Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards

• Published in: Ecology and evolution Vol. 14; no. 3; pp. e11117 - n/a
• Main Authors: Sakamoto, Fuku, Kanamori, Shunsuke, Díaz, Luis M., Cádiz, Antonio, Ishii, Yuu, Yamaguchi, Katsushi, Shigenobu, Shuji, Nakayama, Takuro, Makino, Takashi, Kawata, Masakado
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01.03.2024; John Wiley and Sons Inc; Wiley
• Subjects: accelerated evolution; Adaptation; Anolis; Circadian rhythm; Circadian rhythms; Climate change; comparative genomics; Conserved sequence; Endangered & extinct species; Energy consumption; Evolution & development; Evolutionary conservation; Forests; Gene expression; Genes; Genomes; Genomics; Global warming; Habitats; Lizards; reptiles; Temperature; thermal adaptation; Thermal environments; Cuba; Anolis; accelerated evolution; thermal adaptation; reptiles; comparative genomics
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.11117

Understanding the genetic basis for adapting to thermal environments is important due to 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 alignment. 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. Whole genomes were used from eight Anolis lizard species that repeatedly adapted to similar thermal habitats in multiple lineages and we identified evolutionarily conserved or accelerated genomic regions.