Australasian plant conservation : journal of the Australian network for plant conservation, Dec 1, 2014
The large-scale translocation of species for agricultural, forestry or fisheries purposes has cre... more The large-scale translocation of species for agricultural, forestry or fisheries purposes has created numerous environmental issues world-wide that require management for industry sustainability and certification purposes. One such issue is ‘exotic gene flow’, where translocated ‘industrial-species’ can alter the gene pool of indigenous species through hybridisation and introgression. This exotic gene flow could have flow on effects to dependent native communities, especially where foundation species such as forest trees are involved (Potts et al. 2003; Whitham et al. 2006).
Understanding the capacity of forest tree species to adapt to climate change is of increasing imp... more 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...
In plants where seed dispersal is limited compared with pollen dispersal, hybridisation may enhan... more 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 ...
With climate change impacting trees worldwide, enhancing adaptation capacity has become an import... more 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 varia...
SummaryWe overview an array of common garden genetics trials established across multiple sites an... more SummaryWe 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.
Background and AimsHybridization is increasingly recognized as an integral part of the dynamics o... more Background and AimsHybridization 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.MethodsWe 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 ResultsIn the hybrid zone, E. amygdalina adults showed greater mortality than E. risdonii, and the current seedling cohort is still dominated by E. risdonii phenotypes. M...
Widespread species spanning strong environmental (e.g., climatic) gradients frequently display mo... more 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.
In order to assist breeding and gene pool conservation in tropical Acacias, we aimed to develop a... more In order to assist breeding and gene pool conservation in tropical Acacias, we aimed to develop a set of multipurpose SSR markers for use in both Acacia mangium and A. auriculiformis. A total of 51 SSR markers (developed in A. mangium and natural A. mangium x A. auriculiformis hybrid) were tested. A final set of 16 well-performing SSR markers were identified, six of which were species diagnostic. The markers were optimized for assay in four multiplex mixes and used to genotype range-wide samples of A. mangium, A. auriculiformis, and putative F1 hybrids. Simulation analysis was used to investigate the power of the markers for identifying the pure species and their F1, F2, and backcross hybrids. The six species diagnostic markers were particularly powerful for detecting F1 hybrids from pure species but could also discriminate the pure species from F2 and backcross progenies in most cases (97 %). STRUCTURE analysis using all 16 markers was likewise able to distinguish these cross types and pure species sets. Both sets of markers had difficulties in distinguishing F2 and backcross progenies. However, identifying F1 from pure species is the current primary concern in countries where these species are planted. The SSR marker set also has direct application in DNA profiling (probability of identity = 4.1 × 10−13), breeding system analysis, and population genetics.
Eucalyptus globulusis grown extensively in plantations outside its native range in Australia. Con... more Eucalyptus globulusis grown extensively in plantations outside its native range in Australia. Concerns have been raised that the species may pose a genetic risk to native eucalypt species through hybridisation and introgression. Methods for identifying hybrids are needed to enable assessment and management of this genetic risk. This paper assesses the efficiency of a Bayesian approach for identifying hybrids between the plantation speciesE. globulusandE. nitensand four at-risk native eucalypts. Range-wide DNA samples ofE. camaldulensis,E. cypellocarpa,E. globulus,E. nitens,E. ovataandE. viminalis, and pedigreed and putative hybrids (n= 606), were genotyped with 10 microsatellite loci. Using a two-way simulation analysis (two species in the model at a time), the accuracy of identification was 98% for first and 93% for second generation hybrids. However, the accuracy of identifying simulated backcross hybrids was lower (74%). A six-way analysis (all species in the model together) show...
Australasian plant conservation : journal of the Australian network for plant conservation, Dec 1, 2014
The large-scale translocation of species for agricultural, forestry or fisheries purposes has cre... more The large-scale translocation of species for agricultural, forestry or fisheries purposes has created numerous environmental issues world-wide that require management for industry sustainability and certification purposes. One such issue is ‘exotic gene flow’, where translocated ‘industrial-species’ can alter the gene pool of indigenous species through hybridisation and introgression. This exotic gene flow could have flow on effects to dependent native communities, especially where foundation species such as forest trees are involved (Potts et al. 2003; Whitham et al. 2006).
Understanding the capacity of forest tree species to adapt to climate change is of increasing imp... more 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...
In plants where seed dispersal is limited compared with pollen dispersal, hybridisation may enhan... more 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 ...
With climate change impacting trees worldwide, enhancing adaptation capacity has become an import... more 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 varia...
SummaryWe overview an array of common garden genetics trials established across multiple sites an... more SummaryWe 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.
Background and AimsHybridization is increasingly recognized as an integral part of the dynamics o... more Background and AimsHybridization 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.MethodsWe 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 ResultsIn the hybrid zone, E. amygdalina adults showed greater mortality than E. risdonii, and the current seedling cohort is still dominated by E. risdonii phenotypes. M...
Widespread species spanning strong environmental (e.g., climatic) gradients frequently display mo... more 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.
In order to assist breeding and gene pool conservation in tropical Acacias, we aimed to develop a... more In order to assist breeding and gene pool conservation in tropical Acacias, we aimed to develop a set of multipurpose SSR markers for use in both Acacia mangium and A. auriculiformis. A total of 51 SSR markers (developed in A. mangium and natural A. mangium x A. auriculiformis hybrid) were tested. A final set of 16 well-performing SSR markers were identified, six of which were species diagnostic. The markers were optimized for assay in four multiplex mixes and used to genotype range-wide samples of A. mangium, A. auriculiformis, and putative F1 hybrids. Simulation analysis was used to investigate the power of the markers for identifying the pure species and their F1, F2, and backcross hybrids. The six species diagnostic markers were particularly powerful for detecting F1 hybrids from pure species but could also discriminate the pure species from F2 and backcross progenies in most cases (97 %). STRUCTURE analysis using all 16 markers was likewise able to distinguish these cross types and pure species sets. Both sets of markers had difficulties in distinguishing F2 and backcross progenies. However, identifying F1 from pure species is the current primary concern in countries where these species are planted. The SSR marker set also has direct application in DNA profiling (probability of identity = 4.1 × 10−13), breeding system analysis, and population genetics.
Eucalyptus globulusis grown extensively in plantations outside its native range in Australia. Con... more Eucalyptus globulusis grown extensively in plantations outside its native range in Australia. Concerns have been raised that the species may pose a genetic risk to native eucalypt species through hybridisation and introgression. Methods for identifying hybrids are needed to enable assessment and management of this genetic risk. This paper assesses the efficiency of a Bayesian approach for identifying hybrids between the plantation speciesE. globulusandE. nitensand four at-risk native eucalypts. Range-wide DNA samples ofE. camaldulensis,E. cypellocarpa,E. globulus,E. nitens,E. ovataandE. viminalis, and pedigreed and putative hybrids (n= 606), were genotyped with 10 microsatellite loci. Using a two-way simulation analysis (two species in the model at a time), the accuracy of identification was 98% for first and 93% for second generation hybrids. However, the accuracy of identifying simulated backcross hybrids was lower (74%). A six-way analysis (all species in the model together) show...
Uploads