From c839c64626b071f278fe32a78f02a37931bdf4ce Mon Sep 17 00:00:00 2001 From: ggserver Date: Thu, 3 Oct 2024 18:24:49 +0000 Subject: [PATCH] Add updates up until 2024-10-03 18:18:44 --- .../E0/03F0E042C54EFF93FF67F9396317FBB7.xml | 616 +++++++++++++++++ .../A8/069BA8EDEDD751C3A991C489DDA6312D.xml | 312 +++++++++ .../B6/06CEB65661D45D8F8F7527579968CE87.xml | 622 ++++++++++++++++++ .../9A/4E3F9A59B628507BAA558B74BC462D31.xml | 582 ++++++++++++++++ .../5E/B7485EEF769A5EEB96E78957C7D0567B.xml | 326 +++++++++ 5 files changed, 2458 insertions(+) create mode 100644 data/03/F0/E0/03F0E042C54EFF93FF67F9396317FBB7.xml create mode 100644 data/06/9B/A8/069BA8EDEDD751C3A991C489DDA6312D.xml create mode 100644 data/06/CE/B6/06CEB65661D45D8F8F7527579968CE87.xml create mode 100644 data/4E/3F/9A/4E3F9A59B628507BAA558B74BC462D31.xml create mode 100644 data/B7/48/5E/B7485EEF769A5EEB96E78957C7D0567B.xml diff --git a/data/03/F0/E0/03F0E042C54EFF93FF67F9396317FBB7.xml b/data/03/F0/E0/03F0E042C54EFF93FF67F9396317FBB7.xml new file mode 100644 index 00000000000..e73694bae65 --- /dev/null +++ b/data/03/F0/E0/03F0E042C54EFF93FF67F9396317FBB7.xml @@ -0,0 +1,616 @@ + + + +Mitophylogeny of Pangasiid Catfishes and its Taxonomic Implications for Pangasiidae and the Suborder Siluroidei. + + + +Author + +Duong, Thuy Yen +College of Aquaculture and Fisheries, Can Tho University, 3 / 2 street, Can Tho City, Vietnam. E-mail: thuyyen @ ctu. edu. vn (Duong) +thuyyen@ctu.edu.vn + + + +Author + +Pham, Linh Thi Khanh +Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., & Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam + + + +Author + +Le, Xuyen Thi Kim +Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., & Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam + + + +Author + +Nguyen, Ngoc Tran Thi +College of Aquaculture and Fisheries, Can Tho University, 3 / 2 street, Can Tho City, Vietnam. E-mail: thuyyen @ ctu. edu. vn (Duong) +thuyyen@ctu.edu.vn + + + +Author + +Nor, Siti Azizah Mohd +Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia. E-mail: s. azizah @ umt. edu. my (Nor) +s.azizah@umt.edu.my + + + +Author + +Le, Thanh Hoa +Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., & Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam + +text + + +Zoological Studies + + +2023 + +2023-09-22 + + +62 + + +48 + + +1 +17 + + + + +http://dx.doi.org/10.6620/ZS.2023.62-48 + +journal article +10.6620/ZS.2023.62-48 +1810-522X +PMC10641430 +37965298 +12828486 + + + + + +Phylogenetic relationships within +Pangasiidae + + + + + +The complete mtDNA sequence datasets (concatenated 13 PCGs) recovered + +Pangasius + +and + +Pangasianodon + +as sister subclades and the +Pangasiidae +as a monophyletic clade with a 100% bootstrap value ( +Fig. 2 +). The ML tree clarified the monophyly of + +Pangasianodon + +and + +Pangasius + +with 88% bootstrap support. The ML tree clarified the monophyly of + +Pangasianodon + +, with 88% bootstrap support. + +Pangasianodon gigas + +is identified as a sister taxon to a group of + +P. sanitwongsei + +and + +Pn. hypophthalmus + +(5 mitogenomes), and + +Pangasius bocourti + +(as named in GenBank under no. MN842723) is positioned in the + +Pn. hypophthalmus + +group with 100% bootstrap support. Within the + +Pangasius + +, + +P. mekongensis + +was recovered as a sister taxon to the Indian + +Pangasius pangasius +Hamilton-Buchanan, 1822 + +( +Hossain et al. 2009 +) with a very high bootstrap (100%), while + +P. krempfi + +was placed in between + +P. larnaudii + +and the two abovementioned + +Pangasius +species + +( + +P. mekongensis + +and + +P. pangasius + +) with a moderate bootstrap value (68%). The most concerning feature is that + +P. sanitwongsei + +was positioned as a sister taxon to a subgroup of all the + +Pn. hypophthalmus + +sequences (bootstrap 98%), and was in between this subgroup and + +Pn. gigas + +( +Fig. 2 +). Several samples may have been misidentified and, therefore, phylogenetically misplaced. In fact, the sequence named “ + +Pangasianodon_hypophthalmus + +_(BaijinCo-Foshan)-China-MZ286355” is + +Pangasius larnaudii + +, and the “ + +Pangasius bocourti +(QingyuanGD) + +-China-MN842723” sample is + +Pangasianodon hypophthalmus + +. These pangasiid sequences were grouped into their corresponding phylogenetic clades ( +Fig. 2 +). + + +Furthermore, using single-gene datasets, we investigated the close phylogenetic relationships between + +Pangasius + +and + +Pangasianodon + +. Multiple +cox +1 and +cyt +B barcode sequences are available in GenBank and in previous publications; therefore, we downloaded all +cox +1 (551 bp) and +cyt +B (634 bp) sequences and extracted +cox +1 and +cyt +B, respectively, from the complete mitogenomes (listed in +Table S3 +). The +cox +1 and +cyt +B topologies also revealed that the +Pangasiidae +were a sister group to the +Austroglanididae +. All three families ( +Pangasiidae +, +Cranoglanididae +, and +Austroglanididae +) together with the +Ictaluridae +formed a large group that was always a sister group to the +Ariidae +, as discovered in the mitophylogeny constructed based on the complete mitogenome data in our