diff --git a/data/03/A3/B3/03A3B3406E60EF20180EFBFB0D51FD6E.xml b/data/03/A3/B3/03A3B3406E60EF20180EFBFB0D51FD6E.xml new file mode 100644 index 00000000000..36828cce953 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E60EF20180EFBFB0D51FD6E.xml @@ -0,0 +1,333 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Rhoadsiinae Fowler, 1911 + + + + + + + +Type +genus: + + +Rhoadsia +Fowler, 1911 + +. + + +Included genera: + +Carlana +Strand, 1928 + +, + +Nematobrycon + +, + +Parastremma +Eigenmann, 1912 + +, + +Pseudochalceus +Kner, 1863 + +, and + +Rhoadsia +. + + + + + +Definition: +The least inclusive crown clade that contains + +Rhoadsia altipinna +Fowler, 1911 + +and + +Nematobrycon palmeri +Eigenmann 1911 + +. This is a minimum-crown-clade definition. See +Figure 7 +for a reference phylogeny of +Rhoadsiinae +. + + + + +Etymology: +A patronym for Samuel N. Rhoads (1862–1952). + + + + +Remarks: +The phylogeny inferred from the UCE loci resolves a clade we delimit as the subfamily +Rhoadsiinae +that includes + +Nematobrycon + +, + +Pseudochalceus + +, + +Rhoadsia + +, + +Parastremma + +, and + +Carlana + +( +Fig. 7 +). +Rhoadsiinae +was elevated to classify species of + +Rhoadsia + +and + +Parastremma + +, and the monotypic + +Carlana eigenmanni +(Meek, 1912) (Cardoso 2003) + +. Species of +Rhoadsiinae +have a single tooth series in the premaxilla when juveniles and two series when adults, except for + +C. eigenmanni + +, which maintains only the inner tooth series, and the outer teeth series of the premaxilla is composed of two conical teeth and the inner series consists of five multicuspid teeth (Cardoso 2003). Previous molecular phylogenetic analyses resolve + +Carlana eigenmanni + +and + +Nematobrycon + +as sister-lineages ( + +Oliveira +et al +. 2011 + +). Phylogenetic analysis of a combined molecular and morphological dataset resolves a clade containing + +Bario + +, + +Carlana +, +Hollandichthys +, +Inpaichthys +, +Nematobrycon +, +Pseudochalceus +, +Rachooiscus + +, + +Rhoadsia + +, and +Ŋayeria +that is supported by two non-exclusive synapomorphies ( +Mirande 2019 +). + + +Within +Rhoadsiinae +the UCE phylogeny shows successive branching lineages of + +Nematobrycon + +, the two species of + +Pseudochalceus + +, and a clade containing + +Rhoadsia + +, + +Parastremma + +, and + +Carlana + +( +Fig. 7 +). + +Nematobrycon + +contains two species endemic to the Atrato and San Juan rivers of north-western +Colombia +, whereas + +Pseudochalceus + +includes four species distributed in the Pacific versant rivers of +Ecuador +and +Colombia +(Géry 1977). All species of +Rhoadsiinae +are distributed in the western Andes and Central America ( +Fig. 7 +). In addition, species in this clade share an incomplete lateral line, very elongated dorsal-fin rays that may reach the caudal fin in adult males resulting in a pronounced sexual dimorphism, two teeth rows in the premaxilla (except + +Carlana + +), and 10–15 unicuspid to tricuspid teeth on the maxillary. + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E60EF271A85FD530860FD08.xml b/data/03/A3/B3/03A3B3406E60EF271A85FD530860FD08.xml new file mode 100644 index 00000000000..717a240c72b --- /dev/null +++ b/data/03/A3/B3/03A3B3406E60EF271A85FD530860FD08.xml @@ -0,0 +1,439 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Grundulinae Fowler, 1958 +, new usage + + + + + + + +Type +genus: + + +Grundulus +Valenciennes, 1846 + +. + + +Included genera: + +Astyanacinus +Eigenmann, 1907 + +and + +Grundulus +. + + + + + +Definition: +The least inclusive crown clade that contains + +Grundulus bogotensis + +and + +Astyanacinus moorii +(Boulenger, 1892) + +. This is a minimum-crown-clade definition. See +Figure 7 +for a reference phylogeny of +Grundulinae +. + + + + +Etymology: +From the Middle English +grundel +in reference to several species of fishes. + + + + + +Remarks: +Grundulus + +was described for + +Poecilia bogotensis +Humboldt, 1821 + +(Valenciennes in Cuvier and Valenciennes, 1846) and includes three species endemic to lakes in the northern Andes of South America ( + +Román-Valencia +et al. +2005 + +). Morphological phylogenetic analysis resolved + +Grundulus + +as monophyletic, supported with 11 synapomorphies ( + +Román-Valencia +et al. +2010 + +), and + +G +. +quitoensis + +Román-Valencia +et al +., 2005 + + +is the sister-species of a clade including + +G +. +cochae +Román-Valencia + +et al +, 2003 and + +G +. +bogotensis + +. Alternative phylogenetic studies using morphology resolved + +Grundulus + +and + +Coptobrycon + +from eastern +Brazil +as sister-lineages classified in the subfamily +Gymnocharacinae +(Mirande 2009, 2010). Phylogenetic analysis of combined morphological and molecular data resolved + +Grundulus + +as closely related to + +Coptobrycon + +, + +Stygichthys + +, some species of + +Hyphessobrycon + +, + +Phycocharax + +, + +Myxiops + +, + +Probolodus + +, + +Deuterodon + +, and a species of + +Astyanax + +, which were classified in the tribe +Grundulini Fowler, 1958 +( +Mirande 2019 +). This delimitation of +Grundulini +has not been supported in molecular phylogenetic analyses ( +Figs 3–7 +; + +Oliveira +et al. +2011 + +, Melo +et al. +2022a). + + + +Astyanacinus + +was described by Eigenmann (1907: 769) and differentiated from + +Astyanax + +by possessing a ‘lengthened upper jaw’ (Géry 1977: 415). + +Astyanacinus + +was synonymized with + +Astyanax + +based on the phylogenetic resolution of + +Astyanacinus moorii +(Boulenger, 1892) + +as nested within + +Astyanax + +, a result supported by two morphological synapomorphies (Terán +et al. +2020). A phylogenomic study resolved +Grundulus +and Rhoadsia + + +as sister-lineages and + +Astyanacinus + +as the sister-lineage of a clade containing + +Psellogrammus +Eigenmann, 1908 + +, + +Ctenobrycon +Eigenmann, 1908 + +, + +Oligosarcus + +, and + +Astyanax +(Betancur +et al. +2019) + +. An earlier phylogenomic study using UCE loci reflects results presented in +Figure 7 +, with the resolution of a clade containing + +Grundulus + +and + +Astyanacinus + +that is the sister-lineage of a clade containing +Rhoadsiinae +, + +Psellogrammus + +, + +Ctenobrycon + +, + +Oligosarcus + +, and + +Astyanax +(Melo +et al. +2022a) + +. + + +The phylogenetic analysis of UCE loci supports the monophyly of +Grundulinae +, which are the sister-lineage of a species-rich clade that we delimit as the subfamily +Acestrorhamphinae +( +Fig. 7 +). Based on the UCE phylogeny, we recognize the subfamily +Grundulinae +and revalidate + +Astyanacinus + +as a monotypic genus ( +Fig. 7 +; +Table 1 +). A taxonomic revision delimited the + +Astyanax orthodus + +species group that included + +Astyanacinus moori + +(Ruiz-C. +et al. +2018), indicating the presence of additional species currently classified as + +Astyanax + +that may be more closely related to + +Astyanacinus + +. +Grundulinae +exhibit a geographically disjunct distribution with + +Grundulus + +in the Andes and + +Astyanacinus + +in the La Plata basin ( +Fig. 7 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E62EF201A54FCD40B4AFC05.xml b/data/03/A3/B3/03A3B3406E62EF201A54FCD40B4AFC05.xml new file mode 100644 index 00000000000..64c5c947030 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E62EF201A54FCD40B4AFC05.xml @@ -0,0 +1,989 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Thaperiinae Ota, Reia & Benine +, new subfamilp + + + + + + +ZooBank: +urn:lsid:zoobank.org:act:56486412-0A9F-42B8 BBE2-50E138915341. + + + + + +Type +genus: Ŋayeria + +Eigenmann, 1908. + + +Included genera: + +Bario +Myers, 1940 + +, + +Bryconamericus + +(in part), + +Bryconella +Géry, 1965 + +, + +Inpaichthys + +, + +Hollandichthys +Eigenmann, 1910 + +, + +Holopristis +Eigenmann, 1903 + +, + +Hemigrammus + +(in part), + +Hyphessobrycon + +(in part), + +Parapristella +Géry, 1964 + +, +Rachooiscus +, + +Ramirezella +Fernández-Yépez, 1949 + +, and +Ŋayeria. + + + + +Definition: +The least inclusive crown clade that contains + +Ŋayeria +obliqua + +, + +Holopristis ocellifer +(Steindachner, 1882) + +, and + +Inpaichthys kerri +Géry and Junk, 1977 + +. This is a minimum-crown-clade definition. See +Figure 7 +for a reference phylogeny of Thayeriinae. + + + + +Etymology: +A patronym for Nathaniel Thayer (1808–1883). + + + + +Remarks: +The phylogeny inferred from the UCE loci resolves a clade of three species that includes + +Inpaichthys kerri + +, + +Bryconamericus orinocoense +Román-Valencia, 2003 + +, and + +Hyphessobrycon +sp. + +Jari as the sister-lineage of all other species of Thayeriinae ( +Fig. 7 +). A DNA barcoding study did not resolve + +B. orinocoense + +with a clade containing + +Bryconamericus + +or other species of +Stevardiidae +(García-Melo +et al. +2019). The undescribed species identified here as + +Hyphessobrycon +sp. + +Jari has the morphological characteristics consistent with the genus + +Hyphessobrycon +(Eigenmann 1917) + +but is distantly related to + +H. compressus + +. This clade must be investigated further in order to understand the species composition, as many species may be absent from the present study. + + +There is an interesting clade in Thayeriinae that contains species distributed in Atlantic coastal rivers ( +Fig. 7 +). + +Hyphessobrycon flammeus +Myers, 1924 + +and + +H. griemi +Hoedeman + +, 1957 are similar morphologically and found in coastal rivers in + + +the Atlantic rainforest from +Rio de Janeiro +to +Santa Catarina +, +Brazil +(Weitzman +et al. +1988). + +Hollandichthys multifasciatus +(Eigenmann and Norris, 1900) + +is resolved as the sister-species of +Rachooiscus crassiceps +Myers, 1926 and + +R. graciliceps +Weitzman and Cruz, 1981 + +( +Fig. 7 +), corroborating results from previous phylogenetic analyses ( + +Quagio-Grassioto +et al. +2012 + +, Betancur-R +et al. +2019, +Mirande 2019 +, Melo +et al. +2022a). Several phenotypic traits are consistent with a close phylogenetic relationship between + +Hollandichthys + +and +Rachooiscus +that includes a unique +type +of spermiogenesis, presence of a long and spiralling mitochondria in the midpiece of the spermatozoa in both genera, and presence of a ventral body cavity between pelvic and anal fins that houses internally the anus and the urogenital opening in both males and females (Bertaco and Malabarba 2013). + + + +Ramirezella newboldi +Fernández-Yépez, 1949 + +and + +R. pyrophthalma + +(Costa, 1994) (former + +Hemigrammus newboldi + +and + +Moenkhausia pyrophthalma + +) form a monophyletic group resolved as the sister-lineage of +Ŋayeria +( +Fig. 7 +). + +Ramirezella newboldi + +was described as a new species and new monotypic genus, initially diagnosed by the presence of scales covering the basal portion of caudal fin, incomplete lateral-line, and short maxilla (Fernández-Yépez 1949). The species was subsequently transferred to + +Hemigrammus +( +Taphorn 1992 +) + +, which also highlighted a similar colour paưern shared with + +Moenkhausia cotinho +Eigenmann, 1908 + +. Recently, + +Ramirezella newboldi + +was redescribed and diagnosed from comparisons to + +M. cotinho +(Mathubara and Toledo-Piza 2020) + +. + +Moenkhausia pyrophthalma + +was described by Costa (1994), who hypothesized a close relationship with + +M. oligolepis +(Günther, 1864) + +, + +M. sanctaefilomenae +(Steindachner, 1907) + +(herein classified as a species of + +Bario + +; +Table 1 +), and + +M. cotinho + +based on a reticulate colour paưern, a relationship not supported in the UCE phylogeny ( +Fig. 7 +). Considering that the clade + +Hemigrammus newboldi + +and + +Moenkhausia pyrophthalma + +is phylogenetically distant from both + +M. xinguensis + +( +type +species of + +Moenkhausia + +) and + +H. unilineatus + +( +type +species of + +Hemigrammus + +), we revalidate + +Ramirezella +Fernández-Yépez, 1949 + +to include + +Ramirezella newboldi + +new combination +, and + +Ramirezella pyrophthalma + +new combination +( +Table 1 +). + +Ramirezella + +and + +Bario + +possess a reticulate colour paưern, but according to the phylogeny, this feature seems to have evolved independently in these two lineages ( +Fig. 7 +). + +Moenkhausia cotinho + +was not included in the UCE phylogenomic dataset, but ongoing research is investigating the phylogenetic placement of this species (L. Reia, unpublished data). + + +Ŋayeria +is unique among characids in that the lower caudal-fin lobe is longer than the upper caudal-fin lobe, there is a dark stripe across the lower caudal-fin lobe that is continuous with a longitudinal stripe, and the body is directed slightly upwards when swimming ( + +Moreira and +Lima +2017 + +). Previous molecular phylogenetic analyses resolved + +T. boehlkei +Weitzman, 1957 + +and + +T. ifati +Géry, 1959 + +as a monophyletic group sister to + +Moenkhausia sanctaefilomenae +(Javonillo +et al. +2010) + +. Morphological phylogenetic analysis resolved + +T. boehlkei + +and + +T. obliqua +Eigenmann, 1908 + +as monophyletic based on four synapomorphies, and as the sister-group of + +Hemigrammus +(Mirande 2010) + +. An expanded morphological dataset of Mirande (2010) resulted in phylogenies where a monophyletic +Ŋayeria +was the + + +sister-lineage of a clade containing + +Petitella bleheri + +(Géry and Mahnert, 1986) and + +Petitella georgiae +( + +Ohara +et al. +2017 + +) + +. The resolution of +Ŋayeria +in Thayeriinae reflects results from a previous phylogenomic study of UCE loci (Melo +et al. +2022a). + + + +Ramirezella + +and +Ŋayeria +form a clade sister to a more inclusive group with + +Bario + +, some species assigned to + +Hemigrammus + +, + +Parapristella + +, and + +Bryconella + +(fourth to seventh lineages; +Fig. 7 +). With the exception of + +Bryconella + +and a few + +Bario +species + +, which have green to blue eyes when alive, the majority of taxa belonging to this lineage present the upper margin of the eye red in live specimens ( + +Ohara and +Lima +2015 + +). + + + +Bario + +and several species of + +Moenkhausia + +and + +Hemigrammus skolioplatus +Bertaco and Carvalho, 2005 + +are resolved as a clade of Thayeriinae ( +Fig. 7 +). The genus + +Bario + +was described by +Myers (1940) +asser a complex taxonomic history involving + +Tetragonopterus lineatus +Steindachner, 1891 + +( +Steindachner 1891 +). Eigenmann (1893) observed that + +T. lineatus + +was preoccupied by a species described by Perugia and replaced it with + +T. steindachneri +Eigenmann, 1893 + +. Eigenmann (1917) transferred this species to the monotypic genus + +Entomolepis + +. +Myers (1940) +described + +Bario + +to replace + +Entomolepis + +, since that name was preoccupied in Crustacea ( + +Entomolepis +Brady + +). Molecular and morphological phylogenetic studies have shown a close relationship between + +B. steindachneri + +and species of + +Moenkhausia + +: + +M. oligolepis + +, + +M. sanctaefilomenae + +, + +M. forestii +Benine +et al +., 2009 + +, and + +M. australis +Eigenmann, 1908 + +(Mirande 2009, 2010, 2019, Mariguela +et al. +2013, Melo +et al. +2022a). These species comprise the + +Moenkhausia oligolepis + +/ + +M. sanctaefilomenae + +complex (Costa 1994, +Lima +et al. +2007, + +Ohara and +Lima +2015 + +). The group was defined by a colour paưern characterized by a higher concentration of dark chromatophores in the distal margins of the scales, a vertically elongate humeral blotch, and a conspicuous dark blotch on the caudal peduncle preceded by a lighter area (Costa 1994). Two subgroups in the species complex were proposed based on the degree of flaưening in the pre- and post-pelvic region: laterally compressed in + +M. australis + +, + +M. forestii + +, + +M. oligolepis + +, + +M. sanctaefilomenae + +, and + +Bario steindachneri + +, and ventrally flattened in + +M. cosmops + +Lima +et al +., 2007, + +M. uirapuru +Ohara and Lima, 2015 + +, + +M. diktyota + +Lima +and Toledo-Piza, 2001, and + +M. lineomaculata +Dagosta +et al +., 2015 + +( + +Reia +et al. +2019 + +). + + +The genus + +Bario + +is expanded to include all the eight species analysed here of the + +M. oligolepis + +/ + +M. sanctaefilomenae + +complex ( +Fig. 7 +; +Table 1 +). The phylogeny inferred from the UCE loci provides some corroboration for the species groups delimited in + +Reia +et al. +(2019) + +, and the UCE phylogeny resolves + +Bario skolioplatus + +as the sister-lineage of a clade containing + +Bario uirapuru + +and + +Bario cosmops + +that was proposed in a previous taxonomic revision ( + +Ohara and +Lima +2015 + +). + + +One of the clades resolved in the UCE phylogeny is the + +Hemigrammus ocellifer + +group that includes + +H. aguaruna + +Lima +et al +., 2016, + +H. falsus +Meinken, 1959 + +, + +H. haraldi +Géry, 1961 + +, + +H. guyanensis +Géry, 1959 + +, + +H. luelingi +Géry, 1964 + +, + +H. neptunus +Zarske and Géry, 2002 + +, + +H. ocellifer + +, + +H. pulcher +Ladiges, 1938 + +, and + +H. yinyang + +Lima +and Sousa, 2009 ( +Fig. 7 +; +Lima +and Sousa 2009, +Lima +et al. +2016). Species in this clade possess two humeral blotches, a dark blotch on the caudal peduncle, a red upper eye margin in life, and a single medium-sized hook per anal-fin ray that are arranged in a row along the last unbranched + + +and seven anteriormost branched anal-fin rays in adult males ( +Lima +and Sousa 2009). + +Holopristis + +was described to include + +Tetragonopterus ocellifer +(Eigenmann, 1903) + +, later synonymized in + +Hemigrammus +(Géry 1959) + +. Considering the morphological and phylogenomic support for monophyly of this group ( +Fig. 7 +; +Lima +and Sousa 2009, +Lima +et al. +2016), we revalidate the genus + +Holopristis + +to accommodate + +Holopristis aguaruna + +, + +H. falsus + +, + +H. guyanensis + +, + +H. haraldi + +, + +H. luelingi + +, + +H. neptunus + +, + +H. ocellifer + +, + +H. pulcher + +, and + +H. yinyang + +. Three species of + +Holopristis + +were not sampled in the UCE phylogeny: + +H. falsus + +, + +H. luelingi + +, and + +H. yinyang + +. + + +Species of + +Parapristella + +are resolved as a monophyletic group in Thayeriinae ( +Fig. 7 +). + +Parapristella + +was described to include + +P. georgiae +Géry, 1964 + +and + +Pristella aubynei +Eigenmann, 1909 + +(Géry 1964a). In the UCE phylogeny, + +Parapristella + +is resolved as the sister-lineage of a clade containing + +Bryconella + +and + +Hemigrammus oorderwinkleri +Géry, 1963 + +( +Fig. 7 +). + +Bryconella + +is a monotypic genus described to allocate + +Cheirodon pallidiþons +Fowler, 1946 + +(Géry 1965). Although future studies may suggest that + +H. oorderwinkleri + +should be moved to + +Bryconella + +, we avoid this transference until further detailed studies are conducted into the taxonomy and phylogeny of species of Thayeriinae. The subfamily contains several clades associated with distinct biogeographic regions. The clade has predominance across the Amazon–Orinoco–Guianas with + +Bario + +reaching the La Plata and São Francisco, and the clade with + +Hyphessobrycon flammeus + +, + +H. griemi + +, + +Hollandichthys + +, and +Rachooiscus +distributed in the Atlantic coastal rivers of eastern +Brazil +( +Fig. 7 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E63EF2219A6FA800DFEFCE8.xml b/data/03/A3/B3/03A3B3406E63EF2219A6FA800DFEFCE8.xml new file mode 100644 index 00000000000..fa257017f6b --- /dev/null +++ b/data/03/A3/B3/03A3B3406E63EF2219A6FA800DFEFCE8.xml @@ -0,0 +1,823 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + + +Hpphessobrpconinae +Lima +, Carvalho & Faria + +, new subfamilp + + + + + + +ZooBank: + +urn:lsid:zoobank.org:act: +B7A1E353-CC55-4480- 842E-CFA88155FA94 + +. + + + + + +Type +genus: + + +Hyphessobrycon +Durbin + +in Eigenmann, 1908. + + +Included genera: + +Dinotopterygium +Frainer +et al +., 2021 + +, + +Erythrocharax + +Netto-Ferreira +et al +., 2013 + + +, + +Hemigrammus + +(in part), + +Hyphessobrycon + +(in part), + +Jupiaba + +(in part), + +Macropsobrycon + +(in part), + +Moenkhausia + +(in part), + +Parecbasis + +, and + +Phycocharax + +Ohara +et al +., 2017 + + +. + + + + +Definition: +The least inclusive crown clade that contains + +Hyphessobrycon agulha +Fowler, 1913 + +and + +Jupiaba polylepis +(Günther, 1864) + +. This is a minimum-crown-clade definition. See +Figure 6 +for a reference phylogeny of +Hyphessobryconinae +. + + + + +Etymology: +From the ancient Greek ὑϕήσσων (hˈuːfɑːsˌo͡ʊn) meaning of lesser stature and ΒΡύκω (bɹˈʊka͡ʊ) meaning to bite. + + + + +Remarks: +The new subfamily +Hyphessobryconinae +is delimited as containing many species and genera that have long been challenged in the systematics and taxonomy of +Characiformes +( +Fig. 6 +). A clade comprising eight species currently classified in + +Jupiaba + +and + +Hyphessobrycon moniliger + +is the sister-lineage of all other species of +Hyphessobryconinae +( +Fig. 6 +). Within +Hyphessobryconinae +there is a clade that includes several species with large bony hooks on the anal fin of males: + +Parecbasis cyclolepis +Eigenmann, 1914 + +, eight species of + +Hyphessobrycon + +, one species of + +Macropsobrycon + +, three species of + +Moenkhausia + +, and three species of + +Hemigrammus + +( +Fig. 6 +). A close phylogenetic affinity of species sharing large bony hooks on the anal fins of males had been suggested for the + +Hyphessobrycon panamensis + +group (Ota +et al +. 2020), + +H. bayleyi + +Lima +et al +., 2022, + +H. diancistrus + +, and + +H. otrynus + +( +Lima +et al +. 2022). + + + +Hyphessobrycon compressus + +is the +type +species of the genus and in the UCE phylogeny resolves in a monophyletic group that also contains + +H. columbianus +Zarske and Géry, 2002 + +, + +H. ecuadorensis +(Eigenmann, 1915) + +, + +H. panamensis +Durbin, 1908 + +, and + +Hyphessobrycon +sp. + +Dagua ( +Fig. 6 +). This monophyletic trans-Andean lineage was supported in other phylogenetic studies that included + +H. bussingi +Ota +et al +., 2020 + +, + +H. columbianus + +, + +H. compressus + +, + +H. condotensis +Regan, 1913 + +, + +H. ecuadoriensis +Eigenmann and Henn, 1914 + +, + +H. panamensis + +, + +H. saoagei +Bussing, 1967 + +, and + +H. tortuguerae +Böhlke, 1958 + +(Melo +et al +. 2022a, Elías +et al +. 2023), which differs from the hypothesis based on morphology of a close relationship with cis-Andean species of the rosy tetra clade (Weitzman and Palmer 1997, Carvalho and Malabarba 2015). Pending additional taxonomic and phylogenetic research, we refrain from proposing changes in the generic classification and nomenclature for + +Moenkhausia gracilima + +, + +Moenkhausia mikia + +, + +Hemigrammus leois + +, + +Macropsobrycon xinguensis + +, + +Moenkhausia ceros + +, and + +Hemigrammus hyanuary + +. + + +The specimen identified as + +Hyphessobrycon +sp. + +Dagua (15715) from Río Dagua in south-western +Colombia +in the UCE phylogeny has the morphological features of + +Astyanax daguae +Eigenmann, 1913 + +, such as complete lateral line and absence of scales over caudal-fin lobes (Eigenmann 1913). The species was recently analysed based on a single mitochondrial gene and transferred to + +Tetragonopterus +( + +Terán +et al +., 2020 + +) + +. Due to the phylogenetic position of the specimen relatively close to + +Hyphessobrycon compressus + +( +Fig. 6 +), and the presence of a second species + +Hyphessobrycon daguae +(Eigenmann, 1922) + +in that river, we use the provisional name + +Hyphessobrycon +sp. + +Dagua, with an indication that future research will evaluate the status of both species. This also reveals that the species should not be placed in the genus + +Tetragonopterus + +( +Tetragonopterinae +) within +Characidae +( +Fig. 3 +). The genus + +Macropsobrycon + +requires additional taxonomic research because + +Macropsobrycon xinguensis + +phylogenetically resolved as a lineage of +Hyphessobryconinae +, but the +type +species of the genus + +Macropsobrycon uruguayanae + +is placed in +Cheirodontinae +( +Characidae +) in the UCE phylogeny ( +Figs 3 +, +6 +). + + + +Erythrocharax + +, + +Dinotopterygium + +, and + +Phycocharax + +are speciesdepauperate genera described over the past 10 years that are nested in a clade of +Hyphessobryconinae +that includes several species of + +Hyphessobrycon + +( +Fig. 6 +; + +Netto-Ferreira +et al. +2013 + +, Ohara +et al +. 2017, Frainer +et al. +2021). Species in this clade are predominantly from the Brazilian Shield and possess up to + + +seven cusps, with +Hyphessobrycon psitacus +Dagosta +et al +., 2016 being the exception with five cusps. Some species have a higher number of cusps, such as + +Erythrocharax altipinnis + +with up to eight cusps, and + +H. juruna +Faria +et al +., 2018 + +, + +P. rasbora + +Ohara +et al +., 2017 + + +, and + +Dinotopterygium diodon +Frainer +et al +., 2021 + +with up to nine cusps. + + + +Dinotopterygium + +has a unique combination of 10 synapomorphies, including modifications in anal-fin morphology leading to the anal-fin base strongly convex in males, and suggesting a close relationship with + +Erythrocharax + +and + +Phycocharax +(Frainer +et al +. 2021) + +. + +Phycocharax rasbora + +has a unique combination of characters: presence of a single row of relatively compressed premaxillary teeth, large teeth with four to nine cusps on premaxilla and dentary, absence of pseudotympanum, incomplete lateral line, sexually dimorphic males with distal margin of anal fin approximately straight, and presence of a nearly triangular and horizontally elongated blotch from the posterior half of the body to caudal peduncle ( + +Ohara +et al +. 2017 + +). Phylogenetic analysis of morphological characters resolved a clade containing + +Phycocharax + +, + +Paracheirodon axelrodi +(Schultz, 1956) + +, + +Hyphessobrycon elachys +Weitzman, 1985 + +, + +H. loweae + +Costa and Géry, 1994, and + +H. oanzolinii + +Lima +and Flausino Junior, 2016 ( + +Ohara +et al +. 2017 + +). The relationships resolved in the UCE phylogeny corroborate the phylogenetic affinities of relationship between + +Phycocharax + +and + +H. loweae + +, but are not consistent with a close phylogenetic relationship with + +P. axelrodi + +. + +Hyphessobrycon elachys + +and + +H. oanzolinii + +were not included in phylogenetic analyses of the UCE loci. + + +The phylogeny resolves a clade containing 14 species of + +Hyphessobrycon + +, + +Hemigrammus +cf. +bellotii +(Steindachner, 1882) + +, + +Hemigrammus rubrostriatus +Zarske, 2015 + +, and + +Hemigrammus +sp. + +Leticia ( +Fig. 6 +). Species in this clade have teeth with up to five cusps; the presence of a longitudinal black stripe typically starting posteriorly to the humeral blotch (when humeral blotch is present) and typically darker on the caudal peduncle region. The black stripe presents interspecific variation, ranging from weakly marked and diffuse (e.g. + +Hyphessobrycon amapaensis +Zarske and Géry, 1998 + +and + +Hemigrammus bellotii + +) to very dark and broad stripe (e.g. + +Hyphessobrycon peruoianus +Ladiges, 1938 + +), and in some cases more than one pattern may occur on the same species (e.g. + +Hyphessobrycon agulha + +). The known species of the group share a thin iridescent stripe above the black stripe and humeral blotch. Our phylogeny indicates that live coloration patterns might support monophyletic assemblages within the +Hyphessobryconinae +, opening new avenues for studies within these clades. + + +Many of the species in this clade were previously classified in the + +Hyphessobrycon agulha + +and + +Hyphessobrycon heterorhabdus +(Ulrey 1894) + +species-groups (Géry 1977, +Lima +et al. +2014, Faria +et al. +2020a, b). The + +Hyphessobrycon agulha + +species group is defined by the presence of ‘a broad, relatively diffuse lateral stripe (typically more discernible ventrally, posterior to the midbody), and a humeral blotch that may or may not coalesce with the stripe (although a humeral blotch is absent in + +H. loretoensis +Ladiges, 1938 + +and + +H. mutabilis + +Costa and Géry, 1994)’ ( + +Ohara and +Lima +2015 + +) and in its most recent proposition is composed of + +Hyphessobrycon agulha + +, + +Hyphessobrycon claoatus +Zarske + +, 2015, +Hyphessobrycon eschwartzae +García-Alzate +et al +., 2013, + + +Hyphessobrycon herbertaxelrodi +Géry, 1961, Hyphessobrycon +klausanni +García-Alzate +et al +., 2017, + +Hyphessobrycon loretoensis + +, + +Hyphessobrycon lucenorum +Ohara and Lima, 2015 + +, + +Hyphessobrycon margitae +Zarske, 2016 + +, + +Hyphessobrycon metae +Eigenmann and Henn, 1914 + +, + +Hyphessobrycon mutabilis + +, + +Hyphessobrycon peruoianus + +, + +Hyphessobrycon wadai +Marinho +et al +., 2016 + +, and + +Hyphessobrycon zoe +Faria +et al +., 2020 + +(Faria +et al. +2020a). The + +Hyphessobrycon heterorhabdus + +species group is currently defined by a tricolor longitudinal pattern along midbody, i.e. dorsal red stripe, middle iridescent stripe and ventral longitudinal black pattern composed by a single humeral blotch, a midlateral black stripe continuous with humeral blotch and increasingly blurred towards caudal peduncle (Faria +et al. +2020b); the group includes + +Hyphessobrycon amapaensis + +, + +Hyphessobrycon cantoi +Faria +et al +., 2021 + +, + +Hyphessobrycon heterorhabdus + +, + +Hyphessobrycon ericae +Moreira and Lima, 2017 + +, + +Hyphessobrycon montagi + +Lima +et al +., 2014, + +Hyphessobrycon sateremawe +Faria +et al +., 2020 + +, and + +Hyphessobrycon wosiackii +Moreira and Lima, 2017 + +(Faria +et al. +2021). The phylogeny inferred from the UCE loci resolves both the + +Hyphessobrycon agulha + +and + +H. heterorhabdus + +species-groups as non-monophyletic ( +Fig. 6 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E67EF2619E6FCF50855FCAA.xml b/data/03/A3/B3/03A3B3406E67EF2619E6FCF50855FCAA.xml new file mode 100644 index 00000000000..796911d43bc --- /dev/null +++ b/data/03/A3/B3/03A3B3406E67EF2619E6FCF50855FCAA.xml @@ -0,0 +1,770 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Acestrorhamphinae Eigenmann 1907 +, new usage + + + + + + + +Type +genus: + + +Acestrorhamphus +Eigenmann and Kennedy 1903 + +, junior synonym of + +Oligosarcus +Günther 1864 + +. + + +Included genera: + +Andromakhe + +Terán +et al +., 2020 + + +, + +Astyanax + +(in part), + +Ctenobrycon + +, + +Hyphessobrycon + +(in part), + +Oligosarcus + +, and + +Psalidodon + +(in part). + + + + +Definition: +The least inclusive crown clade that contains + +Oligosarcus argenteus + +, + +Ctenobrycon olioerai +Benine +et al +., 2010 + +and + +Psalidodon fasciatus +(Cuvier, 1819) + +. This is a minimum-crown-clade definition. See +Figure 7 +for a reference phylogeny of +Acestrorhamphinae +. + + + + +Etymology: +From the ancient Greek ἄκεστΡα (ˈɑːkɛstɹə) meaning a darning needle and ῥάμϕος (ɹˈaemfo͡ʊz) meaning curved beak. + + + + +Remarks: +The subfamily +Acestrorhamphinae +is resolved as monophyletic in the UCE phylogeny and comprises four major lineages ( +Fig. 7 +): + +Ctenobrycon + +, + +Astyanax + +, a clade containing + +Hyphessobrycon + +and + +Oligosarcus + +, and + +Psalidodon + +. There are modifications to the taxonomy for each of these lineages that are outlined below. + + + +Ctenobrycon + +includes four species + +C. spilurus +(Valenciennes, 1850) + +, + +C. olioerai + +, and two species transferred here: + +Ctenobrycon kennedyi +(Eigenmann, 1903) + +(former + +Psellogrammus kennedyi + +) and + +C. magdalenae +(Eigenmann and Henn, 1916) + +(former + +Astyanax magdalenae + +) ( +Fig. 7 +). The taxonomic history starts with the description of + +Ctenobrycon + +with + +Tetragonopterus hauxwellianus +Cope, 1870 + +as the +type +species based on the presence of ctenoid (= spinoid) scales in the pre-ventral region (Eigenmann 1908). The monotypic genus + +Psellogrammus + +, with + +Hemigrammus kennedyi +Eigenmann, 1903 + +as +type +species, was described in the same study (Eigenmann 1908). + +Tetragonopterus spilurus +Valenciennes, 1848 + +was transferred to + +Ctenobrycon +(Eigenmann 1910) + +. A close relationship between +Psellogrammus +and +Ctenobrycon +was suggested based on shared + + +characteristics such as elongated anal fin, ctenoid scales, high body depth, maxilla not extending to the orbit, and absence of scales on the caudal fin (Eigenmann 1927). The hypothesized relationship between + +Psellogrammus + +and + +Ctenobrycon + +in pre-cladistic taxonomic studies was corroborated by molecular and combined molecular and morphological phylogenetic studies ( + +Oliveira +et al. +2011 + +, Betancur-R +et al. +2019, +Mirande 2019 +, Melo +et al. +2022a). A phylogenetic analysis identified a ‘ + +Ctenobrycon + +clade’ supported by three morphological synapomorphies that included + +Ctenobrycon + +, + +Psellogrammus + +, + +Astyanax magdalenae + +, + +A. stilbe +(Cope, 1870) + +, and + +A. atratoensis +Eigenmann, 1907 + +( + +Terán +et al. +2020 + +). In light of the present phylogenetic evidence and morphological similarities ( + +Oliveira +et al. +2011 + +, Betancur-R +et al. +2019, +Mirande 2019 +, + +Terán +et al. +2020 + +, Melo +et al. +2022a), we transfer all species in the ‘ + +Ctenobrycon + +clade’ to + +Ctenobrycon + +, resulting in the new combinations + +Ctenobrycon magdalenae + +and + +Ctenobrycon kennedyi + +( +Table 1 +). + + + +Astyanax + +as defined by + +Terán +et al. +(2020: 9) + +resolves as a lineage of +Acestrorhamphinae +in the UCE phylogeny ( +Fig. 7 +). In addition, + +Moenkhausia pirauba +Zanata +et al +., 2010 + +and + +Genycharax tarpon +Eigenmann, 1912 + +resolve within + +Astyanax + +, thus resulting in + +Astyanax pirauba + +and + +Astyanax tarpon + +, new combinations ( +Fig. 7 +; +Table 1 +). The clade + +Astyanax + +is supported by two morphological synapomorphies, but + +A. tarpon + +and + +A. pirauba + +were not included in the morphological analysis ( + +Terán +et al. +2020 + +). This clade also contains + +A. metae +Eigenmann, 1914 + +and + +A. oenezuelae +Schultz, 1944 + +from the Orinoco, and a clade with widespread species such as + +A. bimaculatus +(Linnaeus, 1758) + +and + +A. lacustris +(Lütken, 1875) + +( +Fig. 7 +). + + +A monophyletic + +Oligosarcus + +is resolved as the sister-lineage of a clade containing two species of + +Hyphessobrycon + +: + +H. bifasciatus +Ellis,1911 + +and + +H.igneus +Miquelarena +et al +., +1980 + +in the UCE phylogeny ( +Fig. 7 +), corroborating results from phylogenetic analyses of morphological and combined molecular and morphological datasets ( +Ribeiro and Menezes 2015 +, +Mirande 2019 +, + +Terán +et al. +2020 + +). The UCE phylogeny results show + +Hyphessobrycon bifasciatus + +and + +H. igneus + +as the sister-lineage of + +Oligosarcus + +( +Fig. 7 +). The two + +Hyphessobrycon +species + +need reallocation to a different genus considering the morphological evidence supporting + +Oligosarcus +( +Ribeiro and Menezes 2015 +) + +. Because the purpose of this study is not to describe new genera or species, we currently consider that the best decision is maintaining it in + +Hyphessobrycon + +until a further generic description and reallocation are published. + + +In the phylogeny inferred from the UCE loci, a monophyletic + +Psalidodon +( +sensu + +Terán +et al. +2020 + +) + +is resolved as a sister-lineage to the clade containing + +Hyphessobrycon + +and + +Oligosarcus + +( +Fig. 7 +). + +Psalidodon + +includes species previously classified in the genera + +Astyanax + +, + +Hasemania + +, + +Hyphessobrycon + +, and + +Moenkhausia + +( +Fig. 7 +). + +Terán +et al. +(2020) + +transferred many species of + +Astyanax + +to the genus + +Psalidodon + +, a clade supported with two morphological synapomorphies, and found monophyly of + +Andromakhe + +supported by 17 molecular synapomorphies. + +Andromakhe saguazu +(Cascioưa +et al +., 2003) + +is resolved inside + +Psalidodon + +in our phylogeny ( +Fig. 7 +). However, we treat + +Andromakhe + +as valid as the +type +species of the genus, + +A. latens +(Mirande +et al +., 2004) + +, was not included in our UCE dataset. However, considering the phylogenetic position of +A. saguazu +, we transfer this species to + + +Psalidodon +, as +Psalidodon saguazu +, new combination (Table 1). Other species are herein transferred to + +Psalidodon + +under the new combinations + +Psalidodon alleni +(Eigenmann and McAtee, 1907) + +, + +Psalidodon balbus +( +Myers, 1927 +) + +, + +Psalidodon biotae +(Castro and Vari, 2004) + +, + +Psalidodon cremnobates +(Bertaco and Malabarba, 2001) + +, + +Psalidodon dissimilis +(Garavello and Sampaio, 2010) + +, + +Psalidodon goyacensis +(Eigenmann, 1908) + +, + +Psalidodon hamatus +(Bertaco and Malabarba, 2005) + +, + +Psalidodon henseli +(de Melo and Buckup, 2006) + +, + +Psalidodon kalunga +(Bertaco and Carvalho, 2010) + +, + +Psalidodon laticeps +(Cope, 1894) + +, + +Psalidodon minor +(Garavello and Sampaio, 2010) + +, + +Psalidodon scabripinnis +(Jenyns, 1842) + +, + +Psalidodon serratus +(Garavello and Sampaio, 2010) + +, + +Psalidodon togoi +(Miquelarena and López, 2006) + +, + +Psalidodon oarzeae +(Abilhoa and Duboc, 2007) + +, + +Psalidodon oermilion +(Zanata and Camelier, 2009) + +, + +Psalidodon uaiso +(Carvalho and Langeani, 2013) + +, and + +Psalidodon uberaba +(Serra and Langeani, 2015) + +( +Fig. 7 +; +Table 1 +). Some of these species were originally assigned to other genera based on morphological features, such as the lack of an adipose fin (e.g. + +Hasemania kalunga + +and + +H. uberaba + +) or incomplete lateral line (e.g. + +Hyphessobrycon balbus + +and + +H. uaiso + +). However, based on the resolution of these species in the UCE phylogeny ( +Fig. 7 +), we hypothesize that these features are homoplastic. + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E6BEF2B19BCFAC10C3EFE12.xml b/data/03/A3/B3/03A3B3406E6BEF2B19BCFAC10C3EFE12.xml new file mode 100644 index 00000000000..4744778abb0 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E6BEF2B19BCFAC10C3EFE12.xml @@ -0,0 +1,228 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Oxpbrpconinae Melo, Mattox & Oliveira +, new subfamilp + + + + + + +ZooBank: + +urn:lsid:zoobank.org:act: +1F86C7A9-015C-4CC6- 9132-9C11CFD4E80E + +. + + + + + +Type +genus: + + +Oxybrycon +Géry, 1964 + +. + + + +Included genus: +Oxybrycon +. + + + + + +Etymology: +From the ancient Greek ὀξύς (hˈe͡ɪke͡ɪs) meaning sharp and ΒΡύκω (bɹˈʊka͡ʊ) meaning to bite. + + + + +Remarks: +The genus and species + +Oxybrycon paroulus + +were described by Géry (1964b), who compared it with + +Leptobrycon +Eigenmann, 1915 + +and + +Macropsobrycon + +. + +Oxybrycon + +was subsequently included in the informal group Aphyoditeina (Géry 1973) that was elevated as the subfamily +Aphyoditeinae (Mirande 2010) +. +Lima +et al +. (2018: 101) summarized the main morphological features of + +Oxybrycon + +as: ‘small adult body size; elongate body shape; large dentary; distinctly upturned mouth; teeth conical, tiny; two tooth rows on the dentary; maxilla + + +toothed; small pseudotympanum present; (...) anal fin very short, with 10–13 branched rays; lateral line not complete, with 2–3 pored scales (...)’. + +Oxybrycon paroulus + +is considered a miniature species ( +sensu +Weitzman and Vari 1988). + + +In the UCE inferred phylogeny, + +Oxybrycon + +is resolved as the sister-lineage of all remaining +Acestrorhamphidae +( +Fig. 5 +), requiring the recognition of a new subfamily, Oxybryconinae. In the maximum likelihood inferred phylogeny, + +Oxybrycon paroulus + +is on a relatively long branch (Supporting Information, +Figs S1– S +3 +), as is the case with other miniature species included in the UCE phylogenomic analyses (e.g. + +Trochilocharax + +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E6BEF2B1AB7FDEF0D45F923.xml b/data/03/A3/B3/03A3B3406E6BEF2B1AB7FDEF0D45F923.xml new file mode 100644 index 00000000000..f6b4347a54b --- /dev/null +++ b/data/03/A3/B3/03A3B3406E6BEF2B1AB7FDEF0D45F923.xml @@ -0,0 +1,253 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Trochilocharacinae Zarske, 2010 +, new usage + + + + + + + +Type +genus: + + +Trochilocharax +Zarske, 2010 + +. + + + +Included genus: +Trochilocharax +. + + + + + +Etymology: +From the ancient Greek τΡοΧιλία (tɹo͡ʊkˈɪliə) meaning a pulley and ΧάΡαξ (kˈɑː͡ɹɹaeks) as a name for species of + +Sparidae + +that exhibit teeth on the oral jaws ( +Thompson 1947: 284–5 +). + + + + +Remarks: +The genus and species + +Trochilocharax ornatus + +were described based on aquarium specimens from +Peru +(Zarske 2010). + +Trochilocharax ornatus + +is a very distinctive characid due to its small size (maximum reported length: +17 mm +standard lenght), absence of body scales (except for a pouch scale in the caudal fin of males), and highly pronounced sexual dimorphism, which includes the presence of numerous extraoral conical teeth on the premaxillary and dentary in males (Zarske 2010). Morphological comparisons between + +Trochilocharax + +and several genera of +Stevardiinae +( +Tytocharax +, + +Argopleura + +, + +Xenurobrycon + +, + +Iotabrycon + +, + +Scopaeocharax + +, + +Ptychocharax + +, and + +Chrysobrycon + +) led to the classification of + +Trochilocharax ornatus + +as the only species in the tribe +Trochilocharacini +within +Stevardiinae (Zarske 2010) +. Among characiforms, the presence of a pouch scale is unique to some genera of +Stevardiidae +, and the presence of extraoral conical teeth in mature males is unique to species of +Tytocharax +. The UCE phylogeny demonstrates that + +Trochilocharax + +is a deeply branching monotypic lineage that is resolved as the sister-group of a clade that contains Stygichthyinae, Megalamphodinae, Stichonodontinae, an unnamed subfamily, +Stethaprioninae, Pristellinae, Jupiabinae, Tyttobryconinae, Hyphessobryconinae, Thayeriinae +, +Rhoadsiinae +, Grundulinae, and Acestrorhamphinae ( +Figs 5–7 +). Based on the resolution of the UCE phylogeny, we elevate +Trochilocharacini +to the subfamily-level Trochilocharacinae to include + +Trochilocharax + +( +Fig. 5 +). + +Trochilocharax ornatus + +and + +Oxybrycon paroulus + +are both endemic to the Amazon basin ( +Fig. 5 +), suggesting that Amazonia might have been the location of the initial diversification of the species and lineages that comprise +Acestrorhamphidae +. + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E6BEF2F1A95F91D0874F96E.xml b/data/03/A3/B3/03A3B3406E6BEF2F1A95F91D0874F96E.xml new file mode 100644 index 00000000000..ac2aa0dccde --- /dev/null +++ b/data/03/A3/B3/03A3B3406E6BEF2F1A95F91D0874F96E.xml @@ -0,0 +1,395 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Stpgichthpinae Gérp, 1972 +, new usage + + + + + + + +Type +genus: + + +Stygichthys +Brittan and Böhlke, 1965 + +. + + + +Included genera: +Astyanax + +(in part), + +Coptobrycon + +, + +Deuterodon + +, +Myxiops +Zanata and Akama, 2004, and Stygichthys. + + + + +Figure 5. +Phylogeny of +Acestrorhamphidae +and subfamilies Oxybryconinae, Trochilocharacinae, Stygichthyinae, Megalamphodinae, and Stichonodontinae based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support. + + + + +Figure 6. +Phylogeny of +Acestrorhamphidae +and subfamilies +Stethaprioninae, Pristellinae, Jupiabinae, Tyttobryconinae, and Hyphessobryconinae +based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support. + + + + +Figure 7. +Phylogeny of +Acestrorhamphidae +and subfamilies Thayeriinae, +Rhoadsiinae +, Grundulinae, and Acestrorhamphinae based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support. + + + + +Definition: +The least inclusive crown clade that contains + +Stygichthys typhlops + +, + +Astyanax mutator +Eigenmann, 1909 + +, and + +Deuterodon iguape +Eigenmann, 1907 + +. This is a minimum-crown-clade definition. See +Figure 5 +for a reference phylogeny of Stygichthyinae. + + + + +Etymology: +The River Styx is the main river in the Underworld of ancient Greek mythology. + + + + +Remarks: +Phylogenetic analysis of the UCE dataset resolves Stygichthyinae as monophyletic and the sister-lineage of all other species of +Acestrorhamphidae +, except for + +Trochilocharax ornatus + +and + +Oxybrycon paroulus + +( +Fig. 5 +). Monophyly of Stygichthyinae was supported in previous phylogenomic studies, but with more limited taxon sampling (Betancur-R +et al +. 2019, Melo +et al +. 2022a). + + +Within Stygichthyinae, the UCE inferred phylogeny includes a clade with three species provisionally classified as + +Astyanax + +that comprise a new and unnamed genus: + +Astyanax +sp. + +Kuribrong that is probably an undescribed species with a very similar pattern as exhibited in + +A. wappi +Valenciennes + +in Cuvier and Valenciennes, 1850, and + +Astyanax mutator +Eigenmann 1909 + +that, contrary to a previous hypothesis, is not resolved in + +Deuterodon +( + +Terán +et al +. 2020 + +) + +. + +Hyphessobrycon eos +Durbin, 1909 + +is probably an unnamed genus. The Brazilian blind characid + +Stygichthys typhlops + +and + +Coptobrycon bilineatus +(Ellis, 1911) + +are both deeply branching monotypic lineages in Stygichthyinae. Based on morphological characters, + +Coptobrycon + +was suggested to be related to + +Grundulus +Valenciennes + +in Cuvier and Valenciennes, 1846 (Langeani and Serra 2010), but the lineages are distantly related in the UCE phylogeny ( +Figs 5 +, +7 +). + + +The two species of + +Myxiops + +[ + +Myxiops aphos +Zanata and Akama, 2004 + +and + +Myxiops pelecus + +(Bertaco and +Lucena +, 2006), new combination (former + +Astyanax pelecus + +); +Table 1 +] are resolved as a monophyletic group and the sister-lineage of + +Deuterodon + +. The genus + +Myxiops + +was described based on an exclusive combination of morphological characteristics (Zanata and Akama 2004). Analysis of morphological characters resulted in phylogenies where species of + +Myxiops + +were nested in + +Deuterodon +( + +Terán +et al +. 2020 + +) + +. Given the relationships inferred from the UCE loci, we revalidate + +Myxiops + +( +Fig. 5 +; +Table 1 +). Similarly, + +Terán +et al. +(2020) + +found + +M. aphos + +and + +M. pelecus + +as belonging to a monophyletic clade reinforcing the new combination + +Myxiops pelecus + +. Eigenmann (1907) described + +Deuterodon + +distinguishing it from other characids by the number and position of premaxillary teeth. Our results corroborate the expansion of + +Deuterodon + +to include several species traditionally classified in + +Astyanax +( + +Terán +et al +. 2020 + +) + +. All species of + +Deuterodon + +are found in the Atlantic rainforest zone, mainly in coastal rivers flowing directly into the Atlantic Ocean ( +Fig. 5 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E6CEF231A4BFD730BE8FABD.xml b/data/03/A3/B3/03A3B3406E6CEF231A4BFD730BE8FABD.xml new file mode 100644 index 00000000000..39cb7c2e6ee --- /dev/null +++ b/data/03/A3/B3/03A3B3406E6CEF231A4BFD730BE8FABD.xml @@ -0,0 +1,390 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Tpttobrpconinae Mattox and Melo +, new subfamilp + + + + + + +ZooBank: + +urn:lsid:zoobank.org:act: +E42BE820-B9A4-4F64- A020-9DB10D7AFBF3 + +. + + + + + +Type +genus: Tytobrycon + +Géry, 1973. + + + +Included genera: +Hyphessobrycon + +(in part), + +Priocharax + +, + +Tucanoichthys +Géry and Römer, 1997 + +, and +Tytobrycon. + + + + +Definition: +The least inclusive crown clade that contains + +Tytobrycon +xeruini + +and + +Priocharax ariel +Weitzman and Vari, 1987 + +. This is a minimum-crown-clade definition. See +Figure 6 +for a reference phylogeny of +Tyttobryconinae +. + + + + +Etymology: +From the ancient Greek τυτθός (tˈʌtθo͡ʊz) meaning small or young and ΒΡύκω (bɹˈʊka͡ʊ) meaning to bite. + + + + +Remarks: +The subfamily +Tyttobryconinae +is delimited here to include four genera ( +Fig. 6 +): the miniatures +Tytobrycon +, + +Tucanoichthys + +, + +Priocharax + +,andthenon-miniature + +Hyphessobrycon boulengeri +(Eigenmann, 1907) + +. Traditionally +Tytobrycon +was classified along with other miniatures in the Aphyoditeinagroup (Géry 1973) that was subsequently classified as the +Aphyoditeinae (Mirande 2010) +. In an earlier phylogenomic analysis of UCE loci, + +Tytobrycon +xeruini + +and the miniature + +Tucanoichthys tucano +Géry and Römer, 1997 + +were resolved as sister-species (Melo +et al. +2022a). In the phylogeny inferred from UCE loci, two of the six species of +Tytobrycon +, + +T. hamatus +Géry, 1973 + +and + +T. xeruini + +, resolve as a clade and are the sister-lineages of the only non-miniature species of +Tyttobryconinae +, the + +Hyphessobrycon boulengeri + +( +Fig. 6 +). The clade comprising +Tytobrycon +and + +H. boulengeri + +is sister to a clade of exclusively miniature species: + +Tucanoichthys tucano + +and species of + +Priocharax + +( +Fig. 6 +). There are no known morphological synapomorphies for the clade we delimit here as +Tyttobryconinae +. + + +Four of the seven valid species of + +Priocharax + +were included in the phylogenetic analysis of the UCE loci and resolved as a monophyletic group ( +Fig. 6 +). This is the first attempt to include + +Priocharax + +in a broad molecular phylogeny, as examination of voucher specimens of the samples of + +Priocharax + +in previous studies revealed an instance of misidentification (see: Souza + + +et al +. 2022). When + +Priocharax + +was described, it was hypothesized as closely related to lineages classified here as +Characinae (Weitzman and Vari, 1987) +. The morphological reductions in + +Priocharax + +, interpreted as developmental truncations, have made it difficult to use morphological characters to resolve the phylogenetic relationships of the lineage among +Characiformes +(Mattox and Toledo-Piza 2012, Mattox +et al +. 2016). + + + +Priocharax + +and the enigmatic + +Tucanoichthys tucano + +resolve as sister-lineages in the UCE phylogeny ( +Fig. 6 +). A detailed anatomical study revealed many similarities between the skeletons of + +T. tucano + +and + +Priocharax +(Mattox and Conway 2021) + +. Many of the skeletal similarities are developmental truncations common to other miniature characid lineages, such as reduction in laterosensory system, reduced squamation, reduced number of fin rays, and specific bones that are absent or exhibit truncated development. Clearly any potential morphological synapomorphies among miniature characid lineages require a cautious interpretation due to the potential for convergent or parallel loss or reduction of traits (Weitzman and Fink 1983). There are two striking morphological characters that may represent reductive morphological synapomorphies for the clade containing + +Priocharax + +and + +Tucanoichthys + +: absence of the claustrum in the Weberian apparatus and the shape of the opercle that is developed ventrally but leaves a gap dorsally exposing part of the branchial chamber (Mattox +et al +. 2016, Mattox and Conway 2021). The claustrum is absent in all species of + +Priocharax + +with the exception of a rudimentary claustrum present in + +P. nanus + +Toledo-Piza +et al +., 2014 + + +and + +P. toledopizae +Mattox +et al +., 2023 + +( + +Toledo-Piza +et al +. 2014 + +, Mattox +et al +. 2023). + +Tucanoichthys + +and + +Priocharax + +also share a peculiar shape of the maxilla, with a long series of strictly conical teeth extending to the distal tip of the bone (Géry and Römer 1997, Mattox and Conway 2021), which is uncommon among small characids. It is interesting to note the relatively long branches of all miniature species throughout the phylogeny inferred from the UCE loci (Supporting Information, +Figs S1–S +3 +), something noted above for other miniature taxa (e.g. + +Oxybrycon + +, + +Trochilocharax + +). Species of +Tyttobryconinae +occur in Amazonia, with the exception of + +Hyphessobrycon boulengeri + +that is distributed in Atlantic coastal rivers ( +Fig. 6 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E6CEF2C19F4FA430D84FD8D.xml b/data/03/A3/B3/03A3B3406E6CEF2C19F4FA430D84FD8D.xml new file mode 100644 index 00000000000..5478ae5a1d2 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E6CEF2C19F4FA430D84FD8D.xml @@ -0,0 +1,294 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Jupiabinae Benine and Ota +, new subfamilp + + + + + + +ZooBank: + +urn:lsid:zoobank.org:act: +A5287E4A-6D3A-4454- B72C-D80AB1AF072C + +. + + + + + +Type +genus: + + +Jupiaba +Zanata, 1997 + +. + + + +Included genus: +Jupiaba + +(in part). + + + + +Etymology: +From the Tupí +ju +meaning thorn and +piaba +meaning small fish. + + + + + +Remarks: +Jupiaba + +was described to include 21 species traditionally classified in + +Astyanax + +or + +Deuterodon + +, based on six synapomorphies related to the structures of the pelvic girdle and adjacent musculature (Zanata 1997). The monophyly of + +Jupiaba + +has never been supported in phylogenetic studies (Oliveira et + + +al +. 2011, Mirande 2019, Melo +et al +. 2022a), which is reflected in substantial differences in the distribution of teeth and the pelvicfin bone morphology (Zanata 1997, Zanata and +Lima +2005). The phylogenetic analysis of UCE loci resolves a monophyletic group containing + +Jupiaba abramoides +(Eigenmann, 1909) + +, + +J. anteroides +(Géry, 1965) + +, + +J. anterior +(Eigenmann, 1908) + +, and + +J. poranga + +( +type +species) that are classified in a newly erected subfamily +Jupiabinae +( +Fig. 6 +), partially corroborating previous phylogenetic analyses ( + +Terán +et al +. 