Genomic vulnerability of a freshwater salmonid under climate change

Abstract

Understanding the adaptive potential of populations and species is pivotal for minimizing the loss of biodiversity in this era of rapid climate change. Adaptive potential has been estimated in various ways, including based on levels of standing genetic variation, presence of potentially beneficial alleles, and/or the severity of environmental change. Kokanee salmon, the non‐migratory ecotype of sockeye salmon (Oncorhynchus nerka), is culturally and economically important and has already been impacted by the effects of climate change. To assess its climate vulnerability moving forward, we integrated analyses of standing genetic variation, genotype‐environment associations, and climate modeling based on sequence and structural genomic variation from 224 whole genomes sampled from 22 lakes in British Columbia and Yukon (Canada). We found that variables for extreme temperatures, particularly warmer temperatures, had the most pervasive signature of selection in the genome and were the strongest predictors of levels of standing variation and of putatively adaptive genomic variation, both sequence and structural. Genomic offset estimates, a measure of climate vulnerability, were significantly correlated with higher increases in extreme warm temperatures, further highlighting the risk of summer heat waves that are predicted to increase in frequency in the future. Levels of standing genetic variation, an important metric for population viability and resilience, were not correlated with genomic offset. Nonetheless, our combined approach highlights the importance of integrating different sources of information and genomic data to formulate more comprehensive and accurate predictions on the vulnerability of populations and species to future climate change.

Advances in salmonid genetics—Insights from Coastwide and beyond

“…Several studies in this Special Issue investigated the crucial role of genomic diversity in maintaining life history variation and enabling natural populations to adapt to local environments. Three papers investigated genomic variation associated with locally adapted traits across populations (Lecomte et al, 2024;Narum et al, 2024;Willis et al, 2024), two others focused on genomic variation to adapt under scenarios of climate change (Tigano et al, 2024) or persist through ecological disturbance (Frei et al, 2024), and another on genomic differences between hatchery reared versus wild stocks (Howe et al, 2024). Lecomte et al (2024) examined SNPs, structural variants (SVs), and small indels between two populations of Atlantic Salmon in North America with differences in life history traits (i.e., age at smoltification and maturity).…”

“…Tigano et al. ( 2024 ) examined the adaptive potential of Kokanee Salmon ( O. nerka ), a non‐migratory ecotype of Sockeye Salmon, in the face of climate change. By integrating analyses of genetic variation, genotype–environment associations, and climate modeling based on genomic data from 224 whole genomes sampled from 22 lakes in Canada, they found that extreme temperatures, particularly warmer temperatures, had the strongest signature of selection in the genome and were the best predictors of adaptive genomic variation.…”

“…The study by Tigano et al. ( 2024 ) thus emphasizes the importance of integrating different sources of information and genomic data to predict the vulnerability of populations and species to climate change accurately.…”

Adaptive potential and genomic vulnerability of keystone forest tree species to climate change: a case study in Scots pine

“…In the face of ongoing environmental changes it is particularly important to consider the possibility of adaptive responses of populations affected by shifting climatic conditions as shown across various study systems [28][29][30][31][32][33] . Species distribution models under various climate change scenarios indicate that many forest tree species will alter their geographical distribution to align with their ecological niche 7,12,[34][35][36] .…”