Population dynamics and genetic connectivity in recent chimpanzee history

Fontsere, Claudia; Kuhlwilm, Martin; Morcillo-Suárez, Carlos; Álvarez-Estapé, Marina; Lester, Jack D.; Gratton, Paolo; Schmidt, Joshua M.; Dieguez, Paula; Aebischer, Thierry; Álvarez-Varona, Paula; Angedakin, Samuel; Assumang, Alfred K.; Ayimisin, Emmanuel Ayuk; Bailey, Emma; Barubiyo, Donatienne; Bessone, Mattia; Carretero-Alonso, Andrea; Chancellor, Rebecca; Cohen, Heather; Danquah, Emmanuel; Deschner, Tobias; Dunn, Andrew; Dupain, Jef; Egbe, Villard Ebot; Feliu, Olga; Goedmakers, Annemarie; Granjon, Anne‐Céline; Head, Josephine; Hedwig, Daniela; Hermans, Veerle; Hernández‐Aguilar, R. Adriana; Imong, Inaoyom; Jones, Sorrel; Junker, Jessica; Kadam, Parag; Kaiser, M. L.; Kambere, Mbangi; Kambale, Magloire V.; Kalan, Ammie K.; Kienast, Ivonne; Kujirakwinja, Deo; Langergraber, Kevin E.; Lapuente, Juan; Larson, Bradley; Laudisoit, Anne; Lee, Kevin; Llana, Manuel; Llorente, Miquel; Marrocoli, Sergio; Morgan, David; Mulindahabi, Felix; Murai, Mizuki; Neil, Emily; Nicholl, Sonia; Nixon, Stuart; Normand, Emma; Orbell, Chris; Ormsby, Lucy Jayne; Pacheco, Liliana; Piel, Alex K.; Riera, Laura; Robbins, Martha M.; Rundus, Aaron; Sanz, Crickette; Sciaky, Lilah; Sommer, Volker; Stewart, Fiona; Tagg, Nikki; Tédonzong, Luc Roscelin Dongmo; Ton, Els; Schijndel, Joost van; Vergnes, Virginie; Wessling, Erin G.; Willie, Jacob; Wittig, Roman M.; Yuh, Yisa Ginath; Yurkiw, Kyle; Zuberbuehler, Klaus; Hecht, Jochen; Vigilant, Linda; Boesch, Christophe; Andrés, Aida M.; Hughes, David A.; Kühl, Hjalmar S.; Lizano, Esther; Arandjelovic, Mimi

doi:10.1016/j.xgen.2022.100133

Cited by 25 publications

(32 citation statements)

References 105 publications

(173 reference statements)

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“…Previous studies on great apes using non-invasive samples have been restricted to analyses of neutral markers, e.g., microsatellites [ 18 , 20 , 59 , 60 , 61 , 62 ], and more recently target enrichment of specific genomic regions, e.g., chromosome 21 [ 45 ]. To date, only one study has obtained WGS data using multiple hairs from a wild-threatened species [ 63 ].…”

Section: Discussionmentioning

confidence: 99%

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Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs

Álvarez-Estapé

Pawar

Fontsere

et al. 2023

Genes

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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.

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Section: Discussionmentioning

confidence: 99%

“…The age of coalescence of the ROH tracks was estimated using the rule of g = 100/(2 × RoH length ) [ 44 ], with g being the number of generations. For this, we assumed a constant recombination rate of 1 cM/1 Mbp following [ 45 , 46 , 47 ].…”

Section: Methodsmentioning

confidence: 99%

Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs

Álvarez-Estapé

Pawar

Fontsere

et al. 2023

Genes

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“…A more fine-grained analysis of the evolutionary history and population structure of gorillas necessitates denser sampling, which most likely will only be possible through advances in the use of non-invasive samples. For example, a reconstruction of recent patterns of connectivity has been demonstrated from a large panel of faecal samples from chimpanzees (Fontsere et al 2022). Furthermore, considering the rapid decline of great ape populations over the past centuries, more temporal sampling from historical specimens (van der Valk et al 2018Valk et al , 2019 has the potential to be highly informative on variation lost over time.…”

Section: Discussionmentioning

confidence: 99%

Ghost admixture in eastern gorillas

Pawar

Cuadros-Espinoza

Manuel

et al. 2022

Preprint

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Archaic admixture has had a significant impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. Within the great apes archaic admixture has been identified in chimpanzees and bonobos, but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using Approximate Bayesian Computation (ABC) with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas, but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, likely more than 40 thousand years ago, and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.

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“…Just as surveys of human genomic and phenotypic diversity require many stakeholders, this project will require partnerships between biomedical scientists, evolutionary biologists, zoos and conservation biologists. This community effort could in turn raise awareness of the value and urgency of conservation, reveal further striking similarities between humans and other apes, produce well-assembled genomes and accompanying barcoding strategies to identify poaching routes and deter illegal trading 291 , and identify species-specific disease vulnerabilities, including to new immunological threats 187 .…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution

et al. 2023

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Our ancestors acquired morphological, cognitive and metabolic modifications that enabled humans to colonize diverse habitats, develop extraordinary technologies and reshape the biosphere. Understanding the genetic, developmental and molecular bases for these changes will provide insights into how we became human. Connecting human-specific genetic changes to species differences has been challenging owing to an abundance of low-effect size genetic changes, limited descriptions of phenotypic differences across development at the level of cell types and lack of experimental models. Emerging approaches for single-cell sequencing, genetic manipulation and stem cell culture now support descriptive and functional studies in defined cell types with a human or ape genetic background. In this Review, we describe how the sequencing of genomes from modern and archaic hominins, great apes and other primates is revealing human-specific genetic changes and how new molecular and cellular approaches — including cell atlases and organoids — are enabling exploration of the candidate causal factors that underlie human-specific traits.

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Population dynamics and genetic connectivity in recent chimpanzee history

Cited by 25 publications

References 105 publications

Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs

Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs

Ghost admixture in eastern gorillas

Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution

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