Ecological genomics of local adaptation

Unravelling drivers of local adaptation through evolutionary functional-structural plant modelling

Local adaptation to contrasting environmental conditions along environmental gradients is a widespread phenomenon in plant populations, yet we lack a mechanistic understanding of how individual agents of selection contribute to this evolutionary process. Here, we developed a novel evolutionary functional-structural plant (E-FSP) model that recreates local adaptation of virtual plants along an environmental gradient. First, we validate the model by testing if it can reproduce two elevational ecotypes of Dianthus carthusianorum occurring in the Swiss Alps. Second, we use the E-FSP model to disentangle the relative contribution of abiotic (temperature) and biotic (competition and pollination) selection pressures to elevational adaptation in D. carthusianorum. Our results suggest that elevational adaptation in D. carthusianorum is predominantly driven by the abiotic environment. The model reproduced the qualitative differences between the elevational ecotypes in two phenological (germination and flowering time) and one morphological trait (stalk height), as well as qualitative differences in four performance variables that emerge from G × E interactions (flowering time, number of stalks, rosette area and seed production). Our approach shows how E-FSP models incorporating physiological, ecological and evolutionary mechanisms can be used in combination with experiments to examine hypotheses about patterns of adaptation observed in the field.

Linking the spatial and genomic structure of adaptive potential for conservation management: a review

We unified the recent literature with the goal to contribute to the discussion on how genetic diversity might best be conserved. We argue that this decision will be guided by how genomic variation is distributed among manageable populations (i.e., its spatial structure), the degree to which adaptive potential is best predicted by variation across the entire genome or the subset of that variation that is identified as putatively adaptive (i.e., its genomic structure), and whether we are managing species as single entities or as collections of diversifying lineages. The distribution of genetic variation and our ultimate goal will have practical implications for on-the-ground management. If adaptive variation is largely polygenic or responsive to change, its spatial structure might be broadly governed by the forces determining genome-wide variation (linked selection, drift, and gene flow), making measurement and prioritization straightforward. If we are managing species as single entities, then population-level prioritization schemes are possible so as to maximize future pooled genetic variation. We outline one such scheme based on the popular Shapley value from cooperative game theory that considers the relative genetic contribution of a population to an unknown future collection of populations.

The systematic codon usage bias has an important effect on genetic adaption in native species

Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.

Demographic History and Adaptive Evolution of Indo-Pacific Bottlenose Dolphins (Tursiops aduncus) in Western Australia

Demographic processes can substantially affect a species' response to changing ecological conditions, necessitating the combined consideration of genetic responses to environmental variables and neutral genetic variation. Using a seascape genomics approach combined with population demographic modelling, we explored the interplay of demographic and environmental factors that shaped the current population structure in Indo-Pacific bottlenose dolphins (Tursiops aduncus) along the Western Australian coastline. We combined large-scale environmental data gathered via remote sensing with RADseq genomic data from 133 individuals at 19 sampling sites. Using population genetic and outlier detection analyses, we identified three distinct genetic clusters, coinciding with tropical, subtropical and temperate provincial bioregions. In contrast to previous studies, our demographic models indicated that populations occupying the paleo-shoreline split into two demographically independent lineages before the last glacial maximum (LGM). A subsequent split after the LGM 12-15 kya gave rise to the Shark Bay population, thereby creating the three currently observed clusters. Although multi-locus heterozygosity declined from north to south, dolphins from the southernmost cluster inhabiting temperate waters had higher heterozygosity in potentially adaptive loci compared to dolphins from subtropical and tropical waters. These findings suggest ongoing adaptation to cold-temperate waters in the southernmost cluster, possibly linked to distinct selective pressures between the different bioregions. Our study demonstrated that in the marine realm, without apparent physical boundaries, only a combined approach can fully elucidate the intricate environmental and genetic interactions shaping the evolutionary trajectory of marine mammals.

Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change

Global climate change is leading to rapid and drastic shifts in environmental conditions, posing threats to biodiversity and nearly all life forms worldwide. Forest trees serve as foundational components of terrestrial ecosystems and play a crucial and leading role in combating and mitigating the adverse effects of extreme climate events, despite their own vulnerability to these threats. Therefore, understanding and monitoring how natural forests respond to rapid climate change is a key priority for biodiversity conservation. Recent progress in evolutionary genomics, driven primarily by cutting-edge multi-omics technologies, offers powerful new tools to address several key issues. These include precise delineation of species and evolutionary units, inference of past evolutionary histories and demographic fluctuations, identification of environmentally adaptive variants, and measurement of genetic load levels. As the urgency to deal with more extreme environmental stresses grows, understanding the genomics of evolutionary history, local adaptation, future responses to climate change, and conservation and restoration of natural forest trees will be critical for research at the nexus of global change, population genomics, and conservation biology. In this review, we explore the application of evolutionary genomics to assess the effects of global climate change using multi-omics approaches and discuss the outlook for breeding of climate-adapted trees.

Signatures of local adaptation and maladaptation to future climate in wild Zizania latifolia

Global climate change poses challenges to agricultural production and food security. Assessing the adaptive capacity of crop wild relatives to future climate is important for protecting key germplasm resources and breeding new crops. We performed population genomics, genotype-environment association analyses, and genomic offset assessment of Chinese wild rice, Zizania latifolia, a crop wild relative and potential new grain crop, based on 168 individuals from 42 populations. We found two genetic lineages in Z. latifolia, corresponding to the south and north of its range, that diverged during the Late Pleistocene. We also identified lineage-specific positively selected genes associated with flower development and flowering, seed shattering, pathogen defense response and cold tolerance. We further found that populations from southeastern China are the most maladapted to future climate and should be prioritized for conservation. Our findings provide important clues for leveraging existing genetic diversity to identify important germplasm resources and create climate-resilient crops.

Limited Migration From Physiological Refugia Constrains the Rescue of Native Gastropods Facing an Invasive Predator

Biological invasions have caused the loss of freshwater biodiversity worldwide. The interplay between adaptive responses and demographic characteristics of populations impacted by invasions is expected to be important for their resilience, but the interaction between these factors is poorly understood. The freshwater gastropod Amnicola limosus is native to the Upper St. Lawrence River and distributed along a water calcium concentration gradient within which high-calcium habitats are impacted by an invasive predator fish (Neogobius melanostomus, round goby), whereas low-calcium habitats provide refuges for the gastropods from the invasive predator. Our objectives were to (1) test for adaptation of A. limosus to the invasive predator and the low-calcium habitats, and (2) investigate if migrant gastropods could move from refuge populations to declining invaded populations (i.e., demographic rescue), which could also help maintain genetic diversity through gene flow (i.e., genetic rescue). We conducted a laboratory reciprocal transplant of wild F0 A. limosus sourced from the two habitat types (high calcium/invaded and low calcium/refuge) to measure adult survival and fecundity in home and transplant treatments of water calcium concentration (low/high) and round goby cue (present/absent). We then applied pooled whole-genome sequencing of 12 gastropod populations from across the calcium/invasion gradient. We identified patterns of life-history traits and genetic differentiation across the habitats that are consistent with local adaptation to low-calcium concentrations in refuge populations and to round goby predation in invaded populations. We also detected restricted gene flow from the low-calcium refugia towards high-calcium invaded populations, implying that the potential for demographic and genetic rescue is limited by natural dispersal. Our study highlights the importance of considering the potentially conflicting effects of local adaptation and gene flow for the resilience of populations coping with invasive predators.

