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


RESULTS
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.


CONCLUSIONS
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.
Laurent A F
LA
Frantz
Joshua G
JG
Schraiber
Ole
O
Madsen
Hendrik-Jan
HJ
Megens
Mirte
M
Bosse
Yogesh
Y
Paudel
Gono
G
Semiadi
Erik
E
Meijaard
Ning
N
Li
Richard P M A
RP
Crooijmans
Alan L
AL
Archibald
Montgomery
M
Slatkin
Lawrence B
LB
Schook
Greger
G
Larson
Martien A M
MA
Groenen
D000349:Africa; D063147:Animal Distribution; D000818:Animals; D001210:Asia, Southeastern; D002874:Chromosome Mapping; D002980:Climate; D051456:Gene Flow; D049810:Genetic Speciation; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome; D010802:Phylogeny; D058974:Phylogeography; D017422:Sequence Analysis, DNA; D013552:Swine / Q000145:classification / Q000235:genetics