Evidence of genomic adaptation to climate in Eucalyptus microcarpa : Implications for adaptive potential to projected climate change

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.

Estimates of heterozygosity from single nucleotide polymorphism markers are context-dependent and often wrong

Genetic diversity is frequently described using heterozygosity, particularly in a conservation context. Often, it is estimated using single nucleotide polymorphisms (SNPs); however, it has been shown that heterozygosity values calculated from SNPs can be biased by both study design and filtering parameters. Though solutions have been proposed to address these issues, our own work has found them to be inadequate in some circumstances. Here, we aimed to improve the reliability and comparability of heterozygosity estimates, specifically by investigating how sample size and missing data thresholds influenced the calculation of autosomal heterozygosity (heterozygosity calculated from across the genome, i.e. fixed and variable sites). We also explored how the standard practice of tri- and tetra-allelic site exclusion could bias heterozygosity estimates and influence eventual conclusions relating to genetic diversity. Across three distinct taxa (a frog, Litoria rubella; a tree, Eucalyptus microcarpa; and a grasshopper, Keyacris scurra), we found heterozygosity estimates to be meaningfully affected by sample size and missing data thresholds, partly due to the exclusion of tri- and tetra-allelic sites. These biases were inconsistent both between species and populations, with more diverse populations tending to have their estimates more severely affected, thus having potential to dramatically alter interpretations of genetic diversity. We propose a modified framework for calculating heterozygosity that reduces bias and improves the utility of heterozygosity as a measure of genetic diversity, whilst also highlighting the need for existing population genetic pipelines to be adjusted such that tri- and tetra-allelic sites be included in calculations.

Rolling with the punches: Organism-environment interactions shape spatial pattern of adaptive differentiation in the widespread mantis shrimp Oratosquilla oratoria

Investigating spatial pattern of adaptive variation and its underlying processes can inform the adaptive potential distributed within species ranges, which is increasingly important in the context of a changing climate. A correct interpretation of adaptive variation pattern requires that population history and the ensuing population genetic structure are taken into account. Here we carried out such a study by integrating population genomic analyses, demographic model testing and species distribution modeling to investigate patterns and causes of adaptive differentiation in a widespread mantis shrimp, Oratosquilla oratoria, along a replicated, broad-scale temperature gradient in the northwestern Pacific (NWP). Our results supported a strong hierarchical ecogeographic structure dominated by habitat-linked divergence among O. oratoria populations accompanied with introgressive hybridization. A combined FST outlier and environmental correlation analyses revealed remarkable temperature-associated clines in allele frequency across paired North-South populations on Chinese and Japanese coasts, and identified a suite of loci associated with temperature adaptation. Further demographic model testing revealed the observed clinal variation derived partly from Pleistocene divergence followed by recent secondary contact. More importantly, the likelihood of hybridization is predicted to increase as climate change progresses, which would break barriers to gene flow and enable the spread of adaptive genetic variation. These results support that not only is temperature-driven adaptive differentiation occurs in O. oratoria but that such pattern is likely attributed to ancient adaptive variation, sustained by contemporary ocean conditions and a semi-permeable barrier to gene flow maintained by selection. They moreover provide genomic insights into the distribution of adaptive potential across O. oratoria' s species range. This work can serve as a case study to characterize adaptive diversity of marine species in the NWP by integrating environmental and genetic data at temporal and spatial scales in a population genomic framework, which would improve management and conservation actions under climate change.

Conservation genetics and potential geographic distribution modeling of Corybas taliensis, a small 'sky Island' orchid species in China

BACKGROUND

Corybas taliensis is an endemic species of sky islands in China. Its habitat is fragile and unstable, and it is likely that the species is threatened. However, it is difficult to determine the conservation priority or unit without knowing the genetic background and the overall distribution of this species. In this study, we used double digest restriction-site associated DNA-sequencing (ddRAD-seq) to investigate the conservation genomics of C. taliensis. At the same time, we modeled the extent of suitable habitat for C. taliensis in present and future (2030 and 2090) habitat using the maximum-entropy (MaxEnt) model.

RESULTS

The results suggested that the related C. fanjingshanensis belongs to C. taliensis and should not be considered a separate species. All the sampling locations were divided into three genetic groups: the Sichuan & Guizhou population (SG population), the Hengduan Mountains population (HD population) and Himalayan population (HM population), and we found that there was complex gene flow between the sampling locations of HD population. MT was distinct genetically from the other sampling locations due to the unique environment in Motuo. The genetic diversity (π, He) of C. taliensis was relatively high, but its contemporary effective population size (Ne) was small. C. taliensis might be currently affected by inbreeding depression, although its large population density may be able to reduce the effect of this. The predicted areas of suitable habitat currently found in higher mountains will not change significantly in the future, and these suitable habitats are predicted to spread to other higher mountains under future climate change. However, suitable habitat in relatively low altitude areas may disappear in the future. This suggests that C. taliensis will be caught in a 'summit trap' in low altitude areas, however, in contrast, the high altitude of the Himalaya and the Hengduan Mountains are predicted to act as 'biological refuges' for C. taliensis in the future.

CONCLUSIONS

These results not only provide a new understanding of the genetic background and potential resource distribution of C. taliensis, but also lay the foundation for its conservation and management.

Hybridization and divergent climatic preferences drive divergence of two allopatric Gentiana species on the Qinghai-Tibet Plateau

BACKGROUND AND AIMS

Exploring how species diverge is vital for understanding the drivers of speciation. Factors such as geographical separation and ecological selection, hybridization, polyploidization and shifts in mating system are all major mechanisms of plant speciation, but their contributions to divergence are rarely well understood. Here we test these mechanisms in two plant species, Gentiana lhassica and G. hoae, with the goal of understanding recent allopatric species divergence on the Qinghai-Tibet Plateau (QTP).

METHODS

We performed Bayesian clustering, phylogenetic analysis and estimates of hybridization using 561 302 nuclear genomic single nucleotide polymorphisms (SNPs). We performed redundancy analysis, and identified and annotated species-specific SNPs (ssSNPs) to explore the association between climatic preference and genetic divergence. We also estimated genome sizes using flow cytometry to test for overlooked polyploidy.

KEY RESULTS

Genomic evidence confirms that G. lhassica and G. hoae are closely related but distinct species, while genome size estimates show divergence occurred without polyploidy. Gentiana hoae has significantly higher average FIS values than G. lhassica. Population clustering based on genomic SNPs shows no signature of recent hybridization, but each species is characterized by a distinct history of hybridization with congeners that has shaped genome-wide variation. Gentiana lhassica has captured the chloroplast and experienced introgression with a divergent gentian species, while G. hoae has experienced recurrent hybridization with related taxa. Species distribution modelling suggested range overlap in the Last Interglacial Period, while redundancy analysis showed that precipitation and temperature are the major climatic differences explaining the separation of the species. The species differ by 2993 ssSNPs, with genome annotation showing missense variants in genes involved in stress resistance.

CONCLUSIONS

This study suggests that the distinctiveness of these species on the QTP is driven by a combination of hybridization, geographical isolation, mating system differences and evolution of divergent climatic preferences.

