• A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

      Tomaszkiewicz, Marta; Rangavittal, Samarth; Cechova, Monika; Sanchez, Rebeca Campos; Fescemyer, Howard W.; Harris, Robert; Ye, Danling; O'Brien, Patricia C. M.; Chikhi, Rayan; Ryder, Oliver A.; et al. (2016)
      The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.
    • Clubs des Amis des Gorilles in the Ebo forest, Cameroon

      Mfossa, Daniel; Abwe, Ekwoge E.; Morgan, Bethan J. (2018)
    • Community-led conservation action in the Ebo forest, Cameroon.

      Abwe, Ekwoge E.; Mfossa, DM; Morgan, Bethan J. (2015)
      The Ebo forest in Littoral Region, Cameroon harbours a rich biodiversity of primates, including gorillas and chimpanzees. The government of Cameroon launched the gazettement of the Ebo forest into a national park in 2006. However, the decree creating the park is still awaited and there is little or no wildlife law enforcement on the ground (Morgan et al. 2011). The proximity of Ebo to major urban centres like Douala, Edea and Yaoundé is a major incentive to the hunting and bushmeat trade, especially as growing agricultural products is not commercially viable given the poor state of the roads around the forest. The forest is thus a main source of livelihood to adjacent communities that depend on unsustainable hunting and the bushmeat trade for protein and income (Morgan 2004). In addition to running two biological research stations in the west and east of the forest, the Ebo Forest Research Project (EFRP) has been working with local communities, traditional and administrative authorities around the forest to conserve its rich biodiversity and habitats while waiting for the official protection of the forest (Abwe and Morgan 2012). This article is aimed at providing a summary of the community-led conservation initiatives by traditional authorities and communities around the Ebo forest since 2012.
    • Conserving the Ebo gorillas through community collaboration

      Mfossa, Daniel; Abwe, Ekwoge E.; Morgan, Bethan J. (2017)
    • First video footage of the elusive Ebo gorillas in Cameroon

      Mfossa, D.; Ndimbe, M.; Abwe, Ekwoge E.; Morgan, Bethan J. (2019)
    • Great ape genetic diversity and population history

      Prado-Martinez, Javier; Sudmant, Peter H.; Kidd, Jeffrey M.; Li, Heng; Kelley, Joanna L.; Lorente-Galdos, Belen; Veeramah, Krishna R.; Woerner, August E.; O’Connor, Timothy D.; Santpere, Gabriel; et al. (2013)
      Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria–Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.
    • Inference of gorilla demographic and selective history from whole-genome sequence data

      McManus, Kimberly F.; Kelley, Joanna L.; Song, Shiya; Veeramah, Krishna R.; Woerner, August E.; Stevison, Laurie S.; Ryder, Oliver A.; Great Ape Genome Project; Kidd, Jeffrey M.; Wall, Jeffrey D.; et al. (2015)
      Although population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole-genome sequences from 14 western lowland gorillas (Gorilla gorilla gorilla), 2 eastern lowland gorillas (G. beringei graueri), and a single Cross River individual (G. gorilla diehli). We infer that the ancestors of western and eastern lowland gorillas diverged from a common ancestor approximately 261 ka, and that the ancestors of the Cross River population diverged from the western lowland gorilla lineage approximately 68 ka. Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of 1.4-fold around 970 ka and a recent 5.6-fold contraction in population size 23 ka. The latter may correspond to a major reduction in African equatorial forests around the Last Glacial Maximum. We also analyze patterns of variation among western lowland gorillas to identify several genomic regions with strong signatures of recent selective sweeps. We find that processes related to taste, pancreatic and saliva secretion, sodium ion transmembrane transport, and cardiac muscle function are overrepresented in genomic regions predicted to have experienced recent positive selection.
    • Revised Regional Action Plan for the Conservation of the Cross River Gorilla (Gorilla gorilla diehli) 2014–2019

      Dunn, Andrew; Bergl, Richard; Byler, Dirck; Eben-Ebai, Samuel; Etiendem, Denis Ndeloh; Fotso, Roger; Ikfuingei, Romanus; Imong, Inaoyom; Jameson, Chris; Macfie, Elizabeth J.; et al. (IUCN/SSC Primate Specialist Group and Wildlife Conservation SocietyNew York, NY, USA, 2014)
      This plan outlines measures that should ensure that Cross River gorilla numbers are able to increase at key core sites, allowing them to extend into areas where they have been absent for many years.