Late Pleistocene-dated divergence between South Hemisphere populations of the non-conventional yeast L. cidri.

Most organisms belonging to the Saccharomycotina subphylum have high genetic diversity and a vast repertoire of metabolisms and lifestyles, which explains its ecological versatility. The yeast Lachancea cidri is an ideal model for exploring the interplay between genetics, ecological function and evolution. L. cidri is a species that diverged from the Saccharomyces lineage before the whole-genome duplication and exhibits a broad distribution across the South Hemisphere, thus displaying an important ecological success. Here, we applied phylogenomics to investigate the adaptive genetic variation of L. cidri isolates obtained from natural environments in Australia and South America. Our approach revealed the presence of two main lineages according to their geographic distribution (Aus and SoAm). Estimation of the divergence time suggest that South American and Australian lineages diverged near the last glacial maximum event during the Pleistocene (64-8 KYA), consistent with the presence of multiple glacial refugia. Interestingly, we found that the French reference strain belongs to the Australian lineage, with a recent divergence (405-51 YA), likely associated to human movements. Additionally, species delimitation analysis identified different evolutionary units within the South American lineage and, together with parameters like Pi (π) and FST, revealed that Patagonia contains most of the genetic diversity of this species. These results agree with phenotypic characterizations, demonstrating a greater phenotypic diversity in the South American lineage. These findings support the idea of a Pleistocene-dated divergence between South Hemisphere lineages, where the Nothofagus and Araucaria ecological niches likely favored the extensive distribution of L. cidri in Patagonia.

A National Multi-Scale Assessment of Regeneration Deficit as an Indicator of Potential Risk of Forest Genetic Variation Loss

Genetic diversity is essential because it provides a basis for adaptation and resilience to environmental stress and change. The fundamental importance of genetic variation is recognized by its inclusion in the Montréal Process sustainability criteria and indicators for temperate and boreal forests. The indicator that focuses on forest species at risk of losing genetic variation, however, has been difficult to address in a systematic fashion. We combined two broad-scale datasets to inform this indicator for the United States: (1) tree species occurrence data from the national Forest Inventory and Analysis (FIA) plot network and (2) climatically and edaphically defined provisional seed zones, which are proxies for among-population adaptive variation. Specifically, we calculated the estimated proportion of small trees (seedlings and saplings) relative to all trees for each species and within seed zone sub-populations, with the assumption that insufficient regeneration could lead to the loss of genetic variation. The threshold between sustainable and unsustainable proportions of small trees reflected the expectation of age–class balance at the landscape scale. We found that 46 of 280 U.S. forest tree species (16.4%) may be at risk of losing genetic variation. California and the Southeast encompassed the most at-risk species. Additionally, 39 species were potentially at risk within at least half of the seed zones in which they occurred. Seed zones in California and the Southwest had the highest proportions of tree species that may be at risk. The results could help focus conservation and management activities to prevent the loss of adaptive genetic variation within tree species.

Climate Change, Crop Wild Relatives and Genomic Data: The persistence and agronomic utility of five Vitis species

Crop wild relatives (CWRs) have the capacity to contribute novel traits to agriculture. Given climate change, these contributions may be especially vital for perennial crops, because perennials are often clonally propagated and consequently do not evolve rapidly. By studying the landscape genomics of five Vitis CWRs (V. arizonica, V. mustangensis, V. riparia, V. berlandieri and V. girdiana) in the context of projected climate change, we addressed two goals. The first was assessing the relative potential of different CWRs to persist in the context of climate change. By integrating species distribution models with adaptive genetic variation, additional genetic features such as genomic load, and a phenotype (resistance to Pierce Disease), we predicted that accessions of V. mustangensis are particularly well-suited to persist. The second goal was identifying candidate CWRs to contribute to bioclimatic adaptation for grapevine (V. vinifera) cultivation. To do so, we first estimated that ~40% of current viticulture sites in the United States will be vulnerable to climate change, based on species distribution models projected to 2070. We then predicted which CWRs have the genomic profile to contribute to bioclimatic adaptation at these vulnerable sites. We identified rootstock candidates from V. mustangensis, V. riparia and V. girdiana and hypothesized that they may prove useful for mitigating climate impacts on viticulture. By identifying candidate germplasm, this work takes a conceptual step toward mitigating the climate impacts on crops by utilizing the genomic and bioclimatic characteristics of CWRs.

