TY - JOUR
T1 - Secondary contact and genomic admixture between rhesus and long-tailed macaques in the Indochina Peninsula
AU - Ito, Tsuyoshi
AU - Kanthaswamy, Sreetharan
AU - Bunlungsup, Srichan
AU - Oldt, Robert F.
AU - Houghton, Paul
AU - Hamada, Yuzuru
AU - Malaivijitnond, Suchinda
N1 - Funding Information:
We would like to thank the members of the Primate Research Unit of Chulalongkorn University for their help and kindness to TI and the owners and staff of Primate Products for the collection and processing of contributed samples. We also thank the Genomic Sequencing and Analysis Facility at the University of Texas for their support with the library preparation and sequencing and the McDonnell Genome Institute, Washington University, St Louis, MO, for making the Mmul_10 assembly sequences available. This work was partly supported by the Thailand Research Fund‐Chinese Academy of Science (DBG6080008), the TSRI Research Team Promotion Grant (RTA6280010), the Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research (K‐CONNEX), established by Human Resource Development Program for Science and Technology, MEXT, and the JSPS Grants‐in‐Aid for Scientific Research (17K15195 to TI and 19K06865 to YH). US National Institutes of Health (NIH) grants: P51 OD011107, 2U42 OD010990 and 5U42 OD021458 also supported SK's contributions to this study.
Funding Information:
We would like to thank the members of the Primate Research Unit of Chulalongkorn University for their help and kindness to TI and the owners and staff of Primate Products for the collection and processing of contributed samples. We also thank the Genomic Sequencing and Analysis Facility at the University of Texas for their support with the library preparation and sequencing and the McDonnell Genome Institute, Washington University, St Louis, MO, for making the Mmul_10 assembly sequences available. This work was partly supported by the Thailand Research Fund-Chinese Academy of Science (DBG6080008), the TSRI Research Team Promotion Grant (RTA6280010), the Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research (K-CONNEX), established by Human Resource Development Program for Science and Technology, MEXT, and the JSPS Grants-in-Aid for Scientific Research (17K15195 to TI and 19K06865 to YH). US National Institutes of Health (NIH) grants: P51 OD011107, 2U42 OD010990 and 5U42 OD021458 also supported SK's contributions to this study.
Publisher Copyright:
© 2020 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2020 European Society For Evolutionary Biology
PY - 2020/9/1
Y1 - 2020/9/1
N2 - Understanding the process and consequences of hybridization is one of the major challenges in evolutionary biology. A growing body of literature has reported evidence of ancient hybridization events or natural hybrid zones in primates, including humans; however, we still have relatively limited knowledge about the pattern and history of admixture because there have been little studies that simultaneously achieved genome-scale analysis and a geographically wide sampling of wild populations. Our study applied double-digest restriction site-associated DNA sequencing to samples from the six localities in and around the provisional hybrid zone of rhesus and long-tailed macaques and evaluated population structure, phylogenetic relationships, demographic history, and geographic clines of morphology and allele frequencies. A latitudinal gradient of genetic components was observed, highlighting the transition from rhesus (north) to long-tailed macaque distribution (south) as well as the presence of one northern population of long-tailed macaques exhibiting unique genetic structure. Interspecific gene flow was estimated to have recently occurred after an isolation period, and the migration rate from rhesus to long-tailed macaques was slightly greater than in the opposite direction. Although some rhesus macaque-biased alleles have widely introgressed into long-tailed macaque populations, the inflection points of allele frequencies have been observed as concentrated around the traditionally recognized interspecific boundary where morphology discontinuously changed; this pattern was more pronounced in the X chromosome than in autosomes. Thus, due to geographic separation before secondary contact, reproductive isolation could have evolved, contributing to the maintenance of an interspecific boundary and species-specific morphological characteristics.
AB - Understanding the process and consequences of hybridization is one of the major challenges in evolutionary biology. A growing body of literature has reported evidence of ancient hybridization events or natural hybrid zones in primates, including humans; however, we still have relatively limited knowledge about the pattern and history of admixture because there have been little studies that simultaneously achieved genome-scale analysis and a geographically wide sampling of wild populations. Our study applied double-digest restriction site-associated DNA sequencing to samples from the six localities in and around the provisional hybrid zone of rhesus and long-tailed macaques and evaluated population structure, phylogenetic relationships, demographic history, and geographic clines of morphology and allele frequencies. A latitudinal gradient of genetic components was observed, highlighting the transition from rhesus (north) to long-tailed macaque distribution (south) as well as the presence of one northern population of long-tailed macaques exhibiting unique genetic structure. Interspecific gene flow was estimated to have recently occurred after an isolation period, and the migration rate from rhesus to long-tailed macaques was slightly greater than in the opposite direction. Although some rhesus macaque-biased alleles have widely introgressed into long-tailed macaque populations, the inflection points of allele frequencies have been observed as concentrated around the traditionally recognized interspecific boundary where morphology discontinuously changed; this pattern was more pronounced in the X chromosome than in autosomes. Thus, due to geographic separation before secondary contact, reproductive isolation could have evolved, contributing to the maintenance of an interspecific boundary and species-specific morphological characteristics.
KW - Indochina
KW - RAD-seq
KW - hybridization
KW - reproductive isolation
KW - speciation
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U2 - 10.1111/jeb.13681
DO - 10.1111/jeb.13681
M3 - Article
C2 - 33448526
AN - SCOPUS:85088792139
SN - 1010-061X
VL - 33
SP - 1164
EP - 1179
JO - Journal of Evolutionary Biology
JF - Journal of Evolutionary Biology
IS - 9
ER -