Early Life History Divergence Mediates Elevational Adaptation in a Perennial Alpine Plant

Spatially divergent natural selection can drive adaptation to contrasting environments and thus the evolution of ecotypes. In perennial plants, selection shapes life history traits by acting on subsequent life stages, each contributing to fitness. While evidence of adaptation in perennial plants is common, the expression of life history traits is rarely characterized, limiting our understanding of their role in adaptive evolution. We conducted a multi-year reciprocal transplant experiment with seedlings from low and high elevation populations of the alpine carnation Dianthus carthusianorum to test for adaptation linked to contrasting climates and inferred specific contributions of early life stages to fitness. We assessed genotype by environment interactions in single fitness components, applied matrix population models to achieve an integrated estimate of fitness through population growth rates, and performed trade-off analyses to investigate the advantage of alternate life history traits across environments. We found evidence of genotype by environment interactions consistent with elevational adaptation at multiple stages of the early life cycle. Estimates of population growth rates corroborated a strong advantage of the local genotype. Early reproduction and survival are alternate major contributors to adaptation at low and high elevation, respectively, and are linked by trade-offs that underlie the evolution of divergent life history traits across environments. While these traits have a strong genetic basis, foreign populations express co-gradient plasticity, reflecting the adaptive strategy of the local populations. Our study reveals that selection associated to climate has driven the evolution of divergent life histories and the formation of elevational ecotypes. While the high energy environment and strong competition favor investment in early reproduction at low elevation, limiting resources favor a more conservative strategy relying on self-maintenance at high elevation. The co-gradient plasticity expressed by high-elevation populations may facilitate their persistence under warming climatic conditions.

Patterns of genetic variation and local adaptation of a native herbivore to a lethal invasive plant

Understanding the evolutionary processes that influence fitness is critical to predicting species' responses to selection. Interactions among evolutionary processes including gene flow, drift and the strength of selection can lead to either local adaptation or maladaptation, especially in heterogenous landscapes. Populations experiencing novel environments or resources are ideal for understanding the mechanisms underlying adaptation or maladaptation, specifically in locally co-evolved interactions. We used the interaction between a native herbivore that oviposits on a patchily distributed introduced plant that in turn causes significant mortality to the larvae to test for signatures of local adaptation in areas where the two co-occurred. We used whole-genome sequencing to explore population structure, patterns of gene flow and signatures of local adaptation. We found signatures of local adaptation in response to the introduced plant in the absence of strong population structure with no genetic differentiation and low genetic variation. Additionally, we found localized allele frequency differences within a single population between habitats with and without the lethal plant, highlighting the effects of strong selection. Finally, we identified that selection was acting on larval ability to feed on the plant rather than on females' ability to avoid oviposition, thus uncovering the specific ontogenetic target of selection. Our work highlights the potential for adaptation to occur in a fine-grained landscape in the presence of gene flow and low genetic variation.

Long-Term Heat Tolerance and Accelerated Metamorphosis: Hot Spring Adaptations of Buergeria japonica

Extreme temperatures are a major threat to the survival of ectotherms such as amphibians. The tree frogs belonging to the genus Buergeria have accomplished a latitudinal distribution and a wide range of thermal adaptations. In particular, Buergeria japonica, referred to as the "hot spring frog", has been reported to tolerate extremely high temperatures. However, it is unclear how the heat tolerance and metamorphic strategies of this species vary among populations at different temperatures. We therefore conducted long-term heat tolerance experiments on multiple populations of B. japonica tadpoles and their congenic species to determine their survivability and development speed. We observed heat tolerance differences between B. japonica/Buergeria choui and Buergeria buergeri. Buergeria japonica exhibited the highest tolerance among all species, and the Seranma hot spring population showed the highest survival rate and accelerated development speed. However, at temperatures higher than 35°C, they could not survive until the completion of metamorphosis, contrary to previous field observations. Our behavioral experiment showed attenuation of the high temperature preference of B. japonica tadpoles associated with developmental stages, suggesting that they can tolerate extreme temperatures for a limited time window during their development until metamorphosis.

Local adaptation of Dromiciops marsupials (Microbiotheriidae) from southern South America: Implications for species management facing climate change

The two species of the microbiotheriid marsupial genus Dromiciops (Dromiciops bozinovici: "Panchos's monito del monte" and Dromiciops gliroides: "monito del monte") exhibit a marked latitudinal genetic differentiation. Nevertheless, it is unclear whether this differentiation results from neutral processes or can be explained, to some extent, by local adaptation to different environmental conditions. Here, we used an SNP panel gathered by Rad-seq and searched for footprints of local adaptation (putative loci under selection) by exploring genetic associations with environmental variables in the two species of Dromiciops in Chilean and Argentinean populations. We applied three methods for detecting outlier SNPs and two genotype-environment associations approaches to quantify associations between allelic frequencies and environmental variables. Both species display strong genetic structure. D. bozinovici exhibited three distinct genetic groups, marking the first report of such structuring in this species using SNPs. In contrast, D. gliroides displayed four genetic clusters, consistent with previous studies. Both species exhibited an association of their genetic structure with environmental variables. D. bozinovici exhibited significant associations of allelic frequencies with elevation, precipitation during the warmest periods, and seasonality in the thermal regime. For D. gliroides, genetic variation appeared to be associated with more variables than D. bozinovici, including precipitation and temperature-related variables, isothermality, and elevation. All the outlier SNPs were mapped to the D. gliroides reference genome to explore if they fell within functionally known genes. These results represent a necessary first step toward identifying the genome regions that harbor genes associated with climate adaptations in Dromiciops. Notably, we identified genes involved in various functions, including carbohydrate synthesis (ALG8), muscle and neuronal regulation (MEF2D), and stress responses (PTGES3). Ultimately, this study contributes valuable insights that can inform targeted conservation strategies aimed at preserving the genetic diversity of Dromiciops in the face of environmental challenges.

Assessing genome-wide adaptations associated with range expansion in the pink rice borer, Sesamia inferens

Understanding the genetic basis of adaptive evolution following habitat expansion can have important implications for pest management. The pink rice borer (PRB), Sesamia inferens (Walker), is a destructive pest of rice that was historically restricted to regions south of 34° N latitude in China. However, with changes in global climate and farming practices, the distribution of this moth has progressively expanded, encompassing most regions in North China. Here, 3 highly differentiated subpopulations were discovered using high-quality single-nucleotide polymorphism and structural variant datasets across China, corresponding to northern, southern China regions, and the Yunnan-Guizhou Plateau, with significant patterns of isolation by geographic and environmental distances. Our estimates of evolutionary history indicate asymmetric migration with varying population sizes across the 3 subpopulations. Selective sweep analyses estimated strong selection at insect cuticle glycine-rich cuticular protein genes which are associated with enhanced desiccation adaptability in the northern group, and at the histone-lysine-N-methyltransferase gene associated with range expansion and local adaptation in the Shandong population. Our findings have significant implications for the development of effective strategies to control this pest.

Ecological and evolutionary dynamics to design and improve ovarian cancer treatment

Ovarian cancer ecosystems are exceedingly complex, consisting of a high heterogeneity of cancer cells. Development of drugs such as poly ADP-ribose polymerase (PARP) inhibitors, targeted therapies and immunotherapies offer more options for sequential or combined treatments. Nevertheless, mortality in metastatic ovarian cancer patients remains high because cancer cells consistently develop resistance to single and combination therapies, urging a need for treatment designs that target the evolvability of cancer cells. The evolutionary dynamics that lead to resistance emerge from the complex tumour microenvironment, the heterogeneous populations, and the individual cancer cell's plasticity. We propose that successful management of ovarian cancer requires consideration of the ecological and evolutionary dynamics of the disease. Here, we review current options and challenges in ovarian cancer treatment and discuss principles of tumour evolution. We conclude by proposing evolutionarily designed strategies for ovarian cancer, with the goal of integrating such principles with longitudinal, quantitative data to improve the treatment design and management of drug resistance. KEY POINTS/HIGHLIGHTS: Tumours are ecosystems in which cancer and non-cancer cells interact and evolve in complex and dynamic ways. Conventional therapies for ovarian cancer inevitably lead to the development of resistance because they fail to consider tumours' heterogeneity and cellular plasticity. Eco-evolutionarily designed therapies should consider cancer cell plasticity and patient-specific characteristics to improve clinical outcome and prevent relapse.

