干旱区生态环境知识资源中心(Arid): Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation

Arid

DOI	10.1111/1755-0998.13561
	Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation
	Li, Fang; Rane, Rahul, V; Luria, Victor; Xiong, Zijun; Chen, Jiawei; Li, Zimai; Catullo, Renee A.; Griffin, Philippa C.; Schiffer, Michele; Pearce, Stephen; Lee, Siu Fai; McElroy, Kerensa; Stocker, Ann; Shirriffs, Jennifer; Cockerell, Fiona; Coppin, Chris; Sgro, Carla M.; Karger, Amir; Cain, John W.; Weber, Jessica A.; Santpere, Gabriel; Kirschner, Marc W.; Hoffmann, Ary A.; Oakeshott, John G.; Zhang, Guojie
通讯作者	Zhang, GJ (corresponding author), BGI Shenzhen, Shenzhen, Peoples R China. ; Oakeshott, JG (corresponding author), Commonwealth Sci & Ind Res Org, Acton, ACT, Australia. ; Hoffmann, AA (corresponding author), Univ Melbourne, Sch BioSci, Bio21 Inst, Parkville, Vic, Australia.
来源期刊	MOLECULAR ECOLOGY RESOURCES
ISSN	1755-098X
EISSN	1755-0998
出版年	2021-12
英文摘要	Many Drosophila species differ widely in their distributions and climate niches, making them excellent subjects for evolutionary genomic studies. Here, 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. First, phylostratigraphy revealed relatively high rates of recent novel gene gain in three temperate pseudoobscura and five desert-adapted cactophilic mulleri subgroup species. Second, we found differing ratios of nonsynonymous to synonymous substitutions in several hundred orthologues 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, resequencing natural populations of 13 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.
英文关键词	climate adaptation Drosophila incomplete lineage sorting introgression phylogenomics phylostratigraphy
类型	Article ; Early Access
语种	英语
开放获取类型	hybrid
收录类别	SCI-E
WOS记录号	WOS:000728048400001
WOS关键词	MELANOGASTER SPECIES GROUP ; MITOCHONDRIAL-DNA ; DESICCATION RESISTANCE ; DIVERGENCE TIMES ; MUTATION-RATE ; R PACKAGE ; EVOLUTION ; DIPTERA ; GENES ; INTROGRESSION
WOS类目	Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
WOS研究方向	Biochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/374697
作者单位	[Li, Fang; Xiong, Zijun; Chen, Jiawei; Li, Zimai; Zhang, Guojie] BGI Shenzhen, Shenzhen, Peoples R China; [Li, Fang; Zhang, Guojie] Univ Copenhagen, Dept Biol, Sect Ecol & Evolut, Copenhagen, Denmark; [Rane, Rahul, V; Catullo, Renee A.; Pearce, Stephen; Lee, Siu Fai; McElroy, Kerensa; Coppin, Chris; Oakeshott, John G.] Commonwealth Sci & Ind Res Org, Acton, ACT, Australia; [Rane, Rahul, V; Griffin, Philippa C.; Schiffer, Michele; Stocker, Ann; Shirriffs, Jennifer; Hoffmann, Ary A.] Univ Melbourne, Sch BioSci, Bio21 Inst, Parkville, Vic, Australia; [Luria, Victor; Kirschner, Marc W.] Harvard Med Sch, Dept Syst Biol, Boston, MA USA; [Xiong, Zijun; Zhang, Guojie] Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming, Yunnan, Peoples R China; [Xiong, Zijun] Univ Chinese Acad Sci, Coll Life Sci, Beijing, Peoples R China; [Catullo, Renee A.] Australian Natl Univ, Ctr Biodivers Anal, Div Ecol & Evolut, Acton, ACT, Australia; [Schiffer, Michele] James Cook Univ, Daintree Rainforest ...
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],2021.
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).