current study and as in the previously reported analysis ( +Schedel et al. 2022 +). + + +The +cox +1 phylogenetic tree ( +Fig. 3 +) indicated that + +P. mekongensis + +(4 sequences) is a sister taxon to + +P. pangasius + +(8 sequences) with relatively high bootstrap support (88%). In the +cyt +B tree ( +Fig. 4 +), this species is sistered with + +P. pangasius + +with 100% nodal support. + +Pangasius krempfi + +, in the +cox +1 tree, was shown to be close to the + +Helicophagus +species + +( + +Helicophagus leptorhynchus + +and + +Helicophagus waandersii + +) with a low bootstrap of 44%, and was placed as a sister taxon in the +cyt +B tree in a non-stable phylogenetic relationship with a 63% bootstrap, to + +P. macronema + +and + +P. polyuranodon + +. The partial +cox +1 datasets (four sequences, consisting of two from +South Africa +, one from +China +, and one from +Cambodia +) and +cyt +B datasets (two sequences from +Thailand +and one from +China +) of the correctly identified + +P. sanitwongsei + +species placed this taxon into the + +Pangasius + +clade, although with low support (bootstrap 36% and 29%, respectively) ( +Figs. 3 +and +4 +). It should be noted that several + +P. sanitwongsei + +sequences, including Psan-(PB2)-( +China +)-JN020073 and Psan-(PB1)-CN-JN020086, as well as a + +P. bocourti + +sequence, Pboc-(QingyuanGD)-China-MN842723, were placed in the + +Pn. hypophthalmus + +cluster, which could be attributed to missampling or misidentification ( +Figs. 3 +and +4 +). + + + +Fig. 2. +PhyML-phylogeny of the order +Siluriformes +, including 32 catfish families (117 sequences) of three suborders, +Siluroidei +, +Loricarioidei +, and +Diplomystoidei +based on the complete concatenated nucleotide sequences of all 13 mitochondrial protein coding genes (about 11,408 bp in length) (Table S2). Two sequences of +Gonorynchiformes +were used as an outgroup. The alignment was performed by MAFFT ( +Katoh and Standley 2013 +), curated by BMGE v1.12 ( +Criscuolo and Gribaldo 2010 +), the tree was reconstructed in PhyML 3.3 ( +Guindon et al. 2010 +) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 ( +Rambaut 2018 +). The nodal bootstrap support values (shown at each node) were interpreted from the concurrently constructed tree using the above MAFFT-BMGE alignment by MEGA X ( +Kumar et al. 2018 +). The basal nodes of the three suborders ( +Diplomystoidei +, +Loricarioidei +, and +Siluroidei +) as well as the two major “Big Asia” and “Big Africa” groups (background highlighted) are shown by arrows. The + +Pangasius mekongensis + +, + +Pangasianodon hypophthalmus + +, and + +Pangasius krempfi + +sequences in this study are indicated by stars and with the associated families’ background highlighted. The taxa were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies ( +Saitoh et al. 2003 +; +Nakatani et al. 2011 +; +Kappas et al. 2016 +; +Zhang et al. 2021 +; +Schedel et al. 2022 +). The country of origin or geographical regions where the sample was reported are given in full name, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site. + + + + +Fig. 3. +Detailed PhyML-phylogeny based on the analysis of the partial +cox +1 sequences (551 bp) showing the detailed relationships of the family +Pangasiidae +and related families ( +Austroglanididae +, +Ictaluridae +, and +Cranoglanididae +). In total, 83 sequences, including 81 from + +Pangasius + +and + +Pangasianodon + +and 2 outgroup sequences from the order +Gymnotiformes +, were included (Table S3). The alignment was performed by MAFFT ( +Katoh and Standley 2013 +), curated by BMGE v1.12 ( +Criscuolo and Gribaldo 2010 +), the tree was reconstructed in PhyML 3.3 ( +Guindon et al. 2010 +) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 ( +Rambaut 2018 +). The basal nodes of the +Pangasiidae +and two sister groups ( + +Pangasianodon + +and ( + +Pangasius + ++ + +Helicophagus + ++ + +Pseudolais + +)) are shown by arrows. The + +Pangasius mekongensis + +, + +Pangasianodon hypophthalmus + +, and + +Pangasius krempfi + +sequences in this study are bolded. The taxonmisidentified sequences were added with a question mark at the end. The taxa from +Pangasiidae +were shortened and those from other related families were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies ( +Karinthanyakit and Jondeung 2012 +; +Tran and Duong 2019 +; +Schedel et al. 2022 +). The country of origin or where the sample was reported is given in full or in brackets, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site. + + +0 +. +05 + + +Fig. 4. +Detailed PhyML-phylogeny based on the analysis of the partial +cyt +B sequences (634 bp) showing the detailed relationships of the family +Pangasiidae +and related families ( +Austroglanididae +, +Ictaluridae +, and +Cranoglanididae +). In total, 80 sequences, including 78 from + +Pangasius + +and + +Pangasianodon + +and 2 outgroup sequences from the order +Clupeiformes +, were included (Table S3). The alignment was performed by MAFFT ( +Katoh and Standley 2013 +), curated by BMGE v1.12 ( +Criscuolo and Gribaldo 2010 +), the tree was reconstructed in PhyML 3.3 ( +Guindon et al. 2010 +) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 ( +Rambaut 2018 +). The basal nodes of the +Pangasiidae +and two sister groups ( + +Pangasianodon + +and ( + +Pangasius + ++ + +Helicophagus + ++ + +Pseudolais + +)) are shown by arrows. The + +Pangasius mekongensis + +, + +Pangasianodon hypophthalmus + +, and + +Pangasius krempfi + +sequences in this study are bolded. The taxonmisidentified sequences were added with a question mark at the end. The taxa from +Pangasiidae +were shortened and those from other related families were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies. The country of origin or where the sample was reported is given in full or in brackets, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site. + + + +In both the +cox +1 and +cyt +B phylogenies, the + +Pangasianodon + +was clearly resolved as a sister to the + +Pangasius + +with medium nodal support (bootstrap: 86% for +cox +1 and 52% for +cyt +B). While the monophyletic + +Pangasianodon + +was resolved with its two members ( + +Pn. gigas + +was the sister taxon to + +Pn. hypophthalmus + +in both the +cox +1 and the +cyt +B phylogenetic topologies), the + +Pangasius + +cluster included not only + +Pangasius + +but + +Helicophagus + +and + +Pseudolais +species + +as well. Though they had low bootstrap values (28% for +cox +1 and 29% for +cyt +B phylogeny), + +Helicophagus + +and + +Pseudolais +species + +were grouped as sister taxa to some of the + +Pangasius +species. + + + + + \ No newline at end of file diff --git a/data/06/9B/A8/069BA8EDEDD751C3A991C489DDA6312D.xml b/data/06/9B/A8/069BA8EDEDD751C3A991C489DDA6312D.xml new file mode 100644 index 00000000000..6a1940d3c2d --- /dev/null +++ b/data/06/9B/A8/069BA8EDEDD751C3A991C489DDA6312D.xml @@ -0,0 +1,312 @@ + + + +Vicars in the desert: Substrate specialisation and paleo-erosion underpin cryptic speciation in an Australian arid-zone lizard lineage (Diplodactylidae: Diplodactylus) + + + +Author + +McDonald, Peter J. +0000-0001-6875-1466 +Flora and Fauna Division, Northern Territory Department of Environment, Parks and Water Security, Arid Zone Research Institute, south Stuart Highway, Alice Springs, NT, 0870 Australia + + + +Author + +Fenner, Aaron L. +0000-0002-6952-9426 +College of Science and Engineering, Flinders University, Biological Sciences, Sturt Rd, Bedford Park, Adelaide, South Australia, 5042 + + + +Author + +Torkkola, Janne +0000-0001-6587-4655 +Centre for Planetary Health and Food Security, Griffith University, 170 Kessels Rd, Brisbane, Queensland 4121, and Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, Queensland, 4101 Australia + + + +Author + +Oliver, Paul M. +0000-0003-4291-257X +Centre for Planetary Health and Food Security, Griffith University, 170 Kessels Rd, Brisbane, Queensland 4121, and Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, Queensland, 4101 Australia + +text + + +Vertebrate Zoology + + +2024 + +2024-10-03 + + +74 + + +577 +594 + + + +journal article +10.3897/vz.74.e128775 +579E62D6-8A18-4E2D-9F6E-AC0642B48FB3 + + + + + +Diplodactylus galeatus +Kluge, 1973 + + + + + +Figures 5 A, B + + + + +Southern mesa gecko + + + + + +Holotype +. + + + + + +SAMA + +R 973 +, a +male +collected on the +Stuart Range +, +South Australia +( + +29.92 ° S +, +134.67 ° E + +) by +H. Greenfield +; designated by Kluge (1973). + + + + + + +Diagnosis from other species in the + +D. galeatus + +complex. + + + + +Diplodactylus galeatus + +may be distinguished from + +D. tjoritjarinya + + +sp. nov. + +(see below) by the larger ear opening (usually> 6 % of head width or ≥ +0.6 mm +in diameter in adults versus usually <6 % of head width or ≤ +0.5 mm +in diameter in + +D. tjoritjarinya + + +sp. nov. + +), the presence of dorsal blotches descending ≥ 1 / 4 distance down torso when animal is viewed in lateral profile (versus typically descending ~ 1 / 8 down torso in + +D. tjoritjarinya + + +sp. nov. + +), the presence of large white spots (> 3 scales in diameter) in the dorso-lateral region often arranged as mid-lateral row of ‘ portholes’ (versus smaller spots only), and by the dark red background colouration (versus pinkish red or red-brown). + +Diplodactylus galeatus + +may be distinguished from + +D. fyfei + + +sp. nov. + +by the smaller relative rostral scale height (usually ≤ 2.2 % of +SVL +versus usually> 2.2 % +SVL +in + +D. fyfei + + +sp. nov. + +). + +Diplodactylus galeatus + +further differs from the very similar + +D. fyfei + + +sp. nov. + +in at least 20 putatively fixed differences in the mitochondrial +ND 2 +locus (see Table +2 +). + + + + +Description. + + +A medium-sized (to +56 mm +) + +Diplodactylus + +with a robust build; head moderately wide ( +HeadW +/ +HeadL +– mean = 0.65, range = 0.56–0.74) and deep ( +HeadD +/ +HeadL +– mean = 0.44, range = 0.38–0.54); eyes large ( +OrbL +– mean = +3.5 mm +, range = 2.8–4.1); external ear opening relatively large (mean headW / ear = 0.08, range = 0.04–0.11). Supralabials much larger than bordering loreals, wider than high and decreasing in height posteriorly, first supralabial slightly taller or equal in height to second; infralabials 10–12; nostril surrounded by rostral scale, supranasals 2 and postnasals 3–5; relatively low rostral scale ( +Ros +/ +SVL +– mean = 0.021, range = +0.017 +–0.025 +), rostral crease usually present and descending one quarter to halfway from top of scale; mental scale lanceolate in shape and always longer than wide. + + +Scales on dorsum enlarged, up to twice diameter of those on lateral and ventral surfaces; dorsal head scales larger relative to neighbouring sides of head; scales on throat small and granular. Subdigital lamellae in single row of enlarged rounded scales; apical pad pair prominent and enlarged, much wider than proximal width of digit. Males have 3–7 cloacal spurs (median 5); females have rounded scales where the male spurs occur. Original tail short (mean Tail % +SVL +– mean = 0.51, range = 0.45–0.56) and thick, cylindrical, with regular annuli of slightly enlarged tubercles on dorsal and upper lateral surfaces. + +Top of head pale and yellowish-brown bordered posteriorly by a rounded dark line, dorsum dark red brown with four to five dark-edged pale blotches (rarely merged to form a continuous vertebral stripe; 14 % of individuals) that descend ≥ 1 / 4 distance down torso when animal is viewed in lateral profile, lateral region of torso with numerous white dots (including some> 3 scales wide) and frequently arranged in mid-lateral row, limbs usually with scattered white spots, and ventral surface white. + + + + +Particulars of +holotype +. + + + + +SAMA + +R 973 +adult male +(all measurements in millimetres): +SVL += 52.7, +TrunkL += 23.4, +TailL += 27.0, TArmL = 20.3, TlegL = 25.0, +HeadL += 14.8, +HeadW += 10.4, +RosCre += 0.0, SupNas = 2, SupLab = 9, InfLab = 11, Cspurs = 6, 4 Flam = 7; 4 Tlam = 8. + + + + +Etymology. + + +Derived from the Latin word +galea +meaning covered with a helmet in reference to the dark occipital cap. + + + + +Distribution and ecological notes. + + +Endemic to +South Australia +and restricted to the western Stony Plains +IBRA +region (Thackway and Creswell 1995). Recorded from Prominent Hill in the south, north to approximately +15 km +north of Iwantja and east to near Old Peake Telegraph Station. + + +Occurs on and around dissected tablelands or ‘ breakaway’ hills with sparse tussock grass and lower shrub layers and a very sparse + +Acacia + +shrub overstory. Observed to be abundant in some areas of its range, with large numbers of specimens observed in a relatively short period of spotlighting in the Breakaways near Coober Pedy (P. Oliver pers. obs.). Recorded in syntopy with + +Gehyra versicolor + +and + +Heteronotia binoei +. + + + + + +Suggested IUCN Red List status. + + + +Diplodactylus galeatus + +has a moderately large range (EOO +23,012 km +2 +) spanning areas that are sparsely inhabited, not subject to widespread habitat destruction or disturbance and including several protected areas (6.96 % of the Stony Plains bioregion). Based on these data we suggest that it be considered Least Concern. + + + + \ No newline at end of file diff --git a/data/06/CE/B6/06CEB65661D45D8F8F7527579968CE87.xml b/data/06/CE/B6/06CEB65661D45D8F8F7527579968CE87.xml new file mode 100644 index 00000000000..157c95d9357 --- /dev/null +++ b/data/06/CE/B6/06CEB65661D45D8F8F7527579968CE87.xml @@ -0,0 +1,622 @@ + + + +Vicars in the desert: Substrate specialisation and paleo-erosion underpin cryptic speciation in an Australian arid-zone lizard lineage (Diplodactylidae: Diplodactylus) + + + +Author + +McDonald, Peter J. +0000-0001-6875-1466 +Flora and Fauna Division, Northern Territory Department of Environment, Parks and Water Security, Arid Zone Research Institute, south Stuart Highway, Alice Springs, NT, 0870 Australia + + + +Author + +Fenner, Aaron L. +0000-0002-6952-9426 +College of Science and Engineering, Flinders University, Biological Sciences, Sturt Rd, Bedford Park, Adelaide, South Australia, 5042 + + + +Author + +Torkkola, Janne +0000-0001-6587-4655 +Centre for Planetary Health and Food Security, Griffith University, 170 Kessels Rd, Brisbane, Queensland 4121, and Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, Queensland, 4101 Australia + + + +Author + +Oliver, Paul M. +0000-0003-4291-257X +Centre for Planetary Health and Food Security, Griffith University, 170 Kessels Rd, Brisbane, Queensland 4121, and Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, Queensland, 4101 Australia + +text + + +Vertebrate Zoology + + +2024 + +2024-10-03 + + +74 + + +577 +594 + + + +journal article +10.3897/vz.74.e128775 +579E62D6-8A18-4E2D-9F6E-AC0642B48FB3 + + + + + +Diplodactylus tjoritjarinya + +sp. nov. + + + + +Figures 5 E, F, S 2 + + + + + + + +Tjoritja +gecko + + + + + + + + +Holotype +. + + + + + +NTM +R 20862 + +, a +male +collected in +Alice Springs +( + +23.7 ° S +, +133.87 ° E + +) by +P. Horner +on + + +16 +th +October 1990 + + +. + + + + + + +Paratypes +. + + + + + +NTM +R 20865 + +, +male +, +Alice Springs +( + +23.7 ° S +, +133.87 ° E + +) + +; + + +SAMA +R 38848 + +, +female +, +junction of Larapinta and Namatjira Drives +( + +23.77 ° S +, +133.15 ° E + +) + +; + + +SAMA +R 38861 + +, +male +, +Junction Waterhole + +10 km +north