Mitochondrial Diversity and Historical Demography of Ateles marginatus in Urban Forest Fragments in the Southern Amazon Deforestation Arc

Abstract Primate populations isolated in forest fragments within urban areas often face critical survival challenges due to the negative effects of habitat degradation on genetic diversity, evolutionary potential, and ecological dynamics. The Arc of Deforestation has the highest deforestation rates in the Brazilian Amazon, driven primarily by growth of monocultures, ranching, and urbanisation. However, there are no published studies on urban primate demography and genetic diversity in this region. The range of the white-cheeked spider monkey ( Ateles marginatus ) overlaps significantly with the Arc of Deforestation, where anthropogenic pressures threaten its long-term survival. We assessed the genetic diversity and structure of A. marginatus from five urban forest fragments in Sinop, Mato Grosso, Brazil, by analysing the mitochondrial control region (D-loop). We also compared our data with publicly available Ateles D-loop sequences. Results showed that the study population has high levels of genetic diversity and no signs of spatial substructuring. The haplotype network and phylogenetic tree showed one individual identified as A. marginatus clustered with Genbank sequences of A. chamek , a congeneric species expected only on the opposite bank of the Teles Pires-Tapajós River. Historical demographic analysis showed population expansion between 22–20 kybp, followed by population decline at 10–2 kybp. Recent population fragmentation was probably accompanied by local haplotype extinctions in the study area. Our findings show that urban primate populations can retain genetic diversity and significant evolutionary potential for conservation management and suggest that Amazonian rivers may be more a filter than barrier for Atelid species, allowing the sporadic crossing of individuals.