Avoiding extinction under nonlinear environmental change: models of evolutionary rescue with plasticity

Rapid environmental changes are putting numerous species at risk of extinction. For migration-limited species, persistence depends on either phenotypic plasticity or evolutionary adaptation (evolutionary rescue). Current theory on evolutionary rescue typically assumes linear environmental change. Yet accelerating environmental change may pose a bigger threat. Here, we present a model of a species encountering an environment with accelerating or decelerating change, to which it can adapt through evolution or phenotypic plasticity (within-generational or transgenerational). We show that unless either form of plasticity is sufficiently strong or adaptive genetic variation is sufficiently plentiful, accelerating or decelerating environmental change increases extinction risk compared to linear environmental change for the same mean rate of environmental change.

Land use and life history constrain adaptive genetic variation and reduce the capacity for climate change adaptation in turtles

Background Rapid anthropogenic climate change will require species to adapt to shifting environmental conditions, with successful adaptation dependent upon current patterns of genetic variation. While landscape genomic approaches allow for exploration of local adaptation in non-model systems, most landscape genomics studies of adaptive capacity are limited to exploratory identification of potentially important functional genes, often without a priori expectations as to the gene functions that may be most important for climate change responses. In this study, we integrated targeted sequencing of genes of known function and genotyping of single-nucleotide polymorphisms to examine spatial, environmental, and species-specific patterns of potential local adaptation in two co-occuring turtle species: the Blanding’s turtle (Emydoidea blandingii) and the snapping turtle (Chelydra serpentina). Results We documented divergent patterns of spatial clustering between neutral and putatively adaptive genetic variation in both species. Environmental associations varied among gene regions and between species, with stronger environmental associations detected for genes involved in stress response and for the more specialized Blanding’s turtle. Land cover appeared to be more important than climate in shaping spatial variation in functional genes, indicating that human landscape alterations may affect adaptive capacity important for climate change responses. Conclusions Our study provides evidence that responses to climate change will be contingent on species-specific adaptive capacity and past history of exposure to human land cover change.

Genomic investigations provide insights into the mechanisms of resilience to heterogeneous habitats of the Indian Ocean in a pelagic fish

The adaptive genetic variation in response to heterogeneous habitats of the Indian Ocean was investigated in the Indian oil sardine using ddRAD sequencing to understand the subpopulation structure, stock complexity, mechanisms of resilience, and vulnerability in the face of climate change. Samples were collected from different ecoregions of the Indian ocean and ddRAD sequencing was carried out. Population genetic analyses revealed that samples from the Gulf of Oman significantly diverged from other Indian Ocean samples. SNP allele-environment correlation revealed the presence of candidate loci correlated with the environmental variables like annual sea surface temperature, chlorophyll-a, and dissolved oxygen concentration which might represent genomic regions allegedly diverging as a result of local adaptation. Larval dispersal modelling along the southwest coast of India indicated a high dispersal rate. The two major subpopulations (Gulf of Oman and Indian) need to be managed regionally to ensure the preservation of genetic diversity, which is crucial for climatic resilience.

Genome assembly of the tayra (Eira barbara, Mustelidae) and comparative genomic analysis reveal adaptive genetic variation in the subfamily Guloninae

Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes, as well as searching for species-specific structural variants (SVs). Among candidate loci that appear to be associated with phenotypic traits, we observed many genes related to diet, body condition and reproduction. For the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observe species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many specific changes in genes associated with diet and body condition. Despite restricting some of our analyses to single-copy orthologs present in all three study species, we observed many candidate loci that may be linked to species traits related to environment-specific challenges in their respective habitats.

