Phylogeny of the holly grevilleas (Proteaceae) based on nuclear ribosomal and chloroplast DNA

Abstract

Abstract. The holly grevilleas are an informal grouping of 15 species (19 taxa) of woody shrubs from south-eastern Australia, with a centre of distribution in central to western Victoria. Many of the species are narrowly endemic. The present study is the first molecular-phylogenetic analysis of the group, with the aim of providing an evolutionary framework for assessing species-level taxonomy and conservation priorities. Analyses using the nrDNA internal transcribed spacer (ITS) regions were complicated by the presence of divergent paralogues, including inferred pseudogenes; analyses restricted to presumed orthologous, functional ITS sequences were uninformative. Combined analyses of three chloroplast intergenic spacers (trnQ-5 0 rps16, trnL-trnF and rpoB-trnC) strongly support the monophyly of a core group of 16 taxa (the 'southern holly grevilleas') from Victoria and South Australia. However, nodes outside this group are poorly resolved and poorly supported, and the relationships of taxa from New South Wales and eastern Victoria (the 'northern holly grevilleas') are unclear. Among the southern holly grevilleas, the following four distinct and partly sympatric cpDNA clades are identified: the 'Grevillea ilicifolia', 'G. aquifolium', 'G. dryophylla' and 'G. repens' clades, among which the earliest and most strongly supported divergence is that of the western-most 'G. ilicifolia' clade. Variation in cpDNA is incongruent with current species-level taxonomy, especially for G. aquifolium (polyphyletic), G. montis-cole (polyphyletic, but the two subspecies each monophyletic) and G. microstegia (nested in G. aquifolium). The effects of incomplete chloroplast lineage sorting, gene flow through hybridisation or introgression, and inappropriate taxonomy are possible explanations for this incongruence. The formal conservation listing for some species within the holly grevillea group requires re-evaluation.

Testing efficacy of distance and tree-based methods for DNA barcoding of grasses (Poaceae tribe Poeae) in Australia

“…Other studies (for example, [ 12 , 15 ]) have also indicated that ITS is an informative marker for DNA barcoding of grasses. However, the presence of multiple paralogous ITS copies [ 54 ], may complicate the interpretation of genetic distances among and within species. For this reason we consider its use, alongside other markers, representing chloroplast and nuclear genomes, to be more optimal than its use individually.…”

Chloroplast variation is incongruent with classification of the Australian bloodwood eucalypts (genus Corymbia, family Myrtaceae)

“…Our dataset included 66 accessions of Corymbia (representing all taxonomic sections), 15 of Angophora (9 of 10 species), 31 of Eucalyptus (the same species as in the cpDNA dataset, representing major lineages), two of Stockwellia , one of Eucalyptopsis , three of Allosyncarpia , and one of Arillastrum (used as outgroup). Partial sequences, or those identified as spacers associated with pseudogenes using established criteria [ 59 , 60 , 61 , 62 ], were excluded from analyses. We used existing nrDNA sequences for analyses, rather than assembling novel sequences from our current genomic data for Corymbia , because of the presence of substantial within-genome variation in our samples (in line with previous reports [ 38 , 59 , 60 ]), and associated difficulties in separating and assembling sequences of the various paralogues/alleles, which is a challenging task worthy of separate investigation and discussion.…”

Grevillea manglesii (Proteaceae: Grevilleoideae: Hakeinae) revisited

“…Results from techniques, not then available to McGillivray, but developed subsequently, to examine phylogeny and analyse relationships, have repeatedly shown that morphology is not necessarily a reliable guide to relationships. Holmes et al (2014) resolved Grevillea montis-cole subsp. brevistyla R.V.Sm.…”