uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
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: 2018-04-20

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full textPubMed

Authority records BETA

van der Valk, TomGuschanski, Katerina

Search in DiVA

By author/editor
van der Valk, TomGuschanski, Katerina
By organisation
Animal ecology
In the same journal
Molecular Ecology Resources
Evolutionary Biology

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 4 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf