机构：[1]BGI-Shenzhen, Shenzhen, 518083, China.[2]Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.[3]Commonwealth Scientific and Industrial Research Organisation, Clunies Ross Street, Acton, ACT, 2601, Australia.[4]Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Road, Parkville, 3010, Australia.[5]Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.[6]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.[7]College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.[8]Division of Ecology and Evolution, and Centre for Biodiversity Analysis, The Australian National University, Acton, ACT, 2601, Australia.[9]Daintree Rainforest Observatory, James Cook University, Cape Tribulation, QLD, 4873, Australia.[10]Applied BioSciences, Macquarie University, North Ryde, NSW, 2109, Australia.[11]School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia.[12]IT - Research Computing, Harvard Medical School, Boston, MA, 02115, USA.[13]Department of Mathematics, Harvard University, Cambridge, MA, 02138, USA.[14]Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.[15]Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra, 08003, Barcelona, Catalonia, Spain.[16]Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, China.
Many Drosophila species differ widely in their distributions and climate niches, making them excellent subjects for evolutionary genomic studies. We have developed a database of high-quality assemblies for 46 Drosophila species and one closely related Zaprionus. Fifteen of the genomes were newly sequenced, and 20 were improved with additional sequencing. New or improved annotations were generated for all 47 species, assisted by new transcriptomes for 19. Phylogenomic analyses of these data resolved several previously ambiguous relationships, especially in the melanogaster species group. However, it also revealed significant phylogenetic incongruence among genes, mainly in the form of incomplete lineage sorting in the subgenus Sophophora but also including asymmetric introgression in the subgenus Drosophila. Using the phylogeny as a framework and taking into account these incongruences, we then screened the data for genome-wide signals of adaptation to different climatic niches. Firstly, phylostratigraphy revealed relatively high rates of recent novel gene gain in three temperate pseudoobscura and five desert-adapted cactophilic mulleri subgroup species. Secondly, we found differing ratios of non-synonymous to synonymous substitutions in several hundred orthologs between climate generalists and specialists, with significant higher trends for those in tropical and lower trends for those in temperate-continental specialists respectively than those in the climate generalists. Finally, re-sequencing natural populations of thirteen species revealed tropics-restricted species generally had smaller population sizes, lower genome diversity and more deleterious mutations than the more widespread species. We conclude that adaptation to different climates in the genus Drosophila has been associated with large-scale and multifaceted genomic changes.This article is protected by copyright. All rights reserved.
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出版当年[2021]版：
大类|2 区生物
小类|1 区生态学2 区生化与分子生物学2 区进化生物学
最新[2023]版：
大类|1 区生物学
小类|1 区生化与分子生物学1 区生态学1 区进化生物学
第一作者：
第一作者机构：[1]BGI-Shenzhen, Shenzhen, 518083, China.[2]Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.
通讯作者：
通讯机构：[1]BGI-Shenzhen, Shenzhen, 518083, China.[2]Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.[3]Commonwealth Scientific and Industrial Research Organisation, Clunies Ross Street, Acton, ACT, 2601, Australia.[4]Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Road, Parkville, 3010, Australia.[6]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.[10]Applied BioSciences, Macquarie University, North Ryde, NSW, 2109, Australia.[16]Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, China.[*1]BGI-Shenzhen, Shenzhen, China.[*2]Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.[*3]Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Vic., Australia.
推荐引用方式(GB/T 7714)：
Li Fang,Rane Rahul V,Luria Victor,et al.Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation.[J].Molecular ecology resources.2021,doi:10.1111/1755-0998.13561.
APA：
Li Fang,Rane Rahul V,Luria Victor,Xiong Zijun,Chen Jiawei...&Zhang Guojie.(2021).Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation..Molecular ecology resources,,
MLA：
Li Fang,et al."Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation.".Molecular ecology resources .(2021)
生物