A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture

Lauren C. White, Claudia Fontsere, Esther Lizano, David A. Hughes, Samuel Angedakin, Mimi Arandjelovic, Anne Céline Granjon, Jörg B. Hans, Jack D. Lester, M. Timothy Rabanus-Wallace, Carolyn Rowney, Veronika Städele, Tomas Marques-Bonet, Kevin Langergraber, Linda Vigilant

Research output: Contribution to journalArticle

Abstract

Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality-assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2%–3%, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies.

Original languageEnglish (US)
Pages (from-to)609-622
Number of pages14
JournalMolecular Ecology Resources
Volume19
Issue number3
DOIs
StatePublished - May 1 2019

Fingerprint

Wild Animals
wild animals
hybridization
DNA
Population
Exome
Pan troglodytes
sampling
wild animal
animal population
Feces
feces
multiple regression
genomics
microorganism
Research Personnel
researchers
microorganisms

Keywords

  • chimpanzees
  • conservation genomics
  • faecal samples
  • population genomics
  • target enrichment

ASJC Scopus subject areas

  • Biotechnology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

White, L. C., Fontsere, C., Lizano, E., Hughes, D. A., Angedakin, S., Arandjelovic, M., ... Vigilant, L. (2019). A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture. Molecular Ecology Resources, 19(3), 609-622. https://doi.org/10.1111/1755-0998.12993

A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture. / White, Lauren C.; Fontsere, Claudia; Lizano, Esther; Hughes, David A.; Angedakin, Samuel; Arandjelovic, Mimi; Granjon, Anne Céline; Hans, Jörg B.; Lester, Jack D.; Rabanus-Wallace, M. Timothy; Rowney, Carolyn; Städele, Veronika; Marques-Bonet, Tomas; Langergraber, Kevin; Vigilant, Linda.

In: Molecular Ecology Resources, Vol. 19, No. 3, 01.05.2019, p. 609-622.

Research output: Contribution to journalArticle

White, LC, Fontsere, C, Lizano, E, Hughes, DA, Angedakin, S, Arandjelovic, M, Granjon, AC, Hans, JB, Lester, JD, Rabanus-Wallace, MT, Rowney, C, Städele, V, Marques-Bonet, T, Langergraber, K & Vigilant, L 2019, 'A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture', Molecular Ecology Resources, vol. 19, no. 3, pp. 609-622. https://doi.org/10.1111/1755-0998.12993
White, Lauren C. ; Fontsere, Claudia ; Lizano, Esther ; Hughes, David A. ; Angedakin, Samuel ; Arandjelovic, Mimi ; Granjon, Anne Céline ; Hans, Jörg B. ; Lester, Jack D. ; Rabanus-Wallace, M. Timothy ; Rowney, Carolyn ; Städele, Veronika ; Marques-Bonet, Tomas ; Langergraber, Kevin ; Vigilant, Linda. / A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture. In: Molecular Ecology Resources. 2019 ; Vol. 19, No. 3. pp. 609-622.
@article{cc35d52e1d914f90a9d3600ba066579b,
title = "A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture",
abstract = "Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality-assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2{\%}–3{\%}, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies.",
keywords = "chimpanzees, conservation genomics, faecal samples, population genomics, target enrichment",
author = "White, {Lauren C.} and Claudia Fontsere and Esther Lizano and Hughes, {David A.} and Samuel Angedakin and Mimi Arandjelovic and Granjon, {Anne C{\'e}line} and Hans, {J{\"o}rg B.} and Lester, {Jack D.} and Rabanus-Wallace, {M. Timothy} and Carolyn Rowney and Veronika St{\"a}dele and Tomas Marques-Bonet and Kevin Langergraber and Linda Vigilant",
year = "2019",
month = "5",
day = "1",
doi = "10.1111/1755-0998.12993",
language = "English (US)",
volume = "19",
pages = "609--622",
journal = "Molecular Ecology Resources",
issn = "1755-098X",
publisher = "Wiley-Blackwell",
number = "3",

}

TY - JOUR

T1 - A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture

AU - White, Lauren C.

AU - Fontsere, Claudia

AU - Lizano, Esther

AU - Hughes, David A.

AU - Angedakin, Samuel

AU - Arandjelovic, Mimi

AU - Granjon, Anne Céline

AU - Hans, Jörg B.

AU - Lester, Jack D.

AU - Rabanus-Wallace, M. Timothy

AU - Rowney, Carolyn

AU - Städele, Veronika

AU - Marques-Bonet, Tomas

AU - Langergraber, Kevin

AU - Vigilant, Linda

PY - 2019/5/1

Y1 - 2019/5/1

N2 - Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality-assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2%–3%, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies.

AB - Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality-assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2%–3%, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies.

KW - chimpanzees

KW - conservation genomics

KW - faecal samples

KW - population genomics

KW - target enrichment

UR - http://www.scopus.com/inward/record.url?scp=85064595943&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85064595943&partnerID=8YFLogxK

U2 - 10.1111/1755-0998.12993

DO - 10.1111/1755-0998.12993

M3 - Article

C2 - 30637963

AN - SCOPUS:85064595943

VL - 19

SP - 609

EP - 622

JO - Molecular Ecology Resources

JF - Molecular Ecology Resources

SN - 1755-098X

IS - 3

ER -