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Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Laurent AF Frantz1*, Joshua G Schraiber2, Ole Madsen1, Hendrik-Jan Megens1, Mirte Bosse1, Yogesh Paudel1, Gono Semiadi3, Erik Meijaard45, Ning Li6, Richard PMA Crooijmans1, Alan L Archibald7, Montgomery Slatkin2, Lawrence B Schook8, Greger Larson9 and Martien AM Groenen1

Author Affiliations

1 Animal Breeding and Genomics Group, Wageningen University, De Elst 1, Wageningen, WD 6708, The Netherlands

2 Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA

3 Puslit Biologi LIPI, Jl. Raya Jakarta-Bogor Km. 46, Cibinong 16911, Jawa Barat, Indonesia

4 People and Nature Consulting International, Vila Lumbung House no. 6, Jl. Kerobokan Raya 1000x, Badung 80361, Bali, Indonesia

5 School of Archaeology and Anthropology, Australian National University, Canberra ACT 0200, Australia

6 State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, PR China

7 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK

8 Department of Animal Sciences, University of Illinois, Urbana-Champaign, Illinois 61801, USA

9 Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham DH1 3LE, UK

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Genome Biology 2013, 14:R107  doi:10.1186/gb-2013-14-9-r107

Published: 26 September 2013



Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog.


Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal.


Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.