Applying genomics in assisted migration under climate change: Framework, empirical applications, and case studies

The potential influence of genome-wide adaptive divergence on conservation translocation outcome in an isolated greater sage-grouse population

Conservation translocations are an important conservation tool commonly employed to augment declining or reestablish extirpated populations. One goal of augmentation is to increase genetic diversity and reduce the risk of inbreeding depression (i.e., genetic rescue). However, introducing individuals from significantly diverged populations risks disrupting coadapted traits and reducing local fitness (i.e., outbreeding depression). Genetic data are increasingly more accessible for wildlife species and can provide unique insight regarding the presence and retention of introduced genetic variation from augmentation as an indicator of effectiveness and adaptive similarity as an indicator of source and recipient population suitability. We used 2 genetic data sets to evaluate augmentation of isolated populations of greater sage-grouse (Centrocercus urophasianus) in the northwestern region of the species range (Washington, USA) and to retrospectively evaluate adaptive divergence among source and recipient populations. We developed 2 statistical models for microsatellite data to evaluate augmentation outcomes. We used one model to predict genetic diversity after augmentation and compared these predictions with observations of genetic change. We used the second model to quantify the amount of observed reproduction attributed to transplants (proof of population integration). We also characterized genome-wide adaptive divergence among source and recipient populations. Observed genetic diversity (HO = 0.65) was higher in the recipient population than predicted had no augmentation occurred (HO = 0.58) but less than what was predicted by our model (HO = 0.75). The amount of shared genetic variation between the 2 geographically isolated resident populations increased, which is evidence of periodic gene flow previously assumed to be rare. Among candidate adaptive genes associated with elevated fixation index (FST) (143 genes) or local environmental variables (97 and 157 genes for each genotype-environment association method, respectively), we found clusters of genes with related functions that may influence the ability of transplants to use local resources and navigate unfamiliar environments and their reproductive potential, all possible reasons for low genetic retention from augmentation.

Habitat remediation followed by managed connectivity reduces unwanted changes in evolutionary trajectory of high extirpation risk populations

As we continue to convert green spaces into roadways and buildings, connectivity between populations and biodiversity will continue to decline. In threatened and endangered species, this trend is particularly concerning because the cessation of immigration can cause increased inbreeding and loss of genetic diversity, leading to lower adaptability and higher extirpation probabilities in these populations. Unfortunately, monitoring changes in genetic diversity from management actions such as assisted migration and predicting the extent of introduced genetic variation that is needed to prevent extirpation is difficult and costly in situ. Therefore, we designed an agent-based model to link population-wide genetic variability and the influx of unique alleles via immigration to population stability and extirpation outcomes. These models showed that management of connectivity can be critical in restoring at-risk populations and reducing the effects of inbreeding depression. However, the rescued populations were more similar to the migrant source population (average FST range 0.05-0.10) compared to the historical recipient population (average FST range 0.23-0.37). This means that these management actions not only recovered the populations from the effects of inbreeding depression, but they did so in a way that changed the evolutionary trajectory that was predicted and expected for these populations prior to the population crash. This change was most extreme in populations with the smallest population sizes, which are representative of critically endangered species that could reasonably be considered candidates for restored connectivity or translocation strategies. Understanding how these at-risk populations change in response to varying management interventions has broad implications for the long-term adaptability of these populations and can improve future efforts for protecting locally adapted allele complexes when connectivity is restored.

Conservation Mitonuclear Replacement: Facilitated mitochondrial adaptation for a changing world

Most species will not be able to migrate fast enough to cope with climate change, nor evolve quickly enough with current levels of genetic variation. Exacerbating the problem are anthropogenic influences on adaptive potential, including the prevention of gene flow through habitat fragmentation and the erosion of genetic diversity in small, bottlenecked populations. Facilitated adaptation, or assisted evolution, offers a way to augment adaptive genetic variation via artificial selection, induced hybridization, or genetic engineering. One key source of genetic variation, particularly for climatic adaptation, are the core metabolic genes encoded by the mitochondrial genome. These genes influence environmental tolerance to heat, drought, and hypoxia, but must interact intimately and co-evolve with a suite of important nuclear genes. These coadapted mitonuclear genes form some of the important reproductive barriers between species. Mitochondrial genomes can and do introgress between species in an adaptive manner, and they may co-introgress with nuclear genes important for maintaining mitonuclear compatibility. Managers should consider the relevance of mitonuclear genetic variability in conservation decision-making, including as a tool for facilitating adaptation. I propose a novel technique dubbed Conservation Mitonuclear Replacement (CmNR), which entails replacing the core metabolic machinery of a threatened species-the mitochondrial genome and key nuclear loci-with those from a closely related species or a divergent population, which may be better-adapted to climatic changes or carry a lower genetic load. The most feasible route to CmNR is to combine CRISPR-based nuclear genetic editing with mitochondrial replacement and assisted reproductive technologies. This method preserves much of an organism's phenotype and could allow populations to persist in the wild when no other suitable conservation options exist. The technique could be particularly important on mountaintops, where rising temperatures threaten an alarming number of species with almost certain extinction in the next century.

