Ancient hybridization and admixture in macaques (genus Macaca) inferred from whole genome sequences

Fan, Zhenxin; Zhou, Anbo; Osada, Naoki; Yu, Jianqiu; Juan, José; Li, Peng; Du, Lianming; Niu, Lili; Deng, Jiabo; Xu, Huailiang; Xing, Jinchuan; Yue, Bisong

doi:10.1016/j.ympev.2018.03.038

Cited by 40 publications

(79 citation statements)

References 63 publications

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“…To examine the phylogenetic relationships among the macaques, we first constructed a tree using mitochondrial genomes Next, we constructed a neighbor-joining tree using the genetic distance between nuclear genomes with the draft genome sequence of OLB as an outgroup ( Figure 3). The tree showed the sister relationship between the sinica and arctoides groups, and between the fascicularis and mulatta groups, as presented in previous studies ( Perelman et al 2011;Fan et al 2014;Fan et al 2018). We also reconstructed a tree using the TreeMix software ( Pickrell and Pritchard 2012) 7 and a graph using the neighbor-net method ( Bryant and Moulton 2004).…”

Section: Species Phylogenymentioning

confidence: 67%

“…Previous studies have revealed that ancient inter-specific gene flow has been common in macaques, not only between sister species such as M. fascicularis and M. mulatta ( Osada et al 2010;Yan et al 2011) but also between different species groups, for example, M. thibetana in the sinica group and M. mulatta in the mulatta group ( Fan et al 2014). Ancient hybridization between the arctoides and mulatta groups was also supported by whole-genome sequencing analysis of M. arctoides ( Fan et al 2018). The divergence of the sinica-arctoides and fascicularis-mulatta groups is estimated to have occurred around 1.5-2.0 Mya, as per fossil evidence ( Delson 1980), but much earlier estimates ( 2.8-4.9 Mya) have been obtained using nucleotide sequences ( Perelman et al 2011;Jiang et al 2016;Matsudaira et al 2018;Roos et al 2019).…”

Section: Individualsmentioning

confidence: 81%

“…In this study, we followed the grouping proposed by , and focused on four out of seven the stump-tailed macaque). Genome-wide phylogenetic analysis showed that the fascicularis and mulatta groups and the sinica and arctoides groups are sister pairs ( Fan et al 2018).…”

Section: Individualsmentioning

confidence: 99%

“…( 1) The mitochondrial genome of M. arctoides was a sister to the mulatta-group species in the mitochondrial phylogenetic tree ( Fan et al 2018;Roos et al 2019); however, a genome sequencing study of M. arctoides showed that the M. arctoides genome had a strong affinity to the genomes of sinica-group species ( Fan et al 2018).…”

Section: Individualsmentioning

confidence: 99%

“…However, hybridization and admixture among genetically divergent populations occasionally occur, impeding further genetic differentiation. Hybridization and admixture have frequently been observed in populations of wild animals and between different species ( Green et al 2010;Osada et al 2010;Meyer et al 2012;Cahill et al 2015;Fan et al 2018). S i m i l a r l y , t he migration of males is expected to have less impact on X chromosomes than on autosomes, because a female carries two X chromosomes but a male has only one.…”

Section: Introductionmentioning

confidence: 99%

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Sex-biased migration and admixture in macaque species revealed by comparison between autosomal and X-chromosomal genomic sequences

