Abstract
BackgroundResolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus Sceloporus. We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution.ResultsThe phylogenomic trees that we obtained for Sceloporus using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the Sceloporus phylogeny approximately 20–25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the Sceloporus species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997).ConclusionsDespite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for Sceloporus that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0628-x) contains supplementary material, which is available to authorized users.
Highlights
Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci
There are at least three fundamental challenges confronting the resolution of rapid radiations using molecular genetic data: 1) quick bursts of speciation limit the opportunities for character changes to accumulate across the genome [1], 2) long-branch attraction artifacts during phylogeny estimation [15], and 3) incomplete lineage sorting [16]
Some of the phylogenomic data were taken from previous studies, including 11 samples from a study of phrynosomatid lizards [13] and 17 samples from a study of the genus Phrynosoma [45]
Summary
Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. The short time intervals separating the speciation events that occur during a rapid radiation leave few opportunities for molecular evolutionary changes to become established in the genome Depending on the method and the model, increasing the amount of data can be positively misleading when faced with long branch attraction and/or incomplete lineage sorting [15, 20, 21] Overcoming these collective challenges, which are not mutually exclusive and are difficult to distinguish, requires the acquisition of large datasets composed of many independent loci together with the implementation of coalescent models of phylogenetic inference; analyzing large datasets is computationally demanding, and this problem is amplified when utilizing complex coalescentbased models. Coalescent methods that utilize gene trees instead of sequence data can dramatically decrease computation times [23], but this comes at the cost of information loss as uncertainty in the sequence data is not taken into account
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