Multiple evolutionary processes drive the patterns of genetic differentiation in a forest tree species complex

Forest trees frequently form species complexes, complicating taxonomic classification and gene pool management. This is certainly the case in Eucalyptus, and well exemplified by the Eucalyptus globulus complex. This ecologically and economically significant complex comprises four taxa (sspp. bicostata, globulus, maidenii, pseudoglobulus) that are geographically and morphologically distinct, but linked by extensive “intergrade” populations. To resolve their genetic affinities, nine microsatellites were used to genotype 1200 trees from throughout the natural range of the complex in Australia, representing 33 morphological core and intergrade populations. There was significant spatial genetic structure (F_ST = 0.10), but variation was continuous. High genetic diversity in southern ssp. maidenii indicates that this region is the center of origin. Genetic diversity decreases and population differentiation increases with distance from this area, suggesting that drift is a major evolutionary process. Many of the intergrade populations, along with other populations morphologically classified as ssp. pseudoglobulus or ssp. globulus, belong to a “cryptic genetic entity” that is genetically and geographically intermediate between core ssp. bicostata, ssp. maidenii, and ssp. globulus. Geography, rather than morphology, therefore, is the best predictor of overall genetic affinities within the complex and should be used to classify germplasm into management units for conservation and breeding purposes.     

Using matK sequence data to unravel the phylogeny of Casuarinaceae

Casuarinaceae are a Gondwanic family with a unique combination of morphological characters not comparable to any other family. Until recently, the 96 species in the family were classified in a single genus, Casuarina s.l. A recent morphological revision of the family resulted in the splitting of Casuarina s.l. into four genera-Allocasuarina, Casuarina s.s., Ceuthostoma, and Gymnostoma. This study uses matK sequence data from 76 species of Casuarinaceae and eight outgroup taxa to examine the phylogenetic structure within the Casuarinaceae. The study demonstrates the monophyly of the four genera and examines the relationships within the family; it tests the validity of the infra-generic subdivision of Allocasuarina; it discovers geography-based infra-generic subdivisions within Gymnostoma and Casuarina; and, finally, provides a molecular framework on which to trace the evolution of xeromorphy in the Casuarinaceae.     

Complete Nucleotide Sequence of the Chloroplast Genome from the Tasmanian Blue Gum, Eucalyptus globulus (Myrtaceae)

The complete nucleotide sequence of the chloroplast genome ofthe hardwood species Eucalyptus globulus is presented and comparedwith chloroplast genomes of tree and non-tree angiosperms andtwo softwood tree species. The 160 286 bp genome is similarin gene order to that of Nicotiana, with an inverted repeat(IR) (26 393 bp) separated by a large single copy (LSC) regionof 89 012 bp and a small single copy region of 18 488 bp. Thereare 128 genes (112 individual gene species and 16 genes duplicatedin the inverted repeat) coding for 30 transfer RNAs, 4 ribosomalRNAs and 78 proteins. One pseudogene (-infA) and one pseudo-ycf(-ycf15) were identified. The chloroplast genome of E. globulusis essentially co-linear with that of another hardwood treespecies, Populus trichocarpa, except that the latter lacks rps16and rpl32, and the IR has expanded in Populus to include rps19(part of the LSC in E. globulus). Since the chloroplast genomeof E. globulus is not significantly different from other treeand non-tree angiosperm taxa, a comparison of hardwood and softwoodchloroplasts becomes, in essence, a comparison of angiospermand gymnosperm chloroplasts. When compared with E. globulus,Pinus chloroplasts have a very small IR, two extra tRNAs andfour additional photosynthetic genes, lack any functional ndhgenes and have a significantly different genome arrangement.There does not appear to be any correlation between plant habitand chloroplast genome composition and arrangement.     

Phylogeny and infrageneric classification of Correa Andrews (Rutaceae) on the basis of nuclear and chloroplast DNA

This paper presents phylogenies of the small but ecologically and horticulturally important Australian genus Correa (Rutaceae). Consensus phylogenies generated using parsimony were congruent with their counterparts generated by Bayesian analysis, although usually less well resolved. The phylogeny generated from the second internal transcribed spacer region of the nuclear ribosomal DNA supported the monophyly of Correa and identified two well supported clades (one comprising C. lawrenceana and C. baeuerlenii and the other containing all other species of the genus). Phylogenetic reconstructions based on the combined trnL-trnF spacer and the trnK intron (including the matK gene) regions of chloroplast DNA also supported the monophyly of Correa and of the C. lawrenceana/C. baeuerlenii clade, but the topology among the other species differed markedly from that in the ITS-based phylogeny. The major clades identified in the chloroplast phylogenies seemed to follow geographic patterns rather than species boundaries, with different samples of C. glabra bearing chloroplast genotypes from different clades. These patterns are likely to be because of independent evolution of the chloroplast and nuclear genomes, and are typical of cases of introgressive hybridisation among species or incomplete lineage sorting of chloroplast genomes leading to incongruence between chloroplast and nuclear phylogenies. Thus, the phylogenies based on nuclear DNA should reflect species relations better than the chloroplast phylogeny in Correa, and we propose a new subgeneric classification of the genus on the basis of the ITS-based phylogeny and morphology. Correa subgenus Persistens Othman, Duretto and G.J. Jord., containing C. lawrenceana and C. baeuerlenii, is formally described.     

