Understanding plant responses to temperature is critical for predicting their vulnerability to global warming and for planning management responses. Germination is a key life-stage, strongly regulated by temperature, that affects the potential for plant populations to persist. Here, we compared the thermal germination niches of three unrelated, declining woodland forb species - Arthropodium fimbriatum (Asparagaceae), Bulbine bulbosa (Asphodelaceae), Microseris walteri (Asteraceae) - across common temperature and precipitation gradients, to characterize the relationships with home-site climate, and associated implications for ecological restoration in a changing climate. Open-pollinated seed were sampled from 14-15 populations per species across an aridity gradient in south-eastern Australia. Germination responses for each population were tested in controlled temperature cabinets under five temperature regimes encompassing contemporary and projected future temperatures. Optimum germination temperature and thermal germination niche were characterized and assessed for associations with home-site climate and potential germination under projected climate change. The three species showed significant intra-specific variation in the thermal germination niche. Optimum germination temperature was correlated with home-site climate, suggesting adaptive variation among populations in germination requirements. However, the pattern of variation in optimum germination across the environmental gradients was not always consistent among the species. Future temperatures projected under climate change tended to be outside the current thermal germination niche for all species, indicating potential benefits of incorporating pre-adapted populations in ecological restoration. Climate-related intra-specific variation in the thermal germination niche provides evidence for local adaptation to climate in all three forb species and suggests potential differences among populations in vulnerability to global warming. These results emphasize the importance of understanding the extent of intra-specific variation in key life history traits to better manage and conserve populations and restore their ecosystems as climates change.

In plants where seed dispersal is limited compared with pollen dispersal, hybridisation may enhance gene exchange and species dispersal. We provide genetic evidence of hybridisation contributing to the expansion of the rare Eucalyptus risdonii into the range of the widespread Eucalyptus amygdalina. These closely related tree species are morphologically distinct, and observations suggest that natural hybrids occur along their distribution boundaries and as isolated trees or in small patches within the range of E. amygdalina. Hybrid phenotypes occur outside the range of normal dispersal for E. risdonii seed, yet in some hybrid patches small individuals resembling E. risdonii occur and are hypothesised to be a result of backcrossing. Using 3362 genome-wide SNPs assessed from 97 individuals of E. risdonii and E. amygdalina and 171 hybrid trees, we show that (i) isolated hybrids match the genotypes expected of F1 /F2 hybrids, (ii) there is a continuum in the genetic composition among the isolated hybrid patches from patches dominated by F1 /F2 -like genotypes to those dominated by E. risdonii-backcross genotypes, and (iii) the E. risdonii-like phenotypes in the isolated hybrid patches are most-closely related to proximal larger hybrids. These results suggest that the E. risdonii phenotype has been resurrected in isolated hybrid patches established from pollen dispersal, providing the first steps in its invasion of suitable habitat by long-distance pollen dispersal and complete introgressive displacement of E. amygdalina. Such expansion accords with the population demographics, common garden performance data, and climate modelling which favours E. risdonii and highlights a role of interspecific hybridisation in climate change adaptation and species expansion.

Habitat loss and fragmentation are critical threats to biodiversity. Consequent decreases in population size and connectivity can impact genetic diversity and, thus, future adaptability and resilience to environmental change. Understanding landscape patterns of genetic diversity, including patterns of adaptive variation, can assist in developing conservation strategies that maximise population persistence and adaptability in the face of environmental change. Using a reduced-representation genomic approach, we investigated genetic diversity, structure, and adaptive variation across an aridity gradient in the woodland forb Arthropodium fimbriatum . Moderate levels of genetic diversity ( H S = 0.14–0.23) were found in all 13 sampled provenances. Inbreeding varied among provenances ( F IS = 0.08–0.42) but was not associated with estimated population size. Four genetic clusters were identified, including one highly differentiated cluster. Higher pairwise F ST (0.23–0.42) between the three provenances of this cluster and the remaining 10 provenances (pairwise F ST between 10 provenances 0.02–0.32) suggested two highly divergent lineages or potentially a cryptic species. After excluding the three highly differentiated populations, outlier and genotype-environment association analysis identified 275 putatively adaptive loci suggesting genomic signatures of climate adaptation in A. fimbriatum is primarily associated with changes in aridity. Combined, these results suggest that all provenances have conservation value, contributing to the maintenance of genetic diversity and adaptive variation in this species. The uncovering of a potential cryptic taxon highlights the power of genomics approaches in conservation genetics and the importance of understanding the role of landscape variation shaping genetic variation to effectively define conservation management units in an era of rapid biodiversity decline.