Beyond cyanogenesis: Temperature gradients drive environmental adaptation in North American white clover (Trifolium repens L.)

Species that repeatedly evolve phenotypic clines across environmental gradients have been highlighted as ideal systems for characterizing the genomic basis of local environmental adaptation. However, few studies have assessed the importance of observed phenotypic clines for local adaptation: conspicuous traits that vary clinally may not necessarily be the most critical in determining local fitness. The present study was designed to fill this gap, using a plant species characterized by repeatedly evolved adaptive phenotypic clines. White clover is naturally polymorphic for its chemical defence cyanogenesis (HCN release with tissue damage); climate-associated cyanogenesis clines have evolved throughout its native and introduced range worldwide. We performed landscape genomic analyses on 415 wild genotypes from 43 locations spanning much of the North American species range to assess the relative importance of cyanogenesis loci vs. other genomic factors in local climatic adaptation. We find clear evidence of local adaptation, with temperature-related climatic variables best describing genome-wide differentiation between sampling locations. The same climatic variables are also strongly correlated with cyanogenesis frequencies and gene copy number variations (CNVs) at cyanogenesis loci. However, landscape genomic analyses indicate no significant contribution of cyanogenesis loci to local adaptation. Instead, several genomic regions containing promising candidate genes for plant response to seasonal cues are identified - some of which are shared with previously identified QTLs for locally adaptive fitness traits in North American white clover. Our findings suggest that local adaptation in white clover is likely determined primarily by genes controlling the timing of growth and flowering in response to local seasonal cues. More generally, this work suggests that caution is warranted when considering the importance of conspicuous phenotypic clines as primary determinants of local adaptation.

Hybridization in the Anthropocene - how pollution and climate change disrupt mate selection in freshwater fish

Chemical pollutants and/or climate change have the potential to break down reproductive barriers between species and facilitate hybridization. Hybrid zones may arise in response to environmental gradients and secondary contact between formerly allopatric populations, or due to the introduction of non-native species. In freshwater ecosystems, field observations indicate that changes in water quality and chemistry, due to pollution and climate change, are correlated with an increased frequency of hybridization. Physical and chemical disturbances of water quality can alter the sensory environment, thereby affecting chemical and visual communication among fish. Moreover, multiple chemical compounds (e.g. pharmaceuticals, metals, pesticides, and industrial contaminants) may impair fish physiology, potentially affecting phenotypic traits relevant for mate selection (e.g. pheromone production, courtship, and coloration). Although warming waters have led to documented range shifts, and chemical pollution is ubiquitous in freshwater ecosystems, few studies have tested hypotheses about how these stressors may facilitate hybridization and what this means for biodiversity and species conservation. Through a systematic literature review across disciplines (i.e. ecotoxicology and evolutionary biology), we evaluate the biological interactions, toxic mechanisms, and roles of physical and chemical environmental stressors (i.e. chemical pollution and climate change) in disrupting mate preferences and inducing interspecific hybridization in freshwater fish. Our study indicates that climate change-driven changes in water quality and chemical pollution may impact visual and chemical communication crucial for mate choice and thus could facilitate hybridization among fishes in freshwater ecosystems. To inform future studies and conservation management, we emphasize the importance of further research to identify the chemical and physical stressors affecting mate choice, understand the mechanisms behind these interactions, determine the concentrations at which they occur, and assess their impact on individuals, populations, species, and biological diversity in the Anthropocene.

Scots pine - panmixia and the elusive signal of genetic adaptation

Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.

Diving into broad-scale and high-resolution population genomics to decipher drivers of structure and climatic vulnerability in a marine invertebrate

Species with widespread distributions play a crucial role in our understanding of climate change impacts on population structure. In marine species, population structure is often governed by both high connectivity potential and selection across strong environmental gradients. Despite the complexity of factors influencing marine populations, studying species with broad distribution can provide valuable insights into the relative importance of these factors and the consequences of climate-induced alterations across environmental gradients. We used the northern shrimp Pandalus borealis and its wide latitudinal distribution to identify current drivers of population structure and predict the species' vulnerability to climate change. A total of 1514 individuals sampled across 24° latitude were genotyped at high geographic (54 stations) and genetic (14,331 SNPs) resolutions to assess genetic variation and environmental correlations. Four populations were identified in addition to finer substructure associated with local adaptation. Geographic patterns of neutral population structure reflected predominant oceanographic currents, while a significant proportion of the genetic variation was associated with gradients in salinity and temperature. Adaptive landscapes generated using climate projections suggest a larger genomic offset in the southern extent of the P. borealis range, where shrimp had the largest adaptive standing genetic variation. Our genomic results combined with recent observations point to further deterioration in southern regions and an impending vulnerable status in the regions at higher latitudes for P. borealis. They also provide rare insights into the drivers of population structure and climatic vulnerability of a widespread meroplanktonic species, which is crucial to understanding future challenges associated with invertebrates essential to ecosystem functioning.

Determining evolutionary origin and phylogenetic relationships of mallard-like ducks of Oceania, greater Indonesia, and the Philippines with ddRAD-seq data

AIM

We aim to determine the evolutionary origins and population genetics of mallard-like ducks of Oceania, greater Indonesia, and the Philippines.

LOCATION

Oceania, greater Indonesia, and the Philippines.

TAXON

Mallard (Anas platyrhynchos), Pacific black duck (A. superciliosa spp.), and Philippine duck (A. luzonica) METHODS: Thousands of nuclear ddRAD-seq loci and the mitochondrial DNA control region were assayed across individuals representative of each species' range. We assessed population structure and phylogenetic relationships, as well as estimated demographic histories to reconstruct the biogeographical history of each species.

RESULTS

Philippine and Pacific black ducks represent unique genetic lineages that diverged from the mallard 1-2 million years ago. We find no support for the Philippine duck representing a hybrid species as once posited; however, their low levels of genetic diversity requires further attention. We find a lack of substructure among Philippine ducks. However, we found pronounced differentiation between subspecies of Pacific black ducks, especially between A. s. superciliosa from New Zealand and A. s. rogersi from Australia, Papua New Guinea, and Timor-Leste, Indonesia. Anas superciliosa pelewensis gave mixed results; individuals from the Solomon Islands were differentiated from the other subspecies, but those from the island of Aunu'u, American Samoa, were genetically more similar to A. s. rogersi than A. s. pelewensis samples from the Solomon Islands. Finally, we find limited evidence of interspecific gene flow at evolutionary scales, and mallard introgression among contemporary samples.

MAIN CONCLUSIONS

Mallard-like ducks radiated across Oceania, greater Indonesia, and the Philippines within the last 2 million years. Only the Pacific black duck showed unique sub-structuring that largely followed known sub-species ranges, except for A. s. pelewensis. We posit that the high interrelatedness among Solomon Island samples suggests that their genetic distinctiveness may simply be the result of high levels of genetic drift. In contrast, we conclude that mainland Australian Pacific black ducks were the most likely source for the recent colonization of American Samoa. As a result, our findings suggest that either the A. s. pelewensis subspecies designations and/or its geographical range may require re-evaluation. Continued re-evaluation of evolutionary and taxonomic relationships is necessary when attempting to reconstruct and understand biogeographical histories, with important implications towards any attempts to implement conservation strategies.