Space-for-time substitutions in climate change ecology and evolution

In an epoch of rapid environmental change, understanding and predicting how biodiversity will respond to a changing climate is an urgent challenge. Since we seldom have sufficient long-term biological data to use the past to anticipate the future, spatial climate-biotic relationships are often used as a proxy for predicting biotic responses to climate change over time. These 'space-for-time substitutions' (SFTS) have become near ubiquitous in global change biology, but with different subfields largely developing methods in isolation. We review how climate-focussed SFTS are used in four subfields of ecology and evolution, each focussed on a different type of biotic variable - population phenotypes, population genotypes, species' distributions, and ecological communities. We then examine the similarities and differences between subfields in terms of methods, limitations and opportunities. While SFTS are used for a wide range of applications, two main approaches are applied across the four subfields: spatial in situ gradient methods and transplant experiments. We find that SFTS methods share common limitations relating to (i) the causality of identified spatial climate-biotic relationships and (ii) the transferability of these relationships, i.e. whether climate-biotic relationships observed over space are equivalent to those occurring over time. Moreover, despite widespread application of SFTS in climate change research, key assumptions remain largely untested. We highlight opportunities to enhance the robustness of SFTS by addressing key assumptions and limitations, with a particular emphasis on where approaches could be shared between the four subfields.

Neutral and adaptive genetic diversity in plants: An overview

Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.

Weak genetic differentiation but strong climate-induced selective pressure toward the rear edge of mountain pine in north-eastern Spain

Local differentiation at distribution limits may influence species' adaptive capacity to environmental changes. However, drivers, such gene flow and local selection, are still poorly understood. We focus on the role played by range limits in mountain forests to test the hypothesis that relict tree populations are subjected to genetic differentiation and local adaptation. Two alpine treelines of mountain pine (Pinus uncinata Ram. ex DC) were investigated in the Spanish Pyrenees. Further, an isolated relict population forming the species' southernmost distribution limit in north-eastern Spain was also investigated. Using genotyping by sequencing, a genetic matrix conformed by single nucleotide polymorphisms (SNPs) was obtained. This matrix was used to perform genotype-environment and genotype-phenotype associations, as well as to model risk of non-adaptedness. Increasing climate seasonality appears as an essential element in the interpretation of SNPs subjected to selective pressures. Genetic differentiations were overall weak. The differences in leaf mass area and radial growth rate, as well as the identification of several SNPs subjected to selective pressures, exceeded neutral predictions of differentiation among populations. Despite genetic drift might prevail in the isolated population, the Fst values (0.060 and 0.066) showed a moderate genetic drift and Nm values (3.939 and 3.555) indicate the presence of gene flow between the relict population and both treelines. Nonetheless, the SNPs subjected to selection pressures provide evidences of possible selection in treeline ecotones. Persistence in range boundaries seems to involve several selective pressures in species' traits, which were significantly related to enhanced drought seasonality at the limit of P. uncinata distribution range. We conclude that gene flow is unlikely to constrain adaptation in the P. uncinata rear edge, although this species shows vulnerability to future climate change scenarios involving warmer and drier conditions.

Genomic signals of local adaptation and hybridization in Asian white birch

Disentangling the numerous processes that affect patterns of genome-wide diversity in widespread tree species has important implications for taxonomy, conservation, and forestry. Here, we investigate the population genomic structure of Asian white birch (Betula platyphylla) in China and seek to explain it in terms of hybridization, demography and adaptation. We generate whole genome sequence data from 83 individuals across the species range in China. Combining this with an existing data set for 79 European and Russian white birches, we show a clear distinction between B. pendula and B. platyphylla, which have sometimes been lumped taxonomically. Genomic diversity of B. platyphylla in north-western China and Central Russia is affected greatly by hybridization with B. pendula. Excluding these hybridized populations, B. platyphylla in China has a linear distribution from north-eastern to south-western China, along the edge of the inland mountainous region. Within this distribution, three genetic clusters are found, which we model as long diverged with subsequent episodes of gene flow. Patterns of covariation between allele frequencies and environmental variables in B. platyphylla suggest the role of natural selection in the distribution of diversity at 7609 SNPs of which 3767 were significantly differentiated among the genetic clusters. The putative adaptive SNPs are distributed throughout the genome and span 1633 genic regions. Of these genic regions, 87 were previously identified as candidates for selective sweeps in Eurasian B. pendula. We use the 7609 environmentally associated SNPs to estimate the risk of nonadaptedness for each sequenced B. platyphylla individual under a scenario of future climate change, highlighting areas where populations may be under future threat from rising temperatures.

Using landscape genomics to assess local adaptation and genomic vulnerability of a perennial herb Tetrastigma hemsleyanum (Vitaceae) in subtropical China

Understanding adaptive genetic variation of plant populations and their vulnerabilities to climate change are critical to preserve biodiversity and subsequent management interventions. To this end, landscape genomics may represent a cost-efficient approach for investigating molecular signatures underlying local adaptation. Tetrastigma hemsleyanum is, in its native habitat, a widespread perennial herb of warm-temperate evergreen forest in subtropical China. Its ecological and medicinal values constitute a significant revenue for local human populations and ecosystem. Using 30,252 single nucleotide polymorphisms (SNPs) derived from reduced-representation genome sequencing in 156 samples from 24 sites, we conducted a landscape genomics study of the T. hemsleyanum to elucidate its genomic variation across multiple climate gradients and genomic vulnerability to future climate change. Multivariate methods identified that climatic variation explained more genomic variation than that of geographical distance, which implied that local adaptation to heterogeneous environment might represent an important source of genomic variation. Among these climate variables, winter precipitation was the strongest predictor of the contemporary genetic structure. F _ST outlier tests and environment association analysis totally identified 275 candidate adaptive SNPs along the genetic and environmental gradients. SNP annotations of these putatively adaptive loci uncovered gene functions associated with modulating flowering time and regulating plant response to abiotic stresses, which have implications for breeding and other special agricultural aims on the basis of these selection signatures. Critically, modelling revealed that the high genomic vulnerability of our focal species via a mismatch between current and future genotype-environment relationships located in central-northern region of the T. hemsleyanum's range, where populations require proactive management efforts such as assistant adaptation to cope with ongoing climate change. Taken together, our results provide robust evidence of local climate adaption for T. hemsleyanum and further deepen our understanding of adaptation basis of herbs in subtropical China.

Between allopatry and secondary contact: differentiation and hybridization among three sympatric Gentiana species in the Qinghai-Tibet Plateau

BACKGROUND

Mountains of the world host a significant portion of all terrestrial biodiversity, and the region of the Qinghai-Tibet Plateau (QTP) stands as one of the most remarkable mountain regions on Earth.  Because many explosive radiations occurred there, the QTP is a natural laboratory which is ideal to investigate patterns and processes linked to speciation and diversification. Indeed, understanding how closely related and sympatric species diverged is vital to explore drivers fostering speciation, a topic only rarely investigated in the QTP. By combining genomic and environmental data, we explored the speciation process among three closely related and sympatric species, Gentiana hexaphylla, G. lawrencei and G. veitchiorum in the QTP region.

