文章基本信息

标题：Parallel genomic responses to historical climate change and high elevation in East Asian songbirds
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作者：Yalin Cheng ; Matthew J. Miller ; Dezhi Zhang 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2021
卷号：118
期号：50
DOI：10.1073/pnas.2023918118
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：Significance A reduction in heterozygosity may limit the opportunity for species facing the same selective pressures to evolve parallel adaptation. Examining 19 East Asian tits’ genomes, we find a pattern of lower heterozygosity in western endemics compared with that found in both eastern endemics and widespread taxa, consistent with expectations of demographic contraction driven by late-Pleistocene climate fluctuations. Comparisons among both endemic and widespread tits find disproportionate levels of genetic differentiation between pairs of lowland and highland tits in genomic regions that are enriched for genes that may be associated with the oxygen transport cascade and/or thermogenesis. However, evolution did not occur in the same genes, and populations with higher heterozygosity did not show higher levels of parallel evolution as predicted. Parallel evolution can be expected among closely related taxa exposed to similar selective pressures. However, parallelism is typically stronger at the phenotypic level, while genetic solutions to achieve these phenotypic similarities may differ. For polygenic traits, the availability of standing genetic variation (i.e., heterozygosity) may influence such genetic nonparallelism. Here, we examine the extent to which high-elevation adaptation is parallel—and whether the level of parallelism is affected by heterozygosity—by analyzing genomes of 19 Paridae species distributed across East Asia with a dramatic east–west elevation gradient. We find that western highlands endemic parids have consistently lower levels of heterozygosity—likely the result of late-Pleistocene demographic contraction—than do parids found exclusively in eastern lowlands, which remained unglaciated during the late Pleistocene. Three widespread species (east to west) have high levels of heterozygosity similar to that observed in eastern species, although their western populations are less variable than eastern ones. Comparing genomic responses to extreme environments of the Qinghai–Tibet Plateau, we find that the most differentiated genomic regions between each high-elevation taxon and its low-elevation relative are significantly enriched for genes potentially related to the oxygen transport cascade and/or thermogenesis. Despite no parallelism at particular genes, high similarity in gene function is found among comparisons. Furthermore, parallelism is not higher in more heterozygous widespread parids than in highland endemics. Thus, in East Asian parids, parallel functional response to extreme elevation appears to rely on different genes, with differences in heterozygosity having no effect on the degree of genetic parallelism.
关键词：parallel evolution; climate change; genetic diversity; demographic history; high-elevation adaptation