Genetic analysis of samples from wild populations opens new perspectives on hybridization between long‐tailed (Macaca fascicularis) and rhesus macaques (Macaca mulatta)

Abstract

In the past decade, many researchers have published papers about hybridization between long-tailed and rhesus macaques. These previous works have proposed unidirectional gene flow with the Isthmus of Kra as the zoogeographical barrier of hybridization. However, these reports analyzed specimens of unknown origin and/or did not include specimens from Thailand, the center of the proposed area of hybridization. Collected specimens of long-tailed and rhesus macaques representing all suspected hybridization areas were examined. Blood samples from four populations each of long-tailed and rhesus macaques inhabiting Thailand, Myanmar, and Laos were collected and analyzed with conspecific references from China (for rhesus macaques) and multiple countries from Sundaic regions (for long-tailed macaques). Ninety-six single nucleotide polymorphism (SNP) markers specifically designed to interrogate admixture and ancestry were used in genotyping. We found genetic admixture maximized at the hybrid zone (15-20°N), as well as admixture signals of varying strength in both directions outside of the hybrid zone. These findings show that the Isthmus of Kra is not a barrier to gene flow from rhesus to long-tailed populations. However, to precisely identify a southernmost barrier, if in fact a boundary rather than simple isolation by distance exists, the samples from peninsular Malaysia must be included in the analysis. Additionally, a long-tailed to rhesus gene flow boundary was found between northern Thailand and Myanmar. Our results suggest that selection of long-tailed and rhesus macaques, the two most commonly used non-human primates for biomedical research, should take into account not only the species identification but also the origin of and genetic admixture within and between the species.

Partial sequence analyses of exon 7 of the ABO locus of cynomolgus (Macaca fascicularis) and rhesus (M. mulatta) macaques: Indeterminate phenotypes show the presence of the O blood group

“…Using Premasuthan et al's methods, Kanthaswamy et al reported the presence of indeterminate blood types in cynomolgus and rhesus macaque populations at frequencies of 2.39% and 1.18%, respectively, and Oldt et al described an enrichment of indeterminate blood phenotypes in the hybrid zone shared by the two species as speculated previously . Multiple macaques in Oldt et al's study exhibited an indeterminate allele caused by failure of the first probe to bind with its target site coupled with the successful detection of the A or B allele with the second probe, suggesting that the indeterminate phenotypes are generated by probe‐target hybridization failures which point to an underlying genetic cause rather than DNA degradation …”

Population genetics of the ABO locus within the rhesus (Macaca mulatta) and cynomolgus (M. fascicularis) macaque hybrid zone

“…DNA samples from 222 free‐ranging macaques, comprising 8 rhesus and cynomolgus populations living in the hybrid zone described in Bunlungsup, Kanthaswamy, et al () as well as 30 wild‐caught cynomolgus macaques from Laos, were subjected to molecular phenotyping using the dual‐amplification qPCR procedure developed by Premasuthan et al (), and blood group frequencies were calculated assuming absence of an O allele. The nine populations studied consist of four rhesus macaque populations from Myanmar, Thailand, and Laos and five cynomolgus macaque populations from Laos and Thailand (both North and South of the IoK; Bunlungsup, Kanthaswamy, et al, ). Blood group frequency reference data (Kanthaswamy et al, ) consisted of two rhesus macaque populations of Chinese and Indian ancestry, three cynomolgus macaque populations of Indonesian, Philippine and Mauritian ancestry, and one population of Vietnam/Cambodia cynomolgus macaque which was treated as the tenth hybrid population.…”

“…The locations of Chinese and Indian rhesus reference populations, hybrid populations of rhesus and cynomolgus macaques, and cynomolgus reference populations were shown in Tables –, and Figure . To compare distributions between the two species, the species status as determined in Bunlungsup, Kanthaswamy, et al () was used.…”

“…However, subsequent SNP‐based research on a Chinese rhesus macaque population suggested a more complex hybridization scenario between the two species (Kanthaswamy, Satkoski, Kou, Malladi, & Glenn Smith, ) that was confirmed later via sex‐linked marker studies (Bunlungsup, Imai, Hamada, Matsudaira, & Malaivijitnond, ). Newer research utilizing markers across the nuclear genome in hybrid zone populations established both bidirectional (albeit unbalanced) gene flow and a wider hybrid zone and cautions that while pure species status need not always be a necessary criterion for use of macaques in biomedical studies (Bunlungsup, Kanthaswamy, et al, ), wide variation among hybrid macaques in their proportions of rhesus and cynomolgus macaque ancestry can influence phenotypic expression of traits under experimental study. Moreover, the more balanced blood group frequencies in Chinese rhesus macaques and Indochinese cynomolgus macaques might reflect gene flow between two species in which blood groups B and A, respectively, would otherwise predominate.…”

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

“…Bunlungsup et al 2017;Liu et al 2018). Therefore, a more detailed and comprehensive evolutionary history of macaques should be performed using species-wide genome sequences in future studies.…”