RESULTS

Combining genome sizes and cytological data, our results showed that G. hexaphylla and G. veitchiorum are diploid, whereas G. lawrencei is tetraploid. Genetic clustering and phylogenetic reconstruction based on genomic SNPs indicated a clear divergence among the three species. Bayesian clustering, migrant, and D-statistic analyses all showed an obvious signature of hybridization among the three species, in particular between G. lawrencei and both G. hexaphylla and G. veitchiorum in almost all populations. Environmental variables related to precipitation and particularly temperature showed significant differences among the three gentians, and in fact a redundancy analysis confirmed that temperature and precipitation were the major climatic factors explaining the genetic differentiation among the three species.

CONCLUSION

Our study suggested that ancient hybridization, polyploidization, geological isolation and the evolution of different climatic preferences were all likely to be involved in the divergence of the three Gentiana species, as may be the case for many other taxa in the QTP region.

Ecological and genomic vulnerability to climate change across native populations of Robusta coffee (Coffea canephora)

The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that is mainly distributed in the lowland rainforests of tropical Africa. Also known as Robusta, its commercial value constitutes a significant revenue for many human populations in tropical countries. Comparing ecological and genomic vulnerabilities within the species' native range can provide valuable insights about habitat loss and the species' adaptive potential, allowing to identify genotypes that may act as a resource for varietal improvement. By applying species distribution models, we assessed ecological vulnerability as the decrease in climatic suitability under future climatic conditions from 492 occurrences. We then quantified genomic vulnerability (or risk of maladaptation) as the allelic composition change required to keep pace with predicted climate change. Genomic vulnerability was estimated from genomic environmental correlations throughout the native range. Suitable habitat was predicted to diminish to half its size by 2050, with populations near coastlines and around the Congo River being the most vulnerable. Whole-genome sequencing revealed 165 candidate SNPs associated with climatic adaptation in C. canephora, which were located in genes involved in plant response to biotic and abiotic stressors. Genomic vulnerability was higher for populations in West Africa and in the region at the border between DRC and Uganda. Despite an overall low correlation between genomic and ecological vulnerability at broad scale, these two components of vulnerability overlap spatially in ways that may become damaging. Genomic vulnerability was estimated to be 23% higher in populations where habitat will be lost in 2050 compared to regions where habitat will remain suitable. These results highlight how ecological and genomic vulnerabilities are relevant when planning on how to cope with climate change regarding an economically important species.

Climate Adaptation, Drought Susceptibility, and Genomic-Informed Predictions of Future Climate Refugia for the Australian Forest Tree Eucalyptus globulus

Understanding the capacity of forest tree species to adapt to climate change is of increasing importance for managing forest genetic resources. Through a genomics approach, we modelled spatial variation in climate adaptation within the Australian temperate forest tree Eucalyptus globulus, identified putative climate drivers of this genomic variation, and predicted locations of future climate refugia and populations at-risk of future maladaptation. Using 812,158 SNPs across 130 individuals from 30 populations (i.e., localities) spanning the species’ natural range, a gradientForest algorithm found 1177 SNPs associated with locality variation in home-site climate (climate-SNPs), putatively linking them to climate adaptation. Very few climate-SNPs were associated with population-level variation in drought susceptibility, signalling the multi-faceted nature and complexity of climate adaptation. Redundancy analysis (RDA) showed 24% of the climate-SNP variation could be explained by annual precipitation, isothermality, and maximum temperature of the warmest month. Spatial predictions of the RDA climate vectors associated with climate-SNPs allowed mapping of genomically informed climate selective surfaces across the species’ range under contemporary and projected future climates. These surfaces suggest over 50% of the current distribution of E. globulus will be outside the modelled adaptive range by 2070 and at risk of climate maladaptation. Such surfaces present a new integrated approach for natural resource managers to capture adaptive genetic variation and plan translocations in the face of climate change.

Comparative population genomics in Tabebuia alliance shows evidence of adaptation in Neotropical tree species

The role of natural selection in shaping spatial patterns of genetic diversity in the Neotropics is still poorly understood. Here, we perform a genome scan with 24,751 probes targeting 11,026 loci in two Neotropical Bignoniaceae tree species: Handroanthus serratifolius from the seasonally dry tropical forest (SDTF) and Tabebuia aurea from savannas, and compared with the population genomics of H. impetiginosus from SDTF. OutFLANK detected 29 loci in 20 genes with selection signal in H. serratifolius and no loci in T. aurea. Using BayPass, we found evidence of selection in 335 loci in 312 genes in H. serratifolius, 101 loci in 92 genes in T. aurea, and 448 loci in 416 genes in H. impetiginosus. All approaches evidenced several genes affecting plant response to environmental stress and primary metabolic processes. The three species shared no SNPs with selection signal, but we found SNPs affecting the same gene in pair of species. Handroanthus serratifolius showed differences in allele frequencies at SNPs with selection signal among ecosystems, mainly between Caatinga/Cerrado and Atlantic Forest, while H. impetiginosus had one allele fixed across all populations, and T. aurea had similar allele frequency distribution among ecosystems and polymorphism across populations. Taken together, our results indicate that natural selection related to environmental stress shaped the spatial pattern of genetic diversity in the three species. However, the three species have different geographical distribution and niches, which may affect tolerances and adaption, and natural selection may lead to different signatures due to the differences in adaptive landscapes in different niches.

Differentiation of Cold Tolerance in an Artificial Population of a Mangrove Species, Kandelia obovata, Is Associated With Geographic Origins

Temperature is one of the climatic factors that shape the geographic distribution of plant populations. Mangroves are temperature-sensitive plants, and their distributions are severely limited by low temperatures. It is unknown, however, to what extent temperature contributes to their population differentiation and evolution. Kandelia obovata (Rhizophoraceae) is a mangrove species with high cold tolerance in the Northern Hemisphere. We investigated the phenotypic responses of an artificial population of K. obovata, with plants transplanted from different source populations, to extremely low temperatures during winter of 2015-2016 in Yueqing County (28°20'N), Zhejiang Province of China. Using two binary traits, "with/without leaves alive on the branches" and "with/without alive buds on the tips of branches," we classified plants in this artificial population into strong, moderate and poor cold resistance groups. We further assessed the genetic diversity, structure and differentiation of these three groups, as well as five natural populations along a latitudinal gradient using ten nuclear and six plastid microsatellite markers. Microsatellite data revealed genetic differentiation among the natural populations along the latitudinal gradient. Molecular data indicated that the cold tolerance of three groups in the artificial population was associated with their geographic origins, and that the most cold-tolerant group came from the northernmost natural population. Our study thus indicates that natural populations of K. obovata may have evolved divergent capacity of cold tolerance.