of + +Alice Springs +( + +23.62 ° S +, +133.88 ° E + +) + +; + + +SAMA +R 40591 + +, +male +, +Upper Stokes Creek +, +Watarrka National Park +(– + +24.28 ° S +, +131.68 ° E + +) + +. + + + + +Referred material. + + + + +NTM +R 15378 + +, + +6 km +SSW of + +Claraville Homestead +, +NT +( + +– +23.417 ° S +, +134.726 ° E + +) + +; + + +NTM +R 15795 + +, + +4 km +SSE of + +Southern Cross Bore +, +Garden Station +, +NT +( + +– +23.417 ° S +, +134.726 ° E + +) + +; + + +NTM +R 32488 + +, +Palm Valley Well No. +, +NT +( + +– +24 ° S +, +132.65 ° E + +) + +; + + +NTM +R 32489 + +, +Alice Springs +, +NT +( + +– +23.7 ° S +, +133.883 ° E + +) + +; + + +NTM +R 32492–4 + +, +Alice Springs +, +NT +( + +– +23.7 ° S +, +133.867 ° E + +) + +. + + + + + +Diagnosis from other species in the + +D. galeatus + +complex. + + + + +Diplodactylus tjoritjarinya + + +sp. nov. + +may be distinguished from + +D. galeatus + +and + +D. fyfei + + +sp. nov. + +by the smaller ear opening (usually ≤ 5 % of head width or ≤ +0.6 mm +in diameter in adults versus usually> 6 % of head width or ≥ +0.6 mm +in diameter in adult + +D. galeatus + +and + +D. tjoritjarinya + + +sp. nov. + +), the presence of dorsal blotches descending <1 / 4 and typically ~ 1 / 8 distance down torso when animal is viewed in lateral profile (versus typically descending ≥ 1 / 4 down torso in + +D. galeatus + +and + +D. fyfei + + +sp. nov. + +), the absence of large white spots (> 3 scales in diameter) in the dorso-lateral region, and by the pinkish red or red-brown background colouration (versus dark red). + + + + +Description. + + +A medium-sized + +Diplodactylus + +(to +56.2 mm +) with robust build; head moderately wide ( +HeadW +/ +HeadL +– mean = 0.66, range = 0.5–0.81) and deep ( +HeadD +/ +HeadL +– mean = 0.47, range = 0.4–0.54); eyes large ( +OrbL +– mean = 3.5, range = 2.7–4.3); external ear opening relatively small (mean +HeadW +/ ear = 0.05, range = 0.02–0.07). Supralabials much larger than bordering loreals, 8–10, wider than high and decreasing in height posteriorly, first supralabial slightly taller or equal in height to second; 10–12 infralabials; nostril surrounded by rostral scale, 2 supranasals and 3–5 postnasals; relatively low rostral scale ( +Ros +/ +SVL +– mean = 0.021, range = +0.015 +–0.032 +), rostral crease usually present and descending one quarter to two thirds down from top of scale; mental scale lanceolate in shape and usually longer than wide. + + +Scales on dorsum enlarged, up to twice diameter of those on lateral and ventral surfaces; dorsal head scales larger relative to neighbouring sides of head; scales on throat small and granular. Subdigital lamellae in single row of enlarged rounded scales; large apical pads, much wider than proximal width of digit. Males have 3–10 cloacal spurs (median 5); females have rounded scales where the male spurs occur. Original tail short (mean Tail / +SVL +– mean = 0.52, range = 0.44–0.57) and thick, cylindrical, covered dorsally with regular annuli of slightly enlarged tubercles. + +Top of head pale yellowish-brown and bordered posteriorly by a rounded dark line, dorsum of body pinkish red to red-brown with 3–8 (median = 5) dark-edged pale yellowish-brown blotches that descend <1 / 4 distance down torso when animal is viewed in lateral profile, lateral region of torso with numerous irregular white dots 1–3 scales wide, dorsal colouration and pattern continue onto original tail (with 2–5 blotches), and ventral surface white. + + + + +Particulars of the +holotype +. + + + +An adult male (Fig. S 2). +SVL += 44.2, +TrunkL += 24.7, +TailL += 24.0, +TailW += 4.4, +ArmL += 7.1, +LegL += 8.7, +HeadL += 12.4, +HeadW += 8.8, +HeadD += 6.6, +IO += 7.4, +NarEye += 3.4, Internar = 1.5, +Ros += 0.9, +RosCre += 0.6, MentalL = 1.5, MentalW = 1.2, SupNas = 2, SupLab = 13, InfLab = 11, CSpurs = 5, 4 Flam = 7; 4 TLam = 9, No. SC = 52. Six pale dorsal blotches present on body and extending <1 / 8 down torso when viewed in lateral profile. Irregular pattern of small white dots (<3 scales wide) on dorso-lateral region. + + + + +Etymology. + + + + +Tjoritja + + +is a Western and Central Aranda name for the MacDonnell Ranges. Aranda people sometimes refer to themselves as + + +Tjoritja + + +- rinya (pronounced ‘ choor-it-ja-rin-ya’) – meaning belonging to + + +Tjoritja + + +. This name respects that + + +Tjoritja + + +is a living cultural landscape to which this gecko belongs and was suggested as a name for this gecko by the Traditional Owners of + + +Tjoritja + + +National Park. Used as a noun in apposition. + + + + +Distribution and ecology. + + +Endemic to the +Northern Territory +and restricted to the MacDonnell Ranges +IBRA +region ( +Thackway and Cresswell 1995 +). The distribution includes the James and Krichauff Ranges in the south, as far southwest as the George Gill Range, east to the Hale River about +40 km +southeast of Ruby Gap Nature Park, northeast to the Harts Range area, and north west to at least Ormiston Gorge in + + +Tjoritja + + +National Park. Recorded at elevations ranging from +416–1102 m +a. s. l. + + +Nocturnally active on the ground on rocky substrates