Frank Udovicic

ETS sequences support the monophyly of the eucalypt genus Corymbia (Myrtaceae)

The generic classification of the eucalypts, especially recognition of the genus Corymbia, has been controversial. The phylogeny of Corymbia and related eucalypt groups was investigated using nuclear ETS sequences, and combined ETS and ITS sequences. Both the ETS and combined datasets support the monophyly of Corymbia. Three major eucalypt clades are confirmed: Corymbia + Angophora; Eucalyptus s.s.; and the Eucalyptopsis group. Within Corymbia, relationships are broadly consistent with phylogenies based on morphological and anatomical characters; sections Ochraria, Blakearia, and Politaria are all supported as monophyletic; sect. Rufaria is monophyletic with the inclusion of the monotypic sect. Apteria. Within Eucalyptus s.s., relationships are generally consistent with those shown by previous molecular studies. Within the Eucalyptopsis group, Allosyncarpia is sister to the clade Stockwellia + Eucalyptopsis. Relationships between the major eucalypt clades are equivocal, but combined analysis of ETS and ITS data shows Corymbia + Angophora as sister to Eucalyptus-the rainforest taxa of the Eucalyptopsis group being outside this clade. Patterns of relationship and distribution are consistent with differentiation of major lineages of Corymbia prior to the isolation of taxa (now relictual) in eastern and south-western Australia, arguably before the midMiocene.

Comment on a new classification of the eucalypts.

Brooker’s classification of the eucalypts, which combines Angophora, Corymbiaand Eucalyptus into one genus, is contrary to phylogenetic evidence based on eight different data sets including morphology, RFLPs, and sequence data for various regions of nuclear and chloroplast DNA (5S rDNA spacer region, ITS1, ITS2, trnL intron, trnL-F spacer and psbA-trnH spacer). On this evidence and the principle of recognising monophyletic taxa, we reject his synonymy of these genera.

Phylogeny, major clades and infrageneric classification of Corymbia (Myrtaceae), based on nuclear ribosomal DNA and morphology

Phylogenetic relationships of sections and species within Corymbia (Myrtaceae), the bloodwood eucalypts, were evaluated by using combined analyses of nuclear rDNA (ETS + ITS) and morphological characters. Combining morphological characters with molecular data provided resolution of relationships within Corymbia. The analyses supported the monophyly of the genus and recognition of the following two major clades, treated here as new subgenera: subgenus Corymbia, including informal sections recognised by Hill and Johnson (1995), namely Rufaria (red bloodwoods), Apteria and Fundoria; and subgenus Blakella, including sections Politaria (spotted gums), Cadagaria, Blakearia (paper-fruited bloodwoods or ghost gums) and Ochraria (yellow bloodwoods). Hill and Johnson’s section Rufaria is monophyletic if Apteria and Fundoria are included. It is evident that, among the red bloodwoods, series are not monophyletic and several morphological characters result from convergent evolution. There was strong morphological and molecular evidence that the three species of red bloodwoods that occur in south-western Western Australia (series Gummiferae: C. calophylla and C. haematoxylon, and series Ficifoliae: C. ficifolia) form a monophyletic group, separate from the eastern C. gummifera (series Gummiferae), which is probably sister to the clade of all other red bloodwoods. Phylogenetic results supported recognition of new taxonomic categories within Corymbia, and these are formalised here.

Molecular phylogeny and biogeography of Melaleuca, Callistemon and related genera (Myrtaceae)

To resolve the relationships of taxa within the Beaufortia suballiance (Myrtaceae), 72 ingroup taxa were analysed by parsimony methods and nrDNA sequence data from the 5S and ITS-1 ribosomal DNA spacer regions. Although basal nodes in the consensus tree (combined data set) are not supported by bootstrap or jackknife values, a number of clades are well supported, showing that Melaleuca is polyphyletic. Monophyletic groups include: endemic species of Melaleuca from New Caledonia (including species of Callistemon recently transferred to Melaleuca); the tropical Melaleuca leucadendra group; Australian species of Callistemon, which relate to species of Melaleuca predominantly from the South-East; and a group of south-western and eastern Australian melaleucas that relate to a clade of three south-western genera, Eremaea, Conothamnus and Phymatocarpus. Calothamnus, Regeliaand Beaufortiamay also relate to this latter group. Lamarchea is possibly related to northern melaleucas. The results have implications for generic revisions of the large genus Melaleuca. Biogeographic subtree analysis, based only on supported nodes of the taxon cladogram, showed New Caledonia, New Guinea, Eastern Queensland and the Northern Desert unresolved at the base of the area cladogram. The position of some of these areas is likely to be artifactual, but New Caledonia is interpreted as in the correct position. At a higher node, the monsoonal northern areas of Australia (Kimberley, Arnhem and Cape York), Atherton, the Pilbara and Western Desert relate to the southern regions, which form a group. The South-West of Australia is related to Eyre and Adelaide (designated area ‘South’) and Tasmania is related to the South-East and MacPherson–Macleay. The vicariance between northern and southern regions in Australia possibly relates to an early major climatic change (from the Early Tertiary). The biogeographic analysis helped illuminate taxon relationships.