2020 + +). The current delimitation of + +Jupiaba + +is polyphyletic in the UCE phylogeny ( +Fig. 6 +), with species resolving in +Hyphessobryconinae +[ + +J. apenima + +, + +J. asymmetrica + +, + +J. iasy +Netto-Ferreira +et al +., 2009 + +, + +J. keithi + +, + +J. ocellata +(Géry, Planquette and Le Bail, 1996) + +, + +J. pirana +Zanata, 1997 + +, + +J. polylepis +(Günther, 1864) + +, and + +J.zonata +(Eigenmann, 1908) + +] and in an unnamed clade with + +Hemigrammus ora + +( + +J. acanthogaster + +, + +J. +cf. +essequibensis + +, and + +J. scologaster + +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E6DEF2C19EBF9E508E1FA7E.xml b/data/03/A3/B3/03A3B3406E6DEF2C19EBF9E508E1FA7E.xml new file mode 100644 index 00000000000..d4242f0b335 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E6DEF2C19EBF9E508E1FA7E.xml @@ -0,0 +1,653 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Pristellinae Gérp and Boutière, 1964 +, new usage + + + + + + + +Type +genus: + + +Pristella +Eigenmann, 1908 + +. + + + +Included genera: +Gymnocorymbus + +, + +Moenkhausia + +(in part), + +Hemigrammus + +(in part), and + +Pristella +. + + + + + +Definition: +The least inclusive crown clade that contains + +Pristella maxillaris + +and + +Gymnocorymbus thayeri +Eigenmann, 1908 + +. This is a minimum-crown-clade definition. See +Figure 6 +for a reference phylogeny of Pristellinae. + + + + +Etymology: +From the ancient Greek πΡίστις (pɹˈɪstiz) a name used by ancient Mediterranean authors for the largetooth sawfish, +Pristis pristis +(Thompson 1947: 219). + + + + +Remarks: +The delimitation of Pristellinae presented here includes + +Hemigrammus unilineatus + +, the +type +species of the genus, and was partially resolved in phylogenetic analyses as the ‘ + +Hemigrammus + +clade’ (Mirande 2009, 2010, 2019). The clade was characterized by homoplastic morphological characters: a dorsal bony process in the rhinosphenoid (Mirande 2009) and incomplete lateral line (Mirande 2010). + + +Within Pristellinae + +Gymnocorymbus + +is the sister-lineage of all other species in the clade ( +Fig. 6 +). In previous phylogenetic studies, + +Gymnocorymbus + +was resolved as closely related to other genera with a very deep body such as + +Brachychalcinus + +, + +Orthospinus + +, + +Poptella + +, + +Stethaprion + +, and + +Stichonodon + +(Javonillo +et al +. 2010, Mirande 2010, 2019, + +Oliveira +et al. +2011 + +, Benine +et al. +2015). The phylogeny inferred from UCE loci strongly resolves + +Gymnocorymbus + +with other lineages of Pristellinae. + + +Lima +et al. +(2021) obtained a clade containing + +Pristella + +and + +Bryconella pallidiþons +(Fowler 1946) + +as the sister-lineage of a clade comprising many of the species included in Pristellinae. In the phylogeny inferred from the UCE loci, + +Pristella + +and + +H. erythrozonus +Durbin, 1909 + +are sister-lineages and they form the sister-group of species currently classified as + +Moenkhausia + +and + +Hemigrammus + +( +Fig. 6 +). + + +In the UCE phylogeny, + +Aphyodite grammica +Eigenmann, 1912 + +is sister to + +Hemigrammus microstomus +Durbin, 1918 + +and nested in a clade of species currently classified as + +Hemigrammus + +( +Fig. 6 +). Morphological phylogenetic analyses resolve + +Aphyodite + +as closely related to + +Atopomesus + +, + +Aphyocharacidium + +, + +Axelrodia + +, + +Leptobrycon + +, + +Microschemobrycon + +, + +Oxybrycon + +, + +Parecbasis + +, and +Tytobrycon +Géry, 1973 (Mirande 2010, Esguícero and Castro 2016). However, molecular ( + +Oliveira +et al. +2011 + +, Mariguela +et al. +2013, Britzke +et al. +2018, Melo +et al +. 2022a) or combined molecular and morphological hypotheses ( +Mirande 2019 +) resolve + +Aphyodite + +more closely related to species classified in Pristellinae, including the +type +species + +Hemigrammus unilineatus + +. As the resolution of + +Aphyodite + +being well supported in the phylogeny inferred from UCE loci and corroborated in other studies, we classify + +Aphyodite grammica + +as a species of + +Hemigrammus + +( +Table 1 +). A recent taxonomic revision of + +Aphyodite + +resulted in the description of two species: + +Aphyodite apiaka +Esguícero and Castro, 2017 + +and + +A. tupebas +Esguícero and Castro, 2017 + +. In addition to + +Aphyodite grammica + +, we classify + +A. apiaka + +and + +A. tupebas + +as species of + +Hemigrammus + +, resulting in the new combinations + +Hemigrammus grammicus + +, + +Hemigrammus apiaka + +, and + +Hemigrammus tupebas + +( +Table 1 +). Considering this new composition of + +Hemigrammus + +, the three species previously classified in + +Aphyodite + +are the only species of + +Hemigrammus + +possessing a single row of premaxillary teeth. + + +Although there are no known morphological synapomorphies for Pristellinae, all species in the clade lack a caudal spot and many species have a broad stripe across the eye and a dark stripe along the anal-fin base. These features were used to define the + +Hemigrammus lunatus +Durbin, 1918 + +species-group ( + +Ota +et al. +2014 + +, +2019 +). It was suggested these shared colour patterns provided evidence for a clade containing + +H. barrigonae +Eigenmann and Henn, 1914 + +, + +H. changae + +Ota +et al +., 2019 + + +, + +H. lunatus + +, + +H. machadoi + +Ota +et al +., 2014 + + +, and + +H. ulreyi +(Boulenger, 1895) + +, possibly related to + +Moenkhausia colletii +(Steindachner, 1882) + +. + +The UCE phylogeny corroborates phylogenies inferred from mitochondrial and nuclear loci in resolving a close relationship + +between +Hemigrammus ulreyi +and +Moenkhausia colletii +(Britzke +et al. +2018). In addition, the UCE phylogeny resolves the + +Hemigrammus lunatus + +species-group as monophyletic ( +Fig. 6 +), but more inclusive than previously ( + +Ota +et al. +2014 + +, +2019 +) ( +Fig. 6 +). Following the phylogenetic relationships resulting from analysis of the UCE loci ( +Fig. 6 +), we are proposing the generic reassignment of + +Moenkhausia colletii + +, + +M.eigenmanni +Géry, 1964 + +, + +M. melogramma +Eigenmann, 1908 + +(present study), and + +M. copei + +and + +M. flaoa + +(based on Britzke +et al. +, 2018) to + +Hemigrammus + +, under the new combinations + +Hemigrammus colletii + +, + +Hemigrammus copei + +, + +Hemigrammus eigenmanni + +, + +Hemigrammus flaous + +, and + +Hemigrammus melogrammus + +( +Fig. 6 +; +Table 1 +). + +Moenkhausia conspicua +Soares and Bührnheim, 2016 + +and + +M. oenerei +Petrolli +et al +., 2016 + +have not been sampled in any molecular phylogenetic analysis, but exhibit a broad stripe across the eye and a dark stripe along the anal-fin base and are probably closely related to species in the + +Hemigrammus lunatus + +species-group; however, pending their inclusion in a phylogenetic analysis we avoid the transfer of these species to + +Hemigrammus + +at this time. Within the + +Hemigrammus lunatus + +species-group, + +H. eigenmanni + +lacks the dark stripe across the eye but has a dark stripe of variable intensity along the anal-fin base. This feature is also shared by + +H. unilineatus + +(with less intensity), + +H. grammicus + +, and + +H. microstomus + +, possibly supporting the close relationship of these species to the + +H. lunatus + +species-group. + + +As pointed out by previous authors (Mirande 2010, Britzke +et al. +2018, + +Soares +et al. +2020 + +, Marinho +et al. +2021), the relationships resolved in the UCE phylogeny highlight the weakness of the degree of lateral line perforation as a diagnostic character to distinguish + +Hemigrammus + +and + +Moenkhausia + +, which can be attributed to the paedomorphic condition retained during a truncated development (Marinho +et al. +2021). The phylogenetic relationships within Pristellinae ( +Fig. 6 +) suggest that pigmentation patterns are more consistent with clades resolved in the phylogeny than is the degree of development of the laterosensory system or caudal-fin squamation. Biogeographically, species of Pristellinae are mostly distributed in Amazon–Orinoco–Guianas; some species of + +Pristella + +and + +Hemigrammus + +are distributed in the São Francisco basin; + +Gymnocorymbus ternetzi + +and + +H. ulreyi + +are distributed in the La Plata, and + +H. lunatus + +is distributed in both Amazon and La Plata basins ( +Fig. 6 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E6EEF2D1A5DFAD10832FA18.xml b/data/03/A3/B3/03A3B3406E6EEF2D1A5DFAD10832FA18.xml new file mode 100644 index 00000000000..c3c7b129a03 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E6EEF2D1A5DFAD10832FA18.xml @@ -0,0 +1,408 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Stethaprioninae Eigenmann, 1907 +, new usage + + + + + + + +Type +genus: + + +Stethaprion +Cope, 1870 + +. + + +Included genera: + +Brachychalcinus +Boulenger, 1892 + +, + +Ectrepopterus +Fowler, 1943 + +, + +Moenkhausia + +(in part), + +Orthospinus +Reis, 1989 + +, + +Poptella +Eigenmann, 1908 + +, and + +Stethaprion +. + + + + + +Definition: +The least inclusive crown clade that contains + +Stethaprion erythrops + +and + +Moenkhausia dasalmas +Bertaco +et al +., 2011 + +. This is a minimum-crown-clade definition. See +Figure 6 +for a reference phylogeny of +Stethaprioninae +. + + + + +Etymology: +From the ancient Greek στῆθος (stˈiːθo͡ʊz) meaning breast and πΡίων (pɹˈa͡ɪən) meaning a saw. + + + + +Remarks: +When first described, the subfamily +Stethaprioninae +included + +Stethaprion + +, + +Fowlerina +Eigenmann, 1907 + +(= + +Poptella + +), and + +Brachychalcinus +(Eigenmann, 1907) + +. A taxonomic revision of Stethaprioninae added +Orthospinus þanciscensis +(Eigenmann, 1914)to the subfamily and identified the presence of a bony spine + + +directed anteriorly, preceding the first dorsal-fin ray as a synapomorphy for the group ( +Reis 1989 +). Within +Acestrorhamphidae +, a predorsal spine is unique to +Stethaprioninae +; however, the trait is present in other lineages of +Characiformes +(as expanded pterygiophore or lepidotrichia e.g. +Curimatidae +, +Prochilodontidae +, and +Serrasalmidae +) ( +Reis 1989 +, Vari 1992, Castro and Vari 2004, Mirande 2010). + + +In the UCE phylogeny, + +Moenkhausia dasalmas + +is resolved as the sister-species of all other lineages of +Stethaprioninae +( +Fig. 6 +). + +Moenkhausia dasalmas + +was described based on the presence of three unbranched and nine branched dorsal-fin rays (Bertaco +et al +. 2011). A more detailed study of the tiny first unbranched ray under the skin of + +M. dasalmas + +may be useful to establish its relationship with the anteriormost spine in the dorsal fin of the remaining +Stethaprioninae +. + +Moenkhausia + +does not resolve as a monophyletic group in the UCE phylogeny, indicating that + +M. dasalmas + +is probably a new and unnamed genus ( +Fig. 6 +). + + +Previous phylogenies inferred from multilocus DNA sequence and combined molecular and morphological datasets resolved +Stethaprioninae +as paraphyletic because + +Gymnocorymbus +Eigenmann, 1908 + +(Pristellinae) was placed as the sister-lineage of a clade of +Stethaprioninae +containing + +Brachychalcinus + +, + +Orthospinus + +, + +Poptella + +, and + +Stethaprion + +( + +Oliveira +et al +. 2011 + +, Benine +et al +. 2015, +Mirande 2019 +). The UCE inferred phylogeny differs from previous phylogenetic analyses and taxonomic delimitations of +Stethaprioninae +in resolving both + +Moenkhausia dasalmas + +and + +Ectrepopterus uruguayensis +(Fowler, 1943) + +as closely related to a clade containing + +Stethaprion + +, + +Poptella + +, + +Brachychalcinus + +, and + +Orthospinus + +( +Fig. 6 +; +Reis 1989 +, + +Oliveira +et al +. 2011 + +, Benine +et al +. 2015). + + + +Ectrepopterus + +was revalidated as distinct from + +Hyphessobrycon +( +sensu +Eigenmann, 1918) + +due to the presence of numerous teeth on maxilla (Malabarba +et al +. 2012), a trait that is absent in all other species of + +Stethaprioninae ( +sensu +Reis 1989 +) + +but present in several other species of the +Acestrorhamphidae +. Analysis of combined molecular and morphological datasets resulted in phylogenies grouping + +E. uruguayensis + +, + +Hyphessobrycon moniliger +Moreira +et al +., 2002 + +, three species of + +Jupiaba + +, and other lineages of + +Stethaprioninae ( +Mirande 2019 +) + +, suggesting future work may discover additional morphological traits consistent with the monophyly of +Stethaprioninae +. The phylogeny and geographic distribution of +Stethaprioninae +indicate that La Plata and the Brazilian Shield had an important role in the diversification of the clade ( +Fig. 6 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E6EEF2E199EFDEF0A7BFDF2.xml b/data/03/A3/B3/03A3B3406E6EEF2E199EFDEF0A7BFDF2.xml new file mode 100644 index 00000000000..431664fd5f2 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E6EEF2E199EFDEF0A7BFDF2.xml @@ -0,0 +1,371 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Stichonodontinae Eigenmann, 1910 +, new usage + + + + + + + +Type +genus: + + +Stichonodon +Eigenmann, 1903 + +. + + + +Included genera: +Hasemania + +, + +Hemigrammus + +(in part), + +Hyphessobrycon + +(in part), + +Moenkhausia + +(in part), + +Nematocharax +Weitzman, Menezes and Britski, 1986 + +, and + +Stichonodon +. + + + + + +Definition: +The least inclusive crown clade that contains + +Stichonodon insignis + +, + +Moenkhausia xinguensis +(Steindachner, 1882) + +, and + +Hyphessobrycon stegemanni +Géry, 1961 + +. This is a minimum-crown-clade definition. See +Figure 5 +for a reference phylogeny of Stichonodontinae. + + + + +Etymology: +From the ancient Greek στίΧος (stˈiːko͡ʊz) meaning a row or line of soldiers or a line of poetry and ὀδών (ˈo͡ʊdɑːn) meaning tooth. + + + + +Remarks: +The phylogeny inferred from the UCE loci resolves Stichonodontinae as monophyletic ( +Fig. 5 +), reflecting previous analysis of molecular characters (Mariguela +et al. +2013, Betancur-R +et al. +2019, Melo +et al. +2022a). + +Moenkhausia + +is paraphyletic with one clade containing + +M. britskii +Azevedo-Santos and Benine,2016 + +, + +M.grandisquamis +(Müller and Troschel, 1845) + +, + +M. pankilopteryx +Bertaco and Lucinda, 2006 + +, + +M. surinamensis +Géry, 1965 + +, + +M. xinguensis +(Steindachner, 1882) + +( +type +species of + +Moenkhausia + +), and + +M. restricta +Soares and Benine, 2019 + +, whereas the other clade includes + +M. abyss +Oliveira and Marinho, 2016 + +, + +M. costae +(Steindachner, 1907) + +, + +M. dichroura +(Kner, 1858) + +, + +M. heikoi +Géry and Zarske, 2004 + +, + +M. intermedia +Eigenmann, 1908 + +, + +M. ischyognatha +Petrolli and Benine, 2015 + +, + +M. lata +Eigenmann, 1908 + +, + +M. sthenosthoma +Petrolli and Benine, 2015 + +, and + +Stichonodon insignis + +( +type +and only species of the genus). + +Moenkhausia lepidura +(Kner, 1858) + +, + +M. nigromarginata + +Costa, 1994, and + +Nematocharax oenustus +Weitzman +et al +., 1986 + +( +type +species of the genus) are successive branching lineages leading to a clade containing + +Hasemania + +, species currently classified with + +Hemigrammus + +and + +Moenkhausia + +, + +Hemigrammus +sp. + +Leticia, + +Hyphessobrycon stegemanni +Géry, 1961 + +, and + +Hyphessobrycon +sp. + +Araguaia ( +Fig. 5 +). + + +Similar to several characid genera, + +Moenkhausia + +is traditionally characterized by a combination of characters that include five multicuspid teeth in the inner premaxillary series, caudal fin partially covered by scales, and complete lateral line (Eigenmann 1917). + +Hasemania + +is diagnosed by the absence of the adipose fin (Ellis 1911). + +Stichonodon + +differs from other characids by the keel-shaped ventral area, two series of teeth in the premaxilla, + + +and dentary in a single series of teeth (Eigenmann and Myers 1929). + +Nematocharax + +is diagnosed by a combination of elongate branched rays of the dorsal, pelvic, and anal fins, two rows of premaxillary teeth in adults, and an almost complete row of teeth along the free ventral maxillary border (Weitzman +et al. +1986). However, all these characters are polymorphic in these lineages, requiring the proposal of new diagnoses based on shared derived features among species within these monophyletic groups. Stichonodontinae probably originated in the Amazon– Orinoco–Guianas with multiple transitions to La Plata and upland rivers of the São Francisco and Atlantic coastal drainages ( +Fig. 5 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E6EEF2E1D21FDCE0D67FAEC.xml b/data/03/A3/B3/03A3B3406E6EEF2E1D21FDCE0D67FAEC.xml new file mode 100644 index 00000000000..e1d6cf18fdb --- /dev/null +++ b/data/03/A3/B3/03A3B3406E6EEF2E1D21FDCE0D67FAEC.xml @@ -0,0 +1,227 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Unnamed +subfamilp + + + + + + + +Included genera: +Hemigrammus + +(in part), + +Jupiaba + +(in part). + + +Definition: +The least inclusive crown clade that contains + +Jupiaba acanthogaster +(Eigenmann, 1911) + +and + +Jupiaba scologaster +(Weitzman and Vari, 1986) + +. This is a minimum-crown-clade definition. See +Figure 6 +for a reference phylogeny of the clade. + + +Remarks: +Analysis of the UCE loci resolves a monophyletic group composed of + +Jupiaba acanthogaster + +, + +J. scologaster + +, + +Hemigrammus ora +Zarske +et al +., 2006 + +, and a new species tentatively identified as + +Jupiaba +cf. +essequibensis +(Eigenmann, 1909) + +( +Fig. 6 +). Species classified as + +Jupiaba + +and + +Hemigrammus + +are consistently resolved among several characid lineages ( + +Oliveira +et al. +2011 + +, +Mirande 2019 +, Melo +et al. +2022a). The unnamed clade resolved in the UCE phylogeny does not include the +type +species of those genera + +Jupiaba poranga + +or + +Hemigrammus unilineatus +(Gill 1858) + +. We understand that smaller named clades are preferable for the sake of classification rather than sinking species in a large subfamily. In addition, this structure retains the existing family-group designations +Stethaprioninae +and Pristellinae. The +type +species of + +Jupiaba + +and + +Hemigrammus + +are not placed inside the clade, which thus requires the description of a new genus before designating the subfamily. + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E6FEF2E19B0F95209F7FE12.xml b/data/03/A3/B3/03A3B3406E6FEF2E19B0F95209F7FE12.xml new file mode 100644 index 00000000000..a0e885db3a6 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E6FEF2E19B0F95209F7FE12.xml @@ -0,0 +1,549 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + + +Megalamphodinae Carvalho, +Lima +& Melo + +, new subfamilp + + + + + + +ZooBank: + +urn:lsid:zoobank.org:act: +5366C168-9D5A-4C10- 83BC-1CC92D99A05A + +. + + + + + +Type +genus: + + +Megalamphodus +Eigenmann, 1915 + +. + + +Included genera: Axelrodia +, +Britanichthys +Géry, 1965, +Hemigrammus +(in part), +Makunaima +Terán +et al +., 2020, + + + + + +Megalamphodus + +, + +Paracheirodon +Géry, 1960 + +, and + +Petitella +Géry + +and Boutière, 1964. + + +Definition: +The least inclusive crown clade that contains + +Megalamphodus megalopterus + +and + +Hemigrammus stictus +(Durbin, 1909) + +. This is a minimum-crown-clade definition. See +Figure 5 +for a reference phylogeny of Megalamphodinae. + + + + +Etymology: +From the ancient Greek μεγαλάμϕοδος (mˌɛɡəlɐmfˈo͡ʊdo͡ʊz) meaning with spacious ways. + + + + +Remarks: +Megalamphodinae are presented as a new subfamily that includes three major clades: a lineage comprising + +Axelrodia stigmatias +Fowler, 1913 + +( +type +species of the genus), + +Petitella georgiae +Géry and Boutière, 1964 + +( +type +species of the genus), + +P. bleheri +Géry and Mahnert, 1986 + +, + +Hemigrammus stictus +(Durbin, 1909) + +, + +Britanichthys axelrodi +Géry, 1965 + +, three species of + +Paracheirodon + +, species of + +Makunaima + +, and species of + +Megalamphodus + +( +Fig. 5 +). + +Hemigrammus stictus + +is a new and undescribed genus from Amazon–Orinoco–Guianas (Melo +et al. +in prep.). The genus + +Makunaima + +was described to include the species + +M. guaporensis +(Eigenmann, 1911) + +, + +M. guianensis +(Eigenmann, 1909) + +, and + +M. multidens +(Eigenmann, 1908) ( + +Terán +et al +. 