Plant pangenomes for crop improvement, biodiversity and evolution

Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes - complete sequences of multiple individuals of a species or higher taxonomic unit - have now entered the geneticists' toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.

Phenotypic covariation predicts diversification in an adaptive radiation of pupfishes

Phenotypic covariation among suites of traits may constrain or promote diversification both within and between species, yet few studies have empirically tested this relationship. In this study, we investigate whether phenotypic covariation of craniofacial traits is associated with diversification in an adaptive radiation of pupfishes found only on San Salvador Island, Bahamas (SSI). The radiation includes generalist, durophagous, and lepidophagous species. We compared phenotypic variation and covariation (i.e., the P matrix) between (1) allopatric populations of generalist pupfish from neighboring islands and estuaries in the Caribbean, (2) SSI pupfish allopatric lake populations with only generalist pupfish, and (3) SSI lake populations containing the full radiation in sympatry. Additionally, we examine patterns observed in the P matrices of two independent lab-reared F2 hybrid crosses of the two most morphologically distinct members of the radiation to make inferences about the underlying mechanisms contributing to the variation in craniofacial traits in SSI pupfishes. We found that the P matrix of SSI allopatric generalist populations exhibited higher levels of mean trait correlation, constraints, and integration with simultaneously lower levels of flexibility compared to allopatric generalist populations on other Caribbean islands and sympatric populations of all three species on SSI. We also document that while many craniofacial traits appear to result from additive genetic effects, variation in key traits such as head depth, maxilla length, and lower jaw length may be produced via non-additive genetic mechanisms. Ultimately, this study suggests that differences in phenotypic covariation significantly contribute to producing and maintaining organismal diversity.

Evaluation of genetic consequences of stocking on the southern-margin populations of white-spotted charr

Coldwater-adapted freshwater fishes, especially their populations along warm-range margins, are most vulnerable to the climate oscillations associated with global warming. Stocking is a major strategy for avoiding the extinction of these species. However, while stocking can reverse the decline of isolated populations, it may also result in a loss of genetic diversity in the native local population due to the introgressive replacement of hatchery genes. To plan an adequate strategy for conserving locally adapted populations, the genetic impacts of stocking on native lineages should be evaluated from small river branches to wide-ranging drainage areas. We investigated the population genetic structure of white-spotted charr (Salvelinus leucomaenis) within its southern range (Lake Biwa basin, Japan). By applying genome-wide SNP analysis to the population's genetic structure, we assessed the extent of genetic introgression resulting from stocking. White-spotted charr in the Lake Biwa watershed constitutes a distinctive genetic group, within which apparent genetic differentiation was observed. The hatchery-reared fish line commonly used for supplementation stocking in the catchment was discernable from the native population, enabling us to analyze genetic introgression across the entire drainage area. Admixed individuals resulting from hatchery introgression were observed in most of the stocked sites that showed relatively high heterozygosity and nucleotide diversity. However, their genetic differentiation was much lower than that of native populations. The supplementation history as well as the road availability contributed substantially to the introgression of hatchery genes. Populations with the native genetic structure remained in the upstream regions of the tested rivers. However, their heterozygosity and nucleotide diversity were low when compared with that of the populations with hatchery supplementation. Our results shed light on the genetic impacts of stocking on isolated native populations and suggest that conventional supplementation methods cannot preserve a unique biodiversity in the distribution margin.

Expression-environment associations in transcriptomic heat stress responses for a global plant lineage

The increasing frequency and severity of heatwaves will intensify stress on plants. Given regional variation in heatwave exposure and expected differences in thermal tolerance between species it is unlikely that all plant species will be affected equally by climate change. However, little is currently known about variation in the responses of plants to heat stress, or how those responses differ among closely related species adapted to different environments. Here we quantify the response of 17 Acacia species (175 RNA-seq libraries), from across Australia's diverse biomes, to a multi-day experimental heatwave treatment to identify variation in transcriptomic and physiological responses to heat stress. Genes with known heat response functions showed consistent responses across Acacia species. Up to 10% of all genes and over 100 gene families showed significant clinal variation in the magnitude of their expression plasticity across species. Specifically, gene families linked to the temperature stress response were overrepresented among significant relationships with home range temperature conditions. Gene expression responses seen on the first day of the heatwave were more frequently associated with home range climates, while expression responses by day four were more commonly related to photosystem II acclimation. Comparative transcriptomics on non-model species has the potential to provide key information on stress response plasticity, especially when linked with our understanding of model species. Our study indicates that the pressing challenge to identifying potentially vulnerable species to climate change could be benefited by the further exploration of clinal variation in transcriptome plasticity.

A genome-guided strategy for climate resilience in American chestnut restoration populations

American chestnut (Castanea dentata) is a deciduous tree species of eastern North America that was decimated by the introduction of the chestnut blight fungus (Cryphonectria parasitica) in the early 20th century. Although millions of American chestnuts survive as root collar sprouts, these trees rarely reproduce. Thus, the species is considered functionally extinct. American chestnuts with improved blight resistance have been developed through interspecific hybridization followed by conspecific backcrossing, and by genetic engineering. Incorporating adaptive genomic diversity into these backcross families and transgenic lines is important for restoring the species across broad climatic gradients. To develop sampling recommendations for ex situ conservation of wild adaptive genetic variation, we coupled whole-genome resequencing of 384 stump sprouts with genotype-environment association analyses and found that the species range can be subdivided into three seed zones characterized by relatively homogeneous adaptive allele frequencies. We estimated that 21 to 29 trees per seed zone will need to be conserved to capture most extant adaptive diversity. We also resequenced the genomes of 269 backcross trees to understand the extent to which the breeding program has already captured wild adaptive diversity, and to estimate optimal reintroduction sites for specific families on the basis of their adaptive portfolio and future climate projections. Taken together, these results inform the development of an ex situ germplasm conservation and breeding plan to target blight-resistant breeding populations to specific environments and provides a blueprint for developing restoration plans for other imperiled tree species.

Chromosome-level genome assembly and annotation of xerophyte secretohalophyte Reaumuria soongarica

Reaumuria soongarica is a xerophytic shrub belonging to the Tamaricaceae family. The species is widely distributed in the deserts of Central Asia and is characterized by its remarkable adaptability to saline and barren desert environments. Using PacBio long-read sequencing and Hi-C technologies, we assembled a chromosome-level genome of R. soongarica. The genome assembly has a size of 1.28 Gb with a scaffold N50 of 116.15 Mb, and approximately 1.25 Gb sequences were anchored in 11 pseudo-chromosomes. A completeness assessment of the assembled genome revealed a BUSCO score of 97.5% and an LTR Assembly Index of 12.37. R. soongarica genome had approximately 60.07% repeat sequences. In total, 21,791 protein-coding genes were predicted, of which 95.64% were functionally annotated. This high-quality genome will serve as a foundation for studying the genomic evolution and adaptive mechanisms to arid-saline environments in R. soongarica, facilitating the exploration and utilization of its unique genetic resources.

Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen

Copy number variation (CNV) can drive rapid evolution in changing environments. In microbial pathogens, such adaptation is a key factor underpinning epidemics and colonization of new niches. However, the genomic determinants of such adaptation remain poorly understood. Here, we systematically investigate CNVs in a large genome sequencing dataset spanning a worldwide collection of 1104 genomes from the major wheat pathogen Zymoseptoria tritici. We found overall strong purifying selection acting on most CNVs. Genomic defense mechanisms likely accelerated gene loss over episodes of continental colonization. Local adaptation along climatic gradients was likely facilitated by CNVs affecting secondary metabolite production and gene loss in general. One of the strongest loci for climatic adaptation is a highly conserved gene of the NAD-dependent Sirtuin family. The Sirtuin CNV locus localizes to an ~68-kb Starship mobile element unique to the species carrying genes highly expressed during plant infection. The element has likely lost the ability to transpose, demonstrating how the ongoing domestication of cargo-carrying selfish elements can contribute to selectable variation within populations. Our work highlights how standing variation in gene copy numbers at the global scale can be a major factor driving climatic and metabolic adaptation in microbial species.