Signatures of natural selection in a foundation tree along Mediterranean climatic gradients

Temperature and precipitation regimes are rapidly changing, resulting in forest dieback and extinction events, particularly in Mediterranean‐type climates (MTC). Forest management that enhance forests’ resilience is urgently required, however adaptation to climates in heterogeneous landscapes with multiple selection pressures is complex. For widespread trees in MTC we hypothesized that: patterns of local adaptation are associated with climate; precipitation is a stronger factor of adaptation than temperature; functionally related genes show similar signatures of adaptation; and adaptive variants are independently sorting across the landscape. We sampled 28 populations across the geographic distribution of Eucalyptus marginata (jarrah), in South‐west Western Australia, and obtained 13,534 independent single nucleotide polymorphic (SNP) markers across the genome. Three genotype‐association analyses that employ different ways of correcting population structure were used to identify putatively adapted SNPs associated with independent climate variables. While overall levels of population differentiation were low (F_ST = 0.04), environmental association analyses found a total of 2336 unique SNPs associated with temperature and precipitation variables, with 1440 SNPs annotated to genic regions. Considerable allelic turnover was identified for SNPs associated with temperature seasonality and mean precipitation of the warmest quarter, suggesting that both temperature and precipitation are important factors in adaptation. SNPs with similar gene functions had analogous allelic turnover along climate gradients, while SNPs among temperature and precipitation variables had uncorrelated patterns of adaptation. These contrasting patterns provide evidence that there may be standing genomic variation adapted to current climate gradients, providing the basis for adaptive management strategies to bolster forest resilience in the future.

Landscape Genomics in Tree Conservation Under a Changing Environment

Understanding the genetic basis of how species respond to changing environments is essential to the conservation of species. However, the molecular mechanisms of adaptation remain largely unknown for long-lived tree species which always have large population sizes, long generation time, and extensive gene flow. Recent advances in landscape genomics can reveal the signals of adaptive selection linking genetic variations and landscape characteristics and therefore have created novel insights into tree conservation strategies. In this review article, we first summarized the methods of landscape genomics used in tree conservation and elucidated the advantages and disadvantages of these methods. We then highlighted the newly developed method "Risk of Non-adaptedness," which can predict the genetic offset or genomic vulnerability of species via allele frequency change under multiple scenarios of climate change. Finally, we provided prospects concerning how our introduced approaches of landscape genomics can assist policymaking and improve the existing conservation strategies for tree species under the ongoing global changes.

Genome-Wide Investigation of the Multiple Origins Hypothesis for Deep-Spawning Kokanee Salmon (Oncorhynchus nerka) across its Pan-Pacific Distribution

Salmonids have emerged as important study systems for investigating molecular processes underlying parallel evolution given their tremendous life history variation. Kokanee, the resident form of anadromous sockeye salmon (Oncorhynchus nerka), have evolved multiple times across the species' pan-Pacific distribution, exhibiting multiple reproductive ecotypes including those that spawn in streams, on lake-shores, and at lake depths >50 m. The latter has only been detected in 5 locations in Japan and British Columbia, Canada. Here, we investigated the multiple origins hypothesis for deep-spawning kokanee, using 9721 single nucleotide polymorphisms distributed across the genome analyzed for the vast majority of known populations in Japan (Saiko Lake) and Canada (Anderson, Seton, East Barrière Lakes) relative to stream-spawning populations in both regions. We detected 397 outlier loci, none of which were robustly identified in paired-ecotype comparisons in Japan and Canada independently. Bayesian clustering and principal components analyses based on neutral loci revealed 6 distinct clusters, largely associated with geography or translocation history, rather than ecotype. Moreover, a high level of divergence between Canadian and Japanese populations, and between deep- and stream-spawning populations regionally, suggests the deep-spawning ecotype independently evolved on the 2 continents. On a finer level, Japanese kokanee populations exhibited low estimates of heterozygosity, significant levels of inbreeding, and reduced effective population sizes relative to Canadian populations, likely associated with transplantation history. Along with preliminary evidence for hybridization between deep- and stream-spawning ecotypes in Saiko Lake, these findings should be considered within the context of on-going kokanee fisheries management in Japan.

Directional Selection on Tree Seedling Traits Driven by Experimental Drought Differs Between Mesic and Dry Populations

We evaluated population differences and drought-induced phenotypic selection on four seedling traits of the Australian forest tree Eucalyptus pauciflora using a glasshouse dry-down experiment. We compared dry and mesic populations and tested for directional selection on lamina length (reflecting leaf size), leaf shape, the node of ontogenetic transition to the petiolate leaf (reflecting the loss of vegetative juvenility), and lignotuber size (reflecting a recovery trait). On average, the dry population had smaller and broader leaves, greater retention of the juvenile leaf state and larger lignotubers than the mesic population, but the populations did not differ in seedling survival. While there was statistical support for directional selection acting on the focal traits in one or other population, and for differences between populations in selection gradient estimates for two traits, only one trait—lamina length—exhibited a pattern of directional selection consistent with the observed population differences being a result of past adaptation to reduce seedling susceptibility to acute drought. The observed directional selection for lamina length in the mesic population suggests that future increases in drought risk in the wild will shift the mean of the mesic population toward that of the dry population. Further, we provide evidence suggesting an early age trade-off between drought damage and recovery traits, with phenotypes which develop larger lignotubers early being more susceptible to drought death. Such trade-offs could have contributed to the absence of population mean differences in survival, despite marked differentiation in seedling traits.

Non-linear genetic diversity and notable population differentiation caused by low gene flow of bermudagrass [Cynodon dactylon (L.) Pers.] along longitude gradients

Background

Environmental variation related to ecological habitat is the main driver of plant adaptive divergence. Longitude plays an important role in the formation of plant population structure, indicating that environmental differentiation can significantly shape population structure.

Methods

Genetic diversity and population genetic structure were estimated using 105 expressed sequence tag-derived simple sequence repeat (EST-SSR) loci. A total of 249 C. dactylon (L.) Pers. (common bermudagrass) individuals were sampled from 13 geographic sites along the longitude (105°57′34″–119°27′06″E).

Results

There was no obvious linear trend of intra-population genetic diversity along longitude and the intra-population genetic diversity was not related to climate in this study. Low gene flow (Nm = 0.7701) meant a rich genetic differentiation among populations of C. dactylon along longitude gradients. Significantly positive Mantel correlation (r = 0.438, P = 0.001) was found between genetic distance and geographical interval while no significant partial Mantel correlation after controlling the effect of mean annual precipitation, which indicated geographic distance correlated with mean annual precipitation affect genetic distance. The genetic diversity of C. dactylon with higher ploidy level was higher than that with lower ploidy level and groups of individuals with higher ploidy level were separated further away by genetic distance from the lower ploidy levels. Understanding the different genetic bases of local adaptation comparatively between latitude and longitude is one of the core findings in the adaptive evolution of plants.

Genomic Approaches for Conservation Management in Australia under Climate Change

Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change.

Prospects and limitations of genomic offset in conservation management

In nature conservation, there is keen interest in predicting how populations will respond to environmental changes such as climate change. These predictions can help determine whether a population can be self-sustaining under future alterations of its habitat or whether it may require human intervention such as protection, restoration, or assisted migration. An increasingly popular approach in this respect is the concept of genomic offset, which combines genomic and environmental data from different time points and/or locations to assess the degree of possible maladaptation to new environmental conditions. Here, we argue that the concept of genomic offset holds great potential, but an exploration of its risks and limitations is needed to use it for recommendations in conservation or assisted migration. After briefly describing the concept, we list important issues to consider (e.g., statistical frameworks, population genetic structure, migration, independent evidence) when using genomic offset or developing these methods further. We conclude that genomic offset is an area of development that still lacks some important features and should be used in combination with other approaches to inform conservation measures.

