The genomic landscape of spider monkeys and northern muriquis from a conservation perspective

• DOI: 10.1101/2025.03.07.641388
• Publication Date: 2025-03-10T19:45:21Z
• Authors: Núria Hermosilla-...; Marc Palmada-Flores; Jèssica Gómez-Gar...; Felipe Ennes Silva; Pol Alentorn-Moron; Armida Faella; Sira Martínez; Hugo Fernández-Be...; Vanessa Almagro; Mariluce Messias; Mariane C. Kaizer; Izeni Farias; Tomas Hrbek; Maria N. F. da Silva; A. Patricia Mendoza; Fernando Vilchez-...; Sam Shanee; José de Souza Sil...; Rogerio Rossi; João Valsecchi; Pedro Mayor; Christina Hvilsom; Esther Lizano; Tyler S. Alioto; Marta Gut; Ivo G. Gut; Lukas F. Kuderna; Jeff Rogers; Kyle Kai-Hao Farh; Tomas Marques-Bonet; Jean P. Boubli

AbstractBackgroundMost populations of spider monkeys (Ateles) and muriquis (Brachyteles), two Neotropical primate genera, are under severe anthropogenic threats. Yet, taxon-wide population-level studies leveraging their degree of endangerment linked to their genetic diversity patterns and demographic history are lacking. To properly address this, there is a need to expand from morphological and genetic marker-based studies.ResultsWe generated high-coverage genome sequencing for 58 individuals sampled across 8Atelidaespecies, in the first population-wide study of all extant spider monkey species, in the wild and captivity, alongside northern muriquis (Brachyteles hypoxanthus). Additionally, we present a high-contiguity reference genome forAteles hybridus. Here, we observe the overall levels of genetic diversity and genetic load of the analyzed populations do not align to their IUCN endangerment category. Moreover, we show that in the wild, genetic load is overall higher compared to the captive populations analyzed. Then, we depict two main trans and cis-Andean sister clades inAteles, and further structure and dynamics outlined by the Madeira River in the latter clade. Lastly, we find that genes in highly divergent regions betweenAtelesandB. hypoxanthusare involved in central nervous system development and photorreception.ConclusionsOur study shows i) the lack of concordance between the genetic diversity levels and extinction risk of these populations, suggestive of recent and strong external drivers; ii) increased genetic load in the wild in contrast to effective captive management, indicating mostly past demographic events; iii) structure and dynamics in spider monkeys that agrees with common biogeographical patterns and iv) genetic divergence betweenAtelesandBrachytelespotentially linked to distinct environmental light levels.