Chloroplast genome analysis of Australian eucalypts--Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae).

We present a phylogenetic analysis and comparison of structural features of chloroplast genomes for 39 species of the eucalypt group (genera Eucalyptus, Corymbia, Angophora, and outgroups Allosyncarpia and Stockwellia). We use 41 complete chloroplast genome sequences, adding 39 finished-quality chloroplast genomes to two previously published genomes. Maximum parsimony and Bayesian analyses, based on >7000 variable nucleotide positions, produced one fully resolved phylogenetic tree (35 supported nodes, 27 with 100% bootstrap support). Eucalyptus and its sister lineage Angophora+Corymbia show a deep divergence. Within Eucalyptus, three lineages are resolved: the 'eudesmid', 'symphyomyrt' and 'monocalypt' groups. Corymbia is paraphyletic with respect to Angophora. Gene content and order do not vary among eucalypt chloroplasts; length mutations, especially frame shifts, are uncommon in protein-coding genes. Some non-synonymous mutations are highly incongruent with the overall phylogenetic signal, notably in rbcL, and may be adaptive. Application of custom informatics pipelines (GYDLE Inc.) enabled direct chloroplast genome assembly, resolving each genome to finished-quality with no need for PCR gap-filling or contig order resolution. Analysis of whole chloroplast genomes resolved major eucalypt clades and revealed variable regions of the genome that will be useful in lower-level genetic studies (including phylogeography and geneflow).

Relationships of the Australo-Malesian genus Paraserianthes (Mimosoideae: Leguminosae) identifies the sister group of Acacia sensu stricto and two biogeographical tracks.

© The Willi Hennig Society 2011. ABSTRACT: Paraserianthes (tribe Ingeae) as circumscribed by Nielsen et al. includes four species and five subspecies in two sections endemic to Australia, Indonesia, New Guinea and the Solomon islands. An alternative classification, proposed by Barneby and Grimes, raised Nielsen's two sections to generic level, thereby reducing Paraserianthes to comprise just species, P. lophantha, and recognizing the genus Falcataria. Neither treatment has been adopted by all. Thus, a phylogenetic and systematic analysis of Paraserianthes is required to clarify the taxonomic circumscription of the genus and relationships among the species and subspecies. Furthermore, elucidation of the phylogenetic relationships of Paraserianthes is significant to an understanding of the evolutionary history and biogeography of Acacia sensu stricto (s.s.). The external transcribed spacer regions of nuclear ribosomal DNA and the rpl32-trnL intergenic spacer of chloroplast DNA were sequenced for all species of Paraserianthes, a representative sample of Acacia s.s. (phyllodinous group) and 18 other members of tribe Ingeae, including an outgroup Samanea tubulosa. These data were analysed with parsimony and Bayesian methods. The topologies of the resultant phylogenetic trees were congruent but with greater resolution in the Bayesian tree. The results show that Paraserianthes sensu Nielsen is paraphyletic and that P. lophantha is the sister group to Acacia, a finding supported by morphological characters. Paraserianthes shows a dual link between Australia and lands to the north. A western biogeographical track relates south-west Western Australia to Sumatra, Java, Bali and Flores (two subspecies of P. lophantha), and an eastern track relates north-east Queensland to the Moluccas, New Guinea, the Bismarck Archipelago and the Solomon Islands (P. toona and its relatives).

A CLADISTIC ANALYSIS OF ANGOPHORA CAV. (MYRTACEAE).

Abstract- A cladistie analysis of Angophora Cav. used a data set dominated by quantitative morphological characters. These were coded into multistates using Generalized Gap-Coding, and treated as ordered sequences of stales. The reasons for choosing an ordered over an unordered sequence are discussed. A branch and bound method yielded one minimal-length, unrooted tree. Because of uncertainty in the position of the root, five cladograms were derived from the unrooted tree. The consensus cladogram comprises four main clades. The consensus cladogram was used for a biogeographic study using component analysis, which generated a single statement of relationships for five areas of eastern Australia. An infra-generic classification of Angophora comprising four series corresponding to the four main clades, and two subseries, is presented. The following new names are published: Angophora series i>Floribundinae, series Subvelutininae, series Bakerinae. subseries Costntitac. Angophora leiocarpa: L. Johnson ex G. Leach) K. R. Thiele and P. Y. Ladiges and A.paludosa (G. Leach) K. R. Thiele and P. Y. Ladiges are published as new combinations.

CLADISTIC AND BIOGEOGRAPHIC ANALYSIS OF THE "BLUE ASH' EUCALYPTS.

