No abstract

Parsimony analysis of matK and rbcL sequence data, together with a nonmolecular database, yielded a well-resolved phylogeny of Cupressaceae sensu lato. Monophyly of Cupressaceae sensu stricto is well supported, and separate northern and southern hemisphere subclades are resolved, with Tetraclinis within the northern subclade; there is no support for any of the tribes sensu Li. Taxodiaceae comprise five separate lineages. Chamaecyparis nootkatensis falls within Cupressus, clustering with a robust clade of New World species. Libocedrus Florin is paraphyletic and should incorporate Pilgerodendron. Evolution of several characters of wood and leaf anatomy and chemistry is discussed in light of this estimate of the phylogeny; numerous parallelisms are apparent. A new infrafamilial classification is proposed in which seven subfamilies are recognized: Callitroideae Saxton, Athrotaxidoideae Quinn, Cunninghamioideae (Sieb. & Zucc.) Quinn, Cupressoideae Rich. ex Sweet, Sequoioideae (Luerss.) Quinn, Taiwanioideae (Hayata) Quinn, Taxodioideae Endl. ex K. Koch. The rbcL sequence for Taxodium distichum is corrected, and the implications for a previously published estimate of the minimum rate of divergence of the gene since the Miocene are highlighted.

Rutaceae is a family of angiosperms well known for the economically important genus Citrus. The division of Rutaceae into subfamilies is still inadequate and provisional. Previous phylogenetic studies at the family level are characterized by a limited sampling of genera and lack several crucial taxa. Here, we present a phylogenetic study based on six nuclear and plastid markers including 87.7% of the currently accepted genera, which is more than twice as many as in previous studies. Seven genera are included in a phylogenetic analysis for the first time. Most clades are resolved with high support, and we propose a new subfamily classification for Rutaceae that comprises the subfamilies Amyridoideae, Aurantioideae, Cneoroideae, Haplophylloideae, Rutoideae and Zanthoxyloideae. Aurantioideae is the only traditional subfamily that is resolved as monophyletic. We tested whether 13 morphological and karyological characters are taxonomically informative in Rutaceae. Chromosome numbers are clearly different in the two main clades of Rutaceae, but fruit characteristics, which have been used to define subfamilies in the past, do not distinguish between the main lineages of the family.

The monophyly of Boronia (Rutaceae) was tested using 134 accessions of 120 species belonging to 39 genera from subfamily Amyridoideae. Taxa included representatives of all eight sections of Boronia plus species of most genera in the two main clades related to Boronia that had been identified by earlier studies. These samples included a good representation of genera from both rainforest and sclerophyllous biomes. Maximum parsimony and Bayesian inference analyses were performed using three plastid markers (psbA‐trnH, trnL‐trnF, rbcL) and two nuclear ribosomal markers (ITS, ETS). Separate analyses of plastid and nuclear sequences using either maximum parsimony or Bayesian inference analyses recovered similar topologies. Apart from Boronia, the broad generic relationships of previous analyses were largely supported. Boronia is polyphyletic with section Cyanothamnus being more closely related to a large clade containing genera found in rainforest, including Melicope, Acronychia and their relatives. The remaining seven sections of Boronia formed a strongly supported and isolated group. Boronia sensu stricto is sister to a clade containing the Cyanothamnus‐Melicope‐Acronychia clade plus a clade containing Euodia, Zieria and other small genera found in rainforest or sclerophyllous communities. Issues with circumscriptions of ingroups and outgroups for previous analyses of Boronia and the complex relationship between Australasian genera found in rainforest and sclerophyllous communities are both discussed. Cyanothamnus is reinstated at generic level. Appropriate nomenclatural changes are made to transfer all currently recognised series, species, subspecies and varieties of Boronia sect. Cyanothamnus to the genus Cyanothamnus.

