Population genetics of captive spider monkeys in Japan for ex situ conservation

Spider monkeys (Ateles sp.) are among the most endangered primates in tropical forests, ranging from Central to South America. The current consensus on their classification is split into 7 species. However, species identification of Ateles individuals is challenging because their intraspecific and interspecific morphological traits gradually change and diversify among species, especially in pelage color and patterning. This problem makes it challenging to perform conservation in both wild (in situ) and captive (ex situ) populations. Currently, there are approximately 150 captive spider monkeys in around 30 Japanese zoos, reflecting more than 120 years of generational changes. To understand the genetic structure of the Ateles population in Japan and promote its ex situ conservation, we performed a population genetic analysis. Genomic DNA was extracted from 127 individuals using their fresh hair follicles. We determined the nucleotide sequences of three mitochondrial DNA regions and the nucleotide lengths of nine nuclear microsatellite loci in all individuals. Our analysis revealed the maternal lineages of four species (A. chamek, A. fusciceps, A. geoffroyi, and A. hybridus) from mitochondrial DNA analysis, and we identified novel haplotypes not previously reported. By comparing the maternal lineages of each individual with zoos' breeding records, we discovered at least 29 hybrid individuals, comprising about 20% of the current Japanese population. The results of the nuclear microsatellite analysis confirmed the genetic structure of hybrid individuals and suggested the presence of additional hybrids that could not be identified based on maternal lineage analysis and zoos' breeding records alone. These findings can contribute to the more appropriate management of spider monkeys toward ex situ conservation.