Next‐generation metrics for monitoring genetic erosion within populations of conservation concern

Abstract

Genetic erosion is a major threat to biodiversity because it can reduce fitness and ultimately contribute to the extinction of populations. Here, we explore the use of quantitative metrics to detect and monitor genetic erosion. Monitoring systems should not only characterize the mechanisms and drivers of genetic erosion (inbreeding, genetic drift, demographic instability, population fragmentation, introgressive hybridization, selection) but also its consequences (inbreeding and outbreeding depression, emergence of large‐effect detrimental alleles, maladaptation and loss of adaptability). Technological advances in genomics now allow the production of data the can be measured by new metrics with improved precision, increased efficiency and the potential to discriminate between neutral diversity (shaped mainly by population size and gene flow) and functional/adaptive diversity (shaped mainly by selection), allowing the assessment of management‐relevant genetic markers. The requirements of such studies in terms of sample size and marker density largely depend on the kind of population monitored, the questions to be answered and the metrics employed. We discuss prospects for the integration of this new information and metrics into conservation monitoring programmes.

Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction

“…Bold text indicates nonoverlapping HPDI values km Assessing genetic erosion in this species is important for identifying areas of management focus, particularly where the monitoring of demographic parameters may be costly and difficult (Leroy et al, 2018). Rows represent the populations from which each individual was sampled, and columns represent the population from which they migrated.…”

“…Although a variety of metrics have been proposed for assessing genetic erosion (Hoban et al, 2014;Leroy et al, 2018) (Galpern, Manseau, & Wilson, 2012;Schaefer, 2003). Although a variety of metrics have been proposed for assessing genetic erosion (Hoban et al, 2014;Leroy et al, 2018) (Galpern, Manseau, & Wilson, 2012;Schaefer, 2003).…”

Genetic and genomic monitoring with minimally invasive sampling methods

“…() surveyed 162 SNPs in golden eagles and found that mean observed heterozygosity (H O ) was 0.32 ± 0.01 in juveniles whereas adult H O was 0.35 ± 0.01, a significant statistical difference consistent with expectations of viability selection. Unfortunately, the types of SNP arrays often used in MIS studies preclude the evaluation of other genetic diversity metrics that will likely be important in the future (e.g., runs‐of‐homozygosity or copy number variants, see Leroy et al., ). This is a factor worth considering when planning a study, as evaluating change in genetic diversity metrics over time is an important task of genetic monitoring (see Box 3).…”

Making use of the social network in conservation genomics: Integrating kinship and network analyses to understand connectivity

“…This highlights the fact that the transition from conservation genetics to conservation genomics will not be limited by the availability of data, but what we do with it. Recent reviews argue that new statistical methods are required to convert this wealth of genomic data into practical management outcomes for endangered populations and species (Leroy et al, 2017). By inferring the impact of a barrier on patterns of relatedness and dispersal using genomic data and the AC, F I G U R E 1 Pyrenean desman (Galemys pyrenaicus; centre right) and the barriers to its dispersal found using kinship and network analyses in Escoda et al (2018).…”