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

Hermosilla-Albala, N.; Palmada-Flores, M.; Gomez-Garrido, J.; Silva, F. E.; Alentorn-Moron, P.; Faella, A.; Martinez, S.; Fernandez-Bellon, H.; Almagro, V.; Messias, M.; Kaizer, M. C.; Farias, I.; Hrbek, T.; da Silva, M. N. F.; Mendoza, A. P.; Vilchez-Delgado, F.; Shanee, S.; de Souza Silva Junior, J.; Rossi, R.; Valsecchi, J.; Mayor, P.; Hvilsom, C.; Lizano, E.; Alioto, T. S.; Gut, M.; Gut, I. G.; Kuderna, L. F.; Rogers, J.; Farh, K. K.-H.; Marques-Bonet, T.; Boubli, J. P.

doi:10.1101/2025.03.07.641388

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bioRxiv · 10.1101/2025.03.07.641388

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

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Abstract

BackgroundMost 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 8 Atelidae species, 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 for Ateles 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 in Ateles, and further structure and dynamics outlined by the Madeira River in the latter clade. Lastly, we find that genes in highly divergent regions between Ateles and B. hypoxanthus are 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 between Ateles and Brachyteles potentially linked to distinct environmental light levels.

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Hermosilla-Albala, N., Palmada-Flores, M., Gomez-Garrido, J., Silva, F. E., Alentorn-Moron, P., Faella, A., Martinez, S., Fernandez-Bellon, H., Almagro, V., Messias, M., Kaizer, M. C., Farias, I., Hrbek, T., da Silva, M. N. F., Mendoza, A. P., Vilchez-Delgado, F., Shanee, S., de Souza Silva Junior, J., Rossi, R., Valsecchi, J., Mayor, P., Hvilsom, C., Lizano, E., Alioto, T. S., Gut, M., Gut, I. G., Kuderna, L. F., Rogers, J., Farh, K. K.-H., Marques-Bonet, T., Boubli, J. P.. 2025-03-10. The genomic landscape of spider monkeys and northern muriquis from a conservation perspective. https://doi.org/10.1101/2025.03.07.641388

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