and geology +types +that include sandstone, limestone, gneiss, quartzite, and conglomerate. Landforms include low rolling hills, stony flats and rugged mountain ranges, with hummock or tussock grassland vegetation, usually with a sparse + +Acacia + +or mallee + +Eucalyptus + +shrub layer. + + +Individuals have been observed emerging from small invertebrate burrows at dusk and have also been found sheltering underneath small rocks during the day in cool weather (P. +McDonald +pers. obs). Frequently observed perched atop small loose or partially embedded rocks rather than actively foraging, suggesting an ambush predation foraging mode. Absent from exposed rock faces and escarpments. Recorded in syntopy with + +Crenadactylus horni + +, + +Diplodactlyus conspicillatus + +, + +Gehyra versicolor + +, + +Heteronotia binoei + +, + +Nephrurus amyae + +, and + +Rhynchoedura ornata + +(P. +McDonald +pers. obs.). Appears to be absent from large boulders, rock faces and escarpments inhabited by the saxicoline Central Ranges endemic geckos + +Gehyra moritzi + +, + +Heteronotia fasciolatus + +, + +Oedura cincta + +, and + +O. luritja + +. + + + + +Suggested IUCN Red List status. + + + +Diplodactylus tjoritjarinya + + +sp. nov. + +has a moderate range size (estimated EOO +9365 km +2 +) spanning areas that are not subject to widespread habitat destruction or disturbance and including several protected areas (e. g., +Tjoritja +National Park; terrestrial protected areas comprise 14.2 % of the MacDonnell Ranges +IBRA +). Recent attempts to locate + +D. tjoritjarinya + + +sp. nov. + +in areas with dense Buffel grass ( + +Cenchrus ciliaris + +) near Alice Springs have failed, suggesting this invasive species impacts habitat suitability for the species (P. +McDonald +pers. obs.). However, Buffel grass is a minor floristic component across most suitable habitats for + +D. tjoritjarinya + + +sp. nov. + +(including both ESU’s). Based on these data we suggest that it be considered Least Concern, but the potential impact of Buffel grass on habitat suitability may warrant further investigation. + + + + \ No newline at end of file diff --git a/data/4E/3F/9A/4E3F9A59B628507BAA558B74BC462D31.xml b/data/4E/3F/9A/4E3F9A59B628507BAA558B74BC462D31.xml new file mode 100644 index 00000000000..dcd592ef417 --- /dev/null +++ b/data/4E/3F/9A/4E3F9A59B628507BAA558B74BC462D31.xml @@ -0,0 +1,582 @@ + + + +Vicars in the desert: Substrate specialisation and paleo-erosion underpin cryptic speciation in an Australian arid-zone lizard lineage (Diplodactylidae: Diplodactylus) + + + +Author + +McDonald, Peter J. +0000-0001-6875-1466 +Flora and Fauna Division, Northern Territory Department of Environment, Parks and Water Security, Arid Zone Research Institute, south Stuart Highway, Alice Springs, NT, 0870 Australia + + + +Author + +Fenner, Aaron L. +0000-0002-6952-9426 +College of Science and Engineering, Flinders University, Biological Sciences, Sturt Rd, Bedford Park, Adelaide, South Australia, 5042 + + + +Author + +Torkkola, Janne +0000-0001-6587-4655 +Centre for Planetary Health and Food Security, Griffith University, 170 Kessels Rd, Brisbane, Queensland 4121, and Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, Queensland, 4101 Australia + + + +Author + +Oliver, Paul M. +0000-0003-4291-257X +Centre for Planetary Health and Food Security, Griffith University, 170 Kessels Rd, Brisbane, Queensland 4121, and Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, Queensland, 4101 Australia + +text + + +Vertebrate Zoology + + +2024 + +2024-10-03 + + +74 + + +577 +594 + + + +journal article +10.3897/vz.74.e128775 +579E62D6-8A18-4E2D-9F6E-AC0642B48FB3 + + + + + +Diplodactylus fyfei + +sp. nov. + + + + +Figures 5 C, D, S 2 + + + + +Fyfe’s mesa gecko + + + + + +Holotype +. + + + + + +NTM +R 39440 + +, a +male +collected in the +foothills east of Mt Beddome on New Crown Station +( + +25.78252 ° S +, +134.35169 ° E + +) by +P. McDonald +on + + +3 +rd +December 2023 + + +. + + + + + + +Paratypes +. + + + + + +NTM +R 39439 + +, +female +, +foothills east Mt Beddome +, +New Crown Station +, +NT +( + +25.78252 ° S +, +134.35169 ° E + +) + +; + + +NTM +R 39441 + +, +female +, +foothills near Mt Beddome +, +New Crown Station +, +NT +( + +25.78252 ° S +, +134.35169 ° E + +) + +; + + +SAMA +R 25851 + +, +male +, +Eringa Station +, + +SA + +( + +26.28 ° S +, +134.72 ° E + +) + +; + + +SAMA +R 47003 + +, +female +, + +10 km +WSW of + +Mosquito Camp Dam +, +New Crown Station +, + +SA + +( + +26.1606 ° S +, +134.3997 ° E + +) + +. + + + + +Referred material. + + + + +NTM +R 39442 + +, +foothills east of Mt Beddome +, +New Crown Station +, +NT +( + +25.78252 ° S +, +134.35169 ° E + +) + +; + + +NTM +R 39443–4 + +, +foothills of Mt Beddome +, +New Crown Station +, +NT +( + +– +25.78122 ° S +, +134.36182 ° E + +) + +; + + +SAMA +R 25852 + +, +Eringa Station +, + +SA + +( + +26.28 ° S +, +134.72 ° E + +) + +; + + +SAMA +R 47002 + +, + +10 km +WSW of + +Mosquito Camp Dam +, +New Crown Station +, + +SA + +( + +26.1606 ° S +, +134.3997 ° E + +) + +; + + +SAMA +R 47004 + +, + +10 km +WSW of + +Mosquito Camp Dam +, +New Crown Station +, + +SA + +( + +26.1606 ° S +, +134.3997 ° E + +) + +. + + + + + +Diagnosis from other species in the + +D. galeatus + +complex. + + + + +Diplodactylus fyfei + + +sp. nov. + +may be distinguished from + +D. tjoritjarinya + + +sp. nov. + +(see below) by the presence of dorsal blotches descending ≥ 1 / 4 distance down torso when animal is viewed in lateral profile (versus typically descending ~ 1 / 8 down torso in + +D. tjoritjarinya + + +sp. nov. + +), the presence of large white spots (> 3 scales in diameter) in the dorso-lateral region often arranged as mid-lateral row of ‘ portholes’ (versus smaller spots only), and by the dark red background colouration (versus pinkish red or red-brown). + +Diplodactylus fyfei + + +sp. nov. + +may be distinguished from + +D. galeatus + +by the larger relative rostral scale height (usually> 2.2 % of +SVL +versus usually ≤ 2.2 % +SVL +in + +D. galeatus + +). + +Diplodactylus fyfei + + +sp. nov. + +further differs from the very similar + +D. galeatus + +in at least 20 putatively fixed differences in the mitochondrial +ND 2 +locus (see Table +2 +). + + + + +Description. + + +A medium-sized + +Diplodactylus + +(to +53 mm +) with robust build; head moderately wide ( +HeadW +/ +HeadL +– mean = 0.66, range = 0.58–0.76) and deep ( +HeadD +/ +HeadL +– mean = 0.45, range = 0.38–0.52); eyes large ( +OrbL +– mean = +3.4 mm +, range = 2.3–3.8); external ear opening relatively large (mean +HeadW +/ +Ear += 0.06, range = 0.05–0.08). Supralabials, 8–10, much larger than bordering loreals, wider than high and decreasing in height posteriorly, first supralabial slighty taller or equal in height to second; infralabials 10–12; nostril surrounded by rostral scale, supranasals 2 and postnasals 3–5; relatively high rostral scale ( +Ros +/ +SVL +– mean = 0.023, range = +0.021 +–0.028 +), rostral crease usually present and descending one quarter to halfway from top of scale; mental scale lanceolate in shape and always longer than wide. + + +Scales on dorsum enlarged, up to twice diameter of those on lateral and ventral surfaces; head scales larger relative to neighbouring sides of head; scales on throat small and granular. Subdigital lamellae in single row of enlarged rounded scales; apical pad pair prominent and enlarged, much wider than proximal width of digit. Males have 5–6 cloacal spurs (median 5); females have rounded scales where the male spurs occur. Original tail short (mean Tail / +SVL +– mean = 0.52, range = 0.47–0.60) and thick, cylindrical, with regular annuli of slightly enlarged tubercles on dorsal and upper lateral surfaces. + +Top of head pale and yellowish-brown bordered posteriorly by a rounded dark line, dorsum of dark red brown with 4–5 (median = 5) dark-edged pale blotches (rarely merged to form a continuous vertebral stripe; 9 % of individuals) that descend ≥ 1 / 4 distance down torso when animal is viewed in lateral profile, lateral region of torso with numerous white dots (including some> 3 scales wide) and frequently arranged in mid-lateral row, limbs usually with scattered white spots, dorsal colouration and pattern continue onto original tail (with 2–5 blotches), and ventral surface white. + + + + +Particulars of the +holotype +. + + + +An adult male (Fig. S 2). +SVL += 46.9, +TrunkL += 19.6, +TailL += 26.5, +TailW += 5.8, +ArmL += 8.3, +LegL += 9.6, +HeadL += 15.1, +HeadW += 10., +HeadD += 7.7, +IO += 7.4, +NarEye += 4.5, Internar = 1.6, +Ros += 1.1, +RosCre += 0.4, MentalL = 1.6, MentalW = 1.2, SupNas = 2, SupLab = 13, InfLab = 12, CSpurs = 5, 4 FLam = 6, 4 TLam = 10, No. SC = 49. Rostral scale height relatively large (2.3 % of +SVL +). Five pale dorsal blotches present on body and extending up to 1 / 3 down torso when viewed in lateral profile. Large white spots (> 3 scale in diameter) present on dorso-lateral region and arranged as mid-lateral row of ‘ portholes’. + + + + +Etymology. + +Named for the pioneering herpetologist Greg Fyfe in recognition of his substantial contribution to the knowledge and conservation of central Australia’s reptile fauna. + + + +Distribution and ecology. + + +Restricted to extreme northern Stony Plains +IBRA +region ( +Thackway and Cresswell 1995 +) straddling the +Northern Territory +/ +South Australia +border. Records in the +Northern Territory +are associated with Beddome Range on New Crown Station. Potentially suitable habitat also occurs further west on Umbeara and Tieyon Stations in +NT +and + +SA + +, respectively. + + +Recorded nocturnally active on the ground in and around dissected tablelands or mesas on sandstone and shale geologies. Vegetation usually includes a sparse tussock grass and lower shrub layers and a very sparse + +Acacia + +shrub overstory. Usually observed perched atop rocks rather than actively foraging and one individual was encountered in a low shrub ( + +Eremophila freelingii + +) (P. +McDonald +pers. obs.). Recorded in syntopy with + +Gehyra versicolor + +, + +Heteronotia binoei + +and + +Underwoodisaurus milii + +. + + + + +Suggested IUCN Red List status. + + + +Diplodactylus fyfei + + +sp. nov. + +has the smallest distribution of the three taxa in