Historical biogeographical patterns in continental Australia: congruence among areas of endemism of two major clades of eucalypts

Published phylogenies of two eucalypt clades, red bloodwoods Corymbia subgenus Corymbia and eudesmids Eucalyptus subgenus Eudesmia (Myrtaceae), were combined for an analysis of historical biogeographical area relationships within continental Australia. The method of paralogy‐free subtree analysis was used to eliminate geographical paralogy; the paralogy‐free subtrees were coded as characters for parsimony analysis to find the minimal and area cladogram, which proved to be informative of a continent‐wide pattern. The eucalypt fossil record and molecular dating studies allow an interpretation of the biogeographical history in terms of major vicariance events that date from the early Paleogene. The summary area cladogram shows the wet jarrah forest region of South‐West Western Australia, a region of high endemism, as the earliest to differentiate from all other areas, isolated by marine inundation across southern Australia and climatic cooling in the Late Eocene–Early Oligocene. From about this time, regionalization continued, with warmer conditions and monsoonal climate developing in central and northern Australia, and cooling in the south‐east. Northern and eastern humid and semi‐humid areas were related as a track, but with increased aridity in the interior of the continent, the monsoonal climate contracted northwards. The Australian Monsoon Tropics (AMT: Kimberley, Top End, Arnhem, Cape York and inland north‐east Queensland) differentiated from eastern areas (Queensland wet tropics to McPherson–Macleay). Our results also show all arid and semi‐arid regions as related, suggestive of a historically cohesive interior biota rather than repeated colonizations of the interior from the periphery of the continent. Climate largely differentiates hot arid areas in the north (Pilbara, Northern and Central deserts) from arid areas in the south (south‐west interzone, Wheatbelt, Goldfields and Great Victoria Desert).

Ribosomal DNA pseudogenes are widespread in the eucalypt group (Myrtaceae): implications for phylogenetic analysis

Pseudogenes from the 18S−5.8S−26S cistron of nuclear ribosomal DNA are reported in the eucalypt group (Myrtaceae), which includes seven genera. Putative pseudogenes are identified by a range of sequence comparisons including: the number of CpG and CpNpG methylation sites, GC content, estimated secondary structure stability of internal transcribed spacer transcripts, the presence of conserved motifs, patterns of sequence relationships and inferred substitution patterns. These comparisons indicate that pseudogenes are widespread, being evident in Eucalyptus (subgenera Eucalyptus and Eudesmia), Corymbia (extracodical sections Rufaria, Ochraria and Blakearia), Angophora, Stockwellia quadrifida and Arillastrum gummiferum. At least six sequences used in previous phylogenetic studies are identified as pseudogenes, and a further 10 pseudogenes are newly sequenced here. Gene trees place pseudogenes in a number of distinct lineages: pseudogenes from Eucalyptus group with other Eucalyptus sequences, those from Corymbia and Angophora group with other Corymbia/Angophora sequences, that from Stockwellia groups with other sequences from the Eucalyptopsis group, and that from Arillastrum is placed as sister to the other included sequence of Arillastrum. Some pseudogenes in Eucalyptus, Corymbia and Angophora represent “deep” ribosomal DNA paralogues that pre‐date species differentiation in these groups, and a recombination analysis shows no evidence of recombination between putative pseudogenes and their functional counterparts. The presence of divergent paralogues presents both challenges and opportunities for the reconstruction of eucalypt phylogenies using ribosomal DNA sequences. Phylogenetic data sets should include only orthologous sequences, but different paralogues potentially provide additional, independent, character sets for phylogenetic analyses.

Molecular phylogeny of three groups of acacias (Acacia subgenus Phyllodineae) in arid Australia based on the internal and external transcribed spacer regions of nrDNA

