Highly Polymorphic Microsatellite Markers for the Assessment of Male Reproductive Skew and Genetic Variation in Critically Endangered Crested Macaques (Macaca nigra)

Abstract

Genetic analyses based on noninvasively collected samples have become an important tool for evolutionary biology and conservation. Crested macaques (Macaca nigra), endemic to Sulawesi, Indonesia, are important for our understanding of primate evolution as Sulawesi macaques represent an exceptional example of primate adaptive radiation. Crested macaques are also Critically Endangered. However, to date we know very little about their genetics. The aim of our study was to find and validate microsatellite markers useful for evolutionary, conservation, and other genetic studies on wild crested macaques. Using fecal samples of 176 wild macaques living in the Tangkoko Reserve, Sulawesi, we identified 12 polymorphic microsatellite loci through cross-species polymerase chain reaction amplification with later modification of some of these primers. We tested their suitability by investigating and exploring patterns of paternity, observed heterozygosity, and evidence for inbreeding. We assigned paternity to 63 of 65 infants with high confidence. Among cases with solved paternity, we found no evidence of extragroup paternity and natal breeding. We found a relatively steep male reproductive skew B index of 0.330 ± 0.267; mean ± SD) and mean alpha paternity of 65% per year with large variation across groups and years (29–100%). Finally, we detected an excess in observed heterozygosity and no evidence of inbreeding across our three study groups, with an observed heterozygosity of 0.766 ± 0.059 and expected heterozygosity of 0.708 ± 0.059, and an inbreeding coefficient of −0.082 ± 0.035. Our results indicate that the selected markers are useful for genetic studies on wild crested macaques, and possibly also on other Sulawesi and closely related macaques. They further suggest that the Tangkoko population of crested macaques is still genetically variable despite its small size, isolation, and the species’ reproductive patterns. This gives us hope that other endangered primate species living in small, isolated populations may also retain a healthy gene pool, at least in the short term.Electronic supplementary materialThe online version of this article (doi:10.1007/s10764-017-9973-x) contains supplementary material, which is available to authorized users.

Bonds of bros and brothers: Kinship and social bonding in postdispersal male macaques

“…Eighty‐eight individuals of the same population had been previously genotyped at 15 autosomal microsatellite loci (Table ; Schülke et al., 2010; Sukmak et al., 2014). We added 48 adult individuals that had not been genotyped yet, following the same procedures, and genotyped all 136 individuals at two additional microsatellite loci (D1s548 & D7s2204; established for crested macaques— Macaca nigra in Engelhardt, Muniz, Perwitasari‐Farajallah, & Widdig, 2017). Genotyping was done following the two‐step multiplex PCR approach (Arandjelovic et al., 2009).…”

Growing into adulthood—a review on sex differences in the development of sociality across macaques

“…While Assamese and rhesus macaques have a less pronounced skew in male reproduction, reproductive skew in male crested macaques is generally much higher (reviewed in Engelhardt et al 2017). This indicates that high-ranking male crested macaques leave more offspring each, which might favour the formation of strong father-offspring bonds in this species.…”

“…As reproductive skew and male breeding tenure differ across primate species, future studies may reveal inter-specific differences in kin structure, kin preferences and mechanisms of kin recognition. In crested macaques with a high skew in paternity (Engelhardt et al 2017) and short breeding tenure (Marty et al 2017a), for instance, paternal kin might most likely be peers, potentially resulting in a kin preferences via age proximity only. In contrast, in species with a lower skew and more relaxed breeding tenure, such as rhesus macaques, paternal siblings are not only restricted to peers (Widdig et al 2002), and other kin recognition mechanisms, such as phenotype matching, might have evolved (e.g.…”

“…Accordingly, macaque groups are characterized by maternally related females organized in matrilines. However, striking variations are apparent, for instance, in male ability to gain or maintain dominance and monopolize fertile females, resulting in different male reproductive skews (compared in Engelhardt et al 2017). This has important consequences for the kin structure of social groups, as differences in male reproductive performance and ability to maintain high dominance lead to differences in the availability of paternally related peers (Widdig 2013).…”

Microsatellite Marker for Cross-Species Amplification: Study Case for Indonesian Sundaland Python (Serpentes: Pythonidae)

“…Best markers were categorized by at least 50% of amplification success and those that were polymorphic with at least three alleles [13]. The observed heterozygosities (Ho) ranged from 0.00-0.60 for P. breitensteini, 0.00-1.00 for P. bivittatus, and 0.00 -1.00 for P. brongersmai.…”