2020 + +) + +. The UCE phylogeny supports + +Makunaima + +as monophyletic and includes two additional species, + +Makunaima pitieri +(Eigenmann, 1920) + +new combination +, and probably an undescribed species from the Tapajós ( +Fig. 5 +; +Table 1 +). + + + +Megalamphodus + +was described by Eigenmann (1915) and classified in +Cheirodontinae +, based on the presence of a single tooth row in the premaxilla. Species subsequently added to + +Megalamphodus + +include + +M +. +uruguayensis +Fowler, 1943 + +, + +M +. +roseus +Géry, 1960 + +, and + +M +. +sweglesi +Géry, 1961 + +. Géry (1977) considered + +Megalamphodus + +as belonging to the ‘ +Pristella- +group’, together with + +Pristella +Eigenmann, 1908 + +. However, Weitzman and Palmer (1997) noticed that large specimens of + +Megalamphodus megalopterus + +, the +type +species of + +Megalamphodus + +, possess two premaxillary tooth rows, and considered + +Megalamphodus + +a junior synonym of + +Hyphessobrycon + +. + + +The present phylogeny supports part of the monophyletic group of rosy tetras ( +sensu +Weitzman and Palmer 1997); thus, we revalidate + +Megalamphodus + +to accommodate these species ( +Table 1 +), namely: + +M. bentosi +(Durbin, 1908) + +(former + +Hyphessobrycon bentosi + +), + +M. copelandi + +(Durbin in Eigenmann, 1908) (former + +Hyphessobrycon copelandi + +), + +M. epicharis +(Weitzman and Palmer, 1997) + +(former + +Hyphessobrycon epicharis + +), + +M.eques +(Steindachner, 1882) + +(former + +Hyphessobrycon eques + +), + +M. erythrostigma +(Fowler, 1943) + +(former + +Hyphessobrycon erythrostigma + +), + +M. haraldschultzi +(Travassos, 1960) + +(former + +Hyphessobrycon haraldschultzi + +), + +M. khardinae +(Zarske, 2008) + +(former + +Hyphessobrycon khardinae + +), + +M. megalopterus + +(former + +Hyphessobrycon megalopterus + +, +type +species), + +M. micropterus +Eigenmann, 1915 + +(former + +Hyphessobrycon micropterus + +), + +M. socolofi +(Weitzman, 1977) + +(former + +Hyphessobrycon socolofi + +), + +M. sweglesi + +(former + +Hyphessobrycon sweglesi + +), and two possibly new species: + +Megalamphodus +cf. +rosaceus + +and + +Megalamphodus +sp. + +Leticia ( +Fig. 5 +; +Table 1 +). + + +Species of + +Megalamphodus + +have been included in molecular and morphological phylogenetic analyses and the resolution of + +M. megalopterus + +in the ‘rosy tetra clade’ justifies the resurrection of +Megalamphodus +as a valid genus (Javonillo +et al +. 2010, Oliveira +et al +. 2011, Mirande 2019). The relationships among lineages of + + +Megalamphodinae have been investigated with morphological and phylogenomic datasets ( + +Terán +et al +. 2020 + +, Melo +et al +. 2022a). A feature shared by the majority of species of Megalamphodinae is the presence of red, reddish, or reddish brown pigmentation over most or entire bodies. + +Megalamphodus + +can be diagnosed by the presence of a conspicuous black blotch on the dorsal fin. Most species of Megalamphodinae are distributed in cis-Andean northern South America ( +Fig. 5 +), and many are popular in the ornamental fish trade as, for example, + +Axelrodia stigmatias + +, + +M. bentosi + +, + +M. eques + +, + +M. erythrostigma + +, + +M. sweglesi + +, + +Paracheirodon + +, and + +Petitella + +. + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E70EF30199DFA3C0D52F8F4.xml b/data/03/A3/B3/03A3B3406E70EF30199DFA3C0D52F8F4.xml new file mode 100644 index 00000000000..fbd21a93855 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E70EF30199DFA3C0D52F8F4.xml @@ -0,0 +1,486 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Aphpocharacinae Eigenmann, 1909 +, new usage + + + + + + + +Type +genus: + + +Aphyocharax +Günther, 1868 + +. + + + +Included genera: +Aphyocharax + +, + +Cyanogaster + +, + +Leptagoniates +Boulenger, 1887 + +, + +Paragoniates +Steindachner, 1876 + +, + +Phenagoniates +Eigenmann and Wilson + +in Eigenmann +et al +., 1914, + +Prionobrama +Fowler, 1913 + +, +Xenagoniate +s Myers, 1942. Not sampled: +Amazonichthys +Esguícero and Mendonça, 2023, and + +Aphyocharacidium + +. + + + + +Definition: +The least inclusive crown clade that contains + +Aphyocharax pusillus +Günther, 1868 + +and + +Cyanogaster noctioaga +Mattox +et al +., 2013 + +. This is a minimum-crown-clade definition. See +Figure 4 +for a reference phylogeny of +Aphyocharacinae +. Species of +Amazonichthys +and + +Aphyocharacidium + +were not sampled in this study. + + + + +Etymology: +From the ancient Greek ἀϕύΗ (ɐfɪˈae), which is a name used by ancient authors for anchovies, smelts, silversides, and the goby + +Aphia minuta +(Risso 1810) + +and ΧάΡαξ (kˈɑː͡ɹɹaeks) as a name for species of + +Sparidae + +that exhibit teeth on the oral jaws ( +Thompson 1947: 21–2 +, 284–5). + + + + +Remarks: +Recent taxonomic treatments of +Characidae +included eight genera in the +Aphyocharacinae +: + +Paragoniates + +, + +Phenagoniates + +, + +Xenagoniates + +, + +Inpaichthys + +, + +Leptagoniates + +(not analysed), +Rachooiscus +Myers, 1926 (not analysed), + +Aphyocharax + +, and + +Prionobrama + +(Mirande 2009, 2010). Phylogenetic studies using molecular data or combined morphological and molecular characters demonstrate that +Rachooiscus +and + +Inpaichthys + +are not closely related to + +Aphyocharacinae ( + +Oliveira +et al +. 2011 + +) + +, resolves + +Aphyocharacidium + +(latter identified as + +Hemigrammus +cf. +geisleri +Zarske and Géry, 2007 + +) within + +Aphyocharacinae ( + +Tagliacollo +et al +. 2012 + +) + +, and resulted in a delimitation of +Aphyocharacinae +that includes + +Aphyocharacidium + +, + +Aphyocharax + +, + +Prionobrama + +, + +Paragoniates + +, + +Phenagoniates + +, + +Leptagoniates + +, and +Xenagoniate +s supported by two dorsal-fin rays articulating with the first dorsal pterygiophore ( + +Tagliacollo +et al +. 2012 + +, + +Vari +et al. +2016 + +). More recently, the composition of +Aphyocharacinae +was expanded to include + +Axelrodia lindeae +Géry, 1973 + +and 12 synapomorphies were identified for the clade ( +Mirande 2019 +); + +A. lindeae + +has been transferred to the newly described +Amazonichthys +(Esguícero and Mendonça 2023). + + +The phylogeny inferred from the UCE loci resolved + +Aphyocharax + +and + +Prionobrama + +as sister-lineages and a clade containing + +Paragoniates + +, + +Phenagoniates + +, + +Leptagoniates + +, and +Xenagoniate +s ( +Fig. 4 +). A result not presented in other phylogenetic studies is the resolution of a clade in +Aphyocharacinae +that contains + +Cyanogaster noctioaga +Mattox +et al +., 2013 + +, four undescribed species of + +Cyanogaster + +(Leticia, Tapajós, Negro, and Apure), and a specimen previously identified as + +Hemigrammus geisleri + +( +Fig. 4 +). + +Cyanogaster noctioaga + +was described as a miniature characid belonging to the +Stevardiinae +based on the presence of ii + 8 dorsal-fin rays and four teeth in the inner premaxillary series (Mattox +et al +. 2013). Phylogenetic analysis of morphological characters resolves + +Cyanogaster + +in the + +Stevardiinae ( +Mirande 2019 +) + +. In the phylogenies inferred from the UCE loci, + +Cyanogaster + +was consistently resolved as the sister-lineage of all other species of +Aphyocharacinae +( +Fig. 4 +). Considering that the +type +species of + +Hemigrammus + +( + +H. unilineatus +Gill, 1858 + +) is phylogenetically placed in the Pristellinae, we transfer + +Hemigrammus geisleri + +to the genus + +Cyanogaster + +as + +Cyanogaster geisleri + +, +new combination +( +Fig. 4 +; +Table 1 +). + +Aphyocharacidium + +remains unsampled in phylogenomic studies and thus with uncertain position and here tentatively included in +Aphyocharacinae +. Species of +Aphyocharacinae +are primarily distributed in Amazon–Orinoco–Guianas; + +Cyanogaster geisleri + +and + +Prionobrama paraguayensis +(Eigenmann 1914) + +extend to the +Paraguay +basin of La Plata, and + +Phenagoniates + +to the trans-Andean region ( +Fig. 4 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E70EF351AA0F8C808D8F908.xml b/data/03/A3/B3/03A3B3406E70EF351AA0F8C808D8F908.xml new file mode 100644 index 00000000000..60d209863e4 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E70EF351AA0F8C808D8F908.xml @@ -0,0 +1,1221 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Cheirodontinae Eigenmann 1915 +, new usage + + + + + + + +Type +genus: + + +Cheirodon +Girard, 1855 + +. + + +Included genera: Acinocheirodon +Malabarba and Weitzman, 1999, +Aphyocheirodon +Eigenmann, 1915, +Cheirodon +, +Cheirodontops +, + + + + +Figure 4. +Phylogeny of +Characidae +and subfamilies +Aphyocharacinae +, +Cheirodontinae +, Exodontinae, +Tetragonopterinae +, and +Characinae +based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support. + + + + +Table 1. +Nomenclature changes at species-level proposed in this study. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Subfamily + + +Names +prior to this study + + +New combination +
+Aphyocharacinae + + +Hemigrammus geisleri + + + +Cyanogaster geisleri +(Zarske and Géry, 2007) + +
Stygichthyinae + +Deuterodon aphos + + + +Myxiops aphos +Zanata and Akama, 2004 + +
+ +Deuterodon pelecus + + + +Myxiops pelecus + +(Bertaco and Lucena, 2006) +
Megalamphodinae + +Hyphessobrycon bentosi + + + +Megalamphodus bentosi +(Durbin, 1908) + +
+ +Hyphessobrycon copelandi + + + +Megalamphodus copelandi +(Durbin, 1908) + +
+ +Hyphessobrycon epicharis + + + +Megalamphodus epicharis +(Weitzman and Palmer, 1997) + +
+ +Hyphessobrycon eques + + + +Megalamphodus eques +(Steindachner, 1882) + +
+ +Hyphessobrycon erythrostigma + + + +Megalamphodus erythrostigmus +(Fowler, 1943) + +
+ +Hyphessobrycon haraldschultzi + + + +Megalamphodus haraldschultzi +(Travassos, 1960) + +
+ +Hyphessobrycon khardinae + + + +Megalamphodus khardinae +(Zarske, 2008) + +
+ +Hyphessobrycon megalopterus + + + +Megalamphodus megalopterus +Eigenmann, 1915 + +
+ +Hyphessobrycon micropterus + + + +Megalamphodus micropterus +Eigenmann, 1915 + +
+ +Hyphessobrycon rosaceus + + + +Megalamphodus rosaceus +(Durbin, 1909) + +
+ +Hyphessobrycon socolofi + + + +Megalamphodus socolofi +(Weitzman, 1977) + +
+ +Hyphessobrycon sweglesi + + + +Megalamphodus sweglesi +Géry, 1961 + +
+ +Moenkhausia pitieri + + + +Makunaima pitieri +(Eigenmann, 1920) + +
Stichonodontinae + +Hyphessobrycon diastatos + + + +Hasemania diastata +(Dagosta, Marinho and Camelier, 2014) + +
+ +Hyphessobrycon negodagua + + + +Hasemania negodagua + +(Lima and Gerhard, 2001) +
+ +Jupiaba zonata + + + +Moenkhausia zonata +(Eigenmann, 1908) + +
Pristellinae + +Aphyodite grammica + + + +Hemigrammus grammicus +(Eigenmann, 1912) + +
+ +Aphyodite apiaka + + + +Hemigrammus apiaka +(Esguícero and Castro, 2017) + +
+ +Aphyodite tupebas + + + +Hemigrammus tupebas +(Esguícero and Castro, 2017) + +
+ +Moenkhausia colletii + + + +Hemigrammus colletii +(Steindachner, 1882) + +
+ +Moenkhausia eigenmanni + + + +Hemigrammus eigenmanni +(Géry, 1964) + +
+ +Moenkhausia melogramma + + + +Hemigrammus melogrammus +(Eigenmann, 1908) + +
Thayeriinae + +Hemigrammus aguaruna + + + +Holopristis aguaruna + +(Lima, Correa and Ota, 2016) +
+ +Hemigrammus guyanensis + + + +Holopristis guyanensis +(Géry, 1959) + +
+ +Hemigrammus haraldi + + + +Holopristis haraldi +(Géry, 1961) + +
+ +Hemigrammus neptunus + + + +Holopristis neptunus +(Zarske and Géry, 2002) + +
+ +Hemigrammus newboldi + + + +Ramirezella newboldi +Fernández-Yépez, 1949 + +
+ +Hemigrammus ocellifer + + + +Holopristis ocellifer +(Steindachner, 1882) + +
+ +Hemigrammus pulcher + + + +Holopristis pulcher +(Ladiges, 1938) + +
+ +Hemigrammus skolioplatus + + + +Bario skolioplatus +(Bertaco and Carvalho, 2005) + +
+ +Moenkhausia australis + + + +Bario australis +(Eigenmann, 1908) + +
+ +Moenkhausia cosmops + + + +Bario cosmops + +(Lima, Britski and Machado, 2007) +
+ +Moenkhausia forestii + + + +Bario forestii +(Benine, Mariguela and Oliveira, 2009) + +
+ +Moenkhausia oligolepis + + + +Bario oligolepis +(Günther, 1864) + +
+ +Moenkhausia pyrophthalma + + + +Ramirezella pyrophthalma + +(Costa, 1994) +
+ +Moenkhausia sanctaefilomenae + + + +Bario sanctaefilomenae +(Steindachner, 1907) + +
+ +Moenkhausia uirapuru + + + +Bario uirapuru + +( +Ohara and Lima, 2015 +) +
+Grundulinae + + +Astyanax moorii + + + +Astyanacinus moorii +(Boulenger, 1892) + +
+Acestrorhamphinae + + +Andromakhe saguazu + + + +Psalidodon saguazu +(Casciotta, Almirón and Azpelicueta, 2003) + +
+ +Astyanax alleni + + + +Psalidodon alleni +(Eigenmann and McAtee, 1907) + +
+ +Astyanax biotae + + + +Psalidodon biotae +(Castro and Vari, 2004) + +
+ +Astyanax cremnobates + + + +Psalidodon cremnobates +(Bertaco and Malabarba, 2001) + +
+ +Astyanax dissimilis + + + +Psalidodon dissimilis +(Garavello and Sampaio, 2010) + +
+ +Astyanax goyanensis + + + +Psalidodon goyanensis + +(Miranda Ribeiro, 1944) +
+ +Astyanax henseli + + + +Psalidodon henseli +(Melo and Buckup, 2006) + +
+ +Astyanax laticeps + + + +Psalidodon laticeps +(Cope, 1894) + +
+ +Astyanax magdalenae + + + +Ctenobrycon magdalenae +(Eigenmann and Heinn, 1916) + +
+ +Astyanax minor + + + + +Psalidodon minor +(Garavello and Sampaio, 2010) + + +
+ + + +Table 1. +Continued + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Subfamily + + +Names +prior to this study + + +New combination +
+ +Astyanax togoi + + + +Psalidodon togoi +(Miquelarena and López, 2006) + +
+ +Astyanax oarzeae + + + +Psalidodon oarzeae +(Abilhoa and Duboc, 2007) + +
+ +Astyanax oermilion + + + +Psalidodon oermilion +(Zanata and Camelier, 2009) + +
+ +Genycharax tarpon + + + +Astyanax tarpon +(Eigenmann, 1912) + +
+ +Hasemania kalunga + + + +Psalidodon kalunga +(Bertaco and Carvalho, 2010) + +
+ +Hasemania uberaba + + + +Psalidodon uberaba +(Serra and Langeani, 2015) + +
+ +Hyphessobrycon balbus + + + +Psalidodon balbus +( +Myers, 1927 +) + +
+ +Hyphessobrycon hamatus + + + +Psalidodon hamatus +(Bertaco and Malabarba, 2005) + +
+ +Hyphessobrycon uaiso + + + +Psalidodon uaiso +(Carvalho and Langeani, 2013) + +
+ +Moenkhausia pirauba + + + +Astyanax pirauba +(Zanata, Birindelli and Moreira, 2010) + +
+ +Psellogrammus kennedyi + + + +Ctenobrycon kennedyi +(Eigenmann, 1903) + +