Scale-dependent signatures of local adaptation in a foundation tree species

Understanding local adaptation is critical for conservation management under rapidly changing environmental conditions. Local adaptation inferred from genotype-environment associations may show different genomic patterns depending on the spatial scale of sampling, due to differences in the slope of environmental gradients and the level of gene flow. We compared signatures of local adaptation across the genome of mountain ash (Eucalyptus regnans) at two spatial scales: A species-wide data set and a topographically-complex subregional data set. We genotyped 367 individual trees at over 3700 single-nucleotide polymorphisms (SNPs), quantified patterns of spatial genetic structure among populations, and used two analytical methods to identify loci associated with at least one of three environmental variables at each spatial scale. Together, the analyses identified 549 potentially adaptive SNPs at the subregion scale, and 435 SNPs at the range-wide scale. A total of 39 genic or near-genic SNPs, associated with 28 genes, were identified at both spatial scales, although no SNP was identified by both methods at both scales. We observed that nongenic regions had significantly higher homozygote excess than genic regions, possibly due to selective elimination of inbred genotypes during stand development. Our results suggest that strong environmental selection occurs in mountain ash, and that the identification of putatively adaptive loci can differ substantially depending on the spatial scale of analyses. We also highlight the importance of multiple adaptive genetic architectures for understanding patterns of local adaptation across large heterogenous landscapes, with comparison of putatively adaptive loci among spatial scales providing crucial insights into the process of adaptation.

Regarding the F-word: The effects of data filtering on inferred genotype-environment associations

Genotype-environment association (GEA) methods have become part of the standard landscape genomics toolkit, yet, we know little about how to best filter genotype-by-sequencing data to provide robust inferences for environmental adaptation. In many cases, default filtering thresholds for minor allele frequency and missing data are applied regardless of sample size, having unknown impacts on the results, negatively affecting management strategies. Here, we investigate the effects of filtering on GEA results and the potential implications for assessment of adaptation to environment. We use empirical and simulated data sets derived from two widespread tree species to assess the effects of filtering on GEA outputs. Critically, we find that the level of filtering of missing data and minor allele frequency affect the identification of true positives. Even slight adjustments to these thresholds can change the rate of true positive detection. Using conservative thresholds for missing data and minor allele frequency substantially reduces the size of the data set, lessening the power to detect adaptive variants (i.e., simulated true positives) with strong and weak strengths of selection. Regardless, strength of selection was a good predictor for GEA detection, but even some SNPs under strong selection went undetected. False positive rates varied depending on the species and GEA method, and filtering significantly impacted the predictions of adaptive capacity in downstream analyses. We make several recommendations regarding filtering for GEA methods. Ultimately, there is no filtering panacea, but some choices are better than others, depending on the study system, availability of genomic resources, and desired objectives.

Genomic vulnerability to rapid climate warming in a tree species with a long generation time

The ongoing increase in global temperature affects biodiversity, especially in mountain regions where climate change is exacerbated. As sessile, long-lived organisms, trees are especially challenged in terms of adapting to rapid climate change. Here, we show that low rates of allele frequency shifts in Swiss stone pine (Pinus cembra) occurring near the treeline result in high genomic vulnerability to future climate warming, presumably due to the species' long generation time. Using exome sequencing data from adult and juvenile cohorts in the Swiss Alps, we found an average rate of allele frequency shift of 1.23 × 10^-2 /generation (i.e. 40 years) at presumably neutral loci, with similar rates for putatively adaptive loci associated with temperature (0.96 × 10^-2 /generation) and precipitation (0.91 × 10^-2 /generation). These recent shifts were corroborated by forward-in-time simulations at neutral and adaptive loci. Additionally, in juvenile trees at the colonisation front we detected alleles putatively beneficial under a future warmer and drier climate. Notably, the observed past rate of allele frequency shift in temperature-associated loci was decidedly lower than the estimated average rate of 6.29 × 10^-2 /generation needed to match a moderate future climate scenario (RCP4.5). Our findings suggest that species with long generation times may have difficulty keeping up with the rapid climate change occurring in high mountain areas and thus are prone to local extinction in their current main elevation range.

Opportunities and challenges in assessing climate change vulnerability through genomics

By investigating how past selection has affected allele frequencies across space, genomic tools are providing new insights into adaptive evolutionary processes. Now researchers are considering how this genomic information can be used to predict the future vulnerability of species under climate change. Genomic vulnerability assessments show promise, but challenges remain.

Genetic mixing for population management: From genetic rescue to provenancing

Animal and plant species around the world are being challenged by the deleterious effects of inbreeding, loss of genetic diversity, and maladaptation due to widespread habitat destruction and rapid climate change. In many cases, interventions will likely be needed to safeguard populations and species and to maintain functioning ecosystems. Strategies aimed at initiating, reinstating, or enhancing patterns of gene flow via the deliberate movement of genotypes around the environment are generating growing interest with broad applications in conservation and environmental management. These diverse strategies go by various names ranging from genetic or evolutionary rescue to provenancing and genetic resurrection. Our aim here is to provide some clarification around terminology and to how these strategies are connected and linked to underlying genetic processes. We draw on case studies from the literature and outline mechanisms that underlie how the various strategies aim to increase species fitness and impact the wider community. We argue that understanding mechanisms leading to species decline and community impact is a key to successful implementation of these strategies. We emphasize the need to consider the nature of source and recipient populations, as well as associated risks and trade-offs for the various strategies. This overview highlights where strategies are likely to have potential at population, species, and ecosystem scales, but also where they should probably not be attempted depending on the overall aims of the intervention. We advocate an approach where short- and long-term strategies are integrated into a decision framework that also considers nongenetic aspects of management.

Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations

Understanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.

Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm

Despite the global importance of tropical ecosystems, few studies have identified how natural selection has shaped their megadiversity. Here, we test for the role of adaptation in the evolutionary success of the widespread, highly abundant Neotropical palm Mauritia flexuosa. We used a genome scan framework, sampling 16,262 single-nucleotide polymorphisms (SNPs) with target sequence capture in 264 individuals from 22 populations in rainforest and savanna ecosystems. We identified outlier loci as well as signal of adaptation using Bayesian correlations of allele frequency with environmental variables and detected both selective sweeps and genetic hitchhiking events. Functional annotation of SNPs with selection footprints identified loci affecting genes related to adaptation to environmental stress, plant development, and primary metabolic processes. The strong differences in climatic and soil variables between ecosystems matched the high differentiation and low admixture in population Bayesian clustering. Further, we found only small differences in allele frequency distribution in loci putatively under selection among widespread populations from different ecosystems, with fixation of a single allele in most populations. Taken together, our results indicate that adaptive selective sweeps related to environmental stress shaped the spatial pattern of genetic diversity in M. flexuosa, leading to high similarity in allele frequency among populations from different ecosystems.

