Dynamic evolution of transposable elements,demographic history,and gene content of paleognathous birds

作     者：Zong-Ji Wang Guang-Ji Chen Guo-Jie Zhang Qi Zhou Zong-Ji Wang;Guang-Ji Chen;Guo-Jie Zhang;Qi Zhou

作者机构：Institute of Animal Sex and DevelopmentZhejiang Wanli UniversityNingboZhejiang 315100China MOE Laboratory of Biosystems Homeostasis&ProtectionLife Sciences InstituteZhejiang UniversityHangzhouZhejiang 310058China Department of Neuroscience and Developmental BiologyUniversity of ViennaVienna 1090Austria BGI-ShenzhenBeishan Industrial ZoneShenzhenGuangdong 518083China State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Section for Ecology and EvolutionDepartment of BiologyUniversity of CopenhagenCopenhagen DK-2100Denmark Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingYunnan 650223China Center for Reproductive MedicineThe Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang 310058China 

出 版 物：《Zoological Research》 (动物学研究（英文）)

年 卷 期：2021年第42卷第1期

页      面：51-61页

核心收录：

学科分类：0710[理学-生物学] 1002[医学-临床医学] 07[理学] 071007[理学-遗传学] 

基　　金：This study was supported by the National Natural Science Foundation of China(31671319,31722050,32061130208) Natural Science Foundation of Zhejiang Province(LD19C190001) European Research Council Starting Grant(grant agreement 677696)to Q.Z. the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31020000,XDB13000000) International Partnership Program of Chinese Academy of Sciences(152453KYSB20170002) Carlsberg Foundation(CF16-0663) Villum Foundation(25900)to G.J.Z We thank China National Genebank at BGI for contributing to the sequencing.We would like to thank Christopher C.Witt,Mariel L.Campbell and Ariel M.Gaffney from the Museum of Southwestern Biology,Gary Graves from Smithsonian Institute,Robb T.Brumfield and Donna L.Dittman from Louisiana State University Museum of Natural Science,Jack Withrow and Andy Kratter from Florida Museum of Natural History,University of New Mexico for providing bird DNA samples for this work. 

主　　题：Paleognaths Demographic history Transposable elements Gene families Mitochondria 

摘      要：Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution.Here,we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories,which are presently unknown.We found that most species showed a reduction of population size since the beginning of the last glacial period,except for those species distributed in Australasia and in the far south of South America.Different degrees of contraction and expansion of transposable elements(TE)have shaped the paleognathous genome architecture,with a higher transposon removal rate in tinamous than in ratites.One repeat family,AviRTE,likely underwent horizontal transfer from tropical parasites to the ancestor of little and undulated tinamous about 30 million years ago.Our analysis of gene families identified rapid turnover of immune and reproductionrelated genes but found no evidence of gene family changes underlying the convergent evolution of flightlessness among ratites.We also found that mitochondrial genes have experienced a faster evolutionary rate in tinamous than in ratites,with the former also showing more degenerated W chromosomes.This result can be explained by the Hill-Robertson interference affecting genetically linked W chromosomes and mitochondria.Overall,we reconstructed the evolutionary history of the Palaeognathae populations,genes,and TEs.Our findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes.