Mark G. Harrington

Evolution of exceptional species richness among lineages of fleshy-fruited Myrtaceae

BACKGROUND AND AIMS The angiosperm family Myrtaceae comprises 17 tribes with more than half of the estimated 5500 species being referred to the fleshy-fruited and predominantly rainforest associated Syzygieae and Myrteae. Previous studies suggest that fleshy fruits have evolved separately in these lineages, whereas generally shifts in fruit morphology have been variously implicated in diversification rate shifts among angiosperms. A phylogenetic hypothesis and estimate divergence times for Myrtaceae is developed as a basis to explore the evidence for, and drivers of, elevated diversification rates among the fleshy-fruited tribes of Myrtaceae. METHODS Bayesian phylogenetic analyses of plastid and nuclear DNA sequences were used to estimate intertribal relationships and lineage divergence times in Myrtaceae. Focusing on the fleshy-fruited tribes, a variety of statistical approaches were used to assess diversification rates and diversification rate shifts across the family. KEY RESULTS Analyses of the sequence data provide a strongly supported phylogenetic hypothesis for Myrtaceae. Relative to previous studies, substantially younger ages for many of the clades are reported, and it is argued that the use of flexible calibrations to incorporate fossil data provides more realistic divergence estimates than the use of errorless point calibrations. It is found that Syzygieae and Myrteae have experienced elevated diversification rates relative to other lineages of Myrtaceae. Positive shifts in diversification rate have occurred separately in each lineage, associated with a shift from dry to fleshy fruit. CONCLUSIONS Fleshy fruits have evolved independently in Syzygieae and Myrteae, and this is accompanied by exceptional diversification rate shifts in both instances, suggesting that the evolution of fleshy fruits is a key innovation for rainforest Myrtaceae. Noting the scale dependency of this hypothesis, more complex explanations may be required to explain diversification rate shifts occurring within the fleshy-fruited tribes, and the suggested phylogenetic hypothesis provides an appropriate framework for this undertaking.

Phylogenetic Inference in Sapindaceae sensu lato Using Plastid matK and rbcL DNA Sequences

Abstract Phylogenetic relationships within Sapindaceae sensu lato are assessed using sequence data from two plastid genes, analyzed separately and together. A total of 46 rbcL sequences (31 of which are new), and 89 matK sequences (75 new) representing 64 genera were subjected to parsimony and Bayesian analysis. The results support three major lineages, relationships between which are only weakly supported. Xanthoceras sorbifolium is not clearly a member of any of these lineages, and there is some support for it being the first lineage to diverge within the entire assemblage. Support for a broadly defined Sapindaceae incorporating Aceraceae, Hippocastanaceae, and Xanthoceras is very robust. A division into four subfamilies is proposed: Sapindoideae (including Koelreuteria and Ungnadia); Hippocastanoideae (including taxa previously referred to Aceraceae and Hippocastanaceae, plus Handeliodendron); a more narrowly defined Dodonaeoideae; and a monotypic Xanthoceroideae. Tribal groupings are critically evaluated in light of the analyses. Although many of the current tribes appear paraphyletic or polyphyletic, there is support for the monophyly of some core groups of genera that suggest realignments of tribal concepts that would render them more informative of relationships.

Plant DNA Barcodes Can Accurately Estimate Species Richness in Poorly Known Floras

Background Widespread uptake of DNA barcoding technology for vascular plants has been slow due to the relatively poor resolution of species discrimination (∼70%) and low sequencing and amplification success of one of the two official barcoding loci, matK. Studies to date have mostly focused on finding a solution to these intrinsic limitations of the markers, rather than posing questions that can maximize the utility of DNA barcodes for plants with the current technology. Methodology/Principal Findings Here we test the ability of plant DNA barcodes using the two official barcoding loci, rbcLa and matK, plus an alternative barcoding locus, trnH-psbA, to estimate the species diversity of trees in a tropical rainforest plot. Species discrimination accuracy was similar to findings from previous studies but species richness estimation accuracy proved higher, up to 89%. All combinations which included the trnH-psbA locus performed better at both species discrimination and richness estimation than matK, which showed little enhanced species discriminatory power when concatenated with rbcLa. The utility of the trnH-psbA locus is limited however, by the occurrence of intraspecific variation observed in some angiosperm families to occur as an inversion that obscures the monophyly of species. Conclusions/Significance We demonstrate for the first time, using a case study, the potential of plant DNA barcodes for the rapid estimation of species richness in taxonomically poorly known areas or cryptic populations revealing a powerful new tool for rapid biodiversity assessment. The combination of the rbcLa and trnH-psbA loci performed better for this purpose than any two-locus combination that included matK. We show that although DNA barcodes fail to discriminate all species of plants, new perspectives and methods on biodiversity value and quantification may overshadow some of these shortcomings by applying barcode data in new ways.

Molecular systematics of the Acmena alliance (Myrtaceae): phylogenetic analyses and evolutionary implications with reference to Australian taxa

The existence within Australia of several Acmena alliance taxa with morphological features inconsistent with current generic boundaries has meant that phylogenetic assessment of relationships has proved difficult. Sequences of nrDNA from the ITS and ETS regions were obtained for 66 Australian taxa, including representatives from both subfamilies and five genera. The ingroup taxa included 54 Australian endemics and 13 species with distributions that also range outside continental Australia. Parsimony analysis and Bayesian inference of posterior possibilities from the combined molecular datasets do not correlate with the species associations implied by the current taxonomic circumscription of genera: Acmena, Acmenosperma, Anetholea, Syzygium and Waterhousea. The molecular phylogeny recognises five supported lineages within the Acmena alliance, and several novel species associations. The recognition of five species groups indicates a need for a reappraisal of all currently recognised morphological groups within the alliance.

Cenozoic extinction and recolonization in the New Zealand flora: The case of the fleshy-fruited epacrids (Styphelieae, Styphelioideae, Ericaceae)

The origins and evolutionary history of the New Zealand flora has been the subject of much debate. The recent description of Cyathodophyllum novaezelandieae from early Miocene sediments in New Zealand provides possible evidence for the antiquity of the fleshy fruited epacrids (tribe Styphelieae, Ericaceae) in New Zealand. Yet the extant species in this tribe are thought to be very closely related to or conspecific with Australian taxa, suggesting recent trans-Tasman origins. In order to investigate the origins and evolution of the extant New Zealand Styphelieae we produced molecular phylogenetic trees based on sequences of three plastid regions that include representatives of all the genera of the tribe and eight of the ten New Zealand species. We estimated the range of minimum ages of the New Zealand lineages with Bayesian relaxed-clock analyses using different calibration methods and relative dating. We found strong support for each of the eight extant species of New Zealand Styphelieae being a distinct lineage that is nested within an Australian clade. In all except one case the sister is from Tasmania and/or the east coast of mainland Australia; for Acrothamnus colensoi the sister is in New Guinea. Estimated dates indicate that all of the New Zealand lineages diverged from their non-New Zealand sisters within the last 7 Ma. Time discontinuity between the fossil C.novae-zelandiae (20-23 Ma) and the origins of the extant New Zealand lineages (none older than 5 Ma) indicates that the fossil and extant Styphelieae in New Zealand are not related. The relative dating analysis showed that to accept this relationship, it would be necessary to accept that the Styphelieae arose in the early-mid Mesozoic (210-120 Ma), which is starkly at odds with multiple lines of evidence on the age of Ericales and indeed the angiosperms. Therefore, our results do not support the hypothesis that Styphelieae have been continuously present in New Zealand since the early Miocene. Instead they suggest a historical biogeographical scenario in which the lineage to which C. novae-zelandiae belongs went extinct in New Zealand, and the extant New Zealand Styphelieae are derived from Australian lineages that recolonised (presumably by long distance dispersal) no earlier than the late Miocene to Pliocene.

Phylogenetic revision of Backhousieae (Myrtaceae): Neogene divergence, a revised circumscription of Backhousia and two new species

Abstract. Backhousieae is a small tribe of Myrtaceae composed of two genera (Backhousia and Choricarpia) endemic to Australia. Phylogenetic analyses (parsimony, maximum likelihood and Bayesian) were performed on a combined chloroplast (matK, trnH–psbA, trnC–psbM, trnL–F, rps16) and nuclear (internal transcribed spacers) dataset for all nine species of Backhousia, two species of Choricarpia and two undescribed species. Backhousieae is monophyletic; however, Choricarpia is embedded within Backhousia. In all analyses there were four strongly supported clades containing two to four taxa, with no support for relationships among clades, and the relationships of B. bancroftii and B. citriodora remain unresolved. Bayesian relaxed-clock molecular dating indicated that the Backhousieae has been potentially present in rainforest across Australia for more than 50 million years. The current distribution of Backhousia is inferred to be largely due to the contraction of Australian rainforest in the Neogene. New combinations in Backhousia are made for the two species of Choricarpia, and B. gundarara and B. tetraptera are described as new species. B. gundarara is known only from the Kimberley region of Western Australia, widely disjunct from the remaining Backhousia in eastern Queensland and New South Wales, and appears to be a lineage isolated by increasing aridity during the Miocene.

A five-marker molecular phylogeny of the Styphelieae (Epacridoideae, Ericaceae) supports a broad concept of Styphelia

Abstract. The Styphelieae is the largest of the seven tribes within the subfamily Epacridoideae Arn. (Ericaceae Juss.). Recent molecular phylogenetic work has resulted in the recircumscription of some genera and the erection of new ones, but several non-monophyletic genera remain. Most of them are concentrated in the well-supported Styphelia–Astroloma clade, which contains species currently assigned to Leucopogon R.Br., Styphelia Sm., Astroloma R.Br., Croninia J.M. Powell and Coleanthera Stschegl. Parsimony and Bayesian analyses of sequence data from four plastid markers (rbcL, matK, trnH–psbA, and atpB–rbcL), and the nuclear ribosomal internal transcribed spacer (ITS) for 207 taxa corroborate the polyphyly of the genera Astroloma, Leucopogon and Styphelia and resolve 12 well supported groups. Of these groups, two can be distinguished by unique morphological features and another six by different character combinations. The remaining groups are morphologically heterogeneous and inconsistent, and not readily distinguishable. A number of species remain ungrouped either because their phylogenetic relationships are not clear or because they do not show strong morphological affinities with the group to which they have a close phylogenetic relationship. Translating the results into a phylogenetic classification is a choice between accepting a single, large genus or at least 12 smaller genera. The first option would result in a heterogeneous assemblage conveying limited morphological information. The multi-generic option would be a better reflection of the morphological diversity of the clade, but would result in many genera lacking readily observable, diagnostic morphological characters. We prioritise the nomenclatural stability inherent in the former approach and advocate expanding Styphelia to include all taxa in the Styphelia–Astroloma clade.

Phylogenetics of hopbushes and pepperflowers (Dodonaea, Diplopeltis – Sapindaceae), based on nuclear ribosomal ITS and partial ETS sequences incorporating secondary-structure models

Hopbushes and pepperflowers (Dodonaea, Diplopeltis – Sapindaceae) are important components of Australia’s arid zone and sclerophyll and temperate forests and woodlands. Phylogenetic analyses of nuclear ribosomal ITS and partial ETS sequences for near-complete sampling of both genera were performed using a Bayesian statistical method and RNA specific models of nucleotide evolution that incorporate secondary structure (separate models for stems and loops). Diplopeltis is paraphyletic. Diplopeltis stuartii is not closer to other species of the genus than it is to species outside the genus. There are also several evolutionary elements in the molecular data that support D. stuartii as distinct from the other members of the genus. The monophyly of Dodonaea as redefined here to include all species of Distichostemon is unequivocally supported by the molecular data and the morphological synapomorphies of petal-less flowers with a highly reduced intrastaminal disk that is absent in staminate flowers. There do not appear to be any obvious evolutionary trends in the morphological characters (leaf and capsule form, presence or absence of aril, or breeding system) that have been previously used to group taxa. However, there are some morphological characters that may be useful to delineate some of the clades recovered in the present molecular study. New combinations in Dodonaea are made for all species of Distichostemon.

Population genetic structuring in a rare tropical plant: Idiospermum australiense (Diels) S.T. Blake

Idiospermum australiense (Diels) S.T. Blake is considered to be one of the few remaining species of an ancient assemblage to have survived the attrition of Australian tropical rain forest during historically drier periods. This monotypic species is currently restricted to two very wet lowland rain forest locations in Australia’s wet tropical World Heritage Area that are thought to have provided refuge for humid-adapted taxa during the last glacial maximum. Two dominant (RAPD and ISSR) molecular marker sets were employed to investigate whether the genetic structure of Idiospermum could be attributed to its restriction to these quite disjunct localities. The results reveal that neither its restriction to purported Pleistocene refugia nor the geographic distance between populations could fully explain the distribution of variation in the Idiospermum data set, with evidence to suggest that potentially deeper time events have played a role in population structuring and the distribution of diversity. Although there is sufficient evidence in the data to suggest that gene dispersal is quite limited in the species, further investigation is still needed to yield more informative detail on additional factors, such as breeding and germination strategies and their potential influence over population structuring and diversity levels within each population and refugium.