Eucalypts are of great ecological and economic importance. They dominate many woodland and forest landscapes in Australia and are planted in temperate to tropical areas worldwide for forestry. Population genomics research in eucalypts builds on a long history of genetics research, from quantitative trait analysis of field provenance trials to modern molecular genetics studies exploring neutral variation and population structure. It is backed by a high-quality reference genome and, whilst this rapidly expanding field is still in its infancy, it is already providing new insights into both ecological and industry-focused applications. This chapter reviews population genomics research in eucalypts, in the context of past genetics research. After describing the genomic resources available for eucalypts, we show that genomics is enabling greater resolution than ever before of species boundaries and patterns of hybridisation. Landscape genomics studies have revealed various patterns of population structure in natural populations, cryptic lineages within species and low divergence between closely related species. Genomic signatures of adaptation have been identified in several species, highlighting both climatic and edaphic factors as potential drivers of adaptation. In investigating the genetic architecture underlying complex traits, genomic tools are revealing not only associations with genes but also associations with differences in gene expression. With their worldwide importance, eucalypts are at the forefront of developments for integrating genomics into models for the genetic evaluation of forest tree breeding populations. Into the future, an increasing number of population genomics studies of eucalypts will help develop our understanding of the evolution of the genus; how species adapted to varied and changing environments; and the genetic architecture underlying adaptation and complex traits. Such knowledge will help guide species and provenance choices for conservation and ecological restoration under environmental change and will provide a valuable resource to breeding for forestry.

BACKGROUND AND AIMS:Hybridization is increasingly recognized as an integral part of the dynamics of species range expansion and contraction. Thus, it is important to understand the reproductive barriers between co-occurring species. Extending previous studies that argued that the rare Eucalyptus risdonii was expanding into the range of the surrounding E. amygdalina by both seed and pollen dispersal, we here investigate the long-term fitness of both species and their hybrids and whether expansion is continuing.METHODS:We assessed the survival of phenotypes representing a continuum between the two pure species in a natural hybrid swarm after 29 years, along with seedling recruitment. The performance of pure species as well as of artificial and natural hybrids was also assessed over 28 years in a common garden trial.KEY RESULTS:In the hybrid zone, E. amygdalina adults showed greater mortality than E. risdonii, and the current seedling cohort is still dominated by E. risdonii phenotypes. Morphologically intermediate individuals appeared to be the least fit. Similar results were observed after growing artificial first-generation and natural hybrids alongside pure species families in a common garden trial. Here, the survival, reproduction, health and growth of the intermediate hybrids were significantly less than those of either pure species, consistent with hybrid inferiority, although this did not manifest until later reproductive ages. Among the variable progeny of natural intermediate hybrids, the most E. risdonii-like phenotypes were the most fit.CONCLUSIONS:This study contributes to the increasing number of reports of hybrid inferiority in Eucalyptus, suggesting that post-zygotic barriers contribute to the maintenance of species integrity even between closely related species. However, with fitness rapidly recovered following backcrossing, it is argued that hybridization can still be an important evolutionary process, in the present case appearing to contribute to the range expansion of the rare E. risdonii in response to climate change.

