Alvarez-Estape, MarinaPawar, HarvinderFontseré Alemany, Clàudia, 1992-Trujillo, Amber E.Gunson, Jessica L.Bergl, Richard A.Bermejo, MagdalenaLinder, Joshua M.McFarland, KelleyOates, John F.Sunderland-Groves, Jacqueline L.Orkin, Joseph D.Higham, James P.Viaud-Martinez, Karine A.Lizano González, Esther, 1974-Marquès i Bonet, Tomàs, 1975-2023-06-062023-06-062023Alvarez-Estape M, Pawar H, Fontsere C, Trujillo AE, Gunson JL, Bergl RA, Bermejo M, Linder JM, McFarland K, Oates JF, Sunderland-Groves JL, Orkin J, Higham JP, Viaud-Martinez KA, Lizano E, Marques-Bonet T. Past connectivity but recent inbreeding in cross river gorillas determined using whole genomes from single hairs. Genes (Basel). 2023 Mar 18;14(3):743. DOI: 10.3390/genes140307432073-4425http://hdl.handle.net/10230/57048The critically endangered western gorillas (Gorilla gorilla) are divided into two subspecies: the western lowland (G. g. gorilla) and the Cross River (G. g. diehli) gorilla. Given the difficulty in sampling wild great ape populations and the small estimated size of the Cross River gorilla population, only one whole genome of a Cross River gorilla has been sequenced to date, hindering the study of this subspecies at the population level. In this study, we expand the number of whole genomes available for wild western gorillas, generating 41 new genomes (25 belonging to Cross River gorillas) using single shed hairs collected from gorilla nests. By combining these genomes with publicly available wild gorilla genomes, we confirm that Cross River gorillas form three population clusters. We also found little variation in genome-wide heterozygosity among them. Our analyses reveal long runs of homozygosity (>10 Mb), indicating recent inbreeding in Cross River gorillas. This is similar to that seen in mountain gorillas but with a much more recent bottleneck. We also detect past gene flow between two Cross River sites, Afi Mountain Wildlife Sanctuary and the Mbe Mountains. Furthermore, we observe past allele sharing between Cross River gorillas and the northern western lowland gorilla sites, as well as with the eastern gorilla species. This is the first study using single shed hairs from a wild species for whole genome sequencing to date. Taken together, our results highlight the importance of implementing conservation measures to increase connectivity among Cross River gorilla sites.application/pdfeng© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).info:eu-repo/semantics/articlehttp://dx.doi.org/10.3390/genes14030743Cross River gorillaNGSBottleneckGene flowHairsInbreedingNon-invasiveWild gorillasinfo:eu-repo/semantics/openAccess