Osada

Matsudaira

Hamada

et al. 2020

Preprint

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The role of sex-specific demography in hybridization and admixture of genetically diverged species and populations is essential to understand the mechanisms forming the genomic diversity of sexually reproducing organisms. In order to infer how sex-linked genetic loci have been differentiated undergoing frequent hybridization and admixture, we examined 17 whole-genome sequences of seven species of the genus Macaca, which shows frequent inter-specific hybridization and predominantly female philopatry. We found that hybridization and admixture were prevalent within these species. For three cases of suggested hybrid origin of species/subspecies, M. arctoides, M. fascicularis ssp. aurea, and Chinese M. mulatta, we examined the level of admixture of X chromosomes, which is less affected by male-biased migration than that of autosomes. In one case, we were able to determine that M. cyclopis and M. fuscata was genetically closer to Chinese M. mulatta than to the Indian M. mulatta, and the admixture level of Chinese M. mulatta and M. fuscata/cyclopis was more pronounced on the X chromosome than on autosomes. Since the mitochondrial genomes of Chinese M. mulatta, M. cyclopis, and M. fuscata were found to cluster together, and the mitochondrial genome of Indian M. mulatta is more distantly related, the observed pattern of genetic differentiation on X-chromosomal loci is consistent with the nuclear swamping hypothesis, in which strong, continuous male-biased introgression from the ancestral Chinese M. mulatta population to a population related to M. fuscata and M. cyclopis generated incongruencies between the genealogies of the mitochondrial and autosomal genomes.

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Section: Species Phylogenymentioning

confidence: 67%

Section: Individualsmentioning

confidence: 81%

Section: Individualsmentioning

confidence: 99%

Section: Individualsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Sex-biased migration and admixture in macaque species revealed by comparison between autosomal and X-chromosomal genomic sequences

Osada

Matsudaira

Hamada

et al. 2020

Preprint

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Current distribution of two species of Chinese macaques (Macaca arctoides and Macaca thibetana) and the possible influence of climate change on future distribution

Yang

Xia

et al. 2023

American J Primatol

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Predicting the spatial distribution of species and suitable areas under global climate change could provide a reference for species conservation and long‐term management strategies. Macaca thibetana and Macaca arctoides are two endangered species of Chinese macaques. However, limited information is available on their distribution, and their habitat needs lack proper assessment due to complicated taxonomy and less research attention. In recent years, scholars widely used the maximum entropy (MaxEnt) model to predict the impact of global climate and certain environmental factors on species distribution. Therefore, we used the MaxEnt model to predict the spatiotemporal distribution of both macaque species under six climate change scenarios using occurrence and high‐resolution ecological data. We identified climatic factors, elevation, and land cover that shape their distribution range and determined shifts in their habitat range. The results demonstrated that temperature range, annual precipitation, forest land cover, and temperature seasonality, including the precipitation of the driest month are the main factors affecting their distribution. Currently, M. thibetana is mainly concentrated in central, eastern, southern, and southwestern China, and M. arctoides is mainly concentrated in three provinces (Yunnan, Guangxi, and Guangdong) in southern China. The MaxEnt model predicted that the suitable habitat for both species will increase with increased greenhouse emission scenarios. We also found that with the further increase in greenhouse emissions M. thibetana is expected to migrate to western China, and M. arctoides is expected to migrate to western or eastern China. This reinterpretation of the distribution of M. thibetana and M. arctoides in China, and predicted potential suitable habitat and possible migration direction, may provide new insights into the future conservation and management of these two species.

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Admixture in Mammals and How to Understand Its Functional Implications

2019

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Admixture, the genetic exchange between differentiated populations appears to be common in the history of species, but has not yet been comparatively studied across mammals. This limits the understanding of its mechanisms and potential role in mammalian evolution. The authors want to summarize the current knowledge on admixture in non-human primates, and suggest that it is important to establish a comparative framework for this phenomenon in humans. Genetic observations in domesticated mammals and their wild counterparts are discussed, and a brief global overview on other clades is presented. Based on this, some of the consequences of gene flow, including incompatibilities and their genomic footprint, as well as adaptive introgression are discussed, and suggestions for a functional genomics approach are made. It is proposed that the field is moving beyond descriptive observations in single species, to a comprehensive analysis of admixture and its impact. Admixture is becoming an integral part of mammalian evolution.

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Ancient hybridization and admixture in macaques (genus Macaca) inferred from whole genome sequences

Cited by 40 publications

References 63 publications

Sex-biased migration and admixture in macaque species revealed by comparison between autosomal and X-chromosomal genomic sequences

Sex-biased migration and admixture in macaque species revealed by comparison between autosomal and X-chromosomal genomic sequences

Current distribution of two species of Chinese macaques (Macaca arctoides and Macaca thibetana) and the possible influence of climate change on future distribution

Admixture in Mammals and How to Understand Its Functional Implications

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