With climate change impacting trees worldwide, enhancing adaptation capacity has become an important goal of provenance translocation strategies for forestry, ecological renovation, and biodiversity conservation. Given that not every species can be studied in detail, it is important to understand the extent to which climate adaptation patterns can be generalised across species, in terms of the selective agents and traits involved. We here compare patterns of genetic-based population (co)variation in leaf economic and hydraulic traits, climate–trait associations, and genomic differentiation of two widespread tree species (Eucalyptus pauciflora and E. ovata). We studied 2-year-old trees growing in a common-garden trial established with progeny from populations of both species, pair-sampled from 22 localities across their overlapping native distribution in Tasmania, Australia. Despite originating from the same climatic gradients, the species differed in their levels of population variance and trait covariance, patterns of population variation within each species were uncorrelated, and the species had different climate–trait associations. Further, the pattern of genomic differentiation among populations was uncorrelated between species, and population differentiation in leaf traits was mostly uncorrelated with genomic differentiation. We discuss hypotheses to explain this decoupling of patterns and propose that the choice of seed provenances for climate-based plantings needs to account for multiple dimensions of climate change unless species-specific information is available.

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.

Abstract Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, cryptic taxa are often criticized because they are typically detected serendipitously and may not receive the follow‐up study required to verify their geographic or evolutionary limits. Here, we follow‐up a study of Eucalyptus salubris that unexpectedly detected two divergent lineages but was not sampled sufficiently to make clear interpretations. We undertook comprehensive sampling for an independent genomic analysis (3,605 SNPs) to investigate whether the two purported lineages remain discrete genetic entities or if they intergrade throughout the species’ range. We also assessed morphological and ecological traits, and sequenced chloroplast DNA. SNP results showed strong genome‐wide divergence (F ST = 0.252) between two discrete lineages: one dominated the north and one the southern regions of the species’ range. Within lineages, gene flow was high, with low differentiation (mean F ST = 0.056) spanning hundreds of kilometers. In the central region, the lineages were interspersed but maintained their genomic distinctiveness: an indirect demonstration of reproductive isolation. Populations of the southern lineage exhibited significantly lower specific leaf area and occurred on soils with lower phosphorus relative to the northern lineage. Finally, two major chloroplast haplotypes were associated with each lineage but were shared between lineages in the central distribution. Together, these results suggest that these lineages have non‐contemporary origins and that ecotypic adaptive processes strengthened their divergence more recently. We conclude that these lineages warrant taxonomic recognition as separate species and provide fascinating insight into eucalypt speciation.

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.

We overview an array of common garden genetics trials established across multiple sites and embedded in restoration plantings in the harsh, modified Midlands region of the island of Tasmania, Australia. The steps in establishing the common gardens, the diversity of experimental designs employed and their objectives are described. These trials provide a long-term framework to test species choices and provenancing strategies, as well as enhance our understanding of adaptive genetic variation within key eucalypt species used for ecological restoration. Early results signal genetic-based differences in early-age performance, and we showcase the multiple benefits of integrating research infrastructure into restoration plantings.

Eucalyptus globulus is native to southeastern Australia, including the island of Tasmania, but is one of the most widely grown hardwood forestry species in the world and is naturalized on several continents. We studied its naturalization in California, where the species has been planted for over 150 years. We sampled 70 E. globulus trees from 53 locations spanning the entire range of the species in California to quantify the genetic variation present and test whether particular genotypes or native origin affect variation in naturalization among locations. Diversity and native affinities were determined based on six nuclear microsatellite markers and sequences from a highly variable chloroplast DNA region (JLA+). The likely native origin was determined by DNA-based comparison with a range-wide native stand collection. Most of California’s E. globulus originated from eastern Tasmania. Genetic diversity in California is greatly reduced compared with that of the native Australian population, with a single chloroplast haplotype occurring in 66% of the Californian samples. Throughout California, the degree of E. globulus naturalization varies widely but was not associated with genotype or native origin of the trees, arguing that factors such as local climate and disturbance are more important than pre-introduction evolutionary history.

