Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria Author Padial, José M. padialj@carnegiemnh.org Author Grant, Taran taran.grant@ib.usp.br Author Frost, Darrel R. padialj@carnegiemnh.org text Zootaxa 2014 2014-06-26 3825 1 1 132 journal article 10.11646/zootaxa.3825.1.1 1175-5326 4920347 1F6DEC4F-6E2A-45B6-A71C-3D6CF783FEDF Brachycephalidae This taxon includes the sister taxa Brachycephalus and Ischnocnema , a relationship first discovered by Heinicke et al. (2007) , who placed most southeastern Brazilian taxa then referred to “ Eleutherodactylus ” ( Frost et al. , 2006 ) in a redelimited Ischnocnema . Previously, Caramaschi & Canedo (2006) had restricted Ischnocnema to Ischnocnema verrucosa , and placed it in the synonymy of Eleutherodactylus . A new test of the sister relationship of Ischnocnema and Brachycephalus was recently provided by Canedo & Haddad (2012) , who found the taxa to be reciprocally monophyletic in both maximum likelihood and Bayesian analyses. Interestingly, their parsimony analysis of a similarity alignment placed Brachycephalus as the sister of Haddadus binotatus , another taxon from southeastern Brazil . Such a relationship had never been proposed, and although it is not corroborated in our analyses, it surely deserves future attention, particularly with regard to the effects of alignment and optimality criterion. Brachycephalus .—This genus of small, diurnal frogs that usually are brightly colored and contain tetrodotoxin ( Pires et al. 2005 ) is endemic to southeastern Brazil . Its unique pectoral girdle has long been recognized as a synapomorphy of the genus ( Izecksohn, 1971 ; Pombal & Gasparini, 2006 ) and was used to synonymize Psyllophryne ( i.e. , P. didactyla and P. hermogenesi ) with Brachycephalus by Kaplan (2002) , a synonymy subsequently validated by analyses of DNA sequences that found the two species to be nested among other species of Brachycephalus ( Clemente-Carvalho et al. , 2011 ; current results). Frost et al. (2006) , Heinicke et al. (2007) , Hedges et al. (2008a) , and Pyron & Wiens (2011) only included B. ephippium in their analyses, and Canedo & Haddad (2012) added B. cf. didactylus . Clemente-Carvalho et al. (2011) provided the first extensive molecular phylogenetic analysis of the genus by including 14 of the 18 currently recognized species ( Pombal & Izecksohn, 2011 ). Inadequate outgroup sampling (the tree was rooted on a single terminal of Ischnocnema ) prevented the monophyly of Brachycephalus , the position of Psyllophryne within Brachycephaloidea, or the sister relationships with Ischnocnema from being tested in that study. Nevertheless, our results agree with Clemente-Carvalho et al. ’s (2011) Bayesian analysis of the concatenated nuclear and mitochondrial data in recovering two major sister clades, a southern clade formed by locally endemic species restricted to the high and humid Atlantic Forest of Paraná ( B. brunneus , B. ferruginus , B. izecksohni , B. pernix , and B. pombali ) and the northern clade, allopatric to the first, distributed from farther north in Paraná to Espírito Santo ( B. alipioi , B. didactylus , B. ephippium , B. garbeanus , B. hermogenesi , B. nodoterga , B. pitanga , B. toby , and B. vertebralis ), with the two species of the former Psyllophryne placed separately in the second clade. Ischnocnema .— This genus is distributed within the Atlantic Forest of south, southeastern, and northeastern Brazil and Misiones , Argentina ( Canedo & Haddad, 2012 ; Frost, 2014 ). The monophyly of the genus was hypothesized by Heinicke et al. (2007) and Hedges et al. (2008a) , who analyzed 5 of the 33 species. A more complete test of generic monophyly was recently provided by Canedo & Haddad (2012) in a study that was published while the present manuscript was being written, which unfortunately precluded the use of their data in our analyses. Nevertheless, their taxon sampling of other brachycephalids was large enough (214 species) to provide a strong test of the monophyly of Ischnocnema . Their major finding was a polyphyletic Ischnocnema sensu Hedges et al. (2008a) with three named species ( I. paulodutrai , I. ramagii , and I. vinhai ) and two unnamed species recovered as part of the Pristimantis conspicillatus species group. Also, Ischnocnema bilineata was found to be the sister of a clade composed of the genera Noblella and Barycholos in Holoadeninae . Accordingly, Canedo & Haddad (2012) placed three nominal species of Ischnocnema in Pristimantis , but left " Eleutherodactylus " bilineatus Bokermann, 1975 "1974" as incertae sedis within Holoadeninae 6 (of Craugastoridae , below). For the remaining species of Ischnocnema , they recognized four monophyletic species series and left two species unassigned to any group, although five species were only tentatively assigned to groups based on their morphology. We follow their assignment of species to species series (see Appendix 2).