The maintenance of standing genetic variation: gene flow versus selective neutrality in Atlantic stickleback fish

Adaptation to derived habitats often occurs from standing genetic variation (SGV). The maintenance within ancestral populations of genetic variants favorable in derived habitats is commonly ascribed to long-term antagonism between purifying selection and gene flow resulting from hybridization across habitats. A largely unexplored alternative idea based on quantitative genetic models of polygenic adaptation is that variants favored in derived habitats are neutral in ancestral populations when their frequency is relatively low. To explore the latter, we first identify genetic variants important to the adaptation of threespine stickleback fish to a rare derived habitat – nutrient-depleted acidic lakes – based on whole-genome sequence data. Sequencing marine stickleback from six locations across the Atlantic ocean then allows us to infer that the frequency of these derived variants in the ancestral habitat is unrelated to the likely opportunity for gene flow of these variants from acidic-adapted populations. This result is consistent with the selective neutrality of derived variants within the ancestor. Our study thus supports an underappreciated explanation for the maintenance of SGV, and calls for a better understanding of the fitness consequences of adaptive genetic variation across habitats and genomic backgrounds.

A spectral theory for Wright’s inbreeding coefficients and related quantities

Wright’s inbreeding coefficient, FST, is a fundamental measure in population genetics. Assuming a predefined population subdivision, this statistic is classically used to evaluate population structure at a given genomic locus. With large numbers of loci, unsupervised approaches such as principal component analysis (PCA) have, however, become prominent in recent analyses of population structure. In this study, we describe the relationships between Wright’s inbreeding coefficients and PCA for a model of K discrete populations. Our theory provides an equivalent definition of FST based on the decomposition of the genotype matrix into between and within-population matrices. The average value of Wright’s FST over all loci included in the genotype matrix can be obtained from the PCA of the between-population matrix. Assuming that a separation condition is fulfilled and for reasonably large data sets, this value of FST approximates the proportion of genetic variation explained by the first (K − 1) principal components accurately. The new definition of FST is useful for computing inbreeding coefficients from surrogate genotypes, for example, obtained after correction of experimental artifacts or after removing adaptive genetic variation associated with environmental variables. The relationships between inbreeding coefficients and the spectrum of the genotype matrix not only allow interpretations of PCA results in terms of population genetic concepts but extend those concepts to population genetic analyses accounting for temporal, geographical and environmental contexts.

Diversity begets diversity through shared adaptive genetic variation: discovery of a cryptic wide-mouthed scale-eater

Adaptive radiations involve astounding bursts of phenotypic, ecological, and species diversity. However, the microevolutionary processes that underlie the origins of these bursts are still poorly understood. We report the discovery of a cryptic intermediate wide-mouth scale-eating ecomorph in a recent radiation of Cyprinodon pupfishes which provides crucial information about the evolutionary and ecological transition from a widespread algae-eating generalist to a novel microendemic scale-eating specialist. We first show that this ecomorph occurs in sympatry with generalist C. variegatus and scale-eating specialist C. desquamator across several hypersaline lakes on San Salvador Island, Bahamas, but is genetically differentiated, morphologically distinct when reared in a common garden, and sometimes consumes scales. We then compared the timing of selective sweeps on shared and unique adaptive variants in both scale-eating species to characterize the evolutionary path to scale-eating. We predicted that adaptation to the intermediate wide-mouth scale-eating niche aided in the rapid divergence of the more specialized scale-eater C. desquamator. Therefore, selection for shared adaptive variants would occur first in wide-mouth. Contrary to our prediction, four of the six sets of shared adaptive alleles in both scale-eating species swept significantly earlier in C. desquamator. Adaptive introgression from the specialist into the wide-mouth ancestor may have resulted in parallel evolution of their dietary niche. Conversely, no adaptive alleles for scale-eating were reused in a third sympatric specialist C. brontotheriodes, despite sharing 9% of hard selective sweeps. Our work provides a microevolutionary framework for investigating how diversity begets diversity during adaptive radiation.