Chloroplast DNA variation and population structure in the widespread forest tree, Eucalyptus grandis

Major biogeographic barriers in eastern Australia have shaped the population structure of widely distributed Eucalyptus moluccana and its putative subspecies

We have investigated the impact of recognized biogeographic barriers on genetic differentiation of grey box (Eucalyptus moluccana), a common and widespread tree species of the family Myrtaceae in eastern Australian woodlands, and its previously proposed four subspecies moluccana, pedicellata, queenslandica, and crassifolia. A range of phylogeographic analyses were conducted to examine the population genetic differentiation and subspecies genetic structure in E. moluccana in relation to biogeographic barriers. Slow evolving markers uncovering long term processes (chloroplast DNA) were used to generate a haplotype network and infer phylogeographic barriers. Additionally, fast evolving, hypervariable markers (microsatellites) were used to estimate demographic processes and genetic structure among five geographic regions (29 populations) across the entire distribution of E. moluccana. Morphological features of seedlings, such as leaf and stem traits, were assessed to evaluate population clusters and test differentiation of the putative subspecies. Haplotype network analysis revealed twenty chloroplast haplotypes with a main haplotype in a central position shared by individuals belonging to the regions containing the four putative subspecies. Microsatellite analysis detected the genetic structure between Queensland (QLD) and New South Wales (NSW) populations, consistent with the McPherson Range barrier, an east-west spur of the Great Dividing Range. The substructure was detected within QLD and NSW in line with other barriers in eastern Australia. The morphological analyses supported differentiation between QLD and NSW populations, with no difference within QLD, yet some differentiation within NSW populations. Our molecular and morphological analyses provide evidence that several geographic barriers in eastern Australia, including the Burdekin Gap and the McPherson Range have contributed to the genetic structure of E. moluccana. Genetic differentiation among E. moluccana populations supports the recognition of some but not all the four previously proposed subspecies, with crassifolia being the most differentiated.

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.

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.

Genome scans for divergent selection in natural populations of the widespread hardwood species Eucalyptus grandis (Myrtaceae) using microsatellites

Identification of loci or genes under natural selection is important for both understanding the genetic basis of local adaptation and practical applications, and genome scans provide a powerful means for such identification purposes. In this study, genome-wide simple sequence repeats markers (SSRs) were used to scan for molecular footprints of divergent selection in Eucalyptus grandis, a hardwood species occurring widely in costal areas from 32° S to 16° S in Australia. High population diversity levels and weak population structure were detected with putatively neutral genomic SSRs. Using three FST outlier detection methods, a total of 58 outlying SSRs were collectively identified as loci under divergent selection against three non-correlated climatic variables, namely, mean annual temperature, isothermality and annual precipitation. Using a spatial analysis method, nine significant associations were revealed between FST outlier allele frequencies and climatic variables, involving seven alleles from five SSR loci. Of the five significant SSRs, two (EUCeSSR1044 and Embra394) contained alleles of putative genes with known functional importance for response to climatic factors. Our study presents critical information on the population diversity and structure of the important woody species E. grandis and provides insight into the adaptive responses of perennial trees to climatic variations.

Population and phylogenomic decomposition via genotyping-by-sequencing in Australian Pelargonium

Species delimitation has seen a paradigm shift as increasing accessibility of genomic-scale data enables separation of lineages with convergent morphological traits and the merging of recently diverged ecotypes that have distinguishing characteristics. We inferred the process of lineage formation among Australian species in the widespread and highly variable genus Pelargonium by combining phylogenomic and population genomic analyses along with breeding system studies and character analysis. Phylogenomic analysis and population genetic clustering supported seven of the eight currently described species but provided little evidence for differences in genetic structure within the most widely distributed group that containing P. australe. In contrast, morphometric analysis detected three deep lineages within Australian Pelargonium; with P. australe consisting of five previously unrecognized entities occupying separate geographic ranges. The genomic approach enabled elucidation of parallel evolution in some traits formerly used to delineate species, as well as identification of ecotypic morphological differentiation within recognized species. Highly variable morphology and trait convergence each contribute to the discordance between phylogenomic relationships and morphological taxonomy. Data suggest that genetic divergence among species within the Australian Pelargonium may result from allopatric speciation while morphological differentiation within and among species may be more strongly driven by environmental differences.

Phosphorus limits Eucalyptus grandis seedling growth in an unburnt rain forest soil

Although rain forest is characterized as pyrophobic, pyrophilic giant eucalypts grow as rain forest emergents in both temperate and tropical Australia. In temperate Australia, such eucalypts depend on extensive, infrequent fires to produce conditions suitable for seedling growth. Little is known, however, about constraints on seedlings of tropical giant eucalypts. We tested whether seedlings of Eucalyptus grandis experience edaphic constraints similar to their temperate counterparts. We hypothesized that phosphorous addition would alleviate edaphic constraints. We grew seedlings in a factorial experiment combining fumigation (to simulate nutrient release and soil pasteurization by fire), soil type (E. grandis forest versus rain forest soil) and phosphorus addition as factors. We found that phosphorus was the principal factor limiting E. grandis seedling survival and growth in rain forest soil, and that fumigation enhanced survival of seedlings in both E. grandis forest and rain forest soil. We conclude that similar to edaphic constraints on temperate giant eucalypts, mineral nutrient and biotic attributes of a tropical rain forest soil may hamper E. grandis seedling establishment. In rain forest soil, E. grandis seedlings benefited from conditions akin to a fire-generated ashbed (i.e., an "ashbed effect").

Giant eucalypts - globally unique fire-adapted rain-forest trees?

