Applying genomic data in wildlife monitoring : Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels

ORCID
0000-0001-9060-0912
Affiliation
Senckenberg Research Institute and Natural History Museum Frankfurt
von Thaden, Alina;
Affiliation
Senckenberg Research Institute and Natural History Museum Frankfurt
Nowak, Carsten;
Affiliation
Senckenberg Research Institute and Natural History Museum Frankfurt
Tiesmeyer, Annika;
Affiliation
Senckenberg Research Institute and Natural History Museum Frankfurt
Reiners, Tobias E.;
Affiliation
Universidade do Porto
Alves, Paulo C.;
Affiliation
University of Missouri
Lyons, Leslie A.;
Affiliation
ISPRA
Mattucci, Federica;
Affiliation
University of Bologna
Randi, Ettore;
ORCID
0000-0001-7251-8296
Affiliation
Friedrich‐Schiller‐Universität Jena
Cragnolini, Margherita;
Affiliation
Universidad de Murcia
Galián, José;
Affiliation
“Milvus Group” Bird and Nature Protection Association
Hegyeli, Zsolt;
Affiliation
National Museums Scotland
Kitchener, Andrew C.;
Affiliation
University of Liège
Lambinet, Clotilde;
Affiliation
Universidad de Murcia
Lucas, José M.;
Affiliation
BUND für Umwelt und Naturschutz Deutschland (BUND)
Mölich, Thomas;
Affiliation
Universidade do Porto
Ramos, Luana;
Affiliation
University of Liège
Schockert, Vinciane;
ORCID
0000-0002-8427-7861
Affiliation
Senckenberg Research Institute and Natural History Museum Frankfurt
Cocchiararo, Berardino

Abstract The genomic era has led to an unprecedented increase in the availability of genome‐wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat ( Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.

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License Holder: Copyright © 2020 John Wiley & Sons Ltd

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This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.