Genome scans reveal signals of selection associated with pollution in fish populations of Basilichthys microlepidotus, an endemic species of Chile

The Maipo River catchment is one of Chile's most polluted basins. In recent decades, discharges of untreated sewage and organic matter have caused eutrophication and water quality degradation. We employed the indigenous silverfish species Basilichthys microlepidotus as a model organism to investigate the process of adaptation and selection on genes influenced by pollution. Using variation at single nucleotide polymorphisms (SNPs), we determined the temporal stability of the population structure patterns previously identified in this species by varying SNPs. We also examined local adaptation to pollution-selected genes. Using the genotypes of 7684 loci in 180 individuals, we identified 429 and 700 loci that may be undergoing selection. We detected these loci using the FSTHET and ARLEQUIN outlier detection software, respectively. Both software packages simultaneously identified a total of 250 loci. B. microlepidotus' population structure did not change over time at contaminated or unpolluted sites. In addition, our analysis found: (i) selection of genes associated with pollution, consistent with observations in other organisms; (ii) identification of candidate genes that are functionally linked to the same biological processes, molecular functions and/or cellular components that previously showed differential expression in the same populations; and (iii) a candidate gene with differential expression and a non-synonymous substitution.

Integrating very high resolution environmental proxies in genotype-environment association studies

Landscape genomic analyses associating genetic variation with environmental variables are powerful tools for studying molecular signatures of species' local adaptation and for detecting candidate genes under selection. The development of landscape genomics over the past decade has been spurred by improvements in resolutions of genomic and environmental datasets, allegedly increasing the power to identify putative genes underlying local adaptation in non-model organisms. Although these associations have been successfully applied to numerous species across a diverse array of taxa, the spatial scale of environmental predictor variables has been largely overlooked, potentially limiting conclusions to be reached with these methods. To address this knowledge gap, we systematically evaluated performances of genotype-environment association (GEA) models using predictor variables at multiple spatial resolutions. Specifically, we used multivariate redundancy analyses to associate whole-genome sequence data from the plant Arabis alpina L. collected across four neighboring valleys in the western Swiss Alps, with very high-resolution topographic variables derived from digital elevation models of grain sizes between 0.5 m and 16 m. These comparisons highlight the sensitivity of landscape genomic models to spatial resolution, where the optimal grain sizes were specific to variable type, terrain characteristics, and study extent. To assist in selecting variables at appropriate spatial resolutions, we demonstrate a practical approach to produce, select, and integrate multiscale variables into GEA models. After generalizing fine-grained variables to multiple spatial resolutions, a forward selection procedure is applied to retain only the most relevant variables for a particular context. Depending on the spatial resolution, the relevance for topographic variables in GEA studies calls for integrating multiple spatial scales into landscape genomic models. By carefully considering spatial resolutions, candidate genes under selection by a more realistic range of pressures can be detected for downstream analyses, with important applied implications for experimental research and conservation management of natural populations.

Conserving Evolutionary Potential: Combining Landscape Genomics with Established Methods to Inform Plant Conservation

Biodiversity conservation requires conserving evolutionary potential-the capacity for wild populations to adapt. Understanding genetic diversity and evolutionary dynamics is critical for informing conservation decisions that enhance adaptability and persistence under environmental change. We review how emerging landscape genomic methods provide plant conservation programs with insights into evolutionary dynamics, including local adaptation and its environmental drivers. Landscape genomic approaches that explore relationships between genomic variation and environments complement rather than replace established population genomic and common garden approaches for assessing adaptive phenotypic variation, population structure, gene flow, and demography. Collectively, these approaches inform conservation actions, including genetic rescue, maladaptation prediction, and assisted gene flow. The greatest on-the-ground impacts from such studies will be realized when conservation practitioners are actively engaged in research and monitoring. Understanding the evolutionary dynamics shaping the genetic diversity of wild plant populations will inform plant conservation decisions that enhance the adaptability and persistence of species in an uncertain future.

Local adaptation of Pinus leiophylla under climate and land use change models in the Avocado Belt of Michoacán

Climate change and land use change are two main drivers of global biodiversity decline, decreasing the genetic diversity that populations harbour and altering patterns of local adaptation. Landscape genomics allows measuring the effect of these anthropogenic disturbances on the adaptation of populations. However, both factors have rarely been considered simultaneously. Based on a set of 3660 SNPs from which 130 were identified as outliers by a genome-environment association analysis (LFMM), we modelled the spatial turnover of allele frequencies in 19 localities of Pinus leiophylla across the Avocado Belt in Michoacán state, Mexico. Then, we evaluated the effect of climate change and land use change scenarios, in addition to evaluating assisted gene flow strategies and connectivity metrics across the landscape to identify priority conservation areas for the species. We found that localities in the centre-east of the Avocado Belt would be more vulnerable to climate change, while localities in the western area are more threatened by land conversion to avocado orchards. Assisted gene flow actions could aid in mitigating both threats. Connectivity patterns among forest patches will also be modified by future habitat loss, with central and eastern parts of the Avocado Belt maintaining the highest connectivity. These results suggest that areas with the highest priority for conservation are in the eastern part of the Avocado Belt, including the Monarch Butterfly Biosphere Reserve. This work is useful as a framework that incorporates distinct layers of information to provide a more robust representation of the response of tree populations to anthropogenic disturbances.

Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape

Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.

Biotic interactions promote local adaptation to soil in plants

Although different ecological factors shape adaptative evolution in natural habitats, we know little about how their interactions impact local adaptation. Here we used eight generations of experimental evolution with outcrossing Brassica rapa plants as a model system, in eight treatment groups that varied in soil type, herbivory (with/without aphids), and pollination mode (hand- or bumblebee-pollination), to study how biotic interactions affect local adaptation to soil. First, we show that several plant traits evolved in response to biotic interactions in a soil-specific way. Second, using a reciprocal transplant experiment, we demonstrate that significant local adaptation to soil-type evolved in the "number of open flowers", a trait used as a fitness proxy, but only in plants that evolved with herbivory and bee pollination. Whole genome re-sequencing of experimental lines revealed that biotic interactions caused a 10-fold increase in the number of SNPs across the genome with significant allele frequency change, and that alleles with opposite allele frequency change in different soil types (antagonistic pleiotropy) were most common in plants with an evolutionary history of herbivory and bee pollination. Our results demonstrate that the interaction with mutualists and antagonists can facilitate local adaptation to soil type through antagonistic pleiotropy.

Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa

Given the escalating impact of climate change on agriculture and food security, gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation can empower the breeding of climate-resilient crops to face future climate change. Alfalfa (Medicago sativa subsp. sativa), the queen of forages, shows remarkable adaptability across diverse global environments, making it an excellent model for investigating species responses to climate change. In this study, we performed population genomic analyses using genome resequencing data from 702 accessions of 24 Medicago species to unravel alfalfa's climatic adaptation and genetic susceptibility to future climate change. We found that interspecific genetic exchange has contributed to the gene pool of alfalfa, particularly enriching defense and stress-response genes. Intersubspecific introgression between M. sativa subsp. falcata (subsp. falcata) and alfalfa not only aids alfalfa's climatic adaptation but also introduces genetic burden. A total of 1671 genes were associated with climatic adaptation, and 5.7% of them were introgressions from subsp. falcata. By integrating climate-associated variants and climate data, we identified populations that are vulnerable to future climate change, particularly in higher latitudes of the Northern Hemisphere. These findings serve as a clarion call for targeted conservation initiatives and breeding efforts. We also identified pre-adaptive populations that demonstrate heightened resilience to climate fluctuations, illuminating a pathway for future breeding strategies. Collectively, this study enhances our understanding about the local adaptation mechanisms of alfalfa and facilitates the breeding of climate-resilient alfalfa cultivars, contributing to effective agricultural strategies for facing future climate change.

