Complete nucleotide sequence of the chloroplast genome from the Tasmanian Blue Gum, Eucalyptus globulus (Myrtaceae)

The complete nucleotide sequence of the chloroplast genome of the hardwood species Eucalyptus globulus is presented and compared with chloroplast genomes of tree and non-tree angiosperms and two softwood tree species. The 160 286 bp genome is similar in gene order to that of Nicotiana, with an inverted repeat (IR) (26 393 bp) separated by a large single copy (LSC) region of 89 012 bp and a small single copy region of 18 488 bp. There are 128 genes (112 individual gene species and 16 genes duplicated in the inverted repeat) coding for 30 transfer RNAs, 4 ribosomal RNAs and 78 proteins. One pseudogene (-infA) and one pseudo-ycf (-ycf15) were identified. The chloroplast genome of E. globulus is essentially co-linear with that of another hardwood tree species, Populus trichocarpa, except that the latter lacks rps16 and rpl32, and the IR has expanded in Populus to include rps19 (part of the LSC in E. globulus). Since the chloroplast genome of E. globulus is not significantly different from other tree and non-tree angiosperm taxa, a comparison of hardwood and softwood chloroplasts becomes, in essence, a comparison of angiosperm and gymnosperm chloroplasts. When compared with E. globulus, Pinus chloroplasts have a very small IR, two extra tRNAs and four additional photosynthetic genes, lack any functional ndh genes and have a significantly different genome arrangement. There does not appear to be any correlation between plant habit and chloroplast genome composition and arrangement

The occurrence and conservation status of Tasmanian Pterostylis (Orchidaceae)

Orchids belong to one of the largest plant families present in Tasmania and yet they remain poorly researched. In Tasmania, Pterostylis R.Br. comprises about 37 terrestrial species, commonly called greenhoods. Little is understood about Tasmanian Pterostylis ecology and a recent assessment of species’ abundances and distributions have not been conducted. Over a two year period known Pterostylis locations within mainland Tasmania, King Island and Flinders Island were visited for the purpose of collecting detailed data for species abundance, distribution and flowering. Several species within the genus Pterostylis are facing significant threats, and recommendations to prevent the decline of these species are provided

Incongruence between chloroplast and species phylogenies in eucalyptus subgenus monocalyptus (Myrtaceae)

Seventy-eight polymorphic cpDNA (chloroplast DNA) characters were found in 13 closely related taxa from Eucalyptus series Amygdalinae (subgenus Monocalyptus) and seven potential outgroup taxa. The strict consensus of six cladograms generated from cpDNA data confirmed monophyly of Monocalyptus. However, cpDNA phylogeny within Monocalyptus was incongruent with taxonomic classification, being more related to geography, even when accessions were from divergent series. Monocalyptus cpDNA formed two major clades. On the island of Tasmania cpDNA was restricted to a single clade, exhibited very little variation, and was phylogenetically related to cpDNA found in central and western Victoria. In contrast, cpDNA of mainland monocalypt taxa was more variable, even within the Amygdalinae. Four out of six Tasmanian Amygdalinae species were polymorphic. The difference between cpDNA of replicates was often greater than differences between species from different series. The low level of cpDNA variation and extensive morphological intergradation between the Tasmanian endemics suggest recent speciation. However, the transfer of cpDNA through hybridization between lineages is the most likely explanation for the observed sharing of cpDNA across series. This study highlights that the geographical pattern to cpDNA variation in Eucalyptus may be an important source of information on past plant distributions in Australia

Microsatellites retain phylogenetic signals across genera in eucalypts (Myrtaceae)

