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Combined next-generation sequencing and morphology reveal fine-scale speciation in Crocodile Skinks (Squamata: Scincidae:Tribolonotus)

Rittmeyer, Eric N.; Austin, Christopher C.

Description

Next-generation sequencing has vast potential to revolutionize the fields of phylogenetics and population genetics through its ability to collect genomic scale data sets of thousands of orthologous loci. Despite this potential, other types of data (e.g. morphology, ecology) remain important, particularly for studies endeavouring to delimit species. Here, we integrate next-generation sequencing with morphology to examine divergence between populations of Tribolonotus pseudoponceleti on the...[Show more]

dc.contributor.authorRittmeyer, Eric N.
dc.contributor.authorAustin, Christopher C.
dc.date.accessioned2015-08-26T01:26:42Z
dc.date.available2015-08-26T01:26:42Z
dc.identifier.issn0962-1083
dc.identifier.urihttp://hdl.handle.net/1885/14927
dc.description.abstractNext-generation sequencing has vast potential to revolutionize the fields of phylogenetics and population genetics through its ability to collect genomic scale data sets of thousands of orthologous loci. Despite this potential, other types of data (e.g. morphology, ecology) remain important, particularly for studies endeavouring to delimit species. Here, we integrate next-generation sequencing with morphology to examine divergence between populations of Tribolonotus pseudoponceleti on the islands of Buka and Bougainville in the Solomon Archipelago. We used the Ion Torrent PGM to collect over 648 Mbp of sequence data for 12 samples, representing 1526 loci recovered from all samples, and 3342 were recovered from at least six samples. Genetic structure analyses strongly support the distinctiveness of these two populations, and Bayes factor delimitations decisively select speciation between Buka and Bougainville. Principal components and discriminant function analyses reveal concordant morphological divergence. Finally, demographic analyses via diffusion approximation and approximate Bayesian computation prefer a complex model of mid-Pleistocene divergence with migration, and a later decrease or cessation of migration and population size shift, suggesting a scenario in which migration was enabled by Pleistocene merging of these two islands, and limited when isolated by higher sea levels. Further analysis of four Sanger sequenced loci in IMa2 had limited power to distinguish among models including and excluding migration, but resulted in similar population size and divergence time estimates, although with much broader confidence intervals. This study represents a framework for how next-generation sequencing and morphological data can be combined and leveraged towards validating putative species and testing demographic scenarios for speciation.
dc.description.sponsorshipThis research was funded by a Harvard University Museum of Comparative Zoology Ernst Mayr Travel Grant in Animal Systematics to ENR and National Science Foundation grant DEB 1146033 to CCA.
dc.format18 pages
dc.publisherWiley
dc.rights© 2014 John Wiley & Sons Ltd
dc.sourceMolecular Ecology
dc.subjectsolomon archipelago
dc.subjectapproximate bayesian computation
dc.subjectgenomics
dc.subjectspecies delimitation
dc.subjectspecies validation
dc.subjectanimals
dc.subjectbayes theorem
dc.subjectcluster analysis
dc.subjectlizards
dc.subjectmelanesia
dc.subjectmodels, genetic
dc.subjectprincipal component analysis
dc.subjectsequence analysis, dna
dc.subjectgenetic speciation
dc.subjectgenetics, population
dc.titleCombined next-generation sequencing and morphology reveal fine-scale speciation in Crocodile Skinks (Squamata: Scincidae:Tribolonotus)
dc.typeJournal article
local.identifier.citationvolume24
dcterms.dateAccepted2014-11-28
dc.date.issued2015-01
local.publisher.urlhttp://au.wiley.com/
local.type.statusPublished Version
local.contributor.affiliationRittmeyer, Eric N., Division of Evolution, Ecology & Genetics, CMBE Research School of Biology, The Australian National University
local.identifier.essn1365-294X
local.bibliographicCitation.issue2
local.bibliographicCitation.startpage466
local.bibliographicCitation.lastpage483
local.identifier.doi10.1111/mec.13030
CollectionsANU Research Publications

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