Out of Southern East Asia of the Brown Rat Revealed by Large-Scale Genome Sequencing

Lin Zeng; Chen Ming; Yan Li; Ling-Yan Su; Yan-Hua Su; Newton O Otecko; Ambroise Dalecky; Stephen Donnellan; Ken Aplin; Xiao-Hui Liu; Ying Song; Zhi-Bin Zhang; Ali Esmailizadeh; Saeed S Sohrabi; Hojjat Asadollahpour Nanaei; He-Qun Liu; Ming-Shan Wang; Solimane Ag Atteynine; Gérard Rocamora; Fabrice Brescia; Serge Morand; David M Irwin; Ming-Sheng Peng; Yong-Gang Yao; Hai-Peng Li; Dong-Dong Wu; Ya-Ping Zhang

doi:10.1093/molbev/msx276

Out of Southern East Asia of the Brown Rat Revealed by Large-Scale Genome Sequencing

Mol Biol Evol. 2018 Jan 1;35(1):149-158. doi: 10.1093/molbev/msx276.

Authors

Lin Zeng^{1

2}, Chen Ming^{3

4}, Yan Li^{1

5}, Ling-Yan Su^{2

6}, Yan-Hua Su⁷, Newton O Otecko^{1

2

8}, Ambroise Dalecky^{9

10}, Stephen Donnellan¹¹, Ken Aplin¹², Xiao-Hui Liu¹³, Ying Song¹³, Zhi-Bin Zhang¹⁴, Ali Esmailizadeh¹⁵, Saeed S Sohrabi¹⁵, Hojjat Asadollahpour Nanaei¹⁵, He-Qun Liu^{1

2}, Ming-Shan Wang^{1

2}, Solimane Ag Atteynine^{16

17}, Gérard Rocamora¹⁸, Fabrice Brescia¹⁹, Serge Morand²⁰, David M Irwin^{1

21}, Ming-Sheng Peng^{1

2

8}, Yong-Gang Yao^{2

6}, Hai-Peng Li³, Dong-Dong Wu^{1

2

8}, Ya-Ping Zhang^{1

2

5}

Affiliations

¹ State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
² Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
³ CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
⁴ University of Chinese Academy of Sciences, Beijing, China.
⁵ State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming, China.
⁶ Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, China.
⁷ College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.
⁸ Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China.
⁹ Institut de Recherche pour le Développement (Ird), CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro), Montferrier sur Lez cedex, France.
¹⁰ Institut de Recherche pour le Développement (Ird), LPED (UMR AMU/IRD), Marseille, France.
¹¹ University of Adelaide and the South Australian Museum, Adelaide, Australia.
¹² Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC.
¹³ State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
¹⁴ State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
¹⁵ Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
¹⁶ Institut de Recherche pour le Développement (Ird), IMBE (UMR AMU/CNRS/IRD/UAPV), Bamako, Mali.
¹⁷ Faculté des Sciences et Techniques (FST), Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali.
¹⁸ Island Biodiversity & Conservation Center, University of Seychelles, Mahé, Seychelles.
¹⁹ Diversité Biologique et Fonctionnelle des Ecosystèmes, Institut Agronomique néo-Calédonien, Port Laguerre, Paita, New Caledonia.
²⁰ CNRS-CIRAD, Centre d'Infectiologie Christophe Mérieux du Laos, Vientiane, Lao PDR.
²¹ Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.

PMID: 29087519
DOI: 10.1093/molbev/msx276

Abstract

The geographic origin and migration of the brown rat (Rattus norvegicus) remain subjects of considerable debate. In this study, we sequenced whole genomes of 110 wild brown rats with a diverse world-wide representation. We reveal that brown rats migrated out of southern East Asia, rather than northern Asia as formerly suggested, into the Middle East and then to Europe and Africa, thousands of years ago. Comparison of genomes from different geographical populations reveals that many genes involved in the immune system experienced positive selection in the wild brown rat.

Keywords: Rattus norvegicus; demographic history; natural selection; origin.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Africa
Animals
Asia, Southeastern / epidemiology
Biological Evolution
Europe
Evolution, Molecular
Genetic Variation / genetics
Genetics, Population
Genome / genetics
Middle East
Phylogeny
Phylogeography / methods*
Rats / genetics*
Whole Genome Sequencing / methods