DOI: 10.5061/dryad.31zcrjdrk
title: Data from: Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards

description: Understanding the genetic basis for adapting to thermal environments is
 important due to the serious effects of global warming on ectothermic
 species. Various genes associated with thermal adaptation in lizards have
 been identified mainly focusing on changes in gene expression or the
 detection of positively selected genes using coding regions. Only a few
 comprehensive genome-wide analyses have included noncoding regions. This
 study aimed to identify evolutionarily conserved and accelerated genomic
 regions using whole genomes of eight Anolis lizard species that
 have repeatedly adapted to similar thermal environments in multiple
 lineages. Evolutionarily conserved genomic regions were extracted as
 regions with overall sequence conservation (regions with fewer base
 substitutions) across all lineages compared with the neutral model.
 Genomic regions that underwent accelerated evolution in the lineage of
 interest were identified as those with more base substitutions in the
 target branch than in the entire background branch. Conserved elements
 across all branches were relatively abundant in “intergenic” genomic
 regions among noncoding regions. Accelerated regions (ARs) of each lineage
 contained a significantly greater proportion of noncoding RNA genes than
 the entire multiple alignments. Common genes containing ARs within 5 kb of
 their vicinity in lineages with similar thermal habitats were identified.
 Many genes associated with circadian rhythms and behavior were found in
 hot-open and cool-shaded habitat lineages. These genes might play a role
 in contributing to thermal adaptation and assist future studies examining
 the function of genes involved in thermal adaptation via genome editing.
description: # Data from: Detection of evolutionary conserved and accelerated genomic
 regions related to adaptation to thermal niches in *Anolis* lizards
 Contact: Fuku Sakamoto
 ([fukusakamoto29@gmail.com](mailto:fukusakamoto29@gmail.com)), Masakado
 Kawata ([kawata@tohoku.ac.jp](mailto:kawata@tohoku.ac.jp)). ##
 DESCRIPTIONS The files contained under the
 "Sakamoto_etal_2024_anole_pairwise_alignment" directory are
 pairwise alignments of each *Anolis* species using the 13-chromosome
 genome of *Anolis carolinensis* as reference (compressed in gzip format).
 The alignments were generated by LastZ (Harris, 2007), subjected to the
 chaining and netting process introduced by Kent et al. (2003), and then
 filtered by a proprietary script. The naming convention is
 "pairwise_[target species name]_carolinensis_[chromosome name of *A.
 carolinensis*].maf." The files in the
 "Sakamoto_etal_2024_anole_multiple_alignment" directory are
 multiple alignments of *Anolis* species using the 13-chromosome genome of
 *Anolis carolinensis* as reference (compressed in gzip format). Multiple
 alignments were generated by integrating pairwise alignments for each
 species using MultiZ (Blanchette et al., 2004). This dataset contains only
 alignments that are aligned with at least seven of the eight species
 covered in this study. The naming convention is
 "multiple_carolinensis_[chromosome name of *A.
 carolinensis*].maf." The
 "Sakamoto_etal_2024_anole_neutral_phylogenetic_tree" directory
 contains the phylogenetic tree data inferred from the modified 4D sites.
 The directory "Sakamoto_etal_2024_anole_CONorACC_score" contains
 the conserved and accelerated scores calculated by phyloP of the PHAST
 package (Pollard et al., 2010). For each chromosome of *Anolis*
 carolinensis, a conservation or acceleration score of the branch on the
 phylogenetic tree of interest was calculated by comparing a neutral model
 to each genomic region. The naming convention is "logP_[*A.
 carolinensis* chromosome name]_[target branch name]_[score calculation
 options (ACC or CON or CONACC)].gff." The
 "Sakamoto_etal_2024_SCRIPTS" directory contains the codes used
 in this study. Please read the respective README files for details of each
 script. ## REFERENCES * Blanchette, M., Kent, W.J., Riemer, C., Elnitski,
 L., Smit, A.F., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H.,
 Green, E.D., Haussler, D., & Miller, W. (2004). Aligning multiple
 genomic sequences with the threaded blockset aligner. Genome research,
 14(4), 708715. https://doi.org/10.1101/gr.1933104 * Harris, R.S. (2007).
 Improved Pairwise Alignment of Genomic DNA. PhD thesis, Pennsylvania State
 Univ. * Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., &
 Haussler, D. (2003). Evolution's cauldron: Duplication, deletion, and
 rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci., 100,
 1148411489. https://www.pnas.org/doi/10.1073/pnas.1932072100 * Pollard,
 K.S., Hubisz, M.J., Rosenbloom, K.R., & Siepel, A. (2010). Detection
 of nonneutral substitution rates on mammalian phylogenies. Genome
 research, 20(1), 110121. https://doi.org/10.1101/gr.097857.109