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Whole mitochondrial genome capture from faecal samples and museum-preserved specimens
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Toronto, Dept Anthropol, Mississauga, ON, Canada..
Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.ORCID iD: 0000-0002-8493-5457
2017 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 6, p. e111-e121Article in journal (Refereed) Published
Abstract [en]

Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of noninvasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee. We show that the applied method is suitable for a wide range of sample types that differ in endogenous DNA content, increasing the proportion of target reads to over 300-fold. By systematically evaluating biases introduced during target enrichment of pooled museum samples, we show that capture is less efficient for fragments shorter or longer than the baits, that the proportion of human contaminating reads increases postcapture although capture efficiency is lower for human compared to gorilla fragments with a gorilla-generated bait, and that the rate of jumping PCR is considerable, but can be controlled for with a double-barcoding approach. We succeed in capturing complete mitochondrial genomes from faecal samples, but observe reduced capture efficiency as sequence divergence increases between the bait and target species. As previously shown for museum specimens, we demonstrate here that mitochondrial genome capture from field-collected faecal samples is a robust and reliable approach for population-wide studies of nonmodel organisms.

Place, publisher, year, edition, pages
2017. Vol. 17, no 6, p. e111-e121
Keywords [en]
great apes, mtDNA, natural history collections, noninvasive samples, target enrichment
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-342910DOI: 10.1111/1755-0998.12699ISI: 000415921900010PubMedID: 28675688OAI: oai:DiVA.org:uu-342910DiVA, id: diva2:1187054
Funder
Swedish Research Council Formas, 2015-676Available from: 2018-03-02 Created: 2018-03-02 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)
Opponent
Supervisors
Available from: 2019-08-16 Created: 2019-06-04 Last updated: 2019-09-17

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van der Valk, TomGuschanski, Katerina

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