Diversity Patterns of Bermuda Grass along Latitudinal Gradients at Different Temperatures in Southeastern China

Cynodon dactylon (L.) Pers. (common Bermuda grass) has a limited capacity to grow at low temperatures, which limits its geographical range. Exploring its evolutionary relationship across different environmental gradients is necessary to understand the effects of temperature change on the genetics of common Bermuda grass. In this study, high-throughput transcriptome sequencing was performed on 137 samples of C. dactylon from 16 latitudinal gradients to explore the differential molecular markers and analyze genetic diversity and structure along latitudinal gradients at different temperatures. We primarily sampled more high-quality single nucleotide polymorphisms (SNPs) from populations at lower and middle latitudes. Greater intraspecific genetic variation at each level of temperature treatment could be due to factors such as wind pollination and asexual breeding. Populations of C. dactylon at high latitudes differed from populations at middle and low latitudes, which was supported by a principal component analysis (PCA) and genetic structure analysis, performed at different temperatures. We observed more genetic variation for low-latitude populations at 5 °C, according to an analysis of three phylogenetic trees at different temperature levels, suggesting that low temperatures affected samples with low cold resistance. Based on the results of phylogenetic analysis, we found that samples from high latitudes evolved earlier than most samples at low latitudes. The results provide a comprehensive understanding of the evolutionary phenomenon of landscape genetics, laying the groundwork for future structural and comparative genomic studies of C. dactylon.

Anthropogenic and natural barriers affect genetic connectivity in an Alpine butterfly

Dispersal is a key biological process serving several functions including connectivity among populations. Habitat fragmentation caused by natural or anthropogenic structures may hamper dispersal, thereby disrupting genetic connectivity. Investigating factors affecting dispersal and gene flow is important in the current era of anthropogenic global change, as dispersal comprises a vital part of a species' resilience to environmental change. Using finescale landscape genomics, we investigated gene flow and genetic structure of the Sooty Copper butterfly (Lycaena tityrus) in the Alpine Ötz valley system in Austria. We found surprisingly high levels of gene flow in L. tityrus across the region. Nevertheless, ravines, forests, and roads had effects on genetic structure, while rivers did not. The latter is surprising as roads and rivers have a similar width and run largely in parallel in our study area, pointing towards a higher impact of anthropogenic compared with natural linear structures. Additionally, we detected eleven loci potentially under thermal selection, including ones related to membranes, metabolism, and immune function. This study demonstrates the usefulness of molecular approaches in obtaining estimates of dispersal and population processes in the wild. Our results suggest that, despite high gene flow in the Alpine valley system investigated, L. tityrus nevertheless seems to be vulnerable to anthropogenically-driven habitat fragmentation. With anthropogenic rather than natural linear structures affecting gene flow, this may have important consequences for the persistence of species such as the butterfly studied here in altered landscapes.

Spatial, climate and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra

Global climate change poses a significant threat to natural communities around the world, with many plant species showing signs of climate stress. Grassland ecosystems are not an exception, with climate change compounding contemporary pressures such as habitat loss and fragmentation. In this study, we assess the climate resilience of Themeda triandra, a foundational species and the most widespread plant in Australia, by assessing the relative contributions of spatial, environmental and ploidy factors to contemporary genomic variation. Reduced-representation genome sequencing on 472 samples from 52 locations was used to test how the distribution of genomic variation, including ploidy polymorphism, supports adaptation to hotter and drier climates. We explicitly quantified isolation by distance (IBD) and isolation by environment (IBE) and predicted genomic vulnerability of populations to future climates based on expected deviation from current genomic composition. We found that a majority (54%) of genomic variation could be attributed to IBD, while an additional 22% (27% when including ploidy information) could be explained by two temperature and two precipitation climate variables demonstrating IBE. Ploidy polymorphisms were common within populations (31/52 populations), indicating that ploidy mixing is characteristic of T. triandra populations. Genomic vulnerabilities were found to be heterogeneously distributed throughout the landscape, and our analysis suggested that ploidy polymorphism, along with other factors linked to polyploidy, reduced vulnerability to future climates by 60% (0.25-0.10). Our data suggests that polyploidy may facilitate adaptation to hotter climates and highlight the importance of incorporating ploidy in adaptive management strategies to promote the resilience of this and other foundation species.

Genomic evidence of introgression and adaptation in a model subtropical tree species, Eucalyptus grandis

The genetic consequences of adaptation to changing environments can be deciphered using population genomics, which may help predict species' responses to global climate change. Towards this, we used genome-wide SNP marker analysis to determine population structure and patterns of genetic differentiation in terms of neutral and adaptive genetic variation in the natural range of Eucalyptus grandis, a widely cultivated subtropical and temperate species, serving as genomic reference for the genus. We analysed introgression patterns at subchromosomal resolution using a modified ancestry mapping approach and identified provenances with extensive interspecific introgression in response to increased aridity. Furthermore, we describe potentially adaptive genetic variation as explained by environment-associated SNP markers, which also led to the discovery of what is likely a large structural variant. Finally, we show that genes linked to these markers are enriched for biotic and abiotic stress responses.

Genomics of Clinal Local Adaptation in Pinus sylvestris Under Continuous Environmental and Spatial Genetic Setting

Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic basis often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we identified several loci contributing to local adaptation, but only few with large allele frequency changes across latitude. We also discovered a very large (ca. 300 Mbp) putative inversion potentially under selection, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out the need for more attention toward multi-locus analysis of polygenic adaptation.

Local thermal adaptation and limited gene flow constrain future climate responses of a marine ecosystem engineer

Rising ocean temperatures and extreme temperature events have precipitated declines and local extinctions in many marine species globally, but patterns of loss are often uneven across species ranges for reasons that are poorly understood. Knowledge of the extent of local adaptation and gene flow may explain such patterns and help predict future trajectories under scenarios of climate change. We test the extent to which local differentiation in thermal tolerance is influenced by gene flow and local adaptation using a widely distributed intertidal seaweed (Hormosira banksii) from temperate Australia. Population surveys across ~2,000 km of the species range revealed strong genetic structuring at regional and local scales (global F ST = 0.243) reflecting extremely limited gene flow, while common garden experiments (14-day exposures to 15, 18, 21°C) revealed strong site differences in early development and mortality in response to elevated temperature. Embryos from many sites spanning a longitudinal thermal gradient showed suppressed development and increased mortality to elevated water temperatures, but populations originating from warmer and more variable thermal environments tended to be less susceptible to warming. Notably, there was significant local-scale variation in the thermal responses of embryos within regions which was corroborated by the finding of small-scale genetic differences. We expect the observed genetic and phenotypic differentiation to lead to uneven responses to warming sea surface temperatures in this important marine foundation species. The study highlights the challenges of predicting species responses to thermal stress and the importance of management strategies that incorporate evolutionary potential for "climate-proofing" marine ecosystems.

A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia

Amazonia is a major world centre of plant domestication, but the genetics of domestication remains unclear for most Amazonian crops. Manioc (Manihot esculenta) is the most important staple food crop that originated in this region. Although manioc is relatively well-studied, little is known about the diversification of bitter and sweet landraces and how they were dispersed across Amazonia. We evaluated single nucleotide polymorphisms (SNPs) in wild and cultivated manioc to identify outlier SNPs putatively under selection and to assess the neutral genetic structure of landraces to make inferences about the evolution of the crop in Amazonia. Some outlier SNPs were in putative manioc genes possibly related to plant architecture, transcriptional regulation and responses to stress. The neutral SNPs revealed contrasting genetic structuring for bitter and sweet landraces. The outlier SNPs may be signatures of the genomic changes resulting from domestication, while the neutral genetic structure suggests independent dispersals for sweet and bitter manioc, possibly related to the earlier domestication and diversification of the former. Our results highlight the role of ancient peoples and current smallholders in the management and conservation of manioc genetic diversity, including putative genes and specific genetic resources with adaptive potential in the context of climate change.

