Incorporating putatively neutral and adaptive genomic data into marine conservation planning

Abstract

The availability of genomic data for an increasing number of species makes it possible to incorporate evolutionary processes into conservation plans. Recent studies show how genetic data can inform spatial conservation prioritization (SCP), but they focus on metrics of diversity and distinctness derived primarily from neutral genetic data sets. Identifying adaptive genetic markers can provide important information regarding the capacity for populations to adapt to environmental change. Yet, the effect of including metrics based on adaptive genomic data into SCP in comparison to more widely used neutral genetic metrics has not been explored. We used existing genomic data on a commercially exploited species, the giant California sea cucumber (Parastichopus californicus), to perform SCP for the coastal region of British Columbia (BC), Canada. Using a RAD-seq data set for 717 P. californicus individuals across 24 sampling locations, we identified putatively adaptive (i.e., candidate) single nucleotide polymorphisms (SNPs) based on genotype-environment associations with seafloor temperature. We calculated various metrics for both neutral and candidate SNPs and compared SCP outcomes with independent metrics and combinations of metrics. Priority areas varied depending on whether neutral or candidate SNPs were used and on the specific metric used. For example, targeting sites with a high frequency of warm-temperatureassociated alleles to support persistence under future warming prioritized areas in the southern coastal region. In contrast, targeting sites with high expected heterozygosity at candidate loci to support persistence under future environmental uncertainty prioritized areas in the north. When combining metrics, all scenarios generated intermediate solutions, protecting sites that span latitudinal and thermal gradients. Our results demonstrate that distinguishing between neutral and adaptive markers can affect conservation solutions and emphasize the importance of defining objectives when choosing among various genomic metrics for SCP.

Population Genomics and Lagrangian Modeling Shed Light on Dispersal Events in the Mediterranean Endemic Ericaria zosteroides (=Cystoseira zosteroides) (Fucales)

“…The application of genomics in conservation strategy will be essential for monitoring species and taking decisive actions by prioritizing the evolutionary potential of populations (von der Heyden, 2017;Xuereb et al, 2020). The use of genomic information coupled with in situ measurements of the demography and modeling of dispersal is seen to be highly effective to unravel occasional connectivity events in supposed low dispersal marine species.…”

“…The use of this high number of markers allows more precise analysis of genetic differentiation, and increased power to detect genetic differences among populations (Waples, 1998;Gagnaire et al, 2015). Information about the spatial distribution of adaptive genetic diversity can also be considered in management and conservation strategies (Xuereb et al, 2020). Combining population-genomic inferences and Lagrangian dispersal models has helped to elucidate, with unprecedented clarity, how environmental factors and geography drove the genetic structure of marine species (e.g., Benestan et al, 2016;Dalongeville et al, 2017;Paterno et al, 2017;Xuereb et al, 2018a,b;Bracco et al, 2019;Coscia et al, 2020).…”

Genomic signatures of divergent selection are associated with social behaviour for spinner dolphin ecotypes

“…Knowledge about adaptive genomic variation has potential to benefit multiple areas of conservation decision‐making, such as the designation and prioritization of management units, assessment of vulnerability to environmental change, and choosing source populations and recipient sites for assisted gene flow (Allendorf et al, 2010; Funk et al, 2012, 2019; Hoelzel et al, 2019; McMahon et al, 2014). Although the practical aspects of incorporating adaptive genomic information into management decision‐making are complicated and currently the subject of discussion and debate (Hoelzel et al, 2019; Mable, 2019; Shafer et al, 2015; Xuereb et al, 2020), managers have already begun using this type of information and will probably use it with increasing frequency in the future (Funk et al, 2019).…”

“…Although the practical aspects of incorporating adaptive genomic information into management decision-making are complicated and currently the subject of discussion and debate (Hoelzel et al, 2019 ;Mable, 2019 ;Shafer et al, 2015 ;Xuereb et al, 2020 ), managers have already begun using this type of information and will probably use it with increasing frequency in the future (Funk et al, 2019 ).…”

Population genomics ofPocilloporacorals: insights from RAD-sequencing

“…This can be of interest to integrate evolutionary processes in management and conservation (e.g. Xuereb et al, 2020).…”