Shared xerophytic genes and their re-use in local adaptation to aridity in the desert plant Gymnocarpos przewalskii

In order to thrive and survive, plant species need to combine stability in the long term and rapid response to environmental challenges in the short term. The former would be reflected by parallel or convergent adaptation across species, and the latter by pronounced local adaptation among populations of the same species. In the present study, we generated a high-quality genome and re-sequenced 177 individuals for Gymnocarpos przewalskii, an important desert plant species from North-West China, to detect local adaptation. We first focus on ancient adaptation to aridity at the molecular level by comparing the genomic data of 15 species that vary in their ability to withstand aridity. We found that a total of 118 genes were shared across xerophytic species but absent from non-xerophytic species. Of the 65 found in G. przewalskii, 63 were under purifying selection and two under positive selection. We then focused on local adaptation. Up to 20% of the G. przewalskii genome showed signatures of local adaptation to aridity during population divergence. Thirteen of the selected shared xerophytic genes were reused in local adaptation after population differentiation. Hence, only about 20% of the genes shared and specific to xerophytic species and associated with adaptation to aridity were later recruited for local adaptation in G. przewalskii.

Future carbon sequestration potential in a widespread transcontinental boreal tree species: Standing genetic variation matters!

Climate change (CC) necessitates reforestation/afforestation programs to mitigate its impacts and maximize carbon sequestration. But comprehending how tree growth, a proxy for fitness and resilience, responds to CC is critical to maximize these programs' effectiveness. Variability in tree response to CC across populations can notably be influenced by the standing genetic variation encompassing both neutral and adaptive genetic diversity. Here, a framework is proposed to assess tree growth potential at the population scale while accounting for standing genetic variation. We applied this framework to black spruce (BS, Picea mariana [Mill] B.S.P.), with the objectives to (1) determine the key climate variables having impacted BS growth response from 1974 to 2019, (2) examine the relative roles of local adaptation and the phylogeographic structure in this response, and (3) project BS growth under two Shared Socioeconomic Pathways while taking standing genetic variation into account. We modeled growth using a machine learning algorithm trained with dendroecological and genetic data obtained from over 2600 trees (62 populations divided in three genetic clusters) in four 48-year-old common gardens, and simulated growth until year 2100 at the common garden locations. Our study revealed that high summer and autumn temperatures negatively impacted BS growth. As a consequence of warming, this species is projected to experience a decline in growth by the end of the century, suggesting maladaptation to anticipated CC and a potential threat to its carbon sequestration capacity. This being said, we observed a clear difference in response to CC within and among genetic clusters, with the western cluster being more impacted than the central and eastern clusters. Our results show that intraspecific genetic variation, notably associated with the phylogeographic structure, must be considered when estimating the response of widespread species to CC.

Adaptive divergence, historical population dynamics, and simulation of suitable distributions for Picea Meyeri and P. Mongolica at the whole-genome level

The taxonomic classification of Picea meyeri and P. mongolica has long been controversial. To investigate the genetic relatedness, evolutionary history, and population history dynamics of these species, genotyping-by-sequencing (GBS) technology was utilized to acquire whole-genome single nucleotide polymorphism (SNP) markers, which were subsequently used to assess population structure, population dynamics, and adaptive differentiation. Phylogenetic and population structural analyses at the genomic level indicated that although the ancestor of P. mongolica was a hybrid of P. meyeri and P. koraiensis, P. mongolica is an independent Picea species. Additionally, P. mongolica is more closely related to P. meyeri than to P. koraiensis, which is consistent with its geographic distribution. There were up to eight instances of interspecific and intraspecific gene flow between P. meyeri and P. mongolica. The P. meyeri and P. mongolica effective population sizes generally decreased, and Maxent modeling revealed that from the Last Glacial Maximum (LGM) to the present, their habitat areas decreased initially and then increased. However, under future climate scenarios, the habitat areas of both species were projected to decrease, especially under high-emission scenarios, which would place P. mongolica at risk of extinction and in urgent need of protection. Local adaptation has promoted differentiation between P. meyeri and P. mongolica. Genotype‒environment association analysis revealed 96,543 SNPs associated with environmental factors, mainly related to plant adaptations to moisture and temperature. Selective sweeps revealed that the selected genes among P. meyeri, P. mongolica and P. koraiensis are primarily associated in vascular plants with flowering, fruit development, and stress resistance. This research enhances our understanding of Picea species classification and provides a basis for future genetic improvement and species conservation efforts.

Recombinant inbred line panels inform the genetic architecture and interactions of adaptive traits in Drosophila melanogaster

The distribution of allelic effects on traits, along with their gene-by-gene and gene-by-environment interactions, contributes to the phenotypes available for selection and the trajectories of adaptive variants. Nonetheless, uncertainty persists regarding the effect sizes underlying adaptations and the importance of genetic interactions. Herein, we aimed to investigate the genetic architecture and the epistatic and environmental interactions involving loci that contribute to multiple adaptive traits using two new panels of Drosophila melanogaster recombinant inbred lines (RILs). To better fit our data, we re-implemented functions from R/qtl (Broman et al. 2003) using additive genetic models. We found 14 quantitative trait loci (QTL) underlying melanism, wing size, song pattern, and ethanol resistance. By combining our mapping results with population genetic statistics, we identified potential new genes related to these traits. None of the detected QTLs showed clear evidence of epistasis, and our power analysis indicated that we should have seen at least one significant interaction if sign epistasis or strong positive epistasis played a pervasive role in trait evolution. In contrast, we did find roles for gene-by-environment interactions involving pigmentation traits. Overall, our data suggest that the genetic architecture of adaptive traits often involves alleles of detectable effect, that strong epistasis does not always play a role in adaptation, and that environmental interactions can modulate the effect size of adaptive alleles.

Tibetans exhibit lower hemoglobin concentration and decreased heart response to hypoxia during poikilocapnia at intermediate altitude relative to Han Chinese

Background

High-altitude populations exhibit distinct cellular, respiratory, and cardiovascular phenotypes, some of which provide adaptive advantages to hypoxic conditions compared to populations with sea-level ancestry. Studies performed in populations with a history of high-altitude residence, such as Tibetans, support the idea that many of these phenotypes may be shaped by genomic features that have been positively selected for throughout generations. We hypothesize that such traits observed in Tibetans at high altitude also occur in Tibetans living at intermediate altitude, even in the absence of severe sustained hypoxia.

Methodology

We studied individuals of high-altitude ancestry (Tibetans, n = 17 females; n = 12 males) and sea-level ancestry (Han Chinese, n = 6 females; n = 10 males), both who had been living at ∼1300 m (∼4327 ft) for at least 18 months. We measured hemoglobin concentration ([Hb]), hypoxic ventilatory response (HVR), and hypoxic heart rate response (HHRR) with end-tidal CO2 (PetCO2) held constant (isocapnia) or allowed to decrease with hypoxic hyperventilation (poikilocapnia). We also quantified the contribution of CO2 on ventilation and heart rate by calculating the differences of isocapnic versus poikilocapnic hypoxic conditions (Δ V ˙ I /ΔPetCO2 and ΔHR/ΔPetCO2, respectively).

