Incorporating putatively neutral and adaptive genomic data into marine conservation planning

• Published in: Conservation biology 2021-06, Vol.35 (3), p.909-920
• Main Authors: Xuereb, Amanda, D'Aloia, Cassidy C., Andrello, Marco, Bernatchez, Louis, Fortin, Marie‐Josée
• Format: Article
• Language: English
• Subjects: adaptive genetic variation; Adaptive sampling; Alleles; Biodiversity and Ecology; cambio climático; climate change; Coastal zone; Conservation; conservation genetics; Data; Datasets; Environmental changes; Environmental effects; Environmental Sciences; Genetic markers; Genomics; Genotypes; genética de la conservación; Global Changes; Heterozygosity; High frequency; Loci; Marine conservation; Marine invertebrates; marine protected area; Markers; Nucleotides; Ocean floor; Parastichopus californicus; priorización de la conservación espacial; Single-nucleotide polymorphism; spatial conservation prioritization; Spatial data; Temperature; Temperature gradients; variación genética adaptativa; área marina protegida
• ISSN: 0888-8892; 1523-1739
• DOI: 10.1111/cobi.13609

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‐temperature‐associated 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. Incorporación de Datos Genómicos Putativamente Neutros y Adaptativos dentro de la Planeación de la Conservación Marina Resumen La disponibilidad de los datos genómicos para un número creciente de especies posibilita la incorporación de los procesos evolutivos dentro de los planes de conservación. Los estudios recientes muestran cómo los datos genéticos pueden informar a la priorización de la conservación espacial (PCE) pe