Genomics and the challenging translation into conservation practice

Abstract

The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice, and we discuss how scaling-up to genome-wide inference can benefit traditional conservation genetic approaches and provide qualitatively novel insights. Yet, the generation of genomic data and subsequent analyses and interpretations are still challenging and largely confined to academic research in ecology and 20evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners. 3 Conservation biology and genomicsLike most of the life sciences, conservation biology is being confronted with the challenge of how to integrate the collection and analysis of large-scale genomic data into its toolbox. Conservation biologists pull from a wide array of disciplines in an effort to preserve biodiversity and ecosystem services [1]. Genetic data have helped in this regard by 30 detecting, for example, population substructure, measuring genetic connectivity, and identifying potential risks associated with demographic change and inbreeding [2]. Traditionally, conservation genetics (see Glossary) has relied on a handful of molecular markers ranging from a few allozymes to dozens of microsatellites [3]. But for close to a decade [4], genomics -broadly defined high-throughput sampling of nucleic acids [5] -has been touted as an important advancement to the field, a panacea of sorts for the unresolved conservation problems typically addressed 35 with genetic data [6,7]. This transition has led to much promise, but also hyperbole, where concrete empirical examples of genomic data having a conservation impact remain rare.Under the premise that assisting conservation of the world's biota is its ultimate purpose, the emerging field of conservation genomics must openly and pragmatically discuss its potential contribution towards this goal. While there 40are prominent examples where genetic approaches have made inroads influencing conservation efforts (e.g., Florida panther augmentation [8,9]) and wildlife enforcement (i.e., detecting illegal harvest [10]), it is not immediately clear that the conservation community and society more broadly have embraced genomics as a useful tool for conservation.Maintaining genetic diversity has largely been an afterthought when it comes to national biodiversity policies [11,12], and attempts to identify areas that might prove to be essential for conserving biological diversity rarely mention 45 genomics (e.g. [13,14]). An obvious reason for this disconnect is that many of the pressing conservation issues (e.g., [15,16]) simply do not need genomics, but instead need political will.The traditional use of gene...

Understanding and monitoring the consequences of human impacts on intraspecific variation

“…The usefulness of genomic approaches has received increased attention for its value in conservation biology (reviewed in Allendorf, Hohenlohe, & Luikart, 2010; Shafer et al., 2015). Some common NGS approaches include whole genome resequencing, reduced‐representation sequencing (RRS), and pooled DNA sequencing (Pool‐seq).…”

Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation

“…Identifying geographic patterns of local adaptation, the environmental drivers of divergent selection among populations, and genes and their variants involved in local adaptation can inform conservation strategies for species at risk (Allendorf et al., 2010; Shafer et al., 2015), especially in the context of changing environmental conditions (global changes in climate or local changes in land use, fire, hydrology, and other processes altering a species’ local habitat). Genetic variants that help individuals within populations survive or reproduce more under new environmental conditions would be considered adaptive.…”

“…If adaptive genetic variants are identified, individuals with genotypes more likely to have higher fitness in local environments could be used in breeding, reinforcement, or reintroduction programs to help ensure success of those programs (He, Johansson, & Heath, 2016; Kelly & Phillips, 2016; Sgro et al., 2011). Managers could also monitor the frequency of these genetic variants over time to gauge the genetic health of a population, or to assess changes in allele frequencies following management interventions (Schwartz et al., 2007; Shafer et al., 2015). …”

Recent advances in conservation and population genomics data analysis

“…At this time, conservation and evolutionary geneticists can employ the power of genomic tools to answer questions in conservation that could not be answered using traditional genetics approaches (Allendorf, Hohenlohe, & Luikart, 2010; Bernatchez et al., 2017; Garner et al., 2016; Harrisson, Pavlova, Telonis‐Scott, & Sunnucks, 2014; McMahon, Teeling, & Höglund, 2014; Shafer et al., 2015a, 2015b). Technological and analytical advances now allow us to use many thousands of loci, gene expression, or epigenetics to address basic questions of relevance for conservation, such as identifying loci associated with local adaptation or adaptive potential in species face changing environments (Bernatchez, 2016; Flanagan, Forester, Latch, Aitken, & Hoban, 2017; Harrisson et al., 2014; Hoban et al., 2016; Hoffmann et al., 2015; Jensen, Foll, & Bernatchez, 2016; Le Luyer et al., 2017; Wade et al., 2016).…”