Results

Male Tibetans had lower [Hb] compared to Han Chinese males (p < 0.05), consistent with reports for individuals from these populations living at high altitude and sea level. Measurements of ventilation (resting ventilation, HVR, and PetCO2) were similar for both groups. Heart rate responses to hypoxia were similar in both groups during isocapnia; however, HHRR in poikilocapnia was reduced in the Tibetan group (p < 0.03), and the heart rate response to CO2 in hypoxia was lower in Tibetans relative to Han Chinese (p < 0.01).

Conclusion

These results suggest that Tibetans living at intermediate altitude have blunted cardiac responses in the context of hypoxia. Hence, only some of the phenotypes observed in Tibetans living at high altitude are observed in Tibetans living at intermediate altitude. Whereas blunted cardiac responses to hypoxia is revealed at intermediate altitudes, manifestation of other physiological adaptations to high altitude may require exposure to more severe levels of hypoxia.

High-throughput DNA sequence analysis elucidates novel insight into the genetic basis of adaptation in local sheep

Understanding how evolutionary factors related to climate adaptation and human selection have influenced the genetic architecture of domesticated animals is of great interest in biology. In the current study, by using 304 whole genomes from different geographical regions (including Europe, north Africa, Southwest Asia, east Asia, west Africa, south Asia, east Africa, Australia and Turkey), We evaluate global sheep population dynamics in terms of genetic variation and population structure. We further conducted comparative population analysis to study the genetic underpinnings of climate adaption to local environments and also morphological traits. In order to identify genomic signals under selection, we applied fixation index (FST) and also nucleotide diversity (θπ) statistical measurements. Our results revealed several candidate genes on different chromosomes under selection for local climate adaptation (e.g. HOXC12, HOXC13, IRF1, FGD2 and GNAQ), body size (PDGFA, HMGA2, PDE3A) and also morphological related traits (RXFP2). The discovered candidate genes may offer newel insights into genetic underpinning of regional adaptation and commercially significant features in local sheep.

Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data

Islands provide a great system to explore the processes that maintain genetic diversity and promote local adaptation. We explored the genomic diversity of the Balearic lizard Podarcis lilfordi, an endemic species characterized by numerous small insular populations with large phenotypic diversity. Using the newly available genome for this species, we characterized more than 300,000 SNPs, merging genotyping-by-sequencing (GBS) data with previously published restriction site-associated DNA sequencing (RAD-Seq) data, providing a dataset of 16 island populations (191 individuals) across the range of species distribution (Menorca, Mallorca, and Cabrera). Results indicate that each islet hosts a well-differentiated population (F ST = 0.247 ± 0.09), with no recent immigration/translocation events. Contrary to expectations, most populations harbor a considerable genetic diversity (mean nucleotide diversity, P i = 0.144 ± 0.021), characterized by overall low inbreeding values (F IS < 0.1). While the genetic diversity significantly decreased with decreasing islet surface, maintenance of substantial genetic diversity even in tiny islets suggests variable selection or other mechanisms that buffer genetic drift. Maximum-likelihood tree based on concatenated SNP data confirmed the existence of the two major independent lineages of Menorca and Mallorca/Cabrera. Multiple lines of evidence, including admixture and root testing, robustly placed the origin of the species in the Mallorca Island, rather than in Menorca. Outlier analysis mainly retrieved a strong signature of genome differentiation between the two major archipelagos, especially in the sexual chromosome Z. A set of proteins were target of multiple outliers and primarily associated with binding and catalytic activity, providing interesting candidates for future selection studies. This study provides the framework to explore crucial aspects of the genetic basis of phenotypic divergence and insular adaptation.

Predicting gene expression responses to environment in Arabidopsis thaliana using natural variation in DNA sequence

The evolution of gene expression responses are a critical component of adaptation to variable environments. Predicting how DNA sequence influences expression is challenging because the genotype to phenotype map is not well resolved for cis regulatory elements, transcription factor binding, regulatory interactions, and epigenetic features, not to mention how these factors respond to environment. We tested if flexible machine learning models could learn some of the underlying cis-regulatory genotype to phenotype map. We tested this approach using cold-responsive transcriptome profiles in 5 diverse Arabidopsis thaliana accessions. We first tested for evidence that cis regulation plays a role in environmental response, finding 14 and 15 motifs that were significantly enriched within the up- and down-stream regions of cold-responsive differentially regulated genes (DEGs). We next applied convolutional neural networks (CNNs), which learn de novo cis-regulatory motifs in DNA sequences to predict expression response to environment. We found that CNNs predicted differential expression with moderate accuracy, with evidence that predictions were hindered by biological complexity of regulation and the large potential regulatory code. Overall, DEGs between specific environments can be predicted based on variation in cis-regulatory sequences, although more information needs to be incorporated and better models may be required.

Convergent genetic adaptation of Escherichia coli in minimal media leads to pleiotropic divergence

Adaptation in an environment can either be beneficial, neutral or disadvantageous in another. To test the genetic basis of pleiotropic behaviour, we evolved six lines of E. coli independently in environments where glucose and galactose were the sole carbon sources, for 300 generations. All six lines in each environment exhibit convergent adaptation in the environment in which they were evolved. However, pleiotropic behaviour was observed in several environmental contexts, including other carbon environments. Genome sequencing reveals that mutations in global regulators rpoB and rpoC cause this pleiotropy. We report three new alleles of the rpoB gene, and one new allele of the rpoC gene. The novel rpoB alleles confer resistance to Rifampicin, and alter motility. Our results show how single nucleotide changes in the process of adaptation in minimal media can lead to wide-scale pleiotropy, resulting in changes in traits that are not under direct selection.

Spatiotemporal dynamics in butterfly hybrid zones

Evaluating whether hybrid zones are stable or mobile can provide novel insights for evolution and conservation biology. Butterflies exhibit high sensitivity to environmental changes and represent an important model system for the study of hybrid zone origins and maintenance. Here, we review the literature exploring butterfly hybrid zones, with a special focus on their spatiotemporal dynamics and the potential mechanisms that could lead to their movement or stability. We then compare different lines of evidence used to investigate hybrid zone dynamics and discuss the strengths and weaknesses of each approach. Our goal with this review is to reveal general conditions associated with the stability or mobility of butterfly hybrid zones by synthesizing evidence obtained using different types of data sampled across multiple regions and spatial scales. Finally, we discuss spatiotemporal dynamics in the context of a speciation/divergence continuum, the relevance of hybrid zones for conservation biology, and recommend key topics for future investigation.

Fitness surfaces and local thermal adaptation in Drosophila along a latitudinal gradient

Local adaptation is commonly cited to explain species distribution, but how fitness varies along continuous geographical gradients is not well understood. Here, we combine thermal biology and life-history theory to demonstrate that Drosophila populations along a 2500 km latitudinal cline are adapted to local conditions. We measured how heat tolerance and viability rate across eight populations varied with temperature in the laboratory and then simulated their expected cumulative Darwinian fitness employing high-resolution temperature data from their eight collection sites. Simulations indicate a trade-off between annual survival and cumulative viability, as both mortality and the recruitment of new flies are predicted to increase in warmer regions. Importantly, populations are locally adapted and exhibit the optimal combination of both traits to maximize fitness where they live. In conclusion, our method is able to reconstruct fitness surfaces employing empirical life-history estimates and reconstructs peaks representing locally adapted populations, allowing us to study geographic adaptation in silico.

