Darren M. Crayn

Phylogeny, adaptive radiation, and historical biogeography in Bromeliaceae: Insights from an eight-locus plastid phylogeny

PREMISE Bromeliaceae form a large, ecologically diverse family of angiosperms native to the New World. We use a bromeliad phylogeny based on eight plastid regions to analyze relationships within the family, test a new, eight-subfamily classification, infer the chronology of bromeliad evolution and invasion of different regions, and provide the basis for future analyses of trait evolution and rates of diversification. METHODS We employed maximum-parsimony, maximum-likelihood, and Bayesian approaches to analyze 9341 aligned bases for four outgroups and 90 bromeliad species representing 46 of 58 described genera. We calibrate the resulting phylogeny against time using penalized likelihood applied to a monocot-wide tree based on plastid ndhF sequences and use it to analyze patterns of geographic spread using parsimony, Bayesian inference, and the program S-DIVA. RESULTS Bromeliad subfamilies are related to each other as follows: (Brocchinioideae, (Lindmanioideae, (Tillandsioideae, (Hechtioideae, (Navioideae, (Pitcairnioideae, (Puyoideae, Bromelioideae))))))). Bromeliads arose in the Guayana Shield ca. 100 million years ago (Ma), spread centrifugally in the New World beginning ca. 16-13 Ma, and dispersed to West Africa ca. 9.3 Ma. Modern lineages began to diverge from each other roughly 19 Ma. CONCLUSIONS Nearly two-thirds of extant bromeliads belong to two large radiations: the core tillandsioids, originating in the Andes ca. 14.2 Ma, and the Brazilian Shield bromelioids, originating in the Serro do Mar and adjacent regions ca. 9.1 Ma.

Phylogenetic Classification of Ericaceae: Molecular and Morphological Evidence

A new classification of Ericaceae is presented based on phylogenetic analyses of nuclear and chloroplast DNA sequence data, morphology, anatomy, and embryology. Eight subfamilies and 20 tribes are recognized. In this classification Epacridaceae are included as Styphelioideae and Empetraceae as tribe Empetreae within the Ericoideae. The herbaceous taxa previously recognized as Pyrolaceae and Monotropaceae by some authors are also included within Ericaceae, in the subfamily Monotropoideae. A key, morphological descriptions, and representative images are provided for all named groups. Two new combinations inKalmia (K. buxifolia andK. procumbens) are made, and three new taxa are described: Oligarrheneae, Richeeae, and Cosmelieae (all within Styphelioideae).ResumenSe presenta una clasificación nueva de las Ericaceae basada en análisis filogenéticos, empleando secuencias de ADN nuclear y de cloroplasto, morfología, anatomía y embriología. Se reconocen ocho subfamilias y 20 tribus. En esta clasificación las Epacridaceae son incluídas como Styphelioideae y las Empetraceae como la tribu Empetreae dentro de Ericoideae. Los grupos herbáceos previamente reconocidos como Pyrolaceae y Monotropaceae por algunos autores también se incluyen dentro de las Ericaceae, en la subfamilia Monotropoideae. Se dan una clave, descripciones morfológicas e imágenes representativas de todos los grupos nombrados. Se hacen dos combinaciones nuevas enKalmia (K. buxifolia yK. procumbens), y se describen tres nuevos taxones: Oligarrheneae, Richeeae y Cosmelieae (todos dentro de Styphelioideae).

Speciation with gene flow on Lord Howe Island

Understanding the processes underlying the origin of species is a fundamental goal of biology. It is widely accepted that speciation requires an interruption of gene flow between populations: ongoing gene exchange is considered a major hindrance to population divergence and, ultimately, to the evolution of new species. Where a geographic barrier to reproductive isolation is lacking, a biological mechanism for speciation is required to counterbalance the homogenizing effect of gene flow. Speciation with initially strong gene flow is thought to be extremely rare, and few convincing empirical examples have been published. However, using phylogenetic, karyological, and ecological data for the flora of a minute oceanic island (Lord Howe Island, LHI), we demonstrate that speciation with gene flow may, in fact, be frequent in some instances and could account for one in five of the endemic plant species of LHI. We present 11 potential instances of species divergence with gene flow, including an in situ radiation of five species of Coprosma (Rubiaceae, the coffee family). These results, together with the speciation of Howea palms on LHI, challenge current views on the origin of species diversity.

Molecular phylogeny and dating reveals an Oligo-Miocene radiation of dry-adapted shrubs (former Tremandraceae) from rainforest tree progenitors (Elaeocarpaceae) in Australia

To better understand the historical biogeography of the southern hemisphere and evolutionary responses of plants to aridity, we undertook a detailed phylogenetic study of the predominantly southern family Elaeocarpaceae sensu lato (including Tremandraceae). Plastid trnL-trnF and nuclear ITS sequence data were analyzed using parsimony and Bayesian methods and molecular evolutionary rates calibrated using the Oligocene fossil record of Elaeocarpus mesocarps to estimate the minimum divergence dates. The results indicate the monophyly of all recognized genera and a placement for the former Tremandraceae (three genera and about 49 species of shrubby, dry-adapted Australian plants) within the widespread predominantly rainforest tree family Elaeocarpaceae (nine genera, over 500 species). The former Tremandraceae clade diverged from its sister (Aceratium + Elaeocarpus + Sericolea) during the Paleocene, after which it underwent a marked acceleration in evolutionary rate. Furthermore, this lineage diversified during the late Miocene, coincident with widespread aridification in Australian environments and extensive radiations of several sclerophyllous groups. The role of dispersal in explaining the current geographical distribution of Elaeocarpaceae is illustrated by Aristotelia. This genus, whose distribution was previously thought to reflect Gondwanan vicariance, is shown to have arrived in New Zealand from Australia at least 6-7 million yr ago.