Tree species exceeding 70 m in height are rare globally. Giant gymnosperms are concentrated near the Pacific coast of the USA, while the tallest angiosperms are eucalypts (Eucalyptus spp.) in southern and eastern Australia. Giant eucalypts co-occur with rain-forest trees in eastern Australia, creating unique vegetation communities comprising fire-dependent trees above fire-intolerant rain-forest. However, giant eucalypts can also tower over shrubby understoreys (e.g. in Western Australia). The local abundance of giant eucalypts is controlled by interactions between fire activity and landscape setting. Giant eucalypts have features that increase flammability (e.g. oil-rich foliage and open crowns) relative to other rain-forest trees but it is debatable if these features are adaptations. Probable drivers of eucalypt gigantism are intense intra-specific competition following severe fires, and inter-specific competition among adult trees. However, we suggest that this was made possible by a general capacity of eucalypts for 'hyper-emergence'. We argue that, because giant eucalypts occur in rain-forest climates and share traits with rain-forest pioneers, they should be regarded as long-lived rain-forest pioneers, albeit with a particular dependence on fire for regeneration. These unique ecosystems are of high conservation value, following substantial clearing and logging over 150 yr. Contents Summary 1001 I. Introduction 1001 II. Giant eucalypts in a global context 1002 III. Giant eucalypts - taxonomy and distribution 1004 IV. Growth of giant eucalypts 1006 V. Fire and regeneration of giant eucalypts 1008 VI. Are giant eucalypts different from other rain-forest trees? 1009 VII. Conclusions 1010 Acknowledgements 1011 References 1011.

Biotechnologies for the management of genetic resources for food and agriculture

In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.

Phylogeographic divergence in the widespread delicate skink (Lampropholis delicata) corresponds to dry habitat barriers in eastern Australia

BACKGROUND

The mesic habitats of eastern Australia harbour a highly diverse fauna. We examined the impact of climatic oscillations and recognised biogeographic barriers on the evolutionary history of the delicate skink (Lampropholis delicata), a species that occurs in moist habitats throughout eastern Australia. The delicate skink is a common and widespread species whose distribution spans 26° of latitude and nine major biogeographic barriers in eastern Australia. Sequence data were obtained from four mitochondrial genes (ND2, ND4, 12SrRNA, 16SrRNA) for 238 individuals from 120 populations across the entire native distribution of the species. The evolutionary history and diversification of the delicate skink was investigated using a range of phylogenetic (Maximum Likelihood, Bayesian) and phylogeographic analyses (genetic diversity, ΦST, AMOVA, Tajima's D, Fu's F statistic).

RESULTS

Nine geographically structured, genetically divergent clades were identified within the delicate skink. The main clades diverged during the late Miocene-Pliocene, coinciding with the decline and fragmentation of rainforest and other wet forest habitats in eastern Australia. Most of the phylogeographic breaks within the delicate skink were concordant with dry habitat or high elevation barriers, including several recognised biogeographic barriers in eastern Australia (Burdekin Gap, St Lawrence Gap, McPherson Range, Hunter Valley, southern New South Wales). Genetically divergent populations were also located in high elevation topographic isolates inland from the main range of L. delicata (Kroombit Tops, Blackdown Tablelands, Coolah Tops). The species colonised South Australia from southern New South Wales via an inland route, possibly along the Murray River system. There is evidence for recent expansion of the species range across eastern Victoria and into Tasmania, via the Bassian Isthmus, during the late Pleistocene.

CONCLUSIONS

The delicate skink is a single widespread, but genetically variable, species. This study provides the first detailed phylogeographic investigation of a widespread species whose distribution spans virtually all of the major biogeographic barriers in eastern Australia.

Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

A set of over 8000 Diversity Arrays Technology (DArT) markers was tested for its utility in high-resolution population and phylogenetic studies across a range of Eucalyptus taxa. Small-scale population studies of Eucalyptus camaldulensis, Eucalyptus cladocalyx, Eucalyptus globulus, Eucalyptus grandis, Eucalyptus nitens, Eucalyptus pilularis and Eucalyptus urophylla demonstrated the potential of genome-wide genotyping with DArT markers to differentiate species, to identify interspecific hybrids and to resolve biogeographic disjunctions within species. The population genetic studies resolved geographically partitioned clusters in E. camaldulensis, E. cladocalyx, E. globulus and E. urophylla that were congruent with previous molecular studies. A phylogenetic study of 94 eucalypt species provided results that were largely congruent with traditional taxonomy and ITS-based phylogenies, but provided more resolution within major clades than had been obtained previously. Ascertainment bias (the bias introduced in a phylogeny from using markers developed in a small sample of the taxa that are being studied) was not detected. DArT offers an unprecedented level of resolution for population genetic, phylogenetic and evolutionary studies across the full range of Eucalyptus species.

Eucalyptus applied genomics: from gene sequences to breeding tools

Eucalyptus is the most widely planted hardwood crop in the tropical and subtropical world because of its superior growth, broad adaptability and multipurpose wood properties. Plantation forestry of Eucalyptus supplies high-quality woody biomass for several industrial applications while reducing the pressure on tropical forests and associated biodiversity. This review links current eucalypt breeding practices with existing and emerging genomic tools. A brief discussion provides a background to modern eucalypt breeding together with some current applications of molecular markers in support of operational breeding. Quantitative trait locus (QTL) mapping and genetical genomics are reviewed and an in-depth perspective is provided on the power of association genetics to dissect quantitative variation in this highly diverse organism. Finally, some challenges and opportunities to integrate genomic information into directional selective breeding are discussed in light of the upcoming draft of the Eucalyptus grandis genome. Given the extraordinary genetic variation that exists in the genus Eucalyptus, the ingenuity of most breeders, and the powerful genomic tools that have become available, the prospects of applied genomics in Eucalyptus forest production are encouraging.