Phylogeny of Riama (Squamata: Gymnophthalmidae), impact of phenotypic evidence on molecular datasets, and the origin of the Sierra Nevada de Santa Marta endemic fauna

Abstract

Riama is the most speciose genus of the Neotropical lizard family Gymnophthalmidae. Its more than 30 montane species occur throughout the northern Andes, the Cordillera de la Costa (CC) in Venezuela, and Trinidad. We present the most comprehensive phylogenetic analysis of Riama to date based on a total evidence (TE) approach and direct optimization of molecular and morphological evidence. Analyses use DNA sequences from four loci and 35 phenotypic characters. The dataset consists of 55 ingroup terminals representing 25 of the 30 currently recognized species of Riama plus five undescribed taxa, including an endemic species from the Sierra Nevada de Santa Marta (SNSM) in Colombia, and 66 outgroup terminals of 47 species. Analysis results in a well-supported hypothesis in which Riama is polyphyletic, with its species falling into three clades. The Tepuian Anadia mcdiarmidi nests within one clade of Riama, and the recently resurrected Pantodactylus nests within Cercosaura. Accordingly, we propose a monophyletic taxonomy that reflects historical relationships. Analysis of character evolution indicates that the presence/absence of prefrontals-a cornerstone of the early genus-level taxonomy of cercosaurines-is optimally explained as having been plesiomorphically present in the most recent common ancestor of Cercosaurinae and lost in that of the immediately less inclusive clade. Multiple independent reversals to present and subsequent returns to absent occur within this clade. To evaluate the impact of phenotypic evidence on our results, we compare our TE results with results obtained from analyses using only molecular data. Although phenotypic evidence comprises only 1.2% of the TE matrix, its inclusion alters both the topology and support values of the clades that do not differ. Finally, current phylogenetic evidence reveals a SNSM-CC-Trinidad-tepuis biogeographical link. We hypothesize that an ancient connection facilitated the exchange of species between the SNSM and the CC.

A New Species of Andean Gymnophthalmid Lizard (Squamata: Gymnophthalmidae) from the Peruvian Andes, and Resolution of Some Taxonomic Problems

“…Our phylogenetic ML ( Figure 2) tree inferred using fragments of four mitochondrial and one nuclear gene is congruent with other studies [6,11,12,51,52], except that it recovered the monophyly of Proctoporus and that the recently described genus Wilsonosaura is nested within the Proctoporus lineage (Bootstrap: 76). However, trees using only mitochondrial ( Figure S1) and nuclear ( Figure S2) markers are not congruent.…”

“…The ML topology obtained in this study using concatenated sequences of mitochondrial and nuclear genes recovered the monophyly of Proctoporus and included the genus Wilsonosaura within Proctoporus. This topology contrasts with previous studies that did not support the monophyly of Proctoporus, suggesting additional studies are needed to solve the taxonomy and phylogenetic position of Proctoporus [6,11,12,51,52]. Moreover, our study considered 129 terminals and addressed the taxonomy and phylogenetic relationships of the three species of Cercosaura (Cercosaura anomala, "Cercosaura manicata boliviana", and Cercosaura pacha sp.…”

Description and Phylogeny of a New Species of Andean Lizard (Gymnophthalmidae: Cercosaurinae) from the Huancabamba Depression

“…Nonetheless, all species of Macropholidus and Pholidobolus examined to date share a bulge marking the margins of the asulcate face (Nunes, 2011;Torres-Carvajal et al, 2014;Venegas et al, 2016, Parra et al, 2020), which we propose as a putative synapomorphy of the clade Macropholidus + Pholidobolus as it has not been described in other species of Cercosaurine lizards. The conservative hemipenial morphology of this clade contrasts with the variation reported in some clades of gymnophthalmid lizards, in which hemipenes bear diagnostic characters at the species level (e.g., Nunes et al, 2012;Rodrigues et al, 2017;Kok et al, 2018). Only a more comprehensive examination of the hemipenes within the Cercosaurinae will shed some light on their evolution.…”

“…More than one third of the known diversity within Cercosaurinae (i.e., 52 of 147 species) has only been discovered during this century, at a rate of ~2.5 species per year. In addition, recent DNA-based phylogenetic studies have provided major insights into the phylogeny of Cercosaurinae along with numerous taxonomic changes including new generic names and new combinations (e.g., Castoe et al, 2004;Doan and Castoe, 2005;Goicoechea et al, 2012;Sánchez-Pacheco et al, 2017;Moravec et al, 2018). In this context, the sister clades Pholidobolus Peters, 1863 andMacropholidus Noble, 1921, traditionally ranked as genera, were recently redefined.…”

Análise filogenética do clado K92, com ênfase em Gonyleptinae, baseada em caracteres morfológicos e moleculares (Opiliones, Gonyleptidae)

“…A otimização direta testa possíveis hipóteses de homologia dos nucleotídeos de forma dinâmica, otimizando as sequências não-alinhadas diretamente nas árvores disponíveis, ao mesmo tempo em que converte as séries de transformação pré-alinhadas, frutos da otimização (i.e., os nucleotídeos alinhados), em uma matriz estática (Kluge & Grant, 2006;Grant & Kluge, 2009;Sánchez-Pacheco et al, 2017 (Wheeler, 1995;Kluge, 1997Kluge, , 1998Giribet, 2003;Grant & Kluge, 2005;Giribet & Wheeler, 2007;ver um (Goloboff, 1996); Ratchet (Nixon, 1999); e Tree Fusing (Goloboff, 1999 As medidas de suporte calculadas foram Goodman-Bremer (Goodman et al, 1982;Bremer, 1988;Grant & Kluge, 2008) e Bootstrap (Felsenstein, 1985). Os cálculos das medidas de suporte foram feitos no TNT (Goloboff et al, 2003(Goloboff et al, , 2008 As análises baseadas somente em caracteres morfológicos foram realizadas no programa TNT, através de busca heurística usando o algoritmo TBR, com 1000 replicações e salvando 100 árvores por réplica.…”