A reference mitogenome for the yellow-tailed woolly monkey (Lagothrix flavicauda) using Oxford Nanopore sequencing shows no evidence for adaptation to high elevations

Species inhabiting high-elevation environments face energetic and physiological challenges, creating opportunities for adaptive divergence from lowland taxa. The yellow-tailed woolly monkey (Lagothrix flavicauda), a Critically Endangered primate endemic to high-elevation forests in Andean Perú, provides a unique system for investigating the evolutionary consequences of long-term occupation of high elevations. We used Oxford Nanopore Technology (ONT) to generate a high-coverage mitochondrial reference genome using low-quality fecal samples. Using this and a new mitogenome from a closely-related lowland common woolly monkey (L. lagotricha poeppigii), we estimated divergence dates and calculated substitution ratios to investigate the evolutionary history of both Lagothrix taxa and assess whether high-elevation living has left signatures of selection in the mitochondrial oxidative phosphorylation genes of L. flavicauda.

We assembled a high-coverage (9190X) reference mitogenome of 16,603 bp for L. flavicauda from a 15-year-old fecal sample, and a novel mitogenome for L. lagotricha poeppigii from fresh tissue (112X, 16,590 bp). Our phylogenetic reconstruction is consistent with other platyrrhine primate phylogenies with high bootstrap support, with the two Lagothrix taxa showing evidence of having diverged from one another ~ 2.8 million years ago. Substitution (d_N/d_S) ratios suggest purifying selection on protein-coding mitogenomic regions in all assessed lineages.

We found no evidence of positive selection acting on mitochondrial protein-coding genes in either L. flavicauda or the broader genus Lagothrix; all analyses instead support pervasive purifying selection across genes involved in oxidative phosphorylation. These results suggest that unlike in some other non-human primates occupying high elevations, the adaptive response of L. flavicauda to living in the Andes does not appear to involve evolution in the mitochondrial oxidative phosphorylation pathway, and likely involves alternative genetic pathways or mechanisms not captured by mitochondrial sequence evolution. By providing the first publicly available high-coverage mitochondrial genome for L. flavicauda, this study establishes a foundation for future population mitogenomic investigations of adaptation, evolutionary history, and conservation in this Critically Endangered, high-altitude primate.