TY - JOUR

T1 - The ecologist’s field guide to sequence-based identification of biodiversity

AU - Creer, Simon

AU - Deiner, Kristy

AU - Frey, Serita

AU - Porazinska, Dorota

AU - Taberlet, Pierre

AU - Thomas, W. kelley

AU - Potter, Caitlin

AU - Bik, Holly M.

N1 - US National Science Foundation Research Coordination Network. Grant Number: DBI-1262480

PY - 2016/9/13

Y1 - 2016/9/13

N2 - 1. The past 100 years of ecological research has seen substantial progress in understanding the natural worldand likely effects of change, whether natural or anthropogenic. Traditional ecological approaches underpin suchadvances, but would additionally benefit from recent developments in the sequence-based quantification of biodiversityfrom the fields of molecular ecology and genomics. By building on a long and rich history of moleculartaxonomy and taking advantage of the new generation of DNA sequencing technologies, we are gaining previouslyimpossible insights into alpha and beta diversity from all domains of life, irrespective of body size.While anumber of complementary reviews are available in specialist journals, our aim here is to succinctly describe thedifferent technologies available within the omics toolbox and showcase the opportunities available to contemporaryecologists to advance our understanding of biodiversity and its potential roles in ecosystems.2. Starting in the field, we walk the reader through sampling and preservation of genomic material, includingtypical taxonomy marker genes used for species identification. Moving on to the laboratory, we cover nucleicacid extraction approaches and highlight the principal features of using marker gene assessment, metagenomics,metatranscriptomics, single-cell genomics and targeted genome sequencing as complementary approaches toassess the taxonomic and functional characteristics of biodiversity. We additionally provide clear guidance onthe forms of DNA found in the environmental samples (e.g. environmental vs. ancient DNA) and highlight aselection of case studies, including the investigation of trophic relationships/food webs. Given the maturity ofsequence-based identification of prokaryotes and microbial eukaryotes, more exposure is given to macrobialcommunities. We additionally illustrate current approaches to genomic data analysis and highlight the excitingprospects of the publicly available data underpinning published sequence-based studies.3. Given that ecology ‘has to count’, we identify the impact that molecular genetic analyses have had on stakeholdersand end-users and predict future developments for the fields of biomonitoring. Furthermore, we concludeby highlighting future opportunities in the field of systems ecology afforded by effective engagementbetween the fields of traditional and molecular ecology

AB - 1. The past 100 years of ecological research has seen substantial progress in understanding the natural worldand likely effects of change, whether natural or anthropogenic. Traditional ecological approaches underpin suchadvances, but would additionally benefit from recent developments in the sequence-based quantification of biodiversityfrom the fields of molecular ecology and genomics. By building on a long and rich history of moleculartaxonomy and taking advantage of the new generation of DNA sequencing technologies, we are gaining previouslyimpossible insights into alpha and beta diversity from all domains of life, irrespective of body size.While anumber of complementary reviews are available in specialist journals, our aim here is to succinctly describe thedifferent technologies available within the omics toolbox and showcase the opportunities available to contemporaryecologists to advance our understanding of biodiversity and its potential roles in ecosystems.2. Starting in the field, we walk the reader through sampling and preservation of genomic material, includingtypical taxonomy marker genes used for species identification. Moving on to the laboratory, we cover nucleicacid extraction approaches and highlight the principal features of using marker gene assessment, metagenomics,metatranscriptomics, single-cell genomics and targeted genome sequencing as complementary approaches toassess the taxonomic and functional characteristics of biodiversity. We additionally provide clear guidance onthe forms of DNA found in the environmental samples (e.g. environmental vs. ancient DNA) and highlight aselection of case studies, including the investigation of trophic relationships/food webs. Given the maturity ofsequence-based identification of prokaryotes and microbial eukaryotes, more exposure is given to macrobialcommunities. We additionally illustrate current approaches to genomic data analysis and highlight the excitingprospects of the publicly available data underpinning published sequence-based studies.3. Given that ecology ‘has to count’, we identify the impact that molecular genetic analyses have had on stakeholdersand end-users and predict future developments for the fields of biomonitoring. Furthermore, we concludeby highlighting future opportunities in the field of systems ecology afforded by effective engagementbetween the fields of traditional and molecular ecology

U2 - 10.1111/2041-210X.12574

DO - 10.1111/2041-210X.12574

M3 - Article

VL - 7

SP - 1008

EP - 1018

JO - Methods in Ecology and Evolution

JF - Methods in Ecology and Evolution

SN - 2041-210X

ER -