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 (FST), 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 FST(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.Australian Research Council, Grant/Award Number: FT13010004

Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow

Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant ‘islands’. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which ‘islands’ of habitat are most in need of management and protection

The genetic and demographic impacts of contemporary disturbance regimes in mountain ash forests

Timber harvesting, frequent wildfires and a changing climate are influencing ecosystem composition, structure and function globally, with resulting losses to biodiversity and economic indicators. In south-eastern Australia, these factors are causing the rapid ecosystem collapse of montane forests. Here, I characterise and quantify the demographic and genetic impacts that changing environments are having on mountain ash (Eucalyptus regnans), a foundation species and one of the world's tallest trees. To test whether mountain ash populations exhibit variation in susceptibility to increasing fire frequency, I investigated the response of growth rates and seed production to stand age under different environmental conditions. My results show that environmental factors determine the age of maturation, in turn affecting the time taken for populations to develop reproductively viable amounts of seed. This suggests that reduced fire return intervals may result in niche contractions of obligate seeders such as mountain ash. Next, I conducted a range-wide analysis of mountain ash population genetic structure to determine the extent of hybridisation with messmate stringybark (Eucalyptus obliqua), and investigate how genetic diversity parameters are influenced by hybridisation. I found that hybrid occurrence was not distributed evenly across environmental gradients or populations, and after accounting for admixture, mountain ash showed very little population genetic structure, with a small effect of isolation-by-distance and low global FST (0.03). This suggests that decisions around provenancing for restoration may depend on knowledge of how admixture influences population genetic structure, and that for some species there may be little benefit in planning conservation strategies around environmental adaptation of seed sources. Fire and silvicultural practices may be modifying patterns of within- and among-population genetic diversity and fine-scale spatial genetic structure, across a mountain ash-dominated landscape. As chloroplast DNA and nuclear DNA are dispersed via different mechanisms, manual sowing of logged sites using non-local seed is likely to have differing effects on these two genomes. To test this, I utilised chloroplast microsatellites and genome-wide single-nucleotide polymorphisms to compare genetic parameters between undisturbed, burnt, and logged stands. The patterns and extent of genetic diversity and genetic differentiation among stands at nuclear loci were similar among disturbance histories, but chloroplast microsatellites revealed significantly higher levels of genetic diversity in logged stands. This suggests that logging is having minor impacts on the nuclear genome but large impacts on the chloroplast genome, with haplotypes entering the system via the use of non-local seed in the regeneration process. Understanding patterns and drivers of local adaptation is important for conservation management of foundation species. I investigated the genome of mountain ash for signatures of local adaptation at a regional and range-wide spatial scale, using three methods at each scale to identify outlier loci. I found 40 loci that were significantly associated with environmental variables, and demonstrate that investigation of multiple spatial scales provides a greater understanding of local adaptation. This thesis provides novel insights into impacts that modified disturbance regimes have on mountain ash populations. I found geographic variation in vital rates; genetic patterns suggestive of low recolonisation ability; high levels potential adaptive capacity; high potential for adaptive introgression; and identified loci showing signs of local adaptation. Importantly, this knowledge will assist with the conservation management of foundation tree species and forest ecosystems, contributing to the maintenance and/or maximisation of adaptive capacity and allowing forests to persist into a changing and uncertain future

Environmental influences on growth and reproductive maturation of a keystone forest tree: Implications for obligate seeder susceptibility to frequent fire

Anthropogenic modifications to climate and natural fire regimes are occurring globally, leading to the production of environments that may be unsuitable for some species. Fire-intolerant plant species that rely on specific fire regimes for reproduction are at risk of population decline when successive fires occur in less than the time taken to produce seed. Quantifying key fire-related life history traits in such species is therefore critical for developing models of population viability, species distributions and ecosystem persistence. We studied the Australian mountain ash (Eucalyptus regnans), the world's tallest angiosperm and an ecologically and economically important keystone species. We tested whether mountain ash populations exhibit variation in susceptibility to increasing fire frequency by characterising the response of key vital rates to stand age (time since fire) under different environmental conditions. We found that the time taken to produce seed varied geographically. Mean growth rates were greater in areas receiving higher levels of solar radiation, a trend that became stronger with tree age. Tree size and age had the strongest influence on the production of fruit capsules. Mature fruit capsules were found in trees as young as 11 years old, but stands may not contain reproductively viable seed crops until they are more than 21 years old. Our results show that environmental factors influence the primary juvenile period of a keystone obligate seeder, in turn affecting the time taken for a population to develop a reproductively viable seed amount of seed. Reduced fire return intervals may therefore constrain the species’ realised niche (and geographic distribution) to areas where it can tolerate shorter fire return intervals due to faster growth and maturation. We suggest that populations of obligate seeders that reach reproductive viability faster are thus more likely to persist when exposed to multiple fires in short succession. Intra-stand variation in seed crops suggests that selection could also act on rapidly-maturing individuals, resulting in some populations exhibiting high levels of precocious reproductive activity.This work was funded by a Lesslie Research Scholarship in Landscape Conservation and Ecology to B.v.T.D, and an Australian Research Council Future Fellowship (FT130100043) to S.B.