Abstract The phylogeny of three groups of arid Australian acacias ‐ the Acacia victoriae, A. murrayana and A. pyrifolia groups ‐ was constructed based on parsimony analysis of sequence data from the internal and external transcribed spacers (ITS and ETS) of the nuclear ribosomal DNA. Forty ingroup taxa were sequenced, including multiple accessions for some taxa and two species (A platycarpa and A. longispinea) that had been identified in other analyses as relatives of these acacias. Acacia anthochaera was used as the functional outgroup. The ITS and ETS regions proved to be sufficiently variable to resolve relationships at both the specific and intra‐specific level. Two main clades were resolved. One clade confirmed the monophyly of the Acacia murrayana group, and relationships of species were strongly supported. All taxa in this clade have a similar pattern of seedling leaf development. In the second clade, the A. pyrifolia group is nested within the A. victoriae group and all taxa have spinose stipules. Acacia platycarpa and A. longispinea are related to this clade. Phyllode nerve number (uninerved or plurinerved) proved to be homoplasious. Acacia victoriae is a widespread and very variable species. The molecular data identified two major groups: a group of populations occurring across northern Australia and a group of populations from the Western, Central and Eastern deserts. Further analysis of population variation is required to assess the taxonomic status of various forms in this species complex. The geographic distributions of sister taxa suggest predominantly allopatric speciation. The degree of molecular divergence and position of the clades within subgenus Phyllodineae suggest that the lineages are not of recent origin, but have a history that relates to increased aridity in the Australian Eremean region during the Cenozoic.

Phylogenetic analysis of Australian Acacia (Leguminosae: Mimosoideae) by using sequence variations of an intron and two intergenic spacers of chloroplast DNA

Three regions of chloroplast DNA are assessed for their utility for phylogenetic analysis of Acacia subgenus Phyllodineae: psbA–trnH intergenic spacer, the trnL intron and the trnL–trnF intergenic spacer. There are large differences in the lengths of the psbA–trnH spacer (155–440 bp) and trnL–trnF intergenic spacer (101–422 bp) regions, and large multi-residue indels were coded as multistate characters. Overall information content in these regions is relatively low, but the total evidence tree has 12 nodes resolved, five with jackknife support. By using Parkia timoriana as the outgroup, Acacia subgenus Acacia (A. farnesiana) is basal and Acacia subgenus Aculeiferum (A. senegal) is the sister taxon to subgenus Phyllodineae. Although based on a small sample size, within subgenus Phyllodineae, the results of this study have shown that section Alatae is not monophyletic, section Lycopodiifoliae is monophyletic and Botrycephalae is related to members of section Phyllodineae with racemose inflorescences.

Phylogenetic analysis and generic limits of the tribe Pomaderreae (Rhamnaceae) using internal transcribed spacer DNA sequences

The tribe Pomaderreae (Rhamnaceae) currently consists of approximately 180 species in seven genera, endemic to Australia and New Zealand. It is the second largest tribe of Rhamnaceae. We undertook a phylogenetic analysis using internal transcribed spacer (ITS) sequence data from 69 representative species of Pomaderreae and five outgroup taxa. The monophyly of Pomaderreae was confirmed. The clades found in the strict consensus tree are mostly consistent with the currently accepted genera of the tribe. All major clades, except Stenanthemum, received moderate to strong bootstrap and jackknife support. Only the relationship between Siegfriedia and Pomaderris received strong support; relationships between other genera did not receive support above 50%. Taxonomic changes are suggested and a preliminary classification of Pomaderreae is proposed, including the monophyletic genera Cryptandra, Pomaderris, Spyridium and Trymalium. Blackallia and Siegfriedia are monotypic. Two new genera are required: one containing two atypical species of Stenanthemum and the second genus consisting of previously unrelated species from three genera that share a 2-carpellate ovary and a characteristic indumentum. The taxonomic status of Stenanthemum requires further examination. A split of Cryplandra into smaller genera is not supported.

Phylogeny and classification of Eucalyptus subgenus Eudesmia (Myrtaceae) based on nuclear ribosomal DNA, chloroplast DNA and morphology

Phylogenetic analysis of Eucalyptus subgenus Eudesmia is presented on the basis of the following three datasets: sequences of the internal transcribed spacer (ITS) and the external transcribed spacer (ETS) regions from nuclear rDNA, sequences of the psbA–trnH intergenic spacer region from chloroplast DNA, and morphological characters, including stamen bundling, operculum development, seeds and trichomes. Studies of floral development were essential for understanding the morphology of mature flowers and interpretation of synapomorphy and homoplasy. A summary phylogeny was constructed from a maximum parsimony analysis of those nodes coded as characters that had support in the molecular trees together with morphological characters. A revised infra-subgeneric classification is presented on the basis of the summary phylogeny, and compared with classifications of Hill and Johnson (1998) and Brooker (2000). Differences relate to relationships between clades and taxonomic rank (sections, series and subseries) and valid names of Brooker (2000) are conserved where possible. One main clade of 14 species (section Limbatae), many of mallee growth form, was found in all analyses; this clade is distributed in the South-West of Western Australia and adjacent Interzone and desert areas. A second main clade (section Complanatae) occurs in the northern and eastern tropical and subtropical regions of Australia, including Kimberley, Arnhem, Queensland and New South Wales. This section includes E. tetrodonta, previously treated as an isolated taxon in a monotypic section; however, this species is related to E. baileyana, E. similis, E. lirata and series Miniatae. The hypothesised phylogeny provides a framework for further analyses of biogeography and ecology, including functional traits.