Incorporating plant phenological responses into species distribution models reduces estimates of future species loss and turnover

Anthropogenetic climate change has caused range shifts among many species. Species distribution models (SDMs) are used to predict how species ranges may change in the future. However, most SDMs rarely consider how climate-sensitive traits, such as phenology, which affect individuals' demography and fitness, may influence species' ranges. Using > 120 000 herbarium specimens representing 360 plant species distributed across the eastern United States, we developed a novel 'phenology-informed' SDM that integrates phenological responses to changing climates. We compared the ranges of each species forecast by the phenology-informed SDM with those from conventional SDMs. We further validated the modeling approach using hindcasting. When examining the range changes of all species, our phenology-informed SDMs forecast less species loss and turnover under climate change than conventional SDMs. These results suggest that dynamic phenological responses of species may help them adjust their ecological niches and persist in their habitats as the climate changes. Plant phenology can modulate species' responses to climate change, mitigating its negative effects on species persistence. Further application of our framework will contribute to a generalized understanding of how traits affect species distributions along environmental gradients and facilitate the use of trait-based SDMs across spatial and taxonomic scales.

Assessing genetic diversity in critically endangered Chieniodendron hainanense populations within fragmented habitats in Hainan

Habitat fragmentation has led to a reduction in the geographic distribution of species, making small populations vulnerable to extinction due to environmental, demographic, and genetic factors. The wild plant Chieniodendron hainanense, a species with extremely small populations, is currently facing endangerment and thus requires urgent conservation efforts. Understanding its genetic diversity is essential for uncovering the underlying mechanisms of its vulnerability and for developing effective conservation strategies. In our study, we analyzed 35 specimens from six different populations of C. hainanense using genotyping-by-sequencing (GBS) and single nucleotide polymorphism (SNP) methodologies. Our findings indicate that C. hainanense has limited genetic diversity. The observed heterozygosity across the populations ranged from 10.79 to 14.55%, with an average of 13.15%. We categorized the six populations of C. hainanense into two distinct groups: (1) Diaoluoshan and Baishaling, and (2) Wuzhishan, Huishan, Bawangling, and Jianfengling. The genetic differentiation among these populations was found to be relatively weak. The observed loss of diversity is likely a result of the effects of natural selection.

Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens

Climate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers of local adaptation and understanding the underlying genetic variation in random mating indigenous livestock populations informs the design of genetic improvement programmes that aim to increase productivity and resilience. In the present study, we combined environmental, genomic, and phenotypic information of Ethiopian indigenous chickens to investigate their environmental adaptability. Through a hybrid sampling strategy, we captured wide biological and ecological variabilities across the country. Our environmental dataset comprised mean values of 34 climatic, vegetation and soil variables collected over a thirty-year period for 260 geolocations. Our biological dataset included whole genome sequences and quantitative measurements (on eight traits) from 513 individuals, representing 26 chicken populations spread along 4 elevational gradients (6-7 populations per gradient). We performed signatures of selection analyses ([Formula: see text] and XP-EHH) to detect footprints of natural selection, and redundancy analyses (RDA) to determine genotype-environment and genotype-phenotype-associations. RDA identified 1909 outlier SNPs linked with six environmental predictors, which have the highest contributions as ecological drivers of adaptive phenotypic variation. The same method detected 2430 outlier SNPs that are associated with five traits. A large overlap has been observed between signatures of selection identified by[Formula: see text]and XP-EHH showing that both methods target similar selective sweep regions. Average genetic differences measured by [Formula: see text] are low between gradients, but XP-EHH signals are the strongest between agroecologies. Genes in the calcium signalling pathway, those associated with the hypoxia-inducible factor (HIF) transcription factors, and sports performance (GALNTL6) are under selection in high-altitude populations. Our study underscores the relevance of landscape genomics as a powerful interdisciplinary approach to dissect adaptive phenotypic and genetic variation in random mating indigenous livestock populations.

Demographic history and genomic signatures of selection in a widespread vertebrate ectotherm

Environmental conditions vary greatly across large geographic ranges, and yet certain species inhabit entire continents. In such species, genomic sequencing can inform our understanding of colonization history and the impact of selection on the genome as populations experience diverse local environments. As ectothermic vertebrates are among the most vulnerable to environmental change, it is critical to understand the contributions of local adaptation to population survival. Widespread ectotherms offer an opportunity to explore how species can successfully inhabit such differing environments and how future climatic shifts will impact species' survival. In this study, we investigated the widespread painted turtle (Chrysemys picta) to assess population genomic structure, demographic history, and genomic signatures of selection in the western extent of the range. We found support for a substantial role of serial founder effects in shaping population genomic structure: demographic analysis and runs of homozygosity were consistent with bottlenecks of increasing severity from eastern to western populations during and following the Last Glacial Maximum, and edge populations were more strongly diverged and had less genetic diversity than those from the centre of the range. We also detected outlier loci, but allelic patterns in many loci could be explained by either genetic surfing or selection. While range expansion complicates the identification of loci under selection, we provide candidates for future study of local adaptation in a long-lived, widespread ectotherm that faces an uncertain future as the global climate continues to rapidly change.

The relationship between niche breadth and phylogenetic characteristics of eight species of rhubarb on the Qinghai-Tibet Plateau, Asia

The relationship between spatial distribution and phylogeny has been widely debated in recent decades. To understand biogeographic and evolutionary history relationships and to explore the interspecific similarities and phylogenetic correlations of niche characteristics, we collected and recorded all distribution points for eight species of rhubarb on the Qinghai-Tibet Plateau, used different methods to describe the ecological niche, and explored the relationship between phylogeny, ecological niche, and distribution range. The results reveal that: (1) the ranges of optimal environmental variables for species with close kinship are not exactly the same, ecologically similar species are not necessarily sister species, and the overlap of rhubarb has no significant correlation with phylogeny. Therefore, the impact of ecological dimensions on species formation is greater than that of geographical latitude for the eight species of rhubarb. (2) Among the eight species of rhubarb, the breadth of ecological niche is positively correlated with the current suitable habitat area and negatively correlated with fluctuations in future suitable habitat area. In the future, except for Rheum tanguticum and Rheum palmatum, the suitable planting areas for the other six species of rhubarb will decrease as greenhouse gas emissions concentrations and time increase. Therefore, species with smaller ecological niches are at a greater risk of habitat loss compared to species with larger ecological niches. (3) In both existing and future distribution prediction models of rhubarb, we observed that both the widely distributed Rheum spiciforme and the niche narrow Rheum nobile, all eight species of rhubarb are present in the Hengduan Mountains, based on our analysis, we propose that the Hengduan Mountains should be regarded as a priority conservation area for rhubarb, to preserve the species' biodiversity. Our study lays the groundwork for identifying evolutionary trends in ecological specialization.

The soil microbiome affects patterns of local adaptation in an alpine plant under moisture stress

PREMISE

The soil microbiome plays a role in plant trait expression and fitness, and plants may be locally adapted or maladapted to their soil microbiota. However, few studies of local adaptation in plants have incorporated a microbial treatment separate from manipulations of the abiotic environment, so our understanding of microbes in plant adaptation is limited.

METHODS

Here we tested microbial effects on local adaptation in four paired populations of an abundant alpine plant from two community types, dry and moist meadow. In a 5-month greenhouse experiment, we manipulated source population, soil moisture, and soil microbiome and measured plant survival and biomass to assess treatment effects.

RESULTS

Dry meadow populations had higher biomass than moist meadow populations at low moisture, demonstrating evidence of local adaptation to soil moisture in the absence of microbes. In the presence of microbes, dry meadow populations had greater survival than moist meadow populations when grown with dry meadow microbes regardless of moisture. Moist meadow populations showed no signs of adaptation or maladaptation.

CONCLUSIONS

Our research highlights the importance of microbial mutualists in local adaptation, particularly in dry environments with higher abiotic stress. Plant populations from environments with greater abiotic stress exhibit different patterns of adaptation when grown with soil microbes versus without, while plant populations from less abiotically stressful environments do not. Improving our understanding of the role microbes play in plant adaptation will require further studies incorporating microbial manipulations.