Mapping and monitoring genetic diversity of an alpine freshwater top predator by applying newly proposed indicators

Abstract

Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. To test newly proposed indicators, we monitored genetic diversity over 40 years (1970-2010) in metapopulations of brown trout inhabiting 27 small mountain lakes representing 10 water systems in central Sweden. Three of the indicators were previously proposed for broad, international use for the Convention on Biological Diversity (CBD) context, while three others were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations and assess the effective population size (Ne). We used a panel of 96 SNPs and identified 29 discrete populations retained over time. Over 40 percent of the lakes harbored more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne≤500) in 20 populations with five showing Ne<100. Although statistically significant genetic diversity reductions occurred in several populations, they were mostly within proposed threshold limits. Metapopulation structure appears to buffer against diversity loss; when applying the indicators to metapopulations most indicators suggest an acceptable genetic status in all but one system. The CBD indicators agreed with the national ones but provided less detail. We propose that all indicators applied here are appropriate for monitoring genetic diversity within species.

Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator

“…In Sweden, the Swedish Environmental Protection Agency (SEPA) has prioritized species for monitoring (Posledovich et al, 2021a , 2021b ) and have initiated work on a few of these species. The Swedish Agency for Marine and Water Management (SwAM) has run a science‐management collaboration to develop a pilot program for monitoring genetic diversity over contemporary time frames using DNA‐based techniques and three new DNA‐based indicators (Johannesson & Laikre, 2020 ). These indicators measure change in genetic diversity within populations (indicator called Δ H ), between populations (indicator Δ F ST ), and the effective population size (indicator N e ).…”

Bringing together approaches to reporting on within species genetic diversity

“…Several countries are developing national programmes for monitoring genetic diversity. The Swedish Agency for Marine and Water Management (SwAM) has proposed three indicators to integrate genetic diversity into the national aquatic monitoring programme (Andersson et al, 2021). These focus on monitoring genetic diversity within and between populations, and on assessing the genetically effective population size; they are being applied to several marine and freshwater species using different types of DNA data.…”

“…Hoban et al, 2022, d Hollingsworth et al, 2020, e Johannesson & Laikre, 2020Andersson et al, 2021; traditional genetic markers and/or genomics are used depending on species, thus genomic measures are monitored in some cases,f Fischer et al, 2020 …”

Selecting species and populations for monitoring of genetic diversity

“…Two research teams were commissioned, working in close collaboration with SwAM managers. The work identified 12 priority species that were selected based on management questions and several indicators and limiting values to be applied by SwAM (Johannesson & Laikre, 2020;Andersson et al, 2021). Of these, four were selected for pilot monitoring during 2020, i.e., Atlantic herring (Clupea harengus), Atlantic salmon (Salmo salar), eelgrass (Zostera marina) and Atlantic cod (Gadus morhua).…”