Eucalyptus_genotypes_040518

Eucalyptus regnans and Eucalyptus obliqua genotype

The influence of fire and silvicultural practices on the landscape-scale genetic structure of an Australian foundation tree species

Natural disturbance regimes in forest ecosystems are being rapidly modified by anthropogenic pressures, including silvicultural practices and climate change. Australian forests dominated by mountain ash (Eucalyptus regnans) are critically endangered, with wildfires and clearfell logging predicted to cause ecosystem collapse within the next 50 years. To investigate the influence of disturbance on patterns and extent of genetic diversity in mountain ash, we compare replicated sites with three different disturbance histories (undisturbed, burnt, and logged). We employ genetic analysis at five chloroplast microsatellite loci and 2866 nuclear single-nucleotide polymorphisms (SNPs) to estimate within- and among- population genetic diversity, and assess the extent of fine-scale spatial genetic structure among individuals, for the three disturbance treatments. Consistent with the expectation of extensive pollen dispersal but limited seed dispersal, we detected low levels of genetic differentiation at nuclear SNPs (FST = 0.067), and very high levels of differentiation at cpDNA microsatellites (FST = 0.751). While differences among treatments at nuclear SNPs were small, we found stronger spatial genetic structure in the undisturbed treatment, higher levels of genetic differentiation in the logged treatment and greater partitioning of genetic diversity among logged sites. Analysis of cpDNA revealed significantly higher levels of total and within-site genetic diversity in the logged treatment than the burnt or undisturbed treatments, with haplotypes entering the system via the use of non-local seed in the regeneration process. We suggest that artificial regeneration activities should utilise a greater number of maternal parents, which could be achieved via variable retention harvesting or utilising a regional admixture provenancing approach.This study was supported by an Australian Research Council Future Fellowship (FT130100043) to SB, a Lesslie Research Scholarship in Landscape Conservation and Ecology to BvTD, and an Ignition Grant from the Centre for Biodiversity Analysis to BvTD

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

Understanding local adaptation is critical for conservation management under rap idly 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

Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow

Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant 'islands'. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (N(e)), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (N(e)) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which 'islands' of habitat are most in need of management and protection.Damian C. Lettoof, Vicki A. Thomson, Jari Cornelis, Philip W. Bateman, Fabien Aubret, Marthe M. Gagnon, Brenton von Takac

Genomic impact of severe population decline in a nomadic songbird

Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained a SNP dataset from 64 museum specimens (date 1879-1960), 102 'recent' (1989-2012) and 52 'current' (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. Museum sampling showed population structure in regent honeyeaters was historically low, which remains the case despite a severe fragmentation of the breeding range. Population decline has led to minimal loss of genetic diversity since the 1980's. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. A rapid population decline, coupled with the regent honeyeater's high mobility, means a detectable genomic impact of this decline has not yet manifested. Extinction may occur in this nomadic species before a detectable genomic impact of small population size is realised. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.This study was funded through: an environmental offset paid by Cumnock Pty (R. Heinsohn and D.Stojanovic), grants from: the Australian Research Council #DP140104202 (R. Heinsohn); Mohamed bin Zayed Species Conservation Fund (R. Crates); BirdLife Australia (R.Crates); Holsworth Wildlife Research Endowment (R. Crates); Hunter Bird Observers Club (R.Crates); Birding NSW (R.Crates); Oatley Flora and Fauna (R.Crates). Tomasz Suchan was supported by the statutory funds of W. Szafer Institute of Botany, Polish Academy of Sciences