An AFLP marker approach to lower-level systematics in Eucalyptus (Myrtaceae)

Genus Eucalyptus, with over 700 species, presents a number of systematic difficulties including taxa that hybridize or intergrade across environmental gradients. To date, no DNA marker has been found capable of resolving phylogeny below the sectional level in the major subgenera. Molecular markers are needed to support taxonomic revision, assess the extent of genetic divergence at lower taxonomic levels, and inform conservation efforts. We examined the utility of 930 amplified fragment length polymorphisms (AFLPs) for analyzing relationships among Tasmanian taxa of subgenus Symphyomyrtus section Maidenaria. Phenetic and cladistic analyses resolved species into clusters demonstrating significant genetic partitioning, largely concordant with series defined in the most recent taxonomic revision of Eucalyptus. Some departures from current taxonomy were noted, indicating possible cases of morphological convergence and character reversion. Although the resolution obtained using AFLP was greatly superior to that of single sequence markers, the data demonstrated high homoplasy and incomplete resolution of closely related species. The results of this study and others are consistent with recent speciation and reticulate evolution in Maidenaria. We conclude that a combination of phylogenetic and population genetic approaches using multiple molecular markers offers the best prospects for understanding taxonomic relationships below the sectional level in Eucalyptus.     

Chloroplast DNA evidence for reticulate evolution in Eucalyptus (Myrtaceae)

Four highly differentiated chloroplast DNA (cpDNA) lineages were identified in the forest tree species Eucalyptus globulus Labill. (Myrtaceae) in Australia using restriction site polymorphisms from Southern analysis. The cpDNA variation did not conform with ssp. boundaries, yet there was a strong geographical pattern to the distribution of the lineages. One lineage (C) was geographically central and widespread, whereas the other three lineages were found in peripheral populations: Western (W), Northern (N) and Southern (S). Thirteen haplotypes were detected in E. globulus , seven of which belonged to clade C. At least three of the cpDNA lineages (C, N and S) were shared extensively with other species. On the east coast of the island of Tasmania, there was a major north–south difference in cpDNA in the virtually continuous distribution of E. globulus . Northern populations harboured haplotypes from clade C while southeastern populations harboured a single haplotype from clade S. This difference was also reflected in several co-occurring endemic species. It is argued that the extensive cpDNA differentiation within E. globulus is likely to originate from interspecific hybridization and 'chloroplast capture' from different species in different parts of its range. Superficially, this hybridization is not evident in taxonomic traits; however, large-scale common garden experiments have revealed a steep cline in quantitative genetic variation that coincides with the haplotype transition in Tasmania. Our cpDNA results provide the strongest evidence to date that hybridization has had a widespread impact on a eucalypt species and indicate that reticulate evolution may be occurring on an unappreciated scale in Eucalyptus .     

Bioclimatic transect networks: Powerful observatories of ecological change

Transects that traverse substantial climate gradients are important tools for climate change research and allow questions on the extent to which phenotypic variation associates with climate, the link between climate and species distributions, and variation in sensitivity to climate change among biomes to be addressed. However, the potential limitations of individual transect studies have recently been highlighted. Here, we argue that replicating and networking transects, along with the introduction of experimental treatments, addresses these concerns. Transect networks provide cost‐effective and robust insights into ecological and evolutionary adaptation and improve forecasting of ecosystem change. We draw on the experience and research facilitated by the Australian Transect Network to demonstrate our case, with examples, to clarify how population‐ and community‐level studies can be integrated with observations from multiple transects, manipulative experiments, genomics, and ecological modeling to gain novel insights into how species and systems respond to climate change. This integration can provide a spatiotemporal understanding of past and future climate‐induced changes, which will inform effective management actions for promoting biodiversity resilience.     

The impact of intragenic recombination on phylogenetic reconstruction at the sectional level in Eucalyptus when using a single copy nuclear gene (cinnamoyl CoA reductase)

Low copy number nuclear genes have been found to be useful for phylogenetic reconstruction at different taxonomic levels. This study investigated the utility of a single copy gene, cinnamoyl CoA reductase (CCR), for resolving phylogenetic relationships at the sectional level within Eucalyptus. The monophyly of sections Exsertaria and Latoangulatae was explored, using section Maidenaria as an outgroup, and the impact of intragenic recombination on phylogenetic reconstruction examined. Phylogenetic analysis did not resolve monophyletic groups. Latoangulatae and Maidenaria were polyphyletic or paraphyletic. Exsertaria species formed a clade but included a single Latoangulatae species (E. major). Recombination analysis identified two intragenic recombination events that involved species from different sections, which have probably been facilitated by inter-sectional hybridisation. One of the events most likely occurred prior to speciation, with several Latoangulatae species having the recombinant allele. The other event may have occurred after speciation, since only one of two E. globulus samples possessed the recombinant allele. This is the first detailed report of intragenic recombination in both CCR and Eucalyptus, and between species of different sections of a plant genus. The occurrence of intragenic recombination may explain the anomalous positions of some species within the phylogenetic tree, and indicates that phylogenetic analysis of Eucalyptus using nuclear genes will be problematic unless recombination is taken into account.     

Molecular systematics of Clerodendrum (Lamiaceae): ITS sequences and total evidence

Thirty-three species of Clerodendrum s.l. and five outgroup genera were included in a sequence analysis of internal transcribed spacers of the nuclear ribosomal DNA. The results of the cladistic analysis were compared to and combined with cpDNA restriction site data from a previous study. All molecular data identified four major clades within Clerodendrum s.l. and showed the genus to be polyphyletic. Clerodendrum s.s., minus Konocalyx and Cyclonema, is monophyletic and the genus should be restricted to this group. Cyclonema and Konocalyx form a clade distinct from Clerodendrum s.s., which has been recognized as Rotheca Raf.