Genetic diversity ofEucalyptus camaldulensis Dehnh. following population decline in response to drought and altered hydrological regime

Aridity drives clinal patterns in leaf traits and responsiveness to precipitation in a broadly distributed Australian tree species

Aridity shapes species distributions and plant growth and function worldwide. Yet, plant traits often show complex relationships with aridity, challenging our understanding of aridity as a driver of evolutionary adaptation. We grew nine genotypes of Eucalyptus camaldulensis subsp. camaldulensis sourced from an aridity gradient together in the field for ~650 days under low and high precipitation treatments. Eucalyptus camaldulesis is considered a phreatophyte (deep-rooted species that utilizes groundwater), so we hypothesized that genotypes from more arid environments would show lower aboveground productivity, higher leaf gas-exchange rates, and greater tolerance/avoidance of dry surface soils (indicated by lower responsiveness) than genotypes from less arid environments. Aridity predicted genotype responses to precipitation, with more arid genotypes showing lower responsiveness to reduced precipitation and dry surface conditions than less arid genotypes. Under low precipitation, genotype net photosynthesis and stomatal conductance increased with home-climate aridity. Across treatments, genotype intrinsic water-use efficiency and osmotic potential declined with increasing aridity while photosynthetic capacity (Rubisco carboxylation and RuBP regeneration) increased with aridity. The observed clinal patterns indicate that E. camaldulensis genotypes from extremely arid environments possess a unique strategy defined by lower responsiveness to dry surface soils, low water-use efficiency, and high photosynthetic capacity. This strategy could be underpinned by deep rooting and could be adaptive under arid conditions where heat avoidance is critical and water demand is high.

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.

Photosynthesis and carbon allocation are both important predictors of genotype productivity responses to elevated CO2 in Eucalyptus camaldulensis

Intraspecific variation in biomass production responses to elevated atmospheric carbon dioxide (eCO2) could influence tree species' ecological and evolutionary responses to climate change. However, the physiological mechanisms underlying genotypic variation in responsiveness to eCO2 remain poorly understood. In this study, we grew 17 Eucalyptus camaldulensis Dehnh. subsp. camaldulensis genotypes (representing provenances from four different climates) under ambient atmospheric CO2 and eCO2. We tested whether genotype leaf-scale photosynthetic and whole-tree carbon (C) allocation responses to eCO2 were predictive of genotype biomass production responses to eCO2. Averaged across genotypes, growth at eCO2 increased in situ leaf net photosynthesis (Anet) (29%) and leaf starch concentrations (37%). Growth at eCO2 reduced the maximum carboxylation capacity of Rubisco (-4%) and leaf nitrogen per unit area (Narea, -6%), but Narea calculated on a total non-structural carbohydrate-free basis was similar between treatments. Growth at eCO2 also increased biomass production and altered C allocation by reducing leaf area ratio (-11%) and stem mass fraction (SMF, -9%), and increasing leaf mass area (18%) and leaf mass fraction (5%). Overall, we found few significant CO2 × provenance or CO2 × genotype (within provenance) interactions. However, genotypes that showed the largest increases in total dry mass at eCO2 had larger increases in root mass fraction (with larger decreases in SMF) and photosynthetic nitrogen-use efficiency (PNUE) with CO2 enrichment. These results indicate that genetic differences in PNUE and carbon sink utilization (in roots) are both important predictors of tree productivity responsiveness to eCO2.

Relationships between climate of origin and photosynthetic responses to an episodic heatwave depend on growth CO2 concentration for Eucalyptus camaldulensis var. camaldulensis

Stressful episodic weather is likely to affect the C balance of trees as the climate changes, potentially altering survival. However, the role of elevated CO2 concentration ([CO2]) in tolerating off-season episodic extremes is not clear. We tested for interactive effects of elevated CO2 and springtime heat stress on photosynthesis for seven genotypes of Eucalyptus camaldulensis Dehnh. var. camaldulensis, representing its widespread distribution across south-eastern Australia. We grew clonal material under glasshouse conditions of ambient (aCO2; 400 parts per million (ppm)) or elevated (eCO2; 640ppm) [CO2], and air temperatures of 25:17°C (day:night), and measured the electron transport rate in PSII (ETR), stomatal conductance to water vapour (gs) and net CO2 assimilation (A). Measurements were made before, during and after a four-day temperature excursion of 35:27°C. ETR and A were ~17% higher for plants grown in eCO2 than in aCO2. Photosynthesis remained stable for plants in eCO2 during the heatwave. Based on the effect size ratio (eCO2:aCO2), gs and ETR were temporarily affected more by the heatwave than A. A reduction in ETR in eCO2 was the only lasting effect of the heatwave. There were no significant differences among genotypes. Correlations between photosynthesis and climate of origin differed for plants grown in aCO2 compared with eCO2, suggesting potential complex and multiple control points on photosynthesis.

Genomic diversity guides conservation strategies among rare terrestrial orchid species when taxonomy remains uncertain

BACKGROUND AND AIMS

Species are often used as the unit for conservation, but may not be suitable for species complexes where taxa are difficult to distinguish. Under such circumstances, it may be more appropriate to consider species groups or populations as evolutionarily significant units (ESUs). A population genomic approach was employed to investigate the diversity within and among closely related species to create a more robust, lineage-specific conservation strategy for a nationally endangered terrestrial orchid and its relatives from south-eastern Australia.

METHODS

Four putative species were sampled from a total of 16 populations in the Victorian Volcanic Plain (VVP) bioregion and one population of a sub-alpine outgroup in south-eastern Australia. Morphological measurements were taken in situ along with leaf material for genotyping by sequencing (GBS) and microsatellite analyses.

KEY RESULTS

Species could not be differentiated using morphological measurements. Microsatellite and GBS markers confirmed the outgroup as distinct, but only GBS markers provided resolution of population genetic structure. The nationally endangered Diuris basaltica was indistinguishable from two related species ( D. chryseopsis and D. behrii ), while the state-protected D. gregaria showed genomic differentiation.

CONCLUSIONS

Genomic diversity identified among the four Diuris species suggests that conservation of this taxonomically complex group will be best served by considering them as one ESU rather than separately aligned with species as currently recognized. This approach will maximize evolutionary potential among all species during increased isolation and environmental change. The methods used here can be applied generally to conserve evolutionary processes for groups where taxonomic uncertainty hinders the use of species as conservation units.

Landscape genomics reveals altered genome wide diversity within revegetated stands of Eucalyptus microcarpa (Grey Box)

In order to contribute to evolutionary resilience and adaptive potential in highly modified landscapes, revegetated areas should ideally reflect levels of genetic diversity within and across natural stands. Landscape genomic analyses enable such diversity patterns to be characterized at genome and chromosomal levels. Landscape-wide patterns of genomic diversity were assessed in Eucalyptus microcarpa, a dominant tree species widely used in revegetation in Southeastern Australia. Trees from small and large patches within large remnants, small isolated remnants and revegetation sites were assessed across the now highly fragmented distribution of this species using the DArTseq genomic approach. Genomic diversity was similar within all three types of remnant patches analysed, although often significantly but only slightly lower in revegetation sites compared with natural remnants. Differences in diversity between stand types varied across chromosomes. Genomic differentiation was higher between small, isolated remnants, and among revegetated sites compared with natural stands. We conclude that small remnants and revegetated sites of our E. microcarpa samples largely but not completely capture patterns in genomic diversity across the landscape. Genomic approaches provide a powerful tool for assessing restoration efforts across the landscape.