Genomics for monitoring and understanding species responses to global climate change

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.

Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes

Multiple evolutionary processes influence genome-wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead (Oncorhynchus mykiss) populations that have declined in abundance due to anthropogenic impacts. Whole-genome resequencing of 74 populations of steelhead revealed genome-wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.

Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer

Anthropogenic reintroduction can supplement natural recolonization in reestablishing a species' distribution and abundance. However, both reintroductions and recolonizations can give rise to founder effects that reduce genetic diversity and increase inbreeding, potentially causing the accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonizations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonized populations without admixture possessed much lower heterozygosity, higher inbreeding and longer runs of homozygosity, possibly caused by serial population founder effects and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonized populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonization in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.

Regional and global climate risks for reef corals: Incorporating species-specific vulnerability and exposure to climate hazards

Climate change is driving rapid and widespread erosion of the environmental conditions that formerly supported species persistence. Existing projections of climate change typically focus on forecasts of acute environmental anomalies and global extinction risks. The current projections also frequently consider all species within a broad taxonomic group together without differentiating species-specific patterns. Consequently, we still know little about the explicit dimensions of climate risk (i.e., species-specific vulnerability, exposure and hazard) that are vital for predicting future biodiversity responses (e.g., adaptation, migration) and developing management and conservation strategies. Here, we use reef corals as model organisms (n = 741 species) to project the extent of regional and global climate risks of marine organisms into the future. We characterise species-specific vulnerability based on the global geographic range and historical environmental conditions (1900-1994) of each coral species within their ranges, and quantify the projected exposure to climate hazard beyond the historical conditions as climate risk. We show that many coral species will experience a complete loss of pre-modern climate analogs at the regional scale and across their entire distributional ranges, and such exposure to hazardous conditions are predicted to pose substantial regional and global climate risks to reef corals. Although high-latitude regions may provide climate refugia for some tropical corals until the mid-21st century, they will not become a universal haven for all corals. Notably, high-latitude specialists and species with small geographic ranges remain particularly vulnerable as they tend to possess limited capacities to avoid climate risks (e.g., via adaptive and migratory responses). Predicted climate risks are amplified substantially under the SSP5-8.5 compared with the SSP1-2.6 scenario, highlighting the need for stringent emission controls. Our projections of both regional and global climate risks offer unique opportunities to facilitate climate action at spatial scales relevant to conservation and management.

Is now the time? Review of genetic rescue as a conservation tool for brook trout

Brook trout populations have been declining throughout their native range in the east coast of the United States. Many populations are now distributed in small, isolated habitat patches where low genetic diversity and high rates of inbreeding reduce contemporary viability and long-term adaptive potential. Although human-assisted gene flow could theoretically improve conservation outcomes through genetic rescue, there is widespread hesitancy to use this tool to support brook trout conservation. Here, we review the major uncertainties that have limited genetic rescue from being considered as a viable conservation tool for isolated brook trout populations and compare the risks of genetic rescue with other management alternatives. Drawing on theoretical and empirical studies, we discuss methods for implementing genetic rescue in brook trout that could yield long-term evolutionary benefits while avoiding negative fitness effects associated with outbreeding depression and the spread of maladapted alleles. We also highlight the potential for future collaborative efforts to accelerate our understanding of genetic rescue as a viable tool for conservation. Ultimately, while we acknowledge that genetic rescue is not without risk, we emphasize the merits that this tool offers for protecting and propagating adaptive potential and improving species' resilience to rapid environmental change.

Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout

Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low-coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype-environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high-elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high-elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.

Understanding Local Adaptation to Prepare Populations for Climate Change

Adaptation within species to local environments is widespread in nature. Better understanding this local adaptation is critical to conserving biodiversity. However, conservation practices can rely on species’ trait averages or can broadly assume homogeneity across the range to inform management. Recent methodological advances for studying local adaptation provide the opportunity to fine-tune efforts for managing and conserving species. The implementation of these advances will allow us to better identify populations at greatest risk of decline because of climate change, as well as highlighting possible strategies for improving the likelihood of population persistence amid climate change. In the present article, we review recent advances in the study of local adaptation and highlight ways these tools can be applied in conservation efforts. Cutting-edge tools are available to help better identify and characterize local adaptation. Indeed, increased incorporation of local adaptation in management decisions may help meet the imminent demands of managing species amid a rapidly changing world.