Tuesday, April 30, 2013

A new squamate phylogeny



This new study finds rubber boas are not erycines but more closely related to Ungaliophis.
Lizards and snakes (living squamates) number about 9,400 known species. Despite Squamata being one of the most diverse and conspicuous radiations of terrestrial vertebrates, no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Alexander Pyron and colleagues (2013) present the first large-scale phylogenetic estimate for Squamata.

Their estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy.

This study provides a phylogenetic estimate for 4161 squamate species, based on a supermatrix approach. The results provide important confirmation for previous studies based on more limited taxon sampling, and reveal new relationships at the level of families, genera, and species. The authors also provide a phylogenetic framework for future comparative studies, with a large-scale tree including a common set of estimated branch lengths. Also provided is a revised classification for squamates based on this tree, including changes in the higher-level taxonomy of gymnophthalmid and scincid lizards and boid, colubrid, and lamprophiid
snakes.

Some of the more interesting relationships suggested by this work include the following.

(1) The authors found strong support for the basal squamate relationships in the tree. The family Dibamidae is the sister group to all other squamates, and Gekkota is the sister group to all squamates excluding Dibamidae as in some previous studies. The results also corroborate that the New World genus Anelytropsis is nested within the Old World genus Dibamus, but the associated branches are weakly supported.

(2) Within Gekkota, they corroborate both earlier morphological and recent molecular estimates in supporting a clade containing the Australian radiation of "diplodactylid" geckos (Carphodactylidae + Diplodactylidae) and the snakelike pygopodids. As in previous studies, Carphodactylidae is the weakly supported sister group to Pygopodidae, and this strongly supported clade is the sister group to Diplodactylidae. They recover clades within the former Gekkonidae that correspond to the strongly supported families Eublepharidae, Sphaerodactylidae, Phyllodactylidae, and Gekkonidae as in previous studies.

(3) They found find strong support for monophyly of Toxicofera (Anguimorpha, Iguania, and Serpentes), and moderate support for a sister-group relationship between Iguania and Anguimorpha. Relationships among Anguimorpha, Iguania, and they also corroborate previous studies placing Anguimorpha with Iguania.

(4) The more advanced snakes (alethinophidians) showed a mixture of strongly and weakly supported nodes. The authors found strong support for a clade containing Anomochilidae + Cylindrophiidae + Uropeltidae. This clade of three families is strongly supported as the sister taxon to Xenopeltidae + (Loxocemidae + Pythonidae). Together, these six families form a strongly supported clade that is weakly supported as the sister group to the strongly supported clade of Boidae + Calabariidae.

(5) As for the Pythonidae, the genus Python is the sister group to all other genera. Some species traditionally referred to as Python (P. reticulatus and P. timoriensis) are instead sister to an Australasian clade consisting of Antaresia, Apodora, Aspidites, Bothrochilus, Leiopython, Liasis, and Morelia. These taxa (P. reticulatus and P. timoriensis) have been referred to as Broghammerus, a name originating from an act of "taxonomic vandalism" (i.e. an apparently intentional attempt to disrupt stable taxonomy) in a non-peer reviewed organ without data or analyses. The authors suggest this name should be ignored and replaced with a suitable substitute.

(6) Within Boidae this study and other recent studies have converged on estimated relationships that are generally similar to each other but which differ from traditional taxonomy. However, the classification has yet to be modified to reflect this, and we rectify this situation here. The authors found that Calabariidae is nested within Boidae, but this is poorly supported, and contrary to most previous studies. While Calabaria has been classified as an erycine boid in the past, this placement is strongly rejected by this work and other studies. If the current placement of Calabaria is supported in the future, it would require recognition as the subfamily Calabariinae. The Malagasy boine genera Acrantophis and Sanzinia are placed as the sister taxa to a weakly-supported clade containing Calabariidae and a strongly supported clade comprising the currently recognized subfamilies Erycinae, Ungaliophiinae, and other boines . Regardless of the position of Calabariidae, this placement of Malagasy boines renders Boinae paraphyletic. The authors therefore resurrect the subfamily Sanziniinae for Acrantophis and Sanzinia. This subfamily could be recognized as a distinct family if future studies also support placement of this clade as distinct from other Boidae + Calabariidae.

(7) The genera Lichanura and Charina are currently classified as erycines , but are strongly supported as the sister group to Ungaliophiinae, as in previous studies . The authors expand Ungaliophiinae to include these two genera, rather than erect a new subfamily for these taxa. The subfamily Ungaliophiinae is placed as the sister group to a well-supported clade containing the rest of the traditionally recognized Erycinae and Boinae. And, they restrict Erycinae to the Old World genus Eryx.

An early version of the entire article is available on-line.

Citation
Pyron, A. R., F. T. Burbrink, & J.J. Wiens, 2013. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology 2013, 13:93 doi:10.1186/1471-2148-13-93.

No comments:

Post a Comment