+ + + + +Heterocheirodon +Malabarba, 1998 + +, + +Kolpotocheirodon +Malabarba and Weitzman, 2000 + +, + +Macropsobrycon +Eigenmann, 1915 + +(in part), + +Nanocheirodon +Malabarba, 1998 + +, + +Odontostilbe +Cope, 1870 + +, + +Prodontocharax + +, + +Protocheirodon + +Vari +et al +., 2016 + + +, + +Pseudocheirodon +Meek and Hildebrand, 1916 + +, + +Saccoderma +Schultz, 1944 + +, and + +Serrapinnus +Malabarba, 1998 + +. Not sampled: + +Compsura +Eigenmann, 1915 + +and + +Ctenocheirodon +Malabarba and Jerep, 2012 + +. + + +Definition: +The least inclusive crown clade that contains + +Cheirodon pisciculus +Girard 1855 + +and + +Protocheirodon +pi + +(Vari 1978). This is a minimum-crown-clade definition. See +Figure 4 +for a reference phylogeny of +Cheirodontinae +. + + + + +Etymology: +From the ancient Greek ΧειΡόϛ (kˈa͡ɪɹo͡ʊz) meaning hand and ὀδών (ˈo͡ʊdɑːn) meaning tooth. + + + + +Remarks: +Cheirodontinae +are consistently supported as a monophyletic group in molecular ( +Ortí and Meyer 1997 +, Calcagnotto +et al +. 2005, Mirande 2009, 2010, Javonillo +et al +. 2010, Mariguela +et al. +2013) and morphological studies (Malabarba 1998, +Mirande 2019 +). A proposal to include the miniature + +Amazonspinther dalmata + +in + +Cheirodontinae (Bührnheim +et al +. 2008) + +is countered by molecular phylogenetic studies that resolved + +Amazonspinther + +and + +Spintherobolus + +as the sister-lineage to a clade that contains all other species of +Characidae +, +Stevardiidae +, and +Acestrorhamphidae +( + +Oliveira +et al +. 2011 + +, Mariguela +et al. +2013). Molecular phylogenetic analysis led to the description of + +Protocheirodon +( + +Vari +et al +. 2016 + +) + +, which is consistently resolved as the sister-lineage of all other species of +Cheirodontinae +( +Fig. 4 +; + +Vari +et al +. 2016 + +, Melo +et al. +2022a). The phylogeny inferred from the UCE loci includes 14 of the 16 extant genera of +Cheirodontinae +( +Fig. 4 +). The inclusion of + +Compsura + +and + +Ctenocheirodon + +in +Cheirodontinae +is based on previous morphological and molecular studies (Malabarba 1998, Malabarba and Jerep 2012, Mariguela +et al. +2013). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E71EF301A95F9B70BD7FA40.xml b/data/03/A3/B3/03A3B3406E71EF301A95F9B70BD7FA40.xml new file mode 100644 index 00000000000..243f5cb2bde --- /dev/null +++ b/data/03/A3/B3/03A3B3406E71EF301A95F9B70BD7FA40.xml @@ -0,0 +1,327 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Characidae Latreille, 1825 +, new usage + + + + + + + +Type +genus: + + +Charax +Scopoli, 1777 + +. + + +Included subfamilies: +Aphyocharacinae +, +Characinae +, +Cheirodontinae +, Exodontinae, and +Tetragonopterinae +. + + + + +Definition: +The least inclusive crown clade that contains + +Charax gibbosus +(Linnaeus, 1758) + +, + +Aphyocharax pusillus +Günter, 1868 + +, + +Cheirodon pisciculus +Girard, 1855 + +, + +Exodon paradoxus +Müller and Troschel, 1844 + +, and + +Tetragonopterus argenteus +Cuvier 1816 + +. This is a minimum-crown-clade definition. See Figure 4 for a reference phylogeny of Characidae. + + + + +Etymology: +From the ancient Greek ΧάΡαξ (kˈɑː͡ɹɹaeks) as a name for species of +Sparidae +that exhibit teeth on the oral jaws ( +Thompson 1947: 284–5 +). + + + + +Remarks: +There are no known morphological synapomorphies for +Characidae +; however, most species in the clade have a pseudotympanum, a hiatus of the hypaxial muscle along the anterior portion of the gas bladder (Malabarba 1998; Mattox and Toledo-Piza 2012). The pseudotympanum exhibits different shapes, muscles, and rib delimitation among the +Aphyocharacinae +, +Characinae +, +Cheirodontinae +, + +Hyphessobrycon + +(cf. Carvalho 2011), and some species of +Tetragonopterinae +(Malabarba 1998, Mattox and Toledo-Piza 2012). A pseudotympanum is also present in members of +Alestidae +, +Crenuchidae +, +Cynodontidae +, and +Serrasalmidae +(Zanata and Vari 2005; Mattox and Toledo-Piza 2012, Zanata and Camelier 2014, 2015) and may represent a plesiomorphic condition in +Characiformes +as it is present in cithariniforms ( +Vari 1979 +, Mattox and Toledo-Piza 2012), siluriforms ( +Shibatta and Vari 2017 +, + +Slobodian +et al. +2017 + +, +2021 +), gymnotiforms (Dutra +et al. +2015), and cypriniforms (e.g. Britz +et al +. 2021). However, additional investigations are needed to refine our understanding of this character across +Characiformes +and +Ostariophysi +. + + +Several authors have hypothesized a close relationship between +Cheirodontinae +and +Aphyocharacinae +based on morphological similarities (Eigenmann 1917, Géry 1977, Malabarba 1998). Alternatively, Mirande (2010) resolved +Cheirodontinae +as the sister-group of +Aphyoditeinae +and this clade as the sister-group of +Aphyocharacinae +. Molecular phylogenetic studies consistently resolve +Cheirodontinae +and +Aphyocharacinae +as a monophyletic group (Calcagnotto +et al +. 2005, Javonillo +et al. +2010, + +Oliveira +et al +. 2011 + +, + +Tagliacollo +et al +. 2012 + +, Melo +et al +. 2016). + + +In a pre-cladistic study, Géry (1964c) hypothesized a close relationship between +Characinae +and Exodontinae by proposing the tribe +Exodontidi +, which included + +Exodon + +, + +Roeboexodon + +, and + +Roeboides +Günther, 1864 + +. Molecular phylogenies support a close relationship between the +Characinae +and Exodontinae (Javonillo +et al +. 2010, + +Oliveira +et al +. 2011 + +, Melo +et al. +2016), and phylogenomic studies resolve Exodontinae as the sister-lineage of a clade containing +Tetragonopterinae +and +Characinae +( +Fig. 4 +; Betancur-R +et al +. 2019, Melo +et al +. 2022a, + +Souza +et al +. 2022 + +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E71EF311826FE8A080CFAA0.xml b/data/03/A3/B3/03A3B3406E71EF311826FE8A080CFAA0.xml new file mode 100644 index 00000000000..2e28b4a52d4 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E71EF311826FE8A080CFAA0.xml @@ -0,0 +1,317 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Creagrutinae Miles, 1943 +, new usage + + + + + + + +Type +genus + + +Creagrutus +Günther, 1864 + +. + + +Included genera: + +Caiapobrycon +Malabarba and Vari, 2000 + +, + +Creagrutus + +, and + +Microgenys +. + +Not sampled: + +Carlastyanax +. + + + + + +Definition: +The least inclusive crown clade that contains + +Creagrutus muelleri +(Günther 1859) + +, + +Caiapobrycon tucurui +Malabarba and Vari, 2000 + +, and + +Microgenys minuta +Eigenmann, 1913 + +. This is a minimum-crown-clade definition. See +Figure 3 +for a reference phylogeny of Creagrutinae. Although not included in the reference phylogeny, + +Creagrutus muelleri + +resolves in a clade with other species of + +Creagrutus + +in a phylogenetic analysis of morphological characters (Vari and Harlod 2001). + + + + +Etymology: +From the ancient Greek κΡεάγΡευτος (kɹˈiːɡɹuːtˈɑːs) meaning tearing off flesh. + + + + +Remarks: + +Mirande +et al. +(2013) + +and + +Thomaz +et al +. (2015) + +resolved a clade containing + +Creagrutus + +and + +Carlastyanax + +. +Mirande (2019) +later expanded Creagrutini to include + +Planaltina + +, + +Lepidocharax + +, and + +Microgenys + +with two subclades: one with + +L. burnsi +Ferreira +et al +., 2011 + +and + +P. britskii +Menezes +et al +., 2003 + +(see +Planaltininae +), and the second containing + +Microgenys + +, + +Carlastyanax + +, and + +Creagrutus + +. Ferreira +et al +. (2021) delimited Creagrutini to include + +Carlastyanax + +, + +Creagrutus + +, and + +Microgenys + +that was supported with 12 morphological synapomorphies. Our UCE phylogeny resolves + +Microgenys + +as the sister-lineage of a paraphyletic + +Creagrutus + +( +Fig. 3 +). + +Caiapobrycon tucurui + +is nested within + +Creagrutus + +( +Fig. 3 +). We delimit Creagrutinae to include the genera + +Caiapobrycon + +, + +Creagrutus + +, + +Microgenys + +, and + +Carlastyanax +. + + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E71EF3119CAFA970C47F9C9.xml b/data/03/A3/B3/03A3B3406E71EF3119CAFA970C47F9C9.xml new file mode 100644 index 00000000000..be9e313f3d3 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E71EF3119CAFA970C47F9C9.xml @@ -0,0 +1,598 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Diapominae Eigenmann, 1909 +, new usage + + + + + + + +Type +genus: + + +Diapoma +Cope, 1894 + +. + + +Included genera: Atonitus +Vari and Ortega, 2000, + +Aulixidens +Böhlke, 1952 + +, + +Boehlkea + +, + +Bryconamericus + +, + +Ceratobranchia + +, + +Diapoma + +, + +Knodus + +, + +Phallobrycon + +, + +Piabarchus + +, + +Piabina +Reinhardt, 1867 + +,and + +Rhinopetitia +. + +Not sampled: + +Bryconacidnus + +, + +Hypobrycon + +, + +Monotocheirodon +Eigenmann and Pearson, 1924 + +, + +Nantis +Mirande +et al +., 2004 + +, + +Odontostoechus +Gomes, 1947 + +, + +Othonocheirodus +Myers, 1927 + +, and + +Rhinobrycon + +. + + + + +Definition: +The least inclusive crown clade that contains + +Diapoma speculiferum +Cope 1894 + +, + +Diapoma alburnum +(Hensel, 1870) + +, and + +Knodus breoiceps +(Eigenmann, 1908) + +. This is a minimum-crown-clade definition. See +Figure 3 +for a reference phylogeny of +Diapominae +. Although + +Diapoma speculiferum + +is not included in the reference phylogeny it resolves with other species of +Diapoma +in phylogenies inferred from molecular and + + +combined molecular and morphological datasets ( + +Thomaz +et al +. + +2015, Ferreira +et al +. 2021). + + + + +Etymology: +From the ancient Greek διά (dˈa͡ɪə) meaning through and πῶμα(pˈo͡ʊmə) meaning lid or cover. + + + + +Remarks: +Weitzman and Menezes (1998) identified a clade containing + +Diapoma + +, + +Acrobrycon + +,and + +Planaltina + +.Thomaz +etal +.(2015) proposed a delimitation of Diapomini that included +Atonitus +, + +Bryconamericus + +, + +Bryconacidnus + +, + +Ceratobranchia + +, + +Cyanocharax + +, + +Diapoma + +, + +Hypobrycon + +, + +Knodus + +, + +Nantis + +, + +Odontostoechus + +, + +Piabina + +, + +Piabarchus + +, + +Rhinobrycon + +, and tentatively + +Lepidocharax + +and + +Planaltina +. + +Ferreira +et al +. (2021) resolved a monophyletic Diapomini supported by five morphological synapomorphies and two subclades: one containing + +Bryconadenos +Weitzman +et al +., 2005 + +, + +Knodus + +, + +Phallobrycon + +, and + +Rhinobrycon + +, and a second containing +Atonitus +, + +Ceratobranchia + +, + +Bryconacidnus + +, + +Bryconamericus + +, + +Diapoma + +, + +Monotocheirodon + +, + +Nantis + +, + +Odontostoechus + +, + +Piabina + +, and + +Rhinopetitia +. + + + +The UCE phylogeny resolves two monophyletic groups: the first containing a paraphyletic + +Bryconamericus + +, + +Diapoma + +, a paraphyletic + +Piabarchus + +, and + +Piabina + +, and the second containing +Atonitus +, + +Aulixidens + +, + +Boehlkea + +, + +Bryconamericus macarenae + +, + +Ceratobranchia + +, a paraphyletic + +Knodus + +, + +Phallobrycon + +, and + +Rhinopetitia + +( +Fig. 3 +). Given the disparities in clade composition between UCE phylogeny and that of Ferreira +et al +. (2021), we consider a deeper discussion of these relationships premature at this time. + + + +Bryconadenos + +was treated as a synonym of + +Knodus +( + +Thomaz +et al +. 2015 + +) + +. Although the +type +species of + +Knodus + +, + +K. meridae +Eigenmann, 1911 + +, was not sampled in the UCE phylogeny, + +Bryconadenos tanaothoros +Weitzman +et al +., 2005 + +is nested within + +Knodus + +, supporting Thomaz +et al. +’s hypothesis that + +Bryconadenos + +is a junior synonym of + +Knodus +( + +Thomaz +et al +. 2015 + +) + +. + + +Diapominae +are the most species-rich clade of +Stevardiidae +, containing two of the family’s largest genera: + +Bryconamericus + +(54 species) and + +Knodus + +(39 species) (Fricke +et al +. 2023), indicating that numerous taxonomic issues at the specieslevel remain unresolved (García-Melo +et al. +2019, Malabarba +et al. +2021). Following Ferreira +et al +. (2021) and + +Thomaz +et al. +(2015) + +, some genera not sampled in UCE phylogeny were provisionally included in +Diapominae +: + +Bryconacidnus + +, + +Hypobrycon + +, + +Monotocheirodon + +, + +Nantis + +, + +Odontostoechus + +, + +Othonocheirodus + +, and + +Rhinobrycon + +. The UCE phylogeny indicates the diversification of + +Bryconamericus + +, + +Diapoma + +, + +Piabarchus + +, and + +Piabina + +may be associated with the expansion from +Paraguay +basin to the upper Paraná, +Uruguay +, and São Francisco basins ( +Fig. 3 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E72EF311A53FB490BC3FEB6.xml b/data/03/A3/B3/03A3B3406E72EF311A53FB490BC3FEB6.xml new file mode 100644 index 00000000000..a4e462e2c82 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E72EF311A53FB490BC3FEB6.xml @@ -0,0 +1,295 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Planaltininae Oliveira and Souza +, new subfamilp + + + + + + +ZooBank: + +urn:lsid:zoobank.org:act: +06E06366-6662-4FB0- AF63-6CD306320A2B + +. + + + + + +Type +genus: + + +Planaltina +Böhlke, 1954 + +. + + +Included genera: + +Lepidocharax +Ferreira +et al +., 2011 + +and + +Planaltina +. + + + + + +Definition: +The least inclusive crown clade that contains + +Planaltina myersi +Böhlke, 1954 + +and + +Lepidocharax diamantina +Ferreira +et al +., 2011 + +. This is a minimum-crown-clade definition. See +Figure 3 +for a reference phylogeny of +Planaltininae +. + + + + +Etymology: +Planaltina +, +Goiás +, +Brazil +is the +type +locality of + +Planaltina myersi + +. + + + + +Remarks: +Previous authors proposed that + +Planaltina + +is more closely related to + +Acrobrycon + +and + +Diapoma + +and is a sublineage of the Diapomini (Weitzman and Menezes 1998, + +Thomaz +et al +. 2015 + +). Alternatively, +Mirande (2019) +proposed Creagrutini as containing + +Carlastyanax +Géry, 1972 + +, + +Creagrutus +Günther, 1864 + +, + +Microgenys + +, + +Lepidocharax + +, and + +Planaltina + +. Ferreira +et al +. (2021) placed + +Lepidocharax + +and + +Planaltina + +in Diapomini as the sistergroup of the remaining genera and identified 11 morphological synapomorphies for the clade. The UCE phylogeny resolves + + + +Planaltina + +and + +Lepidocharax + +as a monophyletic group and the sister-lineage of a clade containing Creagrutinae and +Diapominae +( +Fig. 3 +); thus, we describe a new subfamily +Planaltininae +that contains + +Lepidocharax + +and + +Planaltina + +. Species of +Planaltininae +are endemic to the Brazilian Shield in upland river systems of the +Paraná +, São Francisco, Paraguaçu, and +Tocantins +( +Fig. 3 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E72EF321820F9250C59FB7B.xml b/data/03/A3/B3/03A3B3406E72EF321820F9250C59FB7B.xml new file mode 100644 index 00000000000..72c86ff5dc5 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E72EF321820F9250C59FB7B.xml @@ -0,0 +1,357 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Stevardiinae Gill, 1858 +, new usage + + + + + + + +Type +genus: Steoardia + +Gill, 1858. + + + +Included genera: +Chrysobrycon + +, + +Corynopoma + +, + +Gephyrocharax +Eigenmann, 1912 + +, + +Pseudocorynopoma +Perugia, 1891 + +, and + +Pterobrycon +Eigenmann, 1913 + +. Not sampled: + +Hysteronotus +Eigenmann, 1911 + +and + +Varicharax + +Vanegas-Ríos +et al +., 2020 + + +. + + + + +Definition: +The least inclusive crown clade that contains + +Chrysobrycon hesperus +(Böhlke, 1958) + +, + +Corynopoma riisei +Gill, 1858 + +, + +Hysteronotus megalostomus +Eigenmann, 1911 + +, and + +Varicharax nigrolineatus + +Vanegas-Ríos +et al +., 2020 + + +. This is a minimum-crown-clade definition. See +Figure 3 +for a reference phylogeny of +Stevardiinae +. Although not included in the reference phylogeny, + +Hysteronotus megalostomus + +resolves in a clade with species of + +Pseudocorynopoma + +and + +Varicharax nigrolineatus + +is placed as the sister-lineage of all other species of +Stevardiinae +in phylogenetic analyses of combined molecular and morphological characters ( + +Vanegas-Ríos +et al +. 2020 + +, Ferreira +et al +. 2021). + + + + +Etymology: Steroardia +Gill, 1858 is a patronym of D. Jackson Steward (1816–1898). + + + + +Remarks: +Weitzman and Menezes (1998) proposed a rearrangement in the +Glandulocaudinae +and defined the tribe +Corynopomini +with + +Corynopoma + +, + +Gephyrocharax + +, and + +Pterobrycon + +, and the tribe +Hysteronotini +with + +Hysteronotus + +and + +Pseudocorynopoma + +. + +Thomaz +et al +. (2015) + +included +Corynopomini +, +Hysteronotini +, and + +Chrysobrycon + +in what they delimited as +Stevardiini +, a result corroborated by Ferreira +et al +. (2021) who identified three morphological synapomorphies supporting the clade. The phylogenies inferred from the UCE loci resolve +Stevardiinae +as a monophyletic group that includes the subclades +Corynopomini +( + +Corynopoma + +, + +Gephyrocharax + +, and + +Pterobrycon + +) and +Hysteronotini +( + +Chrysobrycon + +, + +Pseudocorynopoma + +, and tentatively + +Hysteronotus + +) ( +Fig. 3 +). The UCE phylogeny also suggests + +Gephyrocharax + +is paraphyletic with + +G. oalencia +Eigenmann, 1920 + +more closely related to + +Corynopoma riisei +Gill, 1858 + +than to + +G. oenezuelae +Schultz, 1944 + +, and + +G. machadoi +Ferreira +et al +., 2018 + +and + +Pseudocorynopoma stanleyi +Malabarba +et al +., 2020 + +are sister-species ( +Fig. 3 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E72EF3219C1FDEF080FF95F.xml b/data/03/A3/B3/03A3B3406E72EF3219C1FDEF080FF95F.xml new file mode 100644 index 00000000000..8cec22e4334 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E72EF3219C1FDEF080FF95F.xml @@ -0,0 +1,338 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Hemibrpconinae Gérp, 1966 +, new usage + + + + + + + +Type +genus: + + +Hemibrycon +Günther, 1864 + +. + + +Included genera: + +Acrobrycon +Eigenmann and Pearson + +in Pearson, 1924 and + +Hemibrycon +. + + + + + +Definition: +The least inclusive crown clade that contains + +Acrobrycon ipanquianus +(Cope, 1877) + +, + +Hemibrycon polyodon +(Günther, 1864) + +, and + +Hemibrycon caucanus +(Eigenmann, 1913) + +. This is a minimum-crown-clade definition. See +Figure 3 +for a reference phylogeny of Hemibryconinae. Although + +Hemibrycon polyodon + +is not included in the reference phylogeny, the species resolves with other species of + +Hemibrycon + +in a molecular phylogeny ( + +Thomaz +et al +. 