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

    VL - 19

    SP - 609

    EP - 622

    JO - Molecular Ecology Resources

    JF - Molecular Ecology Resources

    SN - 1755-098X

    IS - 3

    ER -