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Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships

Burbank, Frank T.; Grazziotin, Felipe G.; Pyron, R. Alexander; Cundall, David; Donnellan, S; Irish, Frances; Keogh, J. Scott; Kraus, Fred; Murphy, Robert W.; Noonan, Brice P.; Raxworthy, Christopher J.

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Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75...[Show more]

dc.contributor.authorBurbank, Frank T.
dc.contributor.authorGrazziotin, Felipe G.
dc.contributor.authorPyron, R. Alexander
dc.contributor.authorCundall, David
dc.contributor.authorDonnellan, S
dc.contributor.authorIrish, Frances
dc.contributor.authorKeogh, J. Scott
dc.contributor.authorKraus, Fred
dc.contributor.authorMurphy, Robert W.
dc.contributor.authorNoonan, Brice P.
dc.contributor.authorRaxworthy, Christopher J.
dc.date.accessioned2021-02-09T00:14:41Z
dc.identifier.issn1063-5157
dc.identifier.urihttp://hdl.handle.net/1885/222416
dc.description.abstractGenomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).
dc.description.sponsorshipThis research was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo [grant number BIOTA-FAPESP 2011/50206-9 to H.Z.], National Science Foundation [grant numbers DEB-1257926 to F.T.B., DEB1441719 to R.A.P., DEB-1257610 to C.J.R.], and Australian Research Council Discovery [grant number DP120104146 to J.S.K. and S.C.D.]. F.G.G. benefited from a Postdoctoral grant from Fundação de Amparo à Pesquisa do Estado de São Paulo [FAPESP grant number 2012/08661-3].
dc.format.mimetypeapplication/pdf
dc.language.isoen_AU
dc.publisherOxford University Press (OUP)
dc.rights© The Author(s) 2019. Published by Oxford University Press, on behalf of the Society of Systematic Biologists
dc.sourceSystematic Biology
dc.subjectNeural network
dc.subjectgene interrogation
dc.subjectlizards
dc.subjectsnakes
dc.subjectgenomics
dc.subjectphylogeny
dc.titleInterrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume69
dc.date.issued2020
local.identifier.absfor060309 - Phylogeny and Comparative Analysis
local.identifier.ariespublicationa383154xPUB13625
local.publisher.urlhttp://sysbio.oxfordjournals.org/
local.type.statusPublished Version
local.contributor.affiliationBurbank, Frank T., The American Museum of Natural History
local.contributor.affiliationGrazziotin, Felipe G., Instituto Butantan
local.contributor.affiliationPyron, R. Alexander, The George Washington University
local.contributor.affiliationCundall, David, Lehigh University
local.contributor.affiliationDonnellan, S, University of Adelaide
local.contributor.affiliationIrish, Frances, Moravian College
local.contributor.affiliationKeogh, J Scott, College of Science, ANU
local.contributor.affiliationKraus, Fred, University of Michigan
local.contributor.affiliationMurphy, Robert W., Royal Ontario Museum
local.contributor.affiliationNoonan, Brice P., University of Mississippi
local.contributor.affiliationRaxworthy, Christopher J., The American Museum of Natural History
local.description.embargo2099-12-31
dc.relationhttp://purl.org/au-research/grants/arc/DP120104146
local.bibliographicCitation.issue3
local.bibliographicCitation.startpage502
local.bibliographicCitation.lastpage520
local.identifier.doi10.1093/sysbio/syz062
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciences
dc.date.updated2020-11-08T07:18:00Z
CollectionsANU Research Publications

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