Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances

Abstract

Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.

Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management

“…In addition to providing greater resolution for diversity estimates (e.g., nucleotide diversity, heterozygosity, relatedness [1]), these new genomic approaches provide an opportunity to tackle new questions regarding regions of the genome that underlie fitness-related traits (i.e., adaptive variation [2,3,4]). While the promise of a conservation genomic approach has been heralded for well over a decade [5], the uptake of these technologies by conservation management has been slow [6,7].…”

A multi-omics approach to solving problems in plant disease ecology

“…When designing projects that could benefit from multi-omic approaches, there is a need to move away from strictly observational research questions to those that are hypothesis driven. Although the number of published research articles has grown exponentially in the past decade to reflect breakthroughs in high throughput sequencing, few have been applied to questions within the fields of environmental and conservation genomics that ask experimental questions [178]. A shift from hypotheses that measure correlation to those that decipher an underlying causation for an ecological phenomena would benefit the field of plant disease ecology.…”

A comparison of pedigree, genetic, and genomic estimates of relatedness for informing pairing decisions in two critically endangered birds

“…Given the decreasing cost of high-throughput sequencing (Hayden, 2014) and the increasing amount of genomic resources readily available for non-model species (Galla et al, 2019), producing thousands of SNPs is now possible for many highly threatened species and provides an exciting opportunity for use in conservation breeding programmes (Galla et al, 2016;He, Johansson, & Heath, 2016). Indeed, there are several recent examples of genome-wide SNPs being used for relatedness in conservation, ecology, and evolution (e.g., De Fraga, Lima, Magnusson, Ferrão, & Stow, 2017;Escoda, González-Esteban, Gómez, & Castresana, 2017), with some studies indicating that genome-wide SNPs provide greater accuracy in estimating relatedness and inbreeding compared to robust pedigrees Santure et al, 2010;Wang, 2016) or microsatellites (Attard, Beheregaray, & Möller, 2018;Bérénos, Ellis, Pilkington, & Pemberton, 2014;Hellmann et al, 2016;Keller, Visscher, & Goddard, 2011;Lemopoulos et al, 2019;Li, Strandén, Tiirikka, Sevón-Aimonen, & Kantanen, 2011).…”