TY - JOUR
T1 - Phylogenomic analyses reveal novel relationships among snake families
AU - Streicher, Jeffrey W.
AU - Wiens, John J.
N1 - Funding Information:
We thank M. Fujita, J. Castoe, T. Castoe, and P. Foster for assistance with laboratory methods, sequencing, and computational resources. We thank P. Kapali for use of her python script for removing empty taxa from alignments. We thank E. Smith and T. Gamble for use of their photographs. We thank G. Mathews, E. Miller, and L. Barrientos for laboratory assistance. We thank T. Castoe for many helpful comments on the manuscript. Some photographs were obtained during trips sponsored by NSF DEB-0613802 to J. Campbell and DEB-1146324 to E. Smith and M. Harvey. We are very grateful to the many researchers and institutions who provided (or facilitated access to) tissues and DNA samples for use in this study: see Table S1 for listing of vouchers, specimens, institutions, and individuals (including C. Austin, D. Cannatella, J. Gauthier, S. B. Hedges, M. Kearney, M.S.Y. Lee, J. McGuire, J. Vindum, H. Voris). We especially thank T. Reeder for help in assembling the set of tissues used in the Deep Scaly project (and here). This work was supported by the University of Arizona .
Publisher Copyright:
© 2016 Elsevier Inc.
PY - 2016/7/1
Y1 - 2016/7/1
N2 - Snakes are a diverse and important group of vertebrates. However, relationships among the major groups of snakes have remained highly uncertain, with recent studies hypothesizing very different (and typically weakly supported) relationships. Here, we address family-level snake relationships with new phylogenomic data from 3776 nuclear loci from ultraconserved elements (1.40 million aligned base pairs, 52% missing data overall) sampled from 29 snake species that together represent almost all families, a dataset ~100 times larger than used in previous studies. We found relatively strong support from species-tree analyses (NJst) for most relationships, including three largely novel clades: (1) a clade uniting the boas, pythons and their relatives, (2) a clade placing cylindrophiids and uropeltids with this clade, and (3) a clade uniting bolyeriids (Round Island boas) with pythonids and their relatives (xenopeltids and loxocemids). Relationships among families of advanced snakes (caenophidians) were also strongly supported. The results show the potential for phylogenomic analyses to resolve difficult groups, but also show a surprising sensitivity of the analyses to the inclusion or exclusion of outgroups.
AB - Snakes are a diverse and important group of vertebrates. However, relationships among the major groups of snakes have remained highly uncertain, with recent studies hypothesizing very different (and typically weakly supported) relationships. Here, we address family-level snake relationships with new phylogenomic data from 3776 nuclear loci from ultraconserved elements (1.40 million aligned base pairs, 52% missing data overall) sampled from 29 snake species that together represent almost all families, a dataset ~100 times larger than used in previous studies. We found relatively strong support from species-tree analyses (NJst) for most relationships, including three largely novel clades: (1) a clade uniting the boas, pythons and their relatives, (2) a clade placing cylindrophiids and uropeltids with this clade, and (3) a clade uniting bolyeriids (Round Island boas) with pythonids and their relatives (xenopeltids and loxocemids). Relationships among families of advanced snakes (caenophidians) were also strongly supported. The results show the potential for phylogenomic analyses to resolve difficult groups, but also show a surprising sensitivity of the analyses to the inclusion or exclusion of outgroups.
KW - Phylogenomics
KW - Reptiles
KW - Serpentes
KW - Snakes
KW - Species-tree methods
KW - UCE
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UR - http://www.scopus.com/inward/citedby.url?scp=84963575813&partnerID=8YFLogxK
U2 - 10.1016/j.ympev.2016.04.015
DO - 10.1016/j.ympev.2016.04.015
M3 - Article
C2 - 27083862
AN - SCOPUS:84963575813
VL - 100
SP - 160
EP - 169
JO - Molecular Phylogenetics and Evolution
JF - Molecular Phylogenetics and Evolution
SN - 1055-7903
ER -