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.

The influence of environment and life‐history traits on the distribution of genes and individuals: a comparative study of 11 rainforest trees

This study investigates patterns of genetic connectivity among 11 co‐distributed tropical rainforest tree species from the genus Elaeocarpus across a biogeographic barrier, the Black Mountain Corridor (BMC) in the Australian Wet Tropics (AWT). We analysed a combination of allelic and flanking region sequence data from microsatellite markers, and evaluated the relative influence of environmental preferences and functional traits on genetic diversity and gene flow. The results indicate that only in three species geographic structuring of haplotype distribution reflects a north vs. south of the BMC pattern. Environmental factors linked with altitude were recognized as affecting genetic trends, but the selective processes operating on upland species appear to be associated with competitiveness and regeneration opportunities on poor soil types rather than climate variables alone. In contrast to previous observations within southeastern Australian rainforests, genetic differentiation in the AWT appears to be associated with small‐fruited rather than large‐fruited species, highlighting how external factors can influence the dispersal dimension. Overall, this study emphasizes the importance of considering functional and environmental factors when attempting generalizations on landscape‐level patterns of genetic variation. Understanding how plant functional groups respond to environmental and climatic heterogeneity can help us predict responses to future change.

Australian Oryza: utility and conservation

Australian Oryza are an understudied and underexploited genetic resource for rice improvement. Four species are indigenous: Oryza rufipogon, Oryza meridionalis, Oryza australiensis are widespread across northern Australia, whereas Oryza officinalis is known from two localities only. Molecular analysis of these wild populations is required to better define the distinctness of the taxa and the extent of any gene flow between them and rice. Limited collections of these wild populations are held in seed and DNA banks. These species have potential for domestication in some cases but also have many traits of potential value in the improvement of domesticated rice. Stress tolerance (biotic and abiotic) and grain quality characteristics in these populations may be useful.

Phylodiversity to inform conservation policy: An Australian example

Phylodiversity measures summarise the phylogenetic diversity patterns of groups of organisms. By using branches of the tree of life, rather than its tips (e.g., species), phylodiversity measures provide important additional information about biodiversity that can improve conservation policy and outcomes. As a biodiverse nation with a strong legislative and policy framework, Australia provides an opportunity to use phylogenetic information to inform conservation decision-making. We explored the application of phylodiversity measures across Australia with a focus on two highly biodiverse regions, the south west of Western Australia (SWWA) and the South East Queensland bioregion (SEQ). We analysed seven diverse groups of organisms spanning five separate phyla on the evolutionary tree of life, the plant genera Acacia and Daviesia, mammals, hylid frogs, myobatrachid frogs, passerine birds, and camaenid land snails. We measured species richness, weighted species endemism (WE) and two phylodiversity measures, phylogenetic diversity (PD) and phylogenetic endemism (PE), as well as their respective complementarity scores (a measure of gains and losses) at 20 km resolution. Higher PD was identified within SEQ for all fauna groups, whereas more PD was found in SWWA for both plant groups. PD and PD complementarity were strongly correlated with species richness and species complementarity for most groups but less so for plants. PD and PE were found to complement traditional species-based measures for all groups studied: PD and PE follow similar spatial patterns to richness and WE, but highlighted different areas that would not be identified by conventional species-based biodiversity analyses alone. The application of phylodiversity measures, particularly the novel weighted complementary measures considered here, in conservation can enhance protection of the evolutionary history that contributes to present day biodiversity values of areas. Phylogenetic measures in conservation can include important elements of biodiversity in conservation planning, such as evolutionary potential and feature diversity that will improve decision-making and lead to better biodiversity conservation outcomes.

A molecular estimate of the phylogeny of Styphelieae (Ericaceae)

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.

Phylogenetic relationships of epacrids and vaccinioids (Ericaceae s. l.) based onmatK sequence data

Cladistic relationships of epacrids and vaccinioids (Ericaceae) are investigated using nucleotide sequence data from the chloroplast encodedmatK gene. Sequences of 56 taxa were aligned and analyzed using parsimony methods. Results show thatVaccinioideae as currently recognized are not monophyletic. The epacrids are sister to a clade that includes theLyonia group, theGaultheria group, and theVaccinieae. Arbutus andPyrola branch early inEricaceae, before the rhododendroid group.Enkianthus is sister to the remainingEricaceae (includingEpacridaceae).Vaccinieae are strongly supported as monophyletic, butVaccinium andAgapetes are polyphyletic.