2015 + +) and species in the genus are thought to represent a monophyletic group (Weitzman and Fink 1985). + + + + +Etymology: +From the ancient Greekἡμί- (hˈɛmi) a prefix meaning half and ΒΡύκω (bɹˈuːko͡ʊ) meaning bite or ΒΡύΧω (bɹˈuːko͡ʊ) meaning gnash. + + + + +Remarks: +Géry (1966a) delimited Hemibryconini to include + +Boehlkea +Géry, 1966 + +, + +Bryconacidnus +Myers,1929 + +, + +Bryconamericus + +, + +Ceratobranchia +Eigenmann, 1914 + +, + +Coptobrycon +Géry, 1966 + +, + +Hemibrycon + +, + +Knodus + +, + +Microgenys +Eigenmann,1913 + +, + +Nematobrycon +Eigenmann, 1911 + +, + +Piabarchus +Myers, 1928 + +, + +Rhinobrycon +Myers, 1944 + +, and + +Rhinopetitia +Géry, 1964 + +. + +Thomaz +et al +. (2015) + +resolved Hemibryconini to include + +Acrobrycon + +, + +Hemibrycon + +, and tentatively + +Boehlkea + +(not analysed there). Ferreira +et al +. (2021) resolved + +Acrobrycon + +and + +Hemibrycon + +as a clade supported with five morphological synapomorphies. Phylogenetic analyses of the UCE loci resolve + +Acrobrycon ipanquianus +(Cope, 1877) + +as the sister-lineage of + +Hemibrycon + +( +Fig. 3 +); the +two specimens +of + +Boehlkea + +are placed closer to + +Bryconamericus macarenae + +Román-Valencia +et al +., 2010 + + +, + +Phallobrycon +Menezes +et al +., 2009 + +, and + +Knodus +cf. +delta +Géry, 1972 + +, in the subfamily +Diapominae +( +Fig. 3 +). Hemibryconinae are primarily an Andean lineage, although some species of + +Hemibrycon + +occur in the Amazon and Orinoco basins ( +Fig. 3 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E73EF321A5FFB9D08E0FE12.xml b/data/03/A3/B3/03A3B3406E73EF321A5FFB9D08E0FE12.xml new file mode 100644 index 00000000000..de64d9109d3 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E73EF321A5FFB9D08E0FE12.xml @@ -0,0 +1,262 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Argopleurinae Melo and Oliveira +, new subfamilp + + + + + + +ZooBank: + +urn:lsid:zoobank.org:act: +D266860E-A816-4B4D-84C3-AC7BB9F88CAC + +. + + + + + +Type +genus: + + +Argopleura +Eigenmann, 1913 + +. + + + +Included genus: +Argopleura +. + + + + + +Definition: +The least inclusive crown clade that contains + +Argopleura chocoensis +(Eigenmann, 1913) + +, + +Argopleura conoentus +(Eigenmann, 1913) + +, + +Argopleura diquensis +(Eigenmann, 1913) + +, and + +Argopleura magdalenensis +(Eigenmann, 1913) + +. This is a minimum-crown-clade definition. See +Figure 3 +for a reference phylogeny of Argopleurinae. Although + +Argopleura conoentus + +and + +Argopleura diquensis + +are not sampled in the reference phylogeny, it is assumed that the four species of + +Argopleura + +form a monophyletic group (Weitzman and Fink 1985). + + + + +Etymology: +From the ancient Greek ἀΡγός (ˈɑː͡ɹɡo͡ʊz) meaning shinning or glistening and πλευΡά (plˈoːɹə) meaning rib or side of the body. + + + + +Remarks: +Weitzman and Menezes (1998) placed + +Argopleura + +in +Xenurobryconini +but recognized that the group was based on limited and ambiguous data. According to Weitzman +et al +. (2005), a plesiomorphic pouch scale observed in + +Argopleura + +comprises what appears to be a terminal lateral-line tube, and thus it looks superficially like a scale derived from the lateral-line + + +scale series. The authors suggested that new studies should be conducted to better understand this character. + +Thomaz +et al +. (2015) + +and Ferreira +et al +. (2021) resolved + +Argopleura + +as a deepbranching lineage not closely related to other stevardiine genera and classified it as +incertae sedis +in +Stevardiinae +. +Mirande (2019) +placed + +Argopleura + +within +Stevardiini +but did not discuss its relationships with other genera. Our UCE inferred phylogeny resolves + +Argopleura + +as the sister-lineage of all +Stevardiidae +excluding Landoninae, Xenurobryconinae, and +Glandulocaudinae +( +Fig. 3 +); thus we formally describe the new subfamily, Argopleurinae, endemic to the Andean region ( +Fig. 3 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E73EF331821FA6D0ACDFBA7.xml b/data/03/A3/B3/03A3B3406E73EF331821FA6D0ACDFBA7.xml new file mode 100644 index 00000000000..a5526bb0213 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E73EF331821FA6D0ACDFBA7.xml @@ -0,0 +1,330 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Glandulocaudinae Eigenmann, 1914 + + + + + + + +Type +genus: + + +Glandulocauda +Eigenmann, 1911 + +. + + + +Included genera: +Glandulocauda + +, + +Lophiobrycon +Castro +et al +., 2003 + +, and + +Mimagoniates +Regan, 1907 + +. + + + + +Definition: +The least inclusive crown clade that contains + +Glandulocauda melanopleura +(Ellis 1911) + +and + +Lophiobrycon weitzmani +Castro +et al +., 2003 + +. This is a minimum-crown-clade definition. See +Figure 3 +for a reference phylogeny of +Glandulocaudinae +. + + + + +Etymology: +From Latin +glandulae +(ɡlˈaenduːlˌe͡ɪ) meaning glands of the throat or swollen tonsils and +cauda +(kˈɔːdə) meaning the tail of animals. + + + + +Remarks: +Menezes and Weitzman (2009) reviewed the systematics of the Glandulocaudinae, providing an overview of the long taxonomic history and persistent nomenclatural issues + + +for taxa in the clade. In previous classifications, the clade has been treated as the family +Glandulocaudidae (Fernández-Yépez and Anton 1966) +, the subfamily +Glandulocaudinae +(e.g. Menezes and Weitzman 2009), and the tribe +Glandulocaudini +(e.g. Eigenmann 1914, +Myers and Böhlke 1956 +, Menezes and Weitzman 1990, Mirande 2010). The group’s composition among previous classifications varied until Weitzman +et al +. (2005) restricted +Glandulocaudinae +to + +Glandulocauda + +, + +Lophiobrycon + +, and + +Mimagoniates + +. + + +Several phylogenetic analyses using molecular data or combinations of molecular and morphological datasets resolved + +Glandulocauda + +, + +Lophiobrycon + +, and + +Mimagoniates + +as a monophyletic group, with + +Mimagoniates + +as the sister-lineage of a clade containing + +Lophiobrycon + +and + +Glandulocauda + +( + +Oliveira +et al +. 2011 + +, + +Thomaz +et al +. 2015 + +, +Mirande 2019 +, Ferreira +et al +. 2021). Alternative hypotheses based on analyses of morphological characters resolved + +Lophiobrycon + +as the sister-lineage of a clade containing + +Glandulocauda + +and + +Mimagoniates + +(Castro +et al +. 2003, Menezes and Weitzman 2009). Ferreira +et al +. (2021) identified five morphological synapomorphies for +Glandulocaudinae +. Phylogenetic analysis of mtDNA sequences resolves + +Glandulocauda + +as paraphyletic with + +G. melanopleura +(Ellis, 1911) + +and + +L. weitzmani +Castro +et al +., 2003 + +as sister-taxa, and + +G. caerulea +Menezes and Weitzman, 2009 + +resolved as the sister-lineage of + +Mimagoniates +(Camelier +et al +. 2018) + +. The phylogeny inferred from the UCE loci is consistent with previous studies in resolving +Glandulocaudinae +as monophyletic and + +Glandulocauda + +as paraphyletic ( +Fig. 3 +). The UCE phylogeny indicates that +Glandulocaudinae +represents a La Plata-derived lineage, and that + +Mimagoniates + +diversified into the Atlantic coastal rivers ( +Fig. 3 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E74EF2B1A87FDB10B15FAE3.xml b/data/03/A3/B3/03A3B3406E74EF2B1A87FDB10B15FAE3.xml new file mode 100644 index 00000000000..d56bd6f85d1 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E74EF2B1A87FDB10B15FAE3.xml @@ -0,0 +1,392 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Acestrorhamphidae Eigenmann, 1907 + + + + + + + +Type +genus: + + +Acestrorhamphus +Eigenmann and Kennedy, 1903 + +, junior synonym of + +Oligosarcus +Günther, 1864 + +. + + +Includedsubfamilies: +Acestrorhamphinae +, +Grundulinae +, +Hyphessobryconinae +, +Jupiabinae +, Megalamphodinae, Oxybryconinae, Pristellinae, +Rhoadsiinae +, +Stethaprioninae, Stichonodontinae, Stygichthyinae, Thayeriinae, Trochilocharacinae, Tyttobryconinae +, and an unnamed subfamily. + + + + +Definition: +The least inclusive crown clade that contains + +Oligosarcus argenteus +Günther, 1864 + +, + +Grundulus bogotensis +(Humboldt, 1821) + +, + +Rhoadsia altipinna +Fowler, 1911 + +, +Ŋayeria + +obliqua +Eigenmann, 1908 + +, + +Hyphessobrycon compressus +(Meek, 1904) + +, +Tytobrycon + +xeruini +Géry, 1973 + +, + +Jupiaba poranga +Zanata, 1997 + +, + +Pristella maxillaris +(Ulrey, 1894) + +, + +Stethaprion erythrops +Cope, 1870 + +, + +Stichonodon insignis +( +Steindachner, 1876 +) + +, + +Megalamphodus megalopterus +Eigenmann, 1915 + +, + +Stygichthys typhlops +Brittan and Böhlke, 1965 + +, + +Trochilocharax ornatus +Zarske, 2010 + +, and + +Oxybrycon paroulus +Géry, 1964 + +. This is a minimum-crown-clade definition. See +Figures 5–7 +for a reference phylogeny of +Acestrorhamphidae +. + + + + +Etymology: +From the ancient Greek ἄκεστΡα (ˈɑːkɛstɹə) meaning a darning needle and ῥάμϕος (ɹˈaemfo͡ʊz) meaning curved beak. + + + + +Remarks: +The presence of a very large metacentric pair of chromosomes, at least two times bigger than the second chromosome pair, is a putative synapomorphy for +Acestrorhamphidae +(Sánchez-Romero +et al +. 2015). Studying + +Rhoadsia altipinna +, Sánchez-Romero +et al. +(2015) + +discovered 2n = 50 chromosomes with the first pair being very large metacentric chromosomes that are at least twice as large as the second pair. The authors concluded, based on all available cytogenetic information for characids, that this large pair 1 is present in all karyotyped Clade C species but not in any other karyotyped characid species. The large metacentric pair is present in more than 100 species of +Acestrorhamphidae +and absent in more than 50 species of +Stevardiidae +and +Characidae +s.s. +(Sánchez-Romero +et al +. 2015). We hypothesize that this large first chromosome pair represents a derived condition and is, therefore, synapomorphic for Acestrorhamphidae. + + +Three additional synapomorphies of +Acestrorhamphidae +include: interrupted lateral line, three or fewer maxillary teeth, and three or four unbranched rays articulating with first dorsal fin pterygiophore ( +Mirande 2019 +). Additionally, the majority of species of +Acestrorhamphidae +have two rows of premaxillary teeth with typically five teeth in the inner row, nine branched dorsal-fin rays, and anterior branch of laterosensory canal of sixth infraorbital absent, but recognized that ‘the huge diversity of this clade precludes any diagnosis based on exclusive characters, but the combination of these three characters with the listed synapomorphies should be useful to recognize a species of this subfamily’ ( +Mirande 2019 +). + + +Phylogenetic studies using Sanger-sequenced mitochondrial and nuclear genes (Javonillo +et al +. 2010, + +Oliveira +et al +. 2011 + +, Mariguela +et al. +2013, Melo +et al +. 2016), total evidence analyses ( +Mirande 2019 +), and analysis of phylogenomic datasets ( +Arcila +et al +. 2017, Betancur-R +et al +. 2019, Melo +et al +. 2022a; present study) resolve +Acestrorhamphidae +as a monophyletic group. +Acestrorhamphidae +has been labelled as ‘clade C’ or ‘Stethaprioninae’ in previous phylogenetic studies (Javonillo +et al +. 2010, + +Oliveira +et al +. 2011 + +, +Mirande 2019 +). The name +Stethaprioninae +was proposed by Eigenmann (1907) in a paper published in December of that year,while Eigenmann +et al +.(1907) published the name +Acestrorhamphinae +in July of 1907 ( + +Van der Laan +et al +. 2014 + +). Thus, we recognize +Acestrorhamphidae +as a valid family-group name, with + +Acestrorhamphus +Eigenmann and Kennedy (1903) + +(= + +Oligosarcus + +) as the +type +genus. + + +Given the species-richness and the phylogenetic relationships presented in +Figures 5–7 +, we classify species of +Acestrorhamphidae +among 15 subfamilies. Several genera, including + +Astyanax + +, + +Hemigrammus + +, + +Hyphessobrycon + +, + +Jupiaba + +, and + +Moenkhausia + +, have long been resolved as polyphyletic ( + +Oliveira +et al. +2011 + +, +Mirande 2019 +, Melo +et al. +2022a), a result corroborated in the UCE phylogeny ( +Figs 5–7 +). Future revisionary work on the taxonomy of +Acestrorhamphidae +will require the study of a higher number of species to establish monophyletic genera, which is beyond the scope of this study. + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E74EF3419CDFCD40CA5FDCC.xml b/data/03/A3/B3/03A3B3406E74EF3419CDFCD40CA5FDCC.xml new file mode 100644 index 00000000000..6b534cf90a4 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E74EF3419CDFCD40CA5FDCC.xml @@ -0,0 +1,363 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Characinae Latreille, 1825 +, new usage + + + + + + + +Type +genus: + + +Charax +Scopoli, 1777 + +. + + +Includedgenera: + +Acanthocharax +Eigenmann,1912 + +, + +Acestrocephalus +Eigenmann, 1910 + +, + +Atopomesus + +, + +Charax + +, + +Cynopotamus +Valenciennes, 1850 + +, + +Galeocharax +Fowler, 1910 + +, + +Phenacogaster + +, and + +Roeboides +. + +Not sampled: + +Microschemobrycon + +. + + + + +Definition: +The least inclusive crown clade that contains + +Charax gibbosus +(Linnaeus, 1758) + +, + +Atopomesus pachyodus +Myers, 1927 + +, + +Phenacogaster pectinata +(Cope, 1870) + +, and + +Acestrocephalus anomalus +(Steindachner, 1880) + +. This is a minimum-crown-clade definition. See +Figure 4 +for a reference phylogeny of +Characinae +. + + + + +Etymology: +From the ancient Greek ΧάΡαξ (kˈɑː͡ɹɹaeks) as a name for species of +Sparidae +that exhibit teeth on the oral jaws ( +Thompson 1947: 284–5 +). + + + + +Remarks: +A group that includes + +Charax + +, the +type +genus of +Characiformes +, and small to medium-sized predators such as + +Acanthocharax + +, + +Acestrocephalus + +, + +Cynopotamus + +, + +Galeocharax + +, and + +Roeboides + +have been treated as closely related prior to the application of Hennigian phylogenetic systematics (Howes 1976, Géry 1977). Phylogenetic analysis of morphological characters led to a delimitation of +Characinae +that included + +Phenacogaster + +, + +Priocharax +Weitzman and Vari, 1987 + +, and six genera of heterocharacins ( +Lucena +1998) currently classified in + +Acestrorhynchidae ( + +Oliveira +et al. +2011 + +) + +. Subsequent studies identified a number of morphological synapomorphies, removed the heterocharacins, and added + +Microschemobrycon + +to the +Characinae +(Mirande 2009, 2010, 2019, Mattox and Toledo-Piza 2012). + + +Phylogenomic analysis of UCE loci results in the resolution of four major lineages of +Characinae +delimited as tribes ( + +Souza +et al +. 2022 + +): Phenacogasterini ( + +Phenacogaster + +), Acanthocharacini ( + +Acanthocharax + +), Cynopotamini ( + +Acestrocephalus + +, + +Cynopotamus +, and +Galeocharax +), and Characini ( +Charax +and +Roeboides +). The UCE + +inferred phylogeny presented here is congruent with trees presented by + +Souza +et al +. (2022) + +and includes + +Atopomesus + +as the sister-lineage of all other species of +Characinae +( +Fig. 4 +). Previous morphological phylogenetic studies resolved + +Atopomesus + +in the Spintherobolinae ( +Mirande 2019 +). To investigate this novel phylogenetic hypothesis, specimens from the sequenced lot of + +Atopomesus + +(LBP 23871) were prepared for muscle and skeleton observation, revealing that + +Atopomesus + +possesses four +Characinae +synapomorphies, i.e. characters 3, 7, 8, and 10 of Mattox and Toledo-Piza (2012). + +Microschemobrycon + +was not sampled in the UCE inferred phylogeny but is treated here as +incertae sedis +in +Characinae +following the results from combined multilocus and morphological phylogenetics ( +Mirande 2019 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E75EF341AC6F9CB0B8BFCE8.xml b/data/03/A3/B3/03A3B3406E75EF341AC6F9CB0B8BFCE8.xml new file mode 100644 index 00000000000..7eaae4870d1 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E75EF341AC6F9CB0B8BFCE8.xml @@ -0,0 +1,265 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Tetragonopterinae Gill, 1858 + + + + + + + +Type +genus: + + +Tetragonopterus +Cuvier, 1816 + +. + + +Included genus: + +Tetragonopterus + +. + + + + +Definition: +The least inclusive crown clade that contains + +Tetragonopterus argenteus +Cuvier, 1816 + +and + +Tetragonopterus georgiae +(Géry, 1965) + +. This is a minimum-crown-clade definition. See +Figure 4 +for a reference phylogeny of +Tetragonopterinae +. + + + + +Etymology: +From the ancient Greek τετΡᾰ- (tˈɛtɹə) meaning four, γωνία (ɡˈo͡ʊniə) meaning angle, and πτεΡὀν (tˈɛɹɑːn) meaning fin or wing. + + + + +Remarks: +The initial description of Tetragonopterinae dates to the 19th century and traditionally included many species of +Characidae +(Gill 1858, Géry 1977). The composition changed with the publication of the +Checklist of the Freshwater Fishes of South and Central America +( + +Reis +et al +. 2003 + +), where +Tetragonopterinae +was limited to the genus + +Tetragonopterus +(Reis 2003) + +. The molecular studies in the early 21st century have resulted in recognized species’ diversity in + +Tetragonopterus + +increasing from two to 13 species (Melo +et al. +2011, + +Silva +et al +. 2013 + +, +2016 +, + +Urbanski +et al. +2018 + +). The monophyly of + +Tetragonopterus + +is supported in molecular phylogenies and morphological studies (Melo +et al. +2016, 2022, +Mirande 2019 +), and relaxed clock analyses indicate the lineage diversified in the Miocene (Melo +et al. +2016). The relationships among species of + +Tetragonopterus + +in the UCE phylogeny differ from those inferred from Sanger-sequenced datasets ( +Fig. 4 +), specifically the resolution of + +T. argenteus + +as the sister-species of a clade containing + +T. araguaiensis + +Silva +et al +., 2013 + + +and + +T. ommatus + +Silva +et al +., 2016 + + +( +Fig. 4 +). +Tetragonopterinae +and Exodontinae exhibit a similar biogeographic pattern with many species distributed on the Brazilian Shield; + +T. argenteus + +is the only species distributed in the La Plata basin ( +Fig. 4 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E75EF3519DCF8F40AD5F9F5.xml b/data/03/A3/B3/03A3B3406E75EF3519DCF8F40AD5F9F5.xml new file mode 100644 index 00000000000..1a6e341a778 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E75EF3519DCF8F40AD5F9F5.xml @@ -0,0 +1,218 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Exodontinae Fowler, 1958 +, new usage + + + + + + + +Type +genus: + + +Exodon +Müller and Troschel, 1845 + +. + + +Included genera: Bryconexodon +Géry, 1980, Exodon, Roeboexodon. + + + + +Definition: +The least inclusive crown clade that contains + +Exodon paradoxus +Müller and Troschel, 1844 + +and + +Bryconexodon juruenae +Géry, 1980 + +. This is a minimum-crown-clade definition. See +Figure 4 +for a reference phylogeny of Exodontinae. + + + + +Etymology: +From the ancient Greek ἒξω (ɛɡzˈo͡ʊ) meaning on the outside and ὀδών (ˈo͡ʊdɑːn) meaning tooth. + + + + +Remarks: +The tribe +Exodonidi +was first characterized by ‘the presence of external denticles on outer surface of jaws, clavicle not notched to receive pectoral base, and short anal fin with less than 30 rays’ (Fowler 1958). Phylogenetic analyses of molecular and morphological characters resolve a clade containing three lepidophagous characid genera + +Bryconexodon + +, + +Exodon + +, and + +Roeboexodon + +that is delimited here as Exodontinae (Mirande 2009, 2010, Mattox and Toledo-Piza 2012, Melo +et al +. 