Abstract- A cladistic analysis of the "blue ash" eucalypts (Eucalyptus, Myrtaceae) is presented. Five equally parsimonious trees were found, and a strict consensus tree constructed. A revised informal classification, recognizing five series (Planchonianinae, Sphaerocarpinae, Piperitinae, Fraxininae and Haemastominae, informal subgenus Monocalyptus) is based on the consensus cladogram. A biogeographic analysis applies a new implementation of Assumptions 0 and 1, coding data in the form of three-area statements and using parsimony analysis. These results are used to evaluate hand resolution of Assumption 2. In comparison, Brooks parsimony analysis did not produce area cladograms that best fit the data. Series and subseries were analysed separately for area relationships, which showed a repeated pattern across the blue ash clade; combining all the data in one analysis was seen as equivalent to confounding paralogy and orthology in molecular studies. A resolved area cladogram is presented for southeastern Australia.

SYSTEMATICS AND BIOGEOGRAPHY OF THE AUSTRALIAN "GREEN ASH" EUCALYPTS (MONOCALYPTUS).

Abstract- A cladistic analysis of the "green ash" eucalypts, informal subgenus "Monocalyptus", is presented- As a first step, ordination methods of principal coordinates analysis and multidimensional scaling delineated some terminal taxa. The cladistic analysis, applying parsimony methods to the unweighted data set, yielded 25 equally parsimonious trees, each with a consistency index of 0.57. Farris' successive approximations approach to character weighting produced one tree with a consistency index of 0.74. An informal classification of the group, superseries Eucalyptus, is based on that cladogram. The biogeographic history of superseries Eucalyptus is interpreted from the cladogram as having been caused by lour vicariant events in southeastern Australia, in combination with a suite of ecological features that overlie the biogeographic area-pattern.

Major clades of Australasian Rutoideae (Rutaceae) based on rbcL and atpB sequences.

BACKGROUND: Rutaceae subfamily Rutoideae (46 genera, c. 660 species) is diverse in both rainforests and sclerophyll vegetation of Australasia. Australia and New Caledonia are centres of endemism with a number of genera and species distributed disjunctly between the two regions. Our aim was to generate a high-level molecular phylogeny for the Australasian Rutoideae and identify major clades as a framework for assessing morphological and biogeographic patterns and taxonomy. METHODOLOGY/PRINCIPAL FINDINGS: Phylogenetic analyses were based on chloroplast genes, rbcL and atpB, for 108 samples (78 new here), including 38 of 46 Australasian genera. Results were integrated with those from other molecular studies to produce a supertree for Rutaceae worldwide, including 115 of 154 genera. Australasian clades are poorly matched with existing tribal classifications, and genera Philotheca and Boronia are not monophyletic. Major sclerophyll lineages in Australia belong to two separate clades, each with an early divergence between rainforest and sclerophyll taxa. Dehiscent fruits with seeds ejected at maturity (often associated with myrmecochory) are inferred as ancestral; derived states include woody capsules with winged seeds, samaras, fleshy drupes, and retention and display of seeds in dehisced fruits (the last two states adaptations to bird dispersal, with multiple origins among rainforest genera). Patterns of relationship and levels of sequence divergence in some taxa, mostly species, with bird-dispersed (Acronychia, Sarcomelicope, Halfordia and Melicope) or winged (Flindersia) seeds are consistent with recent long-distance dispersal between Australia and New Caledonia. Other deeper Australian/New Caledonian divergences, some involving ant-dispersed taxa (e.g., Neoschmidia), suggest older vicariance. CONCLUSIONS/SIGNIFICANCE: This comprehensive molecular phylogeny of the Australasian Rutoideae gives a broad overview of the group's evolutionary and biogeographic history. Deficiencies of infrafamilial classifications of Rutoideae have long been recognised, and our results provide a basis for taxonomic revision and a necessary framework for more focused studies of genera and species.

Divergent paralogues of ribosomal DNA in eucalypts (Myrtaceae).

The presence of divergent paralogues of nuclear ribosomal DNA, from the 18S-5.8S-26S cistron, is reported in members of Eucalyptus subg. Eucalyptus. These paralogues, which include non-functional pseudogenes, probably diverged prior to the differentiation of species groups in subg. Eucalyptus. When compared with presumably functional sequences, the pseudogenes show greater sequence variation between species, particularly in the 5.8S gene. They are also characterised by reduced GC content, associated with a reduced number of CpG and CpNpG methylation sites, and an increase in the inferred number of methylation-induced substitutions. Some pseudogenes also lack motifs that are usually conserved in plants, both in ITS1 and the 5.8S gene. Two main lineages of pseudogenes are identified, one isolated from a group of western Australian species, one from a group of eastern Australian species. It is not clear whether these two lineages of pseudogenes are orthologous, or represent independent divergences from functional sequence types. The presence of divergent rDNA paralogues highlights the need for caution when interpreting eucalypt phylogenies based on ITS sequences.

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.