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Genome Biol Evol. 2015 Mar 23;7(3):821-30. doi: 10.1093/gbe/evv033.

Whole-genome sequencing of six Mauritian Cynomolgus macaques (Macaca fascicularis) reveals a genome-wide pattern of polymorphisms under extreme population bottleneck.

Author information

1
Division of Evolutionary Genetics, National Institute of Genetics, Mishima, Japan Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Japan.
2
Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Japan Division of Population Genetics, National Institute of Genetics, Mishima, Japan.
3
Laboratoire d'Immunogénétique Moléculaire (LIMT, EA3034), Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse III, France blancher.a@chu-toulouse.fr.

Abstract

Cynomolgus macaques (Macaca fascicularis) were introduced to the island of Mauritius by humans around the 16th century. The unique demographic history of the Mauritian cynomolgus macaques provides the opportunity to not only examine the genetic background of well-established nonhuman primates for biomedical research but also understand the effect of an extreme population bottleneck on the pattern of polymorphisms in genomes. We sequenced the whole genomes of six Mauritian cynomolgus macaques and obtained an average of 20-fold coverage of the genome sequences for each individual. The overall level of nucleotide diversity was 23% smaller than that of the Malaysian cynomolgus macaques, and a reduction of low-frequency polymorphisms was observed. In addition, we also confirmed that the Mauritian cynomolgus macaques were genetically closer to a representative of the Malaysian population than to a representative of the Indochinese population. Excess of nonsynonymous polymorphisms in low frequency, which has been observed in many other species, was not very strong in the Mauritian samples, and the proportion of heterozygous nonsynonymous polymorphisms relative to synonymous polymorphisms is higher within individuals in Mauritian than Malaysian cynomolgus macaques. Those patterns indicate that the extreme population bottleneck made purifying selection overwhelmed by the power of genetic drift in the population. Finally, we estimated the number of founding individuals by using the genome-wide site frequency spectrum of the six samples. Assuming a simple demographic scenario with a single bottleneck followed by exponential growth, the estimated number of founders (∼20 individuals) is largely consistent with previous estimates.

KEYWORDS:

Mauritian cynomolgus macaque; genome sequence; population bottleneck

PMID:
25805843
PMCID:
PMC5322541
DOI:
10.1093/gbe/evv033
[Indexed for MEDLINE]
Free PMC Article

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