2022a). Within Exodontinae, all three possible relationships among the three genera are resolved: + +Roeboexodon + +as the sister-lineage of all other exodontines (Mirande 2010), + +Exodon + +as the sister to all other exodontines (Mattox and Toledo-Piza 2012), and + +Bryconexodon + +the sister-lineage of the clade containing + +Roeboexodon + +and + +Exodon + +( +Fig.4 +; Melo +et al +. 2022a). Exodontinae are supported by 12 morphological synapomorphies, some of which are associated with reinforcement of the anterior portion of the head and are probably associated with their peculiar way of plucking scales (Mattox and Toledo-Piza 2012). Species of Exodontinae are distributed in the Amazon–Orinoco–Guianas region ( +Fig. 4 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E7CEF331AAAF97309C3FA90.xml b/data/03/A3/B3/03A3B3406E7CEF331AAAF97309C3FA90.xml new file mode 100644 index 00000000000..93d023ce2d0 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E7CEF331AAAF97309C3FA90.xml @@ -0,0 +1,373 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Xenurobrpconinae Mpers and Böhlke, 1956 + + + + + + + +Type +genus: + + +Xenurobrycon +Myers + +and +Miranda +Ribeiro, 1945. + + +Included genera: Tytocharax +Fowler, 1913 and + +Xenurobrycon +. + +Not sampled: + +Iotabrycon + +, + +Ptychocharax +Weitzman +et al +., 1994 + +, and + +Scopaeocharax +Weitzman and Fink, 1985 + +. + + + + +Definition: +The least inclusive crown clade that contains +Xenurobrycon macropus +Myers and Miranda Ribeiro, 1945, + + + + +Iotabrycon praecox +Roberts, 1973 + +, + +Ptychocharax rhyacophila + + +Weitzman +et al +., 1994, + +Scopaeocharax rhinodus +(Böhlke 1958) + +, and + +Tytocharax madeirae +Fowler, 1913 + +. This is a minimum-crown-clade definition. See +Figure 3 +for a reference phylogeny of Xenurobryconinae. Although + +Iotabrycon praecox + +, + +Ptychocharax rhyacophila + +, and + +Scopaeocharax rhinodus + +are not included in the reference phylogeny, they resolve as a monophyletic group with +Tytocharax tambopatensis +and + +Xenurobrycon macropus + +in a phylogenetic analysis of a dataset of mtDNA, nuclear genes, and morphology (Ferreira +et al. +2011:fig. 1). + + + + +Etymology: +From the ancient Greek ξένος (zˈiːno͡ʊz) meaning strange or unusual, οὐΡα (ˈuːɹˈɑː) meaning tail, and ΒΡύκω (bɹˈʊka͡ʊ) meaning to bite. + + + + +Remarks: +Myers and Böhlke (1956) +erected the tribe +Xenurobryconini +to include + +Xenurobrycon + +and +Tytocharax +based on the similarity of their caudal fin morphology. The tribe +Xenurobryconini +was expanded to include + +Argopleura +Eigenmann, 1913 + +, + +Iotabrycon + +, and + +Scopaeocharax +(Weitzman and Fink 1985) + +, and later + +Chrysobrycon +Weitzman and Menezes, 1998 + +and + +Ptychocharax +(Weitzman and Menezes 1998) + +. + +Thomaz +et al +. (2015) + +considered + +Argopleura + +as +incertae sedis +and transferred + +Chrysobrycon + +to their +Stevardiini +. +Mirande (2019) +corroborated the monophyly of +Xenurobryconini +( +sensu + +Thomaz +et al +. 2015 + +), and tentatively included + +Cyanogaster +Mattox +et al +., 2013 + +, in this clade supported by four synapomorphies. Our phylogenetic analysis of the UCE loci indicates that + +Cyanogaster + +is placed closer to species of +Aphyocharacinae +. Ferreira +et al +. (2021) included + +Iotabrycon + +, + +Ptychocharax + +, + +Scopaeocharax +, +Tytocharax + +, and + +Xenurobrycon + +in +Xenurobryconini +based on four morphological synapomorphies. In other phylogenomic analyses, + +Scopaeocharax + +was resolved as the sister-lineage of + +Cyanocharax +Malabarba and Weitzman, 2003 + +or + +Diapoma +Cope, 1894 + +( +Arcila +et al +. 2017, Betancur-R. +et al +. 2019). Although UCE data for + +Iotabrycon + +, + +Ptychocharax + +, and + +Scopaeocharax + +are not yet available, they are included in Xenurobryconinae along with +Tytocharax +and + +Xenurobrycon + +based on phylogenetic analyses of a combined mtDNA, nuclear genes, and morphology dataset (Ferreira +et al +. 2021). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E7CEF3C1820FE4D0B02F90C.xml b/data/03/A3/B3/03A3B3406E7CEF3C1820FE4D0B02F90C.xml new file mode 100644 index 00000000000..2c0332e397d --- /dev/null +++ b/data/03/A3/B3/03A3B3406E7CEF3C1820FE4D0B02F90C.xml @@ -0,0 +1,272 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Stevardiidae Gill, 1858 +, new usage + + + + + + + +Type +genus: Steroardia + +Gill, 1858, junior synonym of + +Corynopoma +Gill, 1858 + +. + + +Included subfamilies: +Argopleurinae, Creagrutinae, +Diapominae +, +Glandulocaudinae +, Hemibryconinae, Landoninae, Planaltininae, and Xenurobryconinae. + + + + +Definition: +The least inclusive crown clade that contains + +Landonia latidens +Eigenmann and Henn, 1914 + +, + +Corynopoma riisei +Gill, 1858 + +, and + +Xenurobrycon macropus +Myers + +and +Miranda +Ribeiro, 1945. This is a minimum-crown-clade definition. See +Figure 3 +for a reference phylogeny of +Stevardiidae +. + + + + +Etymology: Steroardia +Gill, 1858 is a patronym of D. Jackson Steward (1816-1898). + + + + +Remarks: +Synapomorphies for +Stevardiidae +include a short frontal fontanel, up to two-thirds the length of the parietal fontanel, ventral margin of anguloarticular crossing perpendicularly to the dentary laterosensory canal, four teeth in the inner premaxillary row, and ectopterygoid expanded laterally to the blade of the lateral ethmoid ( +Mirande 2019 +); reversals in all characters are observed in several species ( +Mirande 2019 +). + + +Eigenmann(1914) proposedthesubfamilyGlandulocaudinae for characids with a gland in caudal fins of mature males (e.g. + +Corynopoma + +). Weitzman +et al +. (2005) delimited +Stevardiinae +as a lineage distinct from Eigenmann’s +Glandulocaudinae +, and Mirande (2010) on the basis of three synapomorphies merged the two groups under the name +Stevardiinae +. Malabarba and Weitzman (2003) identified a monophyletic group they named Clade A, which contained the +Glandulocaudinae +, + +Stevardiinae ( +sensu +Weitzman +et al +. 2005) + +, and 18 additional genera considered +incertae sedis +within +Characidae +. The monophyly of Clade A has been supported in phylogenetic analyses using morphological (Mirande 2010, Baicere-Silva +et al +. 2011, Ferreira +et al +. 2011, + +Mirande +et al +. 2011 + +), multilocus (Calcagnotto +et al +. 2005, Javonillo +et al +. 2010, + +Oliveira +et al +. 2011 + +, Mariguela +et al +. 2013, + +Thomaz +et al +. 2015 + +), combined multilocus and morphology ( +Mirande 2019 +, Ferreira +et al +. 2021), and phylogenomic data ( +Arcila +et al. +2017, Betancur-R. +et al +. 2019, Melo +et al. +2022a). We have elevated +Stevardiidae +to a family level with nine subfamilies: Landoninae, Xenurobryconinae, +Glandulocaudinae +, Argopleurinae, Hemibryconinae, +Stevardiinae +, Planaltininae, Creagrutinae, and Diapominae ( +Fig. 3 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E7CEF3C19B9F8F00D93F98E.xml b/data/03/A3/B3/03A3B3406E7CEF3C19B9F8F00D93F98E.xml new file mode 100644 index 00000000000..aa6724b0130 --- /dev/null +++ b/data/03/A3/B3/03A3B3406E7CEF3C19B9F8F00D93F98E.xml @@ -0,0 +1,429 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + +Landoninae Weitzman and Menezes, 1998 +, new usage + + + + + + + +Type +genus: + + +Landonia +Eigenmann and Henn, 1914 + +. + + +Included genera: + +Eretmobrycon +Fink, 1976 + +, + +Landonia + +, + +Markiana +Eigenmann, 1903 + +, and + +Phenacobrycon +Eigenmann, 1922 + +. + + + + +Definition: +The least inclusive crown clade that contains Landonia + +latidens + +, + +Eretmobrycon emperador +(Eigenmann and Ogle, 1907) + +, and + +Markiana nigripinnis +(Perugia, 1891) + +. This is a minimum-crown-clade definition. See +Figure 3 +for a reference phylogeny of Landoninae. + + + + + +Etymology: +Landonia + +is a patronym of Hugh McKennan Landon (1867–1947). + + + + +Remarks: +Roberts (1973) +suggested that + +Iotabrycon +Roberts, 1973 + +, + +Landonia + +, and + +Phenacobrycon + +were a monophyletic group derived from a putative ancestor related to + +Bryconamericus + +from the western Andes. + +Oliveira +et al +. (2011) + +identified a monophyletic group including + +Markiana + +and + +Eretmobrycon emperador + +(formerly + +Bryconamericus emperador + +). + +Thomaz +et al +. (2015) + +found the trans-Andean + +Bryconamericus + +more related to + +Markiana + +than to + +B. exodon +Eigenmann 1907 + +( +type +species), and that they should be included in + +Eretmobrycon + +in the tribe +Eretmobryconini +. Ferreira +et al +. (2021) resolved + +Landonia + +inside this clade and renamed the group as Landoniini (= Landonini) based on 19 synapomorphies. +Eretmobryconini + +Thomaz +et al +., 2015 + +(Eretmobryconinae; +type +genus: + +Eretmobrycon + +) is a junior synonym of Landonini Weitzman and Menezes, 1998 (Landoninae; +type +genus: + +Landonia + +). +Vanegas-Ríos (2018) +found that + +Landonia + +was the sister-group of + +Phenacobrycon + +, but this relationship was not corroborated by Ferreira +et al +. (2021), who resurrected the monotypic tribe +Phenacobryconini +proposed by Weitzman and Menezes (1998). Melo +et al +. (2022a) similarly resolved the clade containing + +Markiana + +, + +Phenacobrycon + +, and + +E. emperador + +in a phylogeny inferred from UCE loci. + + +In the UCE phylogeny, Landoninae are monophyletic and composed of + +Markiana + +, + +Eretmobrycon + +, + +Landonia + +, and + +Phenacobrycon + +( +Fig. 3 +). Our phylogenetic analyses revealed that + +Eretmobrycon festae +(Boulenger, 1898) + +(former + +Astyanax festae + +) is more closely related to + +Phenacobrycon + +and + +Landonia + +than to other + +Eretmobrycon + +( +Fig. 3 +). The former + +Astyanax festae +(Boulenger, 1898) + +has been hypothesized to be more related to + +Markiana + +and + +Bryconamericus emperador +( + +Rossini +et al +. 2016 + +) + +and was recently transferred to + +Eretmobrycon +( + +Terán +et al +. 2020 + +) + +. Additional analyses within the group are necessary to evaluate the present hypothesis that + +E. festae + +may belong to a distinct genus. + + +Biogeographically, Landoninae are a group with two lineages: (i) species of + +Markiana + +occurring in Amazon–Orinoco–Guianas and La Plata [ + +M. geayi +(Pellegrin, 1909) + +in Orinoco and + +M. nigripinnis +(Perugia, 1891) + +in the +Paraguay +and Amazon basins], and (ii) species of + +Eretmobrycon + +, + +Phenacobrycon + +, and + +Landonia + +that diversified in the trans-Andean northern South America and lower Central America ( +Fig. 3 +). + + + + \ No newline at end of file diff --git a/data/03/A3/B3/03A3B3406E7EEF3C1AA5FDCE08E7FE70.xml b/data/03/A3/B3/03A3B3406E7EEF3C1AA5FDCE08E7FE70.xml new file mode 100644 index 00000000000..00379a83b9a --- /dev/null +++ b/data/03/A3/B3/03A3B3406E7EEF3C1AA5FDCE08E7FE70.xml @@ -0,0 +1,374 @@ + + + +Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes) + + + +Author + +Melo, Bruno F + + + +Author + +Ota, Rafaela P + + + +Author + +Benine, Ricardo C + + + +Author + +Carvalho, Fernando R + + + +Author + +Lima, Flavio C T + + + +Author + +Mattox, George M T + + + +Author + +Souza, Camila S + + + +Author + +Faria, Tiago C + + + +Author + +Reia, Lais + + + +Author + +Roxo, Fabio F + + + +Author + +Valdez-Moreno, Martha + + + +Author + +Near, Thomas J + + + +Author + +Oliveira, Claudio + +text + + +Zoological Journal of the Linnean Society + + +2024 + +Zool. J. Linn. Soc. + + +2024-09-03 + + +202 + + +1 + + +1 +37 + + + + +https://doi.org/10.1093/zoolinnean/zlae101 + +journal article +10.1093/zoolinnean/zlae101 +0024-4082 +A349939-8BEB-4BAA-9B6D-887B998559B5 + + + + + + + +Spintherobolidae +Mirande, 2019 + +, new usage + + + + + + + +Type +genus: + + +Spintherobolus +Eigenmann, 1911 + +. + + +Included genera: + +Amazonspinther +Bührnheim +et al +., 2008 + +and + +Spintherobolus + +. + + + + +Definition: +The least inclusive crown clade that contains + +Amazonspinther dalmata +Bührnheim +et al +., 2008 + +and + +Spintherobolus papilliferus +Eigenmann, 1911 + +. This is a minimum-crown-clade definition. See +Figure 3 +for a reference phylogeny of +Spintherobolidae +. + + + + +Etymology: +From the ancient Greek σπινθΗΡο (spɪnθˈɜːɹo͡ʊ) meaning a spark and Βόƛος (bˈo͡ʊlo͡ʊz) meaning a throw with a casting net. + + + + +Remarks: +We delimit the family +Spintherobolidae +to include + +Amazonspinther + +and all species of + +Spintherobolus + +as the sister-lineage of a clade containing +Stevardiidae +, +Characidae +, and +Acestrorhamphidae +( +Figs 2 +, +3 +). +Spintherobolidae +are supported by 15 unambiguous synapomorphies relative to + +Cheirodontinae (Bührnheim +et al. +2008) + +, 10 of which are extensively discussed as synapomorphies for + +Spintherobolus + +(Malabarba 1998; (Weitzman and Malabarba 1998) or a clade containing + +A. dalmata + +and + +Spintherobolus +(Bührnheim +et al. +2008) + +. The lack of the mesocoracoid was also proposed as a synapomorphy for + +Amazonspinther + +and + +Spintherobolus +( +Mirande 2019 +) + +, thus reinterpreted here as synapomorphic for the +Spintherobolidae +. + + +Bührnheim +et al. +(2008) hypothesized + +Spintherobolus + +and + +Amazonspinther + +as sister to +Cheirodontinae +. The clade + +Spintherobolus + +and + +Amazonspinther + +has not been resolved as closely related to +Cheirodontinae +, but rather the sister-group of all other characids (Mariguela +et al +. 2013, Melo +et al. +2022a). Phylogenies inferred from a combined molecular and morphological dataset resolved former Spintherobolinae ( + +Amazonspinther + +, + +Atopomesus +Myers, 1927 + +, and + +Spintherobolus + +) as the sister-group of all characids except former + +Stethaprioninae ( +Mirande 2019 +) + +. Only morphological data were available for + +Atopomesus + +and its resolution within Spintherobolinae had low statistical support ( +Mirande 2019 +); phylogenetic analysis of the UCE loci resolves + +Atopomesus + +with high support in a distinct clade within the +Characinae +. The phylogeny inferred from the UCE loci offers a compelling hypothesis that + +Spintherobolus + +and + +Amazonspinther + +form the sister-group of a clade containing Acestrorhamphidae, Stevardiidae, and Characidae (Betancur-R +et al. +2019, Melo +et al +. 2022a; present study). + + + +Figure 3. +Phylogeny of +Spintherobolidae +and +Stevardiidae +and subfamilies Landoninae, Xenurobryconinae, +Glandulocaudinae +, Argopleurinae, Hemibryconinae, +Stevardiinae +, Planaltininae, Creagrutinae, and Diapominae based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support. + + + +Within Spintherobolidae, the Amazonian +Amazonspinther +is the sister-group of the + +Spintherobolus + +from the Atlantic coastal rivers and upper +Paraná +with + +S. papilliferus + +as sister to all other species, and + +S. broccae +Myers, 1925 + +sister to + +S. ankoseion +Weitzman and Malabarba, 1999 + +, and + +S. leptoura +Weitzman and Malabarba, 1999 + +( +Fig. 3 +). The UCE phylogeny and a previous molecular study are congruent with regards to the relationships within + +Spintherobolus +(Mattox +et al. +2023a) + +. + + + + \ No newline at end of file diff --git a/data/2D/3C/88/2D3C8869FFBBD55CFC771B91FC5DFD3C.xml b/data/2D/3C/88/2D3C8869FFBBD55CFC771B91FC5DFD3C.xml new file mode 100644 index 00000000000..47040bda874 --- /dev/null +++ b/data/2D/3C/88/2D3C8869FFBBD55CFC771B91FC5DFD3C.xml @@ -0,0 +1,91 @@ + + + +A revised and annotated checklist of the genus Passiflora L. in French Guiana + + + +Author + +Rome, Maxime +Jardin du Lautaret (SAJF), UAR 3370, CNRS, UGA, CS 40700 – 38058 Grenoble cedex 9 (France) +maxime.rome@univ-grenoble-alpes.fr + + + +Author + +MacDOUGAL, John M. +Missouri Botanical Garden, St. Louis, Missouri 63110 (United States) +decohere@charter.net + + + +Author + +Svoboda, Harlan T. +United States Department of Agriculture, U. S. National Arboretum, Floral and Nursery Plants Research Unit, Washington, D. C. 20002 (United States) +harlan.svoboda@usda.gov + + + +Author + +COPPENS D’EECKENBRUGGE, Geo +CIRAD, AGAP Institut, Avenue Agropolis, 34398 Montpellier (France) and AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier (France) +geo.coppens@cirad.fr + +text + + +Adansonia + + +2024 + +3 + + +2024-12-09 + + +46 + + +20 + + +197 +221 + + + + +https://sciencepress.mnhn.fr/sites/default/files/articles/pdf/adansonia2024v46a20.pdf + +journal article +306420 +10.5252/adansonia2024v46a20 +1e4217e2-ffec-4cca-afee-2d9fdf1ea55c +1639-4798 +14381791 + + + + + +Passiflora +subgen. +Passiflora + + + + + +INCLUDED +SPECIES +. — 27 species. Herbaceous or woody climbers, non-branched tendrils, stipules setaceous to foliaceous, bracts mainly well-developed, large flowers with hypanthium tubular or campanulate to flat. + + + + \ No newline at end of file