1. Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs
- Author
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Marina Alvarez-Estape, Harvinder Pawar, Claudia Fontsere, Amber E. Trujillo, Jessica L. Gunson, Richard A. Bergl, Magdalena Bermejo, Joshua M. Linder, Kelley McFarland, John F. Oates, Jacqueline L. Sunderland-Groves, Joseph Orkin, James P. Higham, Karine A. Viaud-Martinez, Esther Lizano, and Tomas Marques-Bonet
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Cross River gorilla ,NGS ,Wild gorillas ,Genetics ,Inbreeding ,non-invasive ,hairs ,inbreeding ,bottleneck ,gene flow ,wild gorillas ,Hairs ,Non-invasive ,Bottleneck ,Gene flow ,Genetics (clinical) - Abstract
The 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. This research was funded by Ministerio de Ciencia, Universidades e Investigación (FPI, PRE2018) (to M.A.-E.), Generalitat de Catalunya (FI_B100131) (to H.P.), European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 864203), PID2021-126004NB-100 (MICIIN/FEDER, UE), “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018-000792-M), NIH 1R01HG010898-01A1 and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2021 SGR 00177) (to T.M.B.). Illumina Inc. provided support for next-generation library sequencing, Beatriu de Pinós postdoctoral programme of the Government of Catalonia’s Secretariat for Universities and Research of the Ministry of Economy and Knowledge 2017 BP 00265 (to J.O.). The project that gave rise to these results received the support of a fellowship from “la Caixa” Foundation (ID 100010434) and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement (No 847648. The fellowship code is LCF/BQ/PI20/11760004) (to J.O.).
- Published
- 2023
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