@article{09c7f2a6e20a4af184c5f26db7227d6f,
title = "Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards",
abstract = "Squamates include all lizards and snakes, and display some of the most diverse and extreme morphological adaptations among vertebrates. However, compared with birds and mammals, relatively few resources exist for comparative genomic analyses of squamates, hampering efforts to understand the molecular bases of phenotypic diversification in such a speciose clade. In particular, the ∼400 species of anole lizard represent an extensive squamate radiation. Here, we sequence and assemble the draft genomes of three anole species - Anolis frenatus, Anolis auratus, and Anolis apletophallus - for comparison with the available reference genome of Anolis carolinensis. Comparative analyses reveal a rapid background rate of molecular evolution consistent with a model of punctuated equilibrium, and strong purifying selection on functional genomic elements in anoles. We find evidence for accelerated evolution in genes involved in behavior, sensory perception, and reproduction, as well as in genes regulating limb bud development and hindlimb specification. Morphometric analyses of anole fore and hindlimbs corroborated these findings. We detect signatures of positive selection across several genes related to the development and regulation of the forebrain, hormones, and the iguanian lizard dewlap, suggesting molecular changes underlying behavioral adaptations known to reinforce species boundaries were a key component in the diversification of anole lizards.",
keywords = "Anolis, adaptation, genomes, molecular evolution, phenotypic evolution, substitution rates",
author = "Marc Tollis and Hutchins, {Elizabeth D.} and Jessica Stapley and Rupp, {Shawn M.} and Eckalbar, {Walter L.} and Inbar Maayan and Eris Lasku and Infante, {Carlos R.} and Dennis, {Stuart R.} and Robertson, {Joel A.} and May, {Catherine M.} and Crusoe, {Michael R.} and Eldredge Bermingham and Dale Denardo and Hsieh, {Shi Tong Tonia} and Kulathinal, {Rob J.} and McMillan, {William Owen} and Menke, {Douglas B.} and Stephen Pratt and Jeffery Rawls and Oris Sanjur and Norma Wilson-Rawls and {Wilson Sayres}, Melissa and Fisher, {Rebecca E.} and Kenro Kusumi",
note = "Funding Information: We thank Glenn Markov and Peter Marting for their help in the field and Matthew J. Huentelman, John Cornelius, Shannon Gilpin, and Elise Kulik for technical assistance. We also thank Fiona McCarthy for helpful discussion. We thank April Allen and the Collaborative Sequencing Center at the Translational Genomics Research Institute for sequencing assistance. Support for I.M. and E.L. was provided by the School of Life Sciences Undergraduate Research (SOLUR) Program at Arizona State University. This work was supported by funding from a seed grant from Arizona State University (ASU) and the Smithsonian Tropical Research Institute and funding from the College of Liberal Arts and Sciences at ASU to K.K. Additional support to D.B.M. was provided by the National Science Foundation (CAREER IOS1149453). Computational analysis was supported by allocations from the Arizona State University Research Computing and startup from the School of Life Sciences and the Biodesign Institute to M.A.W.S. Funding Information: This work was supported by funding from a seed grant fromArizona State University (ASU) and the Smithsonian Tropical Research Institute and funding from the College of Liberal Arts and Sciences at ASU to K.K. Additional support to D.B.M. was provided by the National Science Foundation (CAREER IOS1149453). Publisher Copyright: {\textcopyright} The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.",
year = "2018",
month = feb,
day = "1",
doi = "10.1093/gbe/evy013",
language = "English (US)",
volume = "10",
pages = "489--506",
journal = "Genome biology and evolution",
issn = "1759-6653",
publisher = "Oxford University Press",
number = "2",
}