In this study we show how the use of exon-primed, intron-crossing (EPIC) polymerase chain reaction (PCR) of a diploid intronic region, in conjunction with temperature gradient gel electrophoresis (TGGE), can be used to detect and rapidly assess allelic variation at the nucleotide level. We developed passerine-specific primers to amplify and sequence a 762 bp region including the second intron of the myoglobin gene in the Gouldian Finch, Erythrura gouldiae. A POLAND plot based on this sequence indicated that TGGE in combination with heteroduplex analysis (TGGE/HA) should reveal nucleotide variation in the 160 bp low-melting domain. Sequencing of the entire fragment from 19 Er. gouldiae revealed five nucleotide substitution differences within the low-melt domain, all of which could be detected and differentiated by TGGE/HA, and an additional substitution in a section of the high-melt domain which characterised another allele. A total of 181 individuals from four populations were screened for these six alleles.

Leptospermum is an ecologically and economically important genus with a long unresolved taxonomic issue concerning polyphyly, as indicated from early molecular analysis on two chloroplast regions. To resolve this, we used genome skimming to obtain high‐copy chloroplast and nuclear ribosomal DNA for a comprehensive phylogenomic analysis of 110 accessions comprising of 38 Leptospermum taxa, 6 closely allied genera and 5 outgroup genera. Maximum likelihood and Bayesian analyses resolved congruent clades for the chloroplast (132,143 bp: 80 CDSs, 4 rRNA genes, 29 tRNA genes, 17 introns and 97 IGSs) and nuclear (1219 bp: ITS1, ITS2, ETS, 5.8S) alignments to provide a robust interpretation of evolutionary relationships. Together, these data confirmed extensive polyphyly of Leptospermum that separated the genus into five monophyletic clades spread amongst clades representing six closely allied genera: Agonis, Asteromyrtus, Homalospermum, Kunzea, Neofabricia and Pericalymma. These five Leptospermum clades share some similarities with morphological and genetic groupings identified previously but provide greater resolution to inform a clear pathway to taxonomic revision. The evidence presented here provides support for resolution of the current polyphyly of Leptospermum through the recognition of five genera, while retaining all other genera of Leptospermeae in their current circumscription.

All enquiries and manuscripts should be directed to:An international journal devoted t o t h e t a x o n o my, b i o g e o g r a p hy and evolution of all plant groups a u s t r a l i a n s y s t e m a t i c b o t a n yAbstract. Analysis of sequence data from the matK gene and the atpβ-rbcL intergenic spacer for 70 representatives of the Chamelaucium alliance sensu Briggs and Johnson (1979) provides strong support for the monophyly of the alliance, but there is no support for their concept of suballiances on the basis of fruit type: indehiscent fruit have arisen in multiple lineages. There is, however, strong support for Calytrix, Homalocalyx and Ochrosperma being the first lineages to diverge within the alliance. A number of genera within the alliance are not monophyletic in this analysis, namely Astartea, Babingtonia, Baeckea sensu lato, Darwinia and Hypocalymma.

Parsimony analyses of sequence data derived from two regions of the chloroplast genome, matK and the atpB-rbcL intergenic spacer, separately and together, are reported for Styphelieae. Taxonomic sampling includes representatives of all currently accepted genera apart from the two non-Australian monotypics, Cyathopsis Brongn. & Gris and Decatoca F.Muell., and of all subgenera or informal infrageneric groups except for Trochocarpa subgenus Pseudocyathodes Sleumer. A well resolved estimate of the phylogeny of the tribe is obtained, with high levels of jackknife support for terminal groupings. The results provide support for the current concepts of Acrotriche R.Br., Androstoma Hook.f., Croninia J.M.Powell, Cyathodes Labill. sensu Weiller, Leptecophylla C.M.Weiller, Leucopogon R.Br. sensu Taaffe et al., Pentachondra R.Br., Planocarpa C.M.Weiller and Trochocarpa R.Br., but the following genera appear paraphyletic: Astroloma R.Br., Brachyloma Sond., Cyathodes sensu Labill., Leucopogon R.Br. sensu lato, Lissanthe R.Br., Monotoca R.Br. and Styphelia Sm. (sensu Bentham). Several robust clades are identified as potential new genera but formalisation of nomenclatural changes is left, pending morphological analyses of the various clades to identify synapomorphies with which to characterise generic groupings. The general approach to be adopted in this endeavour is discussed, with narrower generic concepts being favoured as more informative and less disruptive of the existing nomenclature.