Gillian K. Brown

A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny

The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or cladebased classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

Acacia s.s. and its Relationship Among Tropical Legumes, Tribe Ingeae (Leguminosae: Mimosoideae)

Abstract To search for the sister taxon of Acacia s.s. (tribe Acacieae) and to further knowledge of the phylogeny of the related tribe Ingeae, we have sequenced two regions of nuclear ribosomal DNA (ITS and ETS). Sixty species from tribe Ingeae (26 genera), together with representatives from each of five lineages of tribe Acacieae, have been sampled. Ingeae and Acacia s.s. form a well supported clade, with a monophyletic Acacia s.s. nested within a paraphyletic Ingeae. Based on our sampling, the closest relative of Acacia s.s. is most likely one of the Australian species of the genus Paraserianthes s.l.: Paras. lophantha subsp. lophantha or Paras. toona. Related to Acacia s.s. and Paraserianthes s.l. is a group of Ingeae from Australia and South East Asia: Archidendron p.p., Archidendropsis, Pararchidendron, and Wallaceodendron. This study is a preliminary step in resolving the intergeneric relationships of tribe Ingeae. Genetic relationships within Ingeae appear to conform to morphological groups previously identified as genera and informal alliances; some notable exceptions are discussed.

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.

Phylogenetic connections of phyllodinous species of Acacia outside Australia are explained by geological history and human-mediated dispersal

Abstract. Acacia sensu stricto is found predominantly in Australia; however, there are 18 phyllodinous taxa that occur naturally outside Australia, north from New Guinea to Indonesia, Taiwan, the Philippines, south-western Pacific (New Caledonia to Samoa), northern Pacific (Hawaii) and Indian Ocean (Mascarene Islands). Our aim was to determine the phylogenetic position of these species within Acacia, to infer their biogeographic history. To an existing molecular dataset of 109 taxa of Acacia, we added 51 new accessions sequenced for the ITS and ETS regions of nuclear rDNA, including samples from 15 extra-Australian taxa. Data were analysed using both maximum parsimony and Bayesian methods. The phylogenetic positions of the extra-Australian taxa sampled revealed four geographic connections. Connection A, i.e. northern Australia–South-east Asia–south-western Pacific, is shown by an early diverging clade in section Plurinerves, which relates A. confusa from Taiwan and the Philippines (possibly Fiji) to A. simplex from Fiji and Samoa. That clade is related to A. simsii from southern New Guinea and northern Australia and other northern Australian species. Two related clades in section Juliflorae show a repeated connection (B), i.e. northern Australia–southern New Guinea–south-western Pacific. One of these is the ‘A. auriculiformis clade’, which includes A. spirorbis subsp. spirorbis from New Caledonia and the Loyalty Islands as sister to the Queensland species A. auriculiformis; related taxa include A. mangium, A. leptocarpa and A. spirorbis subsp. solandri. The ‘A. aulacocarpa clade’ includes A. aulacocarpa, A. peregrinalis endemic to New Guinea, A. crassicarpa from New Guinea and Australia, and other Australian species. Acacia spirorbis (syn. A. solandri subsp. kajewskii) from Vanuatu (Melanesia) is related to these two clades but its exact position is equivocal. The third biogeographic connection (C) is Australia–Timor–Flores, represented independently by the widespread taxon A. oraria (section Plurinerves) found on Flores and Timor and in north-eastern Queensland, and the Wetar island endemic A. wetarensis (Juliflorae). The fourth biogeographic connection (D), i.e. Hawaii–Mascarene–eastern Australia, reveals an extreme disjunct distribution, consisting of the Hawaiian koa (A. koa, A. koaia and A. kaoaiensis), sister to the Mascarene (Réunion Island) species A. heterophylla; this clade is sister to the eastern Australian A. melanoxylon and A. implexa (all section Plurinerves), and sequence divergence between taxa is very low. Historical range expansion of acacias is inferred to have occurred several times from an Australian–southern New Guinean source. Dispersal would have been possible as the Australian land mass approached South-east Asia, and during times when sea levels were low, from the Late Miocene or Early Pliocene. The close genetic relationship of species separated by vast distances, from the Indian Ocean to the Pacific, is best explained by dispersal by Austronesians, early Homo sapiens migrants from Asia.

