Advances in Using Non-invasive, Archival, and Environmental Samples for Population Genomic Studies

Andrews, Kimberly R.; De Barba, Marta; Russello, Michael A.; Waits, Lisette P.

doi:10.1007/13836_2018_45

Kimberly R. Andrews^4,5,
Marta De Barba⁶,
Michael A. Russello⁷ &
…
Lisette P. Waits⁴

Part of the book series: Population Genomics ((POGE))

2128 Accesses
21 Citations
2 Altmetric

Abstract

Recent advances in DNA sequencing and genotyping technologies are rapidly building our capacity to address ecological, evolutionary, and conservation questions for wildlife species. However, a large portion of wildlife genetic research relies on samples containing low quantities and quality of DNA, such as non-invasive, archival, and environmental DNA (eDNA) samples. These samples present unique methodological challenges that are largely responsible for a lag in the adoption of new genetic technologies for many areas of wildlife research. Nonetheless, steady progress is being made as researchers test and refine laboratory protocols and bioinformatic methods tailored to low-quality samples. Here we provide an overview of the progress toward low-quality sample applications for amplicon sequencing, single nucleotide polymorphism (SNP) genotyping, DNA capture, mitogenome sequencing, restriction site-associated DNA sequencing (RADseq), and whole-genome sequencing. We also review methods for generating DNA sequence data from samples comprised of multiple individuals and species, such as eDNA or fecal samples, including metagenome sequencing, metabarcoding, metagenome skimming, and metatranscriptomics. The implementation of these approaches has provided insight into a wide range of questions such as modern and historic population genetic structure and diversity, adaptation, inbreeding, ancient hybridization, occupancy, diet composition, microbiome composition, and many more. As the development of methods tailored for low-quality DNA sources continues to advance over the coming years, we expect these samples to provide unprecedented insight into the ecology, evolution, and conservation of wildlife species.

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Acknowledgments

We thank Brendan Epstein and Paul Hohenlohe for helpful comments on the manuscript. K.R.A. and L.P.W. were funded by the College of Natural Resources at the University of Idaho. M.D.B. acknowledges the support of the Laboratoire d’Ecologie Alpine, Grenoble, France. M.A.R acknowledges the support of the NSERC Discovery program (grant # 2014-04736). This is PMEL contribution number 4805 and Joint Institute for the Study of the Atmosphere and Ocean (JISAO) under NOAA Cooperative Agreement NA15OAR4320063 contribution number 2018-0160.

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Authors and Affiliations

Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
Kimberly R. Andrews & Lisette P. Waits
Genetics and Genomics Group, University of Washington JISAO and NOAA Pacific Marine Environmental Lab, Seattle, WA, USA
Kimberly R. Andrews
Laboratoire d’Ecologie Alpine (LECA), CNRS, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, Grenoble, France
Marta De Barba
Department of Biology, University of British Columbia, Kelowna, BC, Canada
Michael A. Russello

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Kimberly R. Andrews
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Marta De Barba
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Michael A. Russello
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Lisette P. Waits
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Correspondence to Kimberly R. Andrews .

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Editors and Affiliations

Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
Paul A. Hohenlohe
Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada
Om P. Rajora

Glossary

Amplicon sequencing: High-throughput sequencing of PCR products from multiple individuals simultaneously
Archival sample: Historic (collected within the last ~200 years) or ancient (usually up to ~100,000 years old) tissue sample
Ascertainment bias: Inference bias resulting from the process by which genetic loci were selected
Bait: Biotinylated oligonucleotide probe used to isolate or “capture” target DNA for sequencing
DNA capture: Method relying on baits to isolate or “capture” target DNA prior to high-throughput sequencing
DNA library: DNA that has been prepared for high-throughput sequencing, with DNA fragments the appropriate length, and with sequencing adapters ligated to ends of fragments
Environmental DNA (eDNA): DNA present in environmental samples such as water, soil, and air
Genetic non-invasive sample (gNIS): DNA sample collected without handling the study organism, e.g., shed hair or fecal sample
Genome skimming: Using low quantities of sequence data from genomic DNA libraries to study high-copy loci like mitogenomes, nuclear ribosomal genes, histone genes, and plastomes
Metabarcoding: High-throughput sequencing of PCR products generated from taxonomic-informative markers for an environmental sample
Metagenome skimming: Using shotgun sequencing data from samples comprised of multiple individuals and/or species (e.g., environmental samples) to study high-copy loci like mitogenomes, nuclear ribosomal genes, histone genes, and plastomes. Often focuses on taxonomic-informative markers to identify community composition
Metatranscriptomics: Sequencing RNA extracted from an environmental sample
Next-generation sequencing: A variety of high-throughput DNA sequencing technologies developed over the last decade
Nextera-tagmented, reductively amplified DNA (NextRAD): High-throughput sequencing of PCR products from genomic regions containing a preselected 9 bp sequence
Restriction site-associated DNA sequencing (RADseq): High-throughput sequencing of genomic regions adjacent to restriction cut sites
Sanger sequencing: “Traditional” low-throughput DNA sequencing technology developed in 1977
Sequencing by synthesis: High-throughput sequencing technology used by Illumina that detects the incorporation of single bases into replicating DNA strands
Shotgun sequencing: Direct sequencing of genomic DNA libraries
Single nucleotide polymorphism (SNP): Variant at a single nucleotide site
SNP genotyping platforms: A variety of technologies that generate SNP genotype data rather than sequence reads

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Andrews, K.R., De Barba, M., Russello, M.A., Waits, L.P. (2018). Advances in Using Non-invasive, Archival, and Environmental Samples for Population Genomic Studies. In: Hohenlohe, P.A., Rajora, O.P. (eds) Population Genomics: Wildlife. Population Genomics. Springer, Cham. https://doi.org/10.1007/13836_2018_45

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DOI: https://doi.org/10.1007/13836_2018_45
Published: 08 September 2018
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-63488-9
Online ISBN: 978-3-030-63489-6
eBook Packages: Computer ScienceComputer Science (R0)

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