AbstractGenotype-environment association (GEA) methods have become part of the standard landscape genomics toolkit, yet, we know little about how to 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. These effects could be amplified in downstream predictions, including management strategies. Here, we investigate the effects of filtering on GEA results and the potential implications for adaptation to environment. Using empirical and simulated datasets 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 dataset, lessening the power to detect adaptive variants (i.e. simulated true positives) with strong and weak strength of selections. Regardless, strength of selection was a good predictor for GEA detection, but even SNPs under strong selection went undetected. We further show that filtering can significantly impact the predictions of adaptive capacity of species 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 largely on the study system, availability of genomic resources, and desired objectives of the study.

Billions of hectares of natural ecosystems have been degraded through human actions. The global community has agreed on targets to halt and reverse these declines, and the restoration sector faces the important but arduous task of implementing programmes to meet these objectives. Existing and emerging genomics tools offer the potential to improve the odds of achieving these targets. These tools include population genomics that can improve seed sourcing, meta-omics that can improve assessment and monitoring of restoration outcomes, and genome editing that can generate novel genotypes for restoring challenging environments. We identify barriers to adopting these tools in a restoration context and emphasize that regulatory and ethical frameworks are required to guide their use.

As climates change, restoration programmes need to maximize the capacity of regenerating ecosystems to adapt to new environments, particularly when planting long-lived trees. By using a combined phenotypic and genomic approach, we assessed evidence of adaptation capacity in Eucalyptus loxophleba ssp. lissophloia, a mallee eucalypt important for restoration and oil production in Western Australia. Assessment of leaf traits in nine wild populations across a rainfall gradient showed that two traits were correlated with long-term moisture availability. Populations in more arid environments had lower specific leaf area and lower stomatal conductance, consistent with a stable plastic or adaptive response. Other leaf size and shape traits were correlated with short-term climate variables, suggesting a dynamic plastic response. Genome-wide scans with 4851 DArTseq markers and outlier analysis detected 50 markers showing signals of disruptive selection, consistent with local adaptation. Sixteen markers showed allele frequencies correlated with aridity; three were also associated with differences in stomatal conductance. Multivariate analysis and marker-environment associations signalled secondary directions of adaptation associated with maximum temperatures and soil phosphorus. We suggest that adaptation and acclimation are both likely determinants of functional phenotype in E. loxophleba, and argue that aridity is a critical driver of adaptation in this widespread species.

Transects that traverse substantial climate gradients are important tools for climate change research and allow questions on the extent to which phenotypic variation associates with climate, the link between climate and species distributions, and variation in sensitivity to climate change among biomes to be addressed. However, the potential limitations of individual transect studies have recently been highlighted. Here, we argue that replicating and networking transects, along with the introduction of experimental treatments, addresses these concerns. Transect networks provide cost-effective and robust insights into ecological and evolutionary adaptation and improve forecasting of ecosystem change. We draw on the experience and research facilitated by the Australian Transect Network to demonstrate our case, with examples, to clarify how population- and community-level studies can be integrated with observations from multiple transects, manipulative experiments, genomics, and ecological modeling to gain novel insights into how species and systems respond to climate change. This integration can provide a spatiotemporal understanding of past and future climate-induced changes, which will inform effective management actions for promoting biodiversity resilience.

Widespread species spanning strong environmental (e.g., climatic) gradients frequently display morphological and physiological adaptations to local conditions. Some adaptations are common to different species that occupy similar environments. However, the genomic architecture underlying such convergent traits may not be the same between species. Using genomic data from previous studies of three widespread eucalypt species that grow along rainfall gradients in southern Australia, our probabilistic approach provides evidence that adaptation to aridity is a genome-wide phenomenon, likely to involve multiple and diverse genes, gene families and regulatory regions that affect a multitude of complex genetic and biochemical processes.