Independent genetic control of drought resistance, recovery, and growth of Eucalyptus globulus seedlings

Drought is a major stress impacting forest ecosystems worldwide. We utilized quantitative trait loci (QTL) analysis to study the genetic basis of variation in (a) drought resistance and recovery and (b) candidate traits that may be associated with this variation in the forest tree Eucalyptus globulus. QTL analysis was performed using a large outcrossed F₂ mapping population from which 300 trees were phenotyped based on the mean performance of their open-pollinated F₃ progeny. Progenies were grown in a glasshouse in a randomized complete block design. A subset of seedlings was subjected to a drought treatment after which they were rewatered and scored for damage and growth postdrought. Nondroughted seedlings were assessed for growth traits as well as lignotuber size and resprouting following severe damage to the main stem. QTL were detected for most traits. Importantly, independent QTL were detected for (a) drought damage and plant size, (b) drought damage and growth recovery, and (c) lignotuber size and resprouting capacity. Such independence argues that trade-offs are unlikely to be a major limitation to the response to selection and at the early life history stage studied; there are opportunities to improve resilience to drought without adverse effects on productivity.

Temperature and Rainfall Are Separate Agents of Selection Shaping Population Differentiation in a Forest Tree

Research highlights: We present evidence indicating that covariation of functional traits among populations of a forest tree is not due to genetic constraints, but rather selective covariance arising from local adaptation to different facets of the climate, namely rainfall and temperature. Background and Aims: Traits frequently covary among natural populations. Such covariation can be caused by pleiotropy and/or linkage disequilibrium, but also may arise when the traits are genetically independent as a direct consequence of natural selection, drift, mutation and/or gene flow. Of particular interest are cases of selective covariance, where natural selection directly generates among-population covariance in a set of genetically independent traits. We here studied the causes of population-level covariation in two key traits in the Australian tree Eucalyptus pauciflora. Materials and Methods: We studied covariation in seedling lignotuber size and vegetative juvenility using 37 populations sampled from throughout the geographic and ecological ranges of E. pauciflora on the island of Tasmania. We integrated evidence from multiple sources: (i) comparison of patterns of trait covariation within and among populations; (ii) climate-trait modelling using machine-learning algorithms; and (iii) selection analysis linking trait variation to field growth in an arid environment. Results: We showed strong covariation among populations compared with the weak genetic correlation within populations for the focal traits. Population differentiation in these genetically independent traits was correlated with different home-site climate variables (lignotuber size with temperature; vegetative juvenility with rainfall), which spatially covaried. The role of selection in shaping the population differentiation in lignotuber size was supported by its relationship with fitness measured in the field. Conclusions: Our study highlights the multi-trait nature of adaptation likely to occur as tree species respond to spatial and temporal changes in climate.

Landscape drivers of genomic diversity and divergence in woodland Eucalyptus

Spatial genetic patterns are influenced by numerous factors, and they can vary even among coexisting, closely related species due to differences in dispersal and selection. Eucalyptus (L'Héritier 1789; the "eucalypts") are foundation tree species that provide essential habitat and modulate ecosystem services throughout Australia. Here we present a study of landscape genomic variation in two woodland eucalypt species, using whole-genome sequencing of 388 individuals of Eucalyptus albens and Eucalyptus sideroxylon. We found exceptionally high genetic diversity (π ≈ 0.05) and low genome-wide, interspecific differentiation (FST  = 0.15) and intraspecific differentiation between localities (FST  ≈ 0.01-0.02). We found no support for strong, discrete population structure, but found substantial support for isolation by geographic distance (IBD) in both species. Using generalized dissimilarity modelling, we identified additional isolation by environment (IBE). Eucalyptus albens showed moderate IBD, and environmental variables have a small but significant amount of additional predictive power (i.e. IBE). Eucalyptus sideroxylon showed much stronger IBD and moderate IBE. These results highlight the vast adaptive potential of these species and set the stage for testing evolutionary hypotheses of interspecific adaptive differentiation across environments.

How well do revegetation plantings capture genetic diversity?

Revegetation plantings are a key management tool for ecological restoration. Revegetation success is usually measured using ecological traits, however, genetic diversity should also be considered as it can influence fitness, adaptive capacity and long-term viability of revegetation plantings and ecosystem functioning. Here we review the global literature comparing genetic diversity in revegetation plantings to natural stands. Findings from 48 studies suggest variable genetic outcomes of revegetation, with 46% demonstrating higher genetic diversity in revegetation than natural stands and 52% demonstrating lower diversity. Levels of genetic diversity were most strongly associated with the number of source sites used-where information was available, 69% of studies showing higher genetic diversity in revegetation reported using multiple provenances, compared with only 33% for those with lower diversity. However, with a few exceptions, it was unclear whether differences in genetic diversity between revegetation and natural stands were statistically significant. This reflected insufficient reporting of statistical error and metadata within the published studies, which limited conclusions about factors contributing to patterns. Nonetheless, our findings indicate that mixed seed sourcing can contribute to higher genetic diversity in revegetation. Finally, we emphasize the type of metadata needed to determine factors influencing genetic diversity in revegetation and inform restoration efforts.

Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes

BACKGROUND

Although the sensory drive hypothesis can explain the geographic variation in echolocation frequencies of some bat species, the molecular mechanisms underlying this phenomenon are still unclear. The three lineages of greater horseshoe bat (Rhinolophus ferrumequinum) in China (northeast, central-east, and southwest) have significant geographic variation in resting frequencies (RF) of echolocation calls. Because their cochleae have an acoustic fovea that is highly sensitive to a narrow range of frequencies, we reported the transcriptomes of cochleae collected from three genetic lineages of R. ferrumequinum, which is an ideal organism for studying geographic variation in echolocation signals, and tried to understand the mechanisms behind this bat phenomenon by analyzing gene expression and sequence variation.

RESULTS

A total of 8190 differentially expressed genes (DEGs) were identified. We identified five modules from all DEGs that were significantly related to RF or forearm length (FL). DEGs in the RF-related modules were significantly enriched in the gene categories involved in neural activity, learning, and response to sound. DEGs in the FL-related modules were significantly enriched in the pathways related to muscle and actin functions. Using 21,945 single nucleotide polymorphisms, we identified 18 candidate unigenes associated with hearing, five of which were differentially expressed among the three populations. Additionally, the gene ERBB4, which regulates diverse cellular processes in the inner ear such as cell proliferation and differentiation, was in the largest module. We also found 49 unigenes that were under positive selection from 4105 one-to-one orthologous gene pairs between the three R. ferrumequinum lineages and three other Chiroptera species.

CONCLUSIONS

The variability of gene expression and sequence divergence at the molecular level might provide evidence that can help elucidate the genetic basis of geographic variation in echolocation signals of greater horseshoe bats.