Bipinnate acacias (Acacia subg. Phyllodineae sect. Botrycephalae) of eastern Australia are polyphyletic based on DNA sequence data

A phylogenetic analysis of Acacia subg. Phyllodineae sect. Botrycephalae, endemic to eastern Australia, is presented based on a combined dataset of ITS and ETS sequences of nrDNA. A smaller set of species was sequenced also for the cpDNA trnK region. A limited number of morphological characters was also combined with the ITS+ETS dataset for most taxa. Thirty-eight of 41 Botrycephalae species were sequenced, together with a sample of ten uninerved phyllodinous species (sect. Phyllodineae). Although these DNA regions showed limited sequence divergence, bootstrap supported nodes of the consensus ITS+ETS tree indicate that Botrycephalae as currently defined is polyphyletic. Eight bipinnate species fell outside the main clade of Botrycephalae species while seven phyllodinous species were nested within it, near the base. The few derived but homoplasious morphological characters that were discovered included: presence of appressed unicellular hairs, presence of jugary and interjugary glands, number of pinnae > 7 and the funicle half–fully encircling the seed. Section Botrycephalae requires redefinition.

Development of microsatellite loci in Triglochin procera (Juncaginaceae), a polyploid wetland plant

Eleven polymorphic microsatellite loci were developed from the polyploid wetland plant Triglochin procera (Juncaginaceae). Loci were screened for variability among 20 individuals from each of two populations in Victoria, Australia. The number of alleles amplified per locus ranged from 5 to 17, with a mean of 9.5. Nei’s genetic diversity (HE) ranged from 0.463 to 0.898 with a mean of 0.725. These primers provide the opportunity to use polymorphic DNA markers to study the population genetic structure, breeding system and dispersal in T. procera and related species.

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.

Microsatellite marker development for two species of holly-leafed Grevillea and cross-species amplification in the Aspleniifolia/Hookeriana Subgroup (Proteaceae)

We identified 14 informative microsatellite loci from two taxa, Grevillea aquifolium (6) and G. infecunda (8), belonging to the Pteridifolia Group, Aspleniifolia/Hookeriana Subgroup (Proteaceae). Loci were screened for variability among 20 individuals of their source species. The number of alleles observed per locus for G. infecunda ranged from 1 to 3. Subsequent chromosome counts revealed between 20 (normal diploid) and 30 (triploid) chromosomes in different individuals. High levels of variability were observed with the number of alleles per locus ranging from 3 to 17, with a mean of 9.8 across all loci. Nei’s genetic diversity (HE) ranged from 0.399 to 0.992 with a mean of 0.783. All loci amplified in a further 9–13 taxa from the same subgroup and under the same amplification conditions. These new markers provide useful tools for evolutionary and conservation studies assessing clonality and polyploidy in this important Australian genus.

Phylogenetic relationships of Rhododendron section Vireya (Ericaceae) inferred from the ITS nrDNA region

Rhododendron L. taxonomy has been tested in recent times by molecular phylogenies based on several DNA regions. Most of these studies have aimed at higher-level relationships, despite the importance of lower ranks, such as sections, to most workers on the genus. Almost one-third of the species of Rhododendron are placed in one of the lepidote (scaly) sections, section Vireya (Blume) Copel.f. Results of phylogenetic analyses of the ITS region (ITS-1, 5.8S and ITS-2) for the genus Rhododendron, with sampling concentrated on section Vireya, are presented. The results of Bayesian and parsimony analyses were predominantly congruent. Subgenus Rhododendron is inferred to be monophyletic, while two of the three sections, Rhododendron and Vireya, are polyphyletic; the monophyly of section Pogonanthum Aitch. & Hemsl. was not tested in this study. Relationships between the species of section Vireya do not correspond to the traditional classification based on morphology, instead correlating strongly with geographic areas, with a disjunction between an Australian–New Guinea clade and clades of west and middle Malesian taxa. The phylogeny also indicates that the ITS region may not undergo complete homogenisation in all species of Rhododendron.

classification of the Vireya group of rhododendron (ericaceae)

A new classification of the Vireya group of Rhododendron, based upon their evolutionary relationships as inferred from analysis of nuclear and plastid DNA sequence data, is presented. Rhododendron sect. Vireya is not monophyletic and its species are herein placed in three sections within subg. Rhododendron, namely sect. Discovireya, sect. Pseudovireya and sect. Vireya, with two subsections recognised within sect. Vireya: subsect. Euvireya and subsect. Malayovireya. Identification keys are provided.