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pp 1-37 | Cite as

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

  • Kimberly R. Andrews
  • Marta De Barba
  • Michael A. Russello
  • Lisette P. Waits
Chapter
Part of the Population Genomics book series

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.

Keywords

Ancient DNA Historical DNA Metagenomics Museum samples Next-generation sequencing 

Notes

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.

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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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Kimberly R. Andrews
    • 1
    • 2
  • Marta De Barba
    • 3
  • Michael A. Russello
    • 4
  • Lisette P. Waits
    • 1
  1. 1.Department of Fish and Wildlife SciencesUniversity of IdahoMoscowUSA
  2. 2.Genetics and Genomics GroupUniversity of Washington JISAO and NOAA Pacific Marine Environmental LabSeattleUSA
  3. 3.Laboratoire d’Ecologie Alpine (LECA)CNRS, Univ. Grenoble Alpes, Univ. Savoie Mont BlancGrenobleFrance
  4. 4.Department of BiologyUniversity of British ColumbiaKelownaCanada

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