The utility of microsatellites (SSRs) in reconstructing phylogenies is largely confined to studies below the genus level, due to the potential of homoplasy resulting from allele size range constraints and poor SSR transferability among divergent taxa. The eucalypt genus Corymbia has been shown to be monophyletic using morphological characters, however, analyses of intergenic spacer sequences have resulted in contradictory hypotheses- showing the genus as either equivocal or paraphyletic. To assess SSR utility in higher order phylogeny in the family Myrtaceae, phylogenetic relationships of the bloodwood eucalypts Corymbia and related genera were investigated using eight polymorphic SSRs. Repeat size variation using the average square and Nei’s distance were congruent and showed Corymbia to be a monophyletic group, supporting morphological characters and a recent combination of the internal and external transcribed spacers dataset. SSRs are selectively neutral and provide data at multiple genomic regions, thus may explain why SSRs retained informative phylogenetic signals despite deep divergences. We show that where the problems of size-range constraints, high mutation rates and size homoplasy are addressed, SSRs might resolve problematic phylogenies of taxa that have diverged for as long as three million generations or 30 million years. Key word

Exploration of the Eucalyptus globulus gene pool

The first Europeans to discover Eucalyptus globulus were French explorers in 1792. Its seed was rapidly spread throughout the world in the 19th century and this was the species by which much of the world first knew the genus. However, it was in the industrial forests of the 20th century that this species, once considered the ‘Prince of Eucalypts’, achieved greatest prominence due to its fast growth and superior pulp qualities. Formal breeding first commenced in 1966 in Portugal and in the late 1980’s large base population trials from open-pollinated seed collections from native stands were established in many countries. These trials have provided unprecedented insights into the quantitative genetic control of numerous traits of economic and ecological importance and how this variation is spatially distributed in the native range of the species. However with large, fully pedigreed breeding populations becoming available for quantitative analysis and the rapidly expanding knowledge of DNA sequence variation, we are now at the threshold of a new understanding of this important eucalypt gene pool. Indications of the significance of non-additive genetic effects are becoming available. The E. globulus chloroplast genome has now been sequenced and several genome maps have been published. Studies of the variation in nuclear microsatellites and the lignin biosynthesis gene CCR confirm the complex, spatially structured nature of the native gene pool. Strong spatial structuring of the chloroplast genome has provided a tool for tracking seed migration and the geographic origin of exotic landraces. Highly divergent lineages of chloroplast DNA have been discovered and studies of the hypervariable JLA+ region argue that some components of the E. globulus gene pool have been assimilated from other species following hybridisation

Development and characterisation of microsatellite loci in Eucalyptus globulus (Myrtaceae)

Eucalyptus globulus Labill. is the premier hardwood plantation species in temperate regions of the world. We developed twelve E. globulus microsatellite loci for fingerprinting and future studies in genome mapping, gene flow and genetic diversity. The microsatellites were highly polymorphic in E. globulus (average number of alleles per locus, 17.8; average observed heterozygosity, 0.66). The loci were robust, amplifying in other Eucalyptus species, Corymbia and Angophora. The high variability and transferability of these molecular markers make them useful in E. globulus, as well as in many of the 700 species of Eucalyptus

Climate adaptation, drought susceptibility, and genomic-informed predictions of future climate refugia for the Australian forest tree Eucalyptus globulus

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

Origins, diversity and naturalization of Eucalyptus globulus (Myrtaceae) in California

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

The double Caldeira-Leggett model: Derivation and solutions of the master equations, reservoir-induced interactions and decoherence

In this paper we analyze the double Caldeira-Leggett model: the path integral approach to two interacting dissipative harmonic oscillators. Assuming a general form of the interaction between the oscillators, we consider two different situations: i) when each oscillator is coupled to its own reservoir, and ii) when both oscillators are coupled to a common reservoir. After deriving and solving the master equation for each case, we analyze the decoherence process of particular entanglements in the positional space of both oscillators. To analyze the decoherence mechanism we have derived a general decay function for the off-diagonal peaks of the density matrix, which applies both to a common and separate reservoirs. We have also identified the expected interaction between the two dissipative oscillators induced by their common reservoir. Such reservoir-induced interaction, which gives rise to interesting collective damping effects, such as the emergence of relaxation- and decoherence-free subspaces, is shown to be blurred by the high-temperature regime considered in this study. However, we find that different interactions between the dissipative oscillators, described by rotating or counter-rotating terms, result in different decay rates for the interference terms of the density matrix.Comment: 42 pages, 7 figures, new discussion added, typos adde