Landscape genetics reveals that adaptive genetic divergence in Pinus bungeana (Pinaceae) is driven by environmental variables relating to ecological habitats

Background

Understanding the genetic basis of local adaptation has long been the concern of biologists. Identifying these adaptive genetic variabilities is crucial not only to improve our knowledge of the genetic mechanism of local adaptation but also to explore the adaptation potential of species.

Results

Using 10 natural populations and 12 start codon targeted (SCoT) markers, a total of 430 unambiguous loci were yielded. The Bayesian analysis of population structure clearly demonstrated that the 10 populations of P. bungeana could be subdivided into three groups. Redundancy analysis showed that this genetic divergence was caused by divergence selection from environmental variables related to the ecological habitats of “avoidance of flooding” and “avoidance of high temperature and humidity.” LFMM results indicated that Bio1, Bio5, Bio8, Bio12, Bio14, and Bio16, which are related to the ecological habitat of P. bungeana, were correlated with the highest numbers of environment-associated loci (EAL).

Conclusions

The results of EAL characterization in P. bungeana clearly supported the hypothesis that environmental variations related to the ecological habitat of species are the key drivers of species adaptive divergence. Moreover, a method to calculate the species landscape adaptation index and quantify the adaptation potential of species was proposed and verified using ecological niche modeling. This model could estimate climatically suitable areas of species spatial distribution. Taking the results together, this study improves the current understanding on the genetic basis of local adaptation.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1489-x) contains supplementary material, which is available to authorized users.

Evolutionary epidemiology predicts the emergence of glyphosate resistance in a major agricultural weed

The evolution of resistance to herbicides is a striking example of rapid, human-directed adaptation with major consequences for food production. Most studies of herbicide resistance are performed reactively and focus on post hoc determination of resistance mechanisms following the evolution of field resistance. If the evolution of resistance can be anticipated, however, pro-active management to slow or prevent resistance traits evolving can be advocated. We report a national-scale study that combines population monitoring, glyphosate sensitivity assays, quantitative genetics and epidemiological analyses to pro-actively identify the prerequisites for adaptive evolution (directional selection and heritable genetic variation) to the world's most widely used herbicide (glyphosate) in a major, economically damaging weed species, Alopecurus myosuroides. Results highlighted pronounced, heritable variability in glyphosate sensitivity amongst UK A. myosuroides populations. We demonstrated a direct epidemiological link between historical glyphosate selection and current population-level sensitivity, and show that current field populations respond to further glyphosate selection. This study provides a novel, pro-active assessment of adaptive potential for herbicide resistance, and provides compelling evidence of directional selection for glyphosate insensitivity in advance of reports of field resistance. The epidemiological approach developed can provide a basis for further pro-active study of resistance evolution across pesticide resistance disciplines.

Safety margins and adaptive capacity of vegetation to climate change

Vegetation is composed of many individual species whose climatic tolerances can be integrated into spatial analyses of climate change risk. Here, we quantify climate change risk to vegetation at a continental scale by calculating the safety margins for warming and drying (i.e., tolerance to projected change in temperature and precipitation respectively) across plants sharing 100 km × 100 km grid cells (locations). These safety margins measure how much warmer, or drier, a location could become before its 'typical' species exceeds its observed climatic limit. We also analyse the potential adaptive capacity of vegetation to temperature and precipitation change (i.e., likelihood of in situ persistence) using median precipitation and temperature breadth across all species in each location. 47% of vegetation across Australia is potentially at risk from increases in mean annual temperature (MAT) by 2070, with tropical regions most vulnerable. Vegetation at high risk from climate change often also exhibited low adaptive capacity. By contrast, 2% of the continent is at risk from reductions in annual precipitation by 2070. Risk from precipitation change was isolated to the southwest of Western Australia where both the safety margin for drier conditions in the typical species is low, and substantial reductions in MAP are projected.

Standing genomic variation within coding and regulatory regions contributes to the adaptive capacity to climate in a foundation tree species

Global climate is rapidly changing, and the ability for tree species to adapt is dependent on standing genomic variation; however, the distribution and abundance of functional and adaptive variants are poorly understood in natural systems. We test key hypotheses regarding the genetics of adaptive variation in a foundation tree: genomic variation is associated with climate, and genomic variation is more likely to be associated with temperature than precipitation or aridity. To test these hypotheses, we used 9,593 independent, genomic single-nucleotide polymorphisms (SNPs) from 270 individuals sampled from Corymbia calophylla's entire distribution in south-western Western Australia, spanning orthogonal temperature and precipitation gradients. Environmental association analyses returned 537 unique SNPs putatively adaptive to climate. We identified SNPs associated with climatic variation (i.e., temperature [458], precipitation [75] and aridity [78]) across the landscape. Of these, 78 SNPs were nonsynonymous (NS), while 26 SNPs were found within gene regulatory regions. The NS and regulatory candidate SNPs associated with temperature explained more deviance (27.35%) than precipitation (5.93%) and aridity (4.77%), suggesting that temperature provides stronger adaptive signals than precipitation. Genes associated with adaptive variants include functions important in stress responses to temperature and precipitation. Patterns of allelic turnover of NS and regulatory SNPs show small patterns of change through climate space with the exception of an aldehyde dehydrogenase gene variant with 80% allelic turnover with temperature. Together, these findings provide evidence for the presence of adaptive variation to climate in a foundation species and provide critical information to guide adaptive management practices.

Pervasive admixture between eucalypt species has consequences for conservation and assisted migration

Conservation management often uses information on genetic population structure to assess the importance of local provenancing for ecological restoration and reintroduction programs. For species that do not exhibit complete reproductive isolation, the estimation of population genetic parameters may be influenced by the extent of admixture. Therefore, to avoid perverse outcomes for conservation, genetically informed management strategies must determine whether hybridization between species is relevant, and the extent to which observed population genetic patterns are shaped by interspecific versus intraspecific gene flow. We used genotyping by sequencing to identify over 2,400 informative single nucleotide polymorphisms across 18 populations of Eucalyptus regnans F. Muell., a foundation tree species of montane forests in south-eastern Australia. We used these data to determine the extent of hybridization with another species, Eucalyptus obliqua L'Hér., and investigate how admixture influences genetic diversity parameters, by estimating metrics of genetic diversity and examining population genetic structure in datasets with and without admixed individuals. We found hybrid individuals at all sites and two highly introgressed populations. Hybrid individuals were not distributed evenly across environmental gradients, with logistic regression identifying hybrids as being associated with temperature. Removal of hybrids resulted in increases in genetic differentiation (F ST), expected heterozygosity, observed heterozygosity and the inbreeding coefficient, and different patterns of isolation by distance. After removal of hybrids and introgressed populations, mountain ash showed very little population genetic structure, with a small effect of isolation by distance, and very low global F ST(0.03). Our study shows that, in plants, decisions around provenancing of individuals for restoration depend on knowledge of whether hybridization is influencing population genetic structure. For species in which most genetic variation is held within populations, there may be little benefit in planning conservation strategies around environmental adaptation of seed sources. The possibility for adaptive introgression may also be relevant when species regularly hybridize.