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The genome of the endangered dryas monkey provides new insights into the evolutionary history of the vervets
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. (Katerina Guschanski)ORCID iD: 0000-0001-6582-3452
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Genomic data can be a powerful tool for inferring ecology, behaviour and conservation needs of highly elusive species, particularly when other sources of information are hard to come by. Here we focus on the dryas monkey, an endangered primate endemic to the Congo Basin with cryptic behaviour and possibly less than 250 remaining individuals. Using whole genome data we show that the dryas monkey represents a sister lineage to the vervet monkeys and has diverged from them at least 1 million years ago with additional bi-directional gene flow 590,000 – 360,000 years ago. After bonobo-chimpanzee admixture, this is the second reported case of gene flow that most likely involved crossing the Congo River, a strong dispersal barrier. As the demographic history of bonobos and dryas monkey shows similar patterns of population increase during this time period, we hypothesise that the fluvial topology of the Congo River might have been more dynamic than previously recognised. As a result of dryas monkey - vervet admixture, genes involved in resistance to the simian immunodeficiency virus (SIV) have been exchanged, possibly indicating adaptive introgression. Despite the presence of several homozygous loss-of-function mutations in genes associated with reduced sperm mobility and immunity, we find high genetic diversity and low levels of inbreeding and genetic load in the studied dryas monkey individual. This suggests that the current population carries sufficient genetic variability for the long-term survival of this species. We thus provide an example of how genomic data can directly improve our understanding of elusive species.

National Category
Genetics
Identifiers
URN: urn:nbn:se:uu:diva-383458DOI: 10.1101/613273OAI: oai:DiVA.org:uu-383458DiVA, id: diva2:1316016
Available from: 2019-05-15 Created: 2019-05-15 Last updated: 2019-06-04
In thesis
1. Genomics of population decline
Open this publication in new window or tab >>Genomics of population decline
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

With human populations forecasted to grow in the next decades, many mammals face increasing anthropogenic threats. The consequential population declines are a precursor to extinctions, as small populations are not only more sensitive to stochastic events, but reduction in population size is generally also followed by a decrease in genetic diversity, which in turn reduces adaptive potential and fitness of the population. By using molecular methods I aimed to estimate the magnitude of the genomic consequences as a result of rapid population declines with a focus on the endangered eastern gorillas. First, I genotyped Grauer’s gorilla (Gorilla beringei graueri) faecal samples, which revealed lower genetic diversity and high differentiation in the peripheral compared to the central populations, indicating a strong effect of genetic drift and limited gene flow among the small, isolated forest fragments (Chapter 1). Next, by using a target capture approach I obtained complete mitochondrial genomes from degraded Grauer’s and mountain (Gorilla beringei beringei) gorilla faecal and museum samples (Chapter 2) which showed a loss of mitochondrial diversity within the last century in Grauer’s gorillas, mainly driven by the extinction of peripheral populations (Chapter 3). Genome-wide sequence data from historical samples suggests that this loss has also affected the nuclear genome, as modern Grauer’s gorillas carry on average more genetic variants with putatively negative fitness consequences than historically. No significant temporal changes were observed in the closely related mountain gorillas, which might be due to their contrasting demographic history (Chapter 4). I then switched study species to the endangered Dryas monkey and find that, despite its possible small population size, the current Dryas monkey population is genetically diverse with low levels of inbreeding and as such likely viable in the long-term if appropriate conservation measures are taken (Chapter 5). Finally, I aimed to estimate the strength of genetic purging across a range of mammalian species. This revealed that although genetic purging might be common among endangered species, it mainly acts on long evolutionary time scales with limited strength during the rapid population declines as experienced by many species today (Chapter 6).

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 57
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1822
Keywords
genetic diversity, minimal-invasive samples, population decline, inbreeding, genetic purging, eastern gorillas, Dryas monkey
National Category
Ecology
Research subject
Biology with specialization in Animal Ecology
Identifiers
urn:nbn:se:uu:diva-384346 (URN)978-91-513-0684-1 (ISBN)
Public defence
2019-09-06, Lindahlsalen, Norbyvägen 18, Uppsala, 10:00 (English)
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Supervisors
Available from: 2019-08-16 Created: 2019-06-04 Last updated: 2019-09-17

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