Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs
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Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs. / Alvarez-Estape, Marina; Pawar, Harvinder; Fontsere, Claudia; Trujillo, Amber E.; Gunson, Jessica L.; Bergl, Richard A.; Bermejo, Magdalena; Linder, Joshua M.; McFarland, Kelley; Oates, John F.; Sunderland-Groves, Jacqueline L.; Orkin, Joseph; Higham, James P.; Viaud-Martinez, Karine A.; Lizano, Esther; Marques-Bonet, Tomas.
In: Genes, Vol. 14, No. 3, 743, 2023.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs
AU - Alvarez-Estape, Marina
AU - Pawar, Harvinder
AU - Fontsere, Claudia
AU - Trujillo, Amber E.
AU - Gunson, Jessica L.
AU - Bergl, Richard A.
AU - Bermejo, Magdalena
AU - Linder, Joshua M.
AU - McFarland, Kelley
AU - Oates, John F.
AU - Sunderland-Groves, Jacqueline L.
AU - Orkin, Joseph
AU - Higham, James P.
AU - Viaud-Martinez, Karine A.
AU - Lizano, Esther
AU - Marques-Bonet, Tomas
N1 - Publisher Copyright: © 2023 by the authors.
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
KW - bottleneck
KW - Cross River gorilla
KW - gene flow
KW - hairs
KW - inbreeding
KW - NGS
KW - non-invasive
KW - wild gorillas
U2 - 10.3390/genes14030743
DO - 10.3390/genes14030743
M3 - Journal article
C2 - 36981014
AN - SCOPUS:85152012215
VL - 14
JO - Genes
JF - Genes
SN - 2073-4425
IS - 3
M1 - 743
ER -
ID: 343342914