<p><strong>Molecular systematics of terraranas (Anura: Brachycephaloidea) </strong><strong>with an assessment of the effects of alignment and optimality criteria</strong></p>

Abstract

Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY. To elucidate the effects of alignment and optimality criterion on phylogenetic inferences, we also used the program MAFFT to obtain a similarity-alignment for analysis under both parsimony and maximum likelihood using the programs TNT and GARLI, respectively. Although all three analytical approaches agreed on numerous points, there was also extensive disagreement. Tree-alignment under parsimony supported the monophyly of the ingroup and the sister group relationship of the monophyletic marsupial frogs (Hemiphractidae), while maximum likelihood and parsimony analyses of the MAFFT similarity-alignment did not. All three methods differed with respect to the position of Ceuthomantis smaragdinus (Ceuthomantidae), with tree-alignment using parsimony recovering this species as the sister of Pristimantis + Yunganastes. All analyses rejected the monophyly of Strabomantidae and Strabomantinae as originally defined, and the tree-alignment analysis under parsimony further rejected the recently redefined Craugastoridae and Pristimantinae. Despite the greater emphasis in the systematics literature placed on the choice of optimality criterion for evaluating trees than on the choice of method for aligning DNA sequences, we found that the topological differences attributable to the alignment method were as great as those caused by the optimality criterion. Further, the optimal tree-alignment indicates that insertions and deletions occurred in twice as many aligned positions as implied by the optimal similarity-alignment, confirming previous findings that sequence turnover through insertion and deletion events plays a greater role in molecular evolution than indicated by similarity-alignments. Our results also provide a clear empirical demonstration of the different effects of wildcard taxa produced by missing data in parsimony and maximum likelihood analyses. Specifically, maximum likelihood analyses consistently (81% bootstrap frequency) provided spurious resolution despite a lack of evidence, whereas parsimony correctly depicted the ambiguity due to missing data by collapsing unsupported nodes. We provide a new taxonomy for the group that retains previously recognized Linnaean taxa except for Ceuthomantidae, Strabomantidae, and Strabomantinae. A phenotypically diagnosable superfamily is recognized formally as Brachycephaloidea, with the informal, unranked name terrarana retained as the standard common name for these frogs. We recognize three familie...

Extinction risk or lack of sampling in a threatened species: Genetic structure and environmental suitability of the neotropical frog Pristimantis penelopus (Anura: Craugastoridae)

“…Phylogenetic relationships within the P. ridens series is in agreement with previous studies (Padial et al, 2014;PintoSánchez et al, 2014). Pristimantis penelopus is recovered as monophyletic and its sister species is P. erythropleura (Fig.…”

“…Pinto-Sánchez et al (2014) and later Padial et al (2014) incorrectly included in their phylogenetic analyses the voucher AJC1344 (MHUAA48119) as Pristimantis paisa. However, after specimen examination and a molecular analysis, we unambiguously identified this specimen as Pristimantis penelopus.…”

“…We included available intraspecific sampling for the species most closely related to P. penelopus: P. erythropleura, P. cruentus (Peters, 1873), P. latidiscus (Boulenger, 1898), and P. museosus (Ibáñez et al, 1994). This group represents the P. ridens series sensu Padial et al (2014). Based on Pinto-Sánchez et al (2014) and our preliminary analyses with the entire genus, we used Pristimantis viejas as the outgroup.…”

“…The frog genus Pristimantis Jiménez de la Espada, 1870, a very species-rich lineage with more than 470 described species, is distributed throughout southern Central America and northern South America (Padial et al, 2014). Currently, 162 species are listed in one of the three IUCN threat categories and most of them under the B criterion (reduced extent of presence or area of occupancy; IUCN, 2016).…”

BOOK REVIEW Leenders, T. 2016 Amphibians of Costa Rica: A field guide. Ítaca, Nueva York, Estados Unidos de América. Zona Tropical Publications.

“…Amphibian Species of The World). Se asume que esto disculparía el hecho que Strabomantinae se mantenga elevada a nivel de familia (Strabomantidae) y no como subfamilia de Craugastoridae (Padial et al, 2014). Por otro lado no se incluyeron en la guía los cambios del reciente artículo de Duellman et al (2016) para Hylidae, que creó a la nueva familia Phyllomedusidae para las vistosas ranas de hojas como Agalychnis callidryas (especie portada del libro), probablemente por el traslape temporal en que ambos textos fueron publicados.…”