Eucalyptus globulus subsp. globulus Labill. (Tasmanian Blue Gum), native to southeast Australia, is a benchmark species for the pulp and paper industry. We genotyped 397 trees from 16 populations of E. globulus representing the native diversity in Australia using 24 microsatellite loci. Eight genetically distinct groups were detected, consistent with genetic groupings detected in previous quantitative and molecular studies. A sample of 29 Portuguese individuals was added to help clarify the origin of the Portuguese landrace. The results suggest a southern and eastern Tasmania origin for the Portuguese landrace. This genetic framework will enable researchers to investigate the provenance of individuals of unknown pedigree and assess the levels of representation of E. globulus natural variation in the Portuguese landrace.

Eucalypts are the cornerstone of ecological restoration efforts across the highly modified agricultural landscapes of southern Australia. ‘Local provenancing’ is the established strategy for sourcing germplasm for ecological restoration plantings, yet this approach gives little consideration to the persistence of these plantings under future climates. This paper provides a synopsis of recent and ongoing research that the authors are undertaking on climate adaptation in eucalypts, combining new genomic approaches with ecophysiological evidence from provenance trials. These studies explore how adaptive diversity is distributed within and among populations, whether populations are buffered against change through capacity for phenotypic plasticity, and how this informs provenancing strategies. Results to date suggest that eucalypts have some capacity to respond to future environmental instability through adaptive phenotypic plasticity or selection of putatively adaptive alleles. Despite this, growing evidence suggests that eucalypts will still be vulnerable to change. Provenancing strategies that exploit adaptations found in non-local provenances could thus confer greater climate-resilience in ecological restoration plantings, although they will also need to account for potential interactions between climate adaptations and other factors (e.g. cryptic evolutionary variation, non-climate-related adaptations, herbivory and elevated CO2).

Most eucalypts are endemic to Australia but they have been introduced into more than 100 countries and there are now over 20 million hectares of eucalypt plantations globally. These plantations are grown mainly for pulpwood but there is expanding interest in their use as a renewable source of solid wood products and energy. In Australia, the eucalypt plantation estate is nearing one million hectares, located mainly in temperate regions and dominated by Eucalyptus globulus and E. nitens (subgenus Symphyomyrtus), which are grown mainly outside their natural ranges. While eucalypt species from different major subgenera do not hybridise, hybrids within subgenera are often reported, including hybrids with plantation species. Concerns were raised in the late 1990s that pollen-mediated gene flow from locally exotic plantation eucalypts may affect the integrity of adjacent native eucalypt gene pools. As Australia is the centre-of-origin of most eucalypt species used in plantations around the world, exotic gene flow is one of the many issues that require management for industry sustainability and certification purposes. We here summarise over a decade of research aimed at providing the framework and biological data to help assess and manage the risk of gene flow from these plantations into native gene pools in Australia.

We used genome-wide markers and an unprecedented scale of sampling to construct a phylogeny for a globally significant Eucalyptus lineage that has been impacted by hybridisation, recent radiation and morphological convergence. Our approach, using 3109 DArT markers distributed throughout the genome and 540 samples covering 185 terminal taxa in sections Maidenaria, Exsertaria, Latoangulatae and related smaller sections, with multiple geographically widespread samples per terminal taxon, produced a phylogeny that largely matched the morphological treatment of sections, though sections Exsertaria and Latoangulatae were polyphyletic. At lower levels there were numerous inconsistencies between the morphological treatment and the molecular phylogeny, and taxa within the three main sections were generally not monophyletic at the series (at least 62% polyphyly) or species (at least 52% polyphyly) level. Some of the discrepancies appear to be the result of morphological convergence or misclassifications, and we propose some taxonomic reassessments to address this. However, many inconsistencies appear to be the products of incomplete speciation and/or hybridisation. Our analysis represents a significant advance on previous phylogenies of these important eucalypt sections (which have mainly used single samples to represent each species), thus providing a robust phylogenetic framework for evolutionary and ecological studies.