the + +D. galeatus + +species complex (EEO = +654 km +2 +) and has not been recorded from any protected areas. However, it is likely that further sampling in areas of dissected tableland along the +NT +/ + +SA + +border to the west will increase its known range. Further, the areas inhabited by + +Diplodactylus fyfei + + +sp. nov. + +are sparsely inhabited and have not been subjected to widespread habitat destruction or disturbance. Based on these data we suggest that it be considered Least Concern. + + + + \ No newline at end of file diff --git a/data/B7/48/5E/B7485EEF769A5EEB96E78957C7D0567B.xml b/data/B7/48/5E/B7485EEF769A5EEB96E78957C7D0567B.xml new file mode 100644 index 00000000000..9ef2dbdd131 --- /dev/null +++ b/data/B7/48/5E/B7485EEF769A5EEB96E78957C7D0567B.xml @@ -0,0 +1,326 @@ + + + +Vicars in the desert: Substrate specialisation and paleo-erosion underpin cryptic speciation in an Australian arid-zone lizard lineage (Diplodactylidae: Diplodactylus) + + + +Author + +McDonald, Peter J. +0000-0001-6875-1466 +Flora and Fauna Division, Northern Territory Department of Environment, Parks and Water Security, Arid Zone Research Institute, south Stuart Highway, Alice Springs, NT, 0870 Australia + + + +Author + +Fenner, Aaron L. +0000-0002-6952-9426 +College of Science and Engineering, Flinders University, Biological Sciences, Sturt Rd, Bedford Park, Adelaide, South Australia, 5042 + + + +Author + +Torkkola, Janne +0000-0001-6587-4655 +Centre for Planetary Health and Food Security, Griffith University, 170 Kessels Rd, Brisbane, Queensland 4121, and Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, Queensland, 4101 Australia + + + +Author + +Oliver, Paul M. +0000-0003-4291-257X +Centre for Planetary Health and Food Security, Griffith University, 170 Kessels Rd, Brisbane, Queensland 4121, and Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, Queensland, 4101 Australia + +text + + +Vertebrate Zoology + + +2024 + +2024-10-03 + + +74 + + +577 +594 + + + +journal article +10.3897/vz.74.e128775 +579E62D6-8A18-4E2D-9F6E-AC0642B48FB3 + + + + +Genus + +Diplodactylus +Gray, 1832 + + + + + + +Type +species. + + + + +Diplodactylus vittatus +Gray, 1832 + +. A genus of +Diplodactylidae +(sensu +Han et al. 2004 +) characterised by robust habitus, wide scansors, numerous (typically> 5) cloacal spurs, two pairs of cloacal bones and an anteriorly enlarged jugal bone entering floor of lacrimal foramen ( +Oliver et al. 2007 +). + + + + + +Diagnosis of the + +Diplodactylus galeatus + +species complex. + + + +All three species in the + +D. galeatus + +complex can be differentiated from all other + +Diplodactylus + +by the following combination of characters: medium size (to +56 mm +); robust build and relatively short (44–60 % of +SVL +) thick tail with regular annuli of slightly enlarged tubercles separated by rows of smaller scales; enlarged dorsal scales up to twice diameter of ventral scales; snout rounded in profile; supralabials and infralabials much larger than bordering loreals; rostral scale in contact with nostril; expanded apical lamellae on all digits; top of head pale yellowish-brown and bordered posteriorly by a rounded dark line; dorsum of body pinkish red to dark red with three to eight dark-edged pale yellowish-brown blotches; and ventral surface uniform white without any pattern. + + +Species in + +D. galeatus + +complex specifically differ from other Australian + +Diplodactylus + +as follows: from + +D. ameyi + +, + +D. barraganae + +, + +D. bilybara + +, + +D. calcicolus + +, + +D. capensis + +, + +D. conspicillatus + +, + +D. custos + +, + +D. fuller + +, + +D. furcosus + +, + +D. galaxias + +, + +D. granariensis + +, + +D. hillii + +, + +D. kenneallyi + +, + +D. laevis + +, + +D. lateroides + +, + +D. mitchelli + +, + +D. nebulosus + +, + +D. ornatus + +, + +D. platyurus + +, + +D. polyophthalmus + +, + +D. savage + +, + +D. tessellatus + +, + +D. vittatus + +, and + +D. wiru + +by the presence of a series of pale yellowish-brown, dark-edged dorsal blotches on the body and tail; from the eight species in the + +D. conspicillatus + +complex ( + +D. ameyi + +, + +D. barraganae + +, + +D. bilybara + +, + +D. conspicillatus + +, + +D. custos + +, + +D. hillii + +, + +D. laevis + +, and + +D. platyurus + +) by the presence of enlarged supralabials (versus absent) and terminal lamellae on fingers noticeably wider than digit (versus not wider); from + +D. galaxias + +, + +D. kenneallyi + +, + +D. pulcher + +, and + +D. savagei + +in having rostral scale in contact with nostril (versus nostril separated from rostral by small scale); from + +D. calcicolus + +, + +D. capensis + +, + +D. furcosus + +, + +D. granariensis + +, + +D. nebulosus + +, + +D. vittatus + +and + +D. wiru + +by the supra and infralabial scales being wider than tall (versus approximately square); from + +D. lateroides + +and + +D. polyophthalmus + +by the presence of dark edges to the dorsal blotches; and from + +D. mitchelli + +and + +D. ornatus + +by the absence of a continuous vertebral stripe (rarely present in the + +D. galeatus + +species complex). + + + + \ No newline at end of file