Boletellus and Heimioporus, two genera of Boletaceae with ornamented basidiospores, are shown to be distinct genera on the basis of phylogenetic analyses of nuclear ribosomal large-subunit and translation elongation-factor 1α DNA sequences. Comparison of spore ornamentation type – longitudinally ribbed in Boletellus v. punctate, alveolate-reticulate in Heimioporus – are further evidence for distinction. Analyses of multiple accessions from the Americas, Asia and Australia support the monophyly of Heimioporus and a ‘core Boletellus’ clade, containing the type species, B. ananas (M.A.Curt.) Murrill, and approximately seven additional species. Tests of alternative phylogenetic topologies could not reject monophyly of a more inclusive group containing the core Boletellus clade and six other species. Heimioporus australis Fechner & Halling, H. cooloolae Fechner & Halling, Boletellus deceptivus Halling & Fechner, B. reminiscens Halling & Fechner and B. sinapipes Fechner, K.Syme, R.Rob. & Halling are described as new species. Phylogenetic analyses also support the following new combinations: Aureoboletus projectellus (Murrill) Halling, A. mirabilis (Murrill) Halling, Hemileccinum subglabripes (Peck) Halling and the new name, Xerocomus tenax Nuhn & Halling.

Several range disjunctions have been identified in the Australian species of the genus Terminalia L. Field studies and examination of herbarium specimens of taxa with range disjunctions have demonstrated that taxonomic changes are justified. Detailed morphological studies of the Terminalia canescens (DC.) Radlk. species complex showed that four taxa should be recognised. The name Terminalia circumalata F.Muell. is resurrected as a taxon endemic to the Pilbara region, with T. canescens not occurring in that region. The distinction of Terminalia bursarina F.Muell., T. canescens and T. pterocarya F.Muell. is also supported. Terminalia cunninghamii C.A.Gardner has been considered to have a disjunct range between the far north and south-west of the Kimberley region of Western Australia. Terminalia kumpaja R.L.Barrett is described as a new species to accommodate the disjunct southern populations because morphological examination has shown them to be distinct. Terminalia kumpaja is restricted to the Dampier Botanical District. Full descriptions and illustrations of key identifying features are provided for these species. Keys to all Australian Terminalia species are presented. Additional species with disjunct distributions that warrant further study are noted. Lectotypes are selected for Terminalia circumalata and T. rogersii W.Fitzg.

Sequence alignment is just as much a part of phylogenetics as is tree building, although it is often viewed solely as a necessary tool to construct trees. However, alignment for the purpose of phylogenetic inference is primarily about homology, as it is the procedure that expresses homology relationships among the characters, rather than the historical relationships of the taxa. Molecular homology is rather vaguely defined and understood, despite its importance in the molecular age. Indeed, homology has rarely been evaluated with respect to nucleotide sequence alignments, in spite of the fact that nucleotides are the only data that directly represent genotype. All other molecular data represent phenotype, just as do morphology and anatomy. Thus, efforts to improve sequence alignment for phylogenetic purposes should involve a more refined use of the homology concept at a molecular level. To this end, we present examples of molecular-data levels at which homology might be considered, and arrange them in a hierarchy. The concept that we propose has many levels, which link directly to the developmental and morphological components of homology. Of note, there is no simple relationship between gene homology and nucleotide homology. We also propose terminology with which to better describe and discuss molecular homology at these levels. Our over-arching conceptual framework is then used to shed light on the multitude of automated procedures that have been created for multiple-sequence alignment. Sequence alignment needs to be based on aligning homologous nucleotides, without necessary reference to homology at any other level of the hierarchy. In particular, inference of nucleotide homology involves deriving a plausible scenario for molecular change among the set of sequences. Our clarifications should allow the development of a procedure that specifically addresses homology, which is required when performing alignment for phylogenetic purposes, but which does not yet exist.

The genus Epacris Cav. (Ericaceae, Epacridoideae, Epacrideae) contains 46 species in south-eastern Australia and two species in New Zealand. Two small genera, Rupicola Maiden & Betche (four spp.) and Budawangia I.Telford (monotypic), both having restricted distributions in the mountains of central eastern New South Wales, have been generally regarded as closely related to but distinct from Epacris. We tested the monophyly and relationships of these three genera using parsimony and Bayesian analysis of morphological and plastid atpB–rbcL DNA sequence datasets. Separate and combined analyses all place Budawangia and Rupicola within Epacris with moderate to strong support. We conclude that there are insufficient grounds for maintaining Rupicola and Budawangia as distinct from Epacris. The required nomenclatural changes are made herein.