Resolving relationships in the radiation of Australia's largest pea clade (Fabaceae tribe Mirbelieae) with target-capture sequencing.

Background And Aims: Tribe Mirbelieae (Fabaceae) represents one of the great species radiations in Australian flora and the largest in the pea-flowered legumes. Traditional amplicon sequencing has failed to resolve relationships within this species-rich and morphologically diverse tribe.

Methods: Target capture sequencing was used to reconstruct relationships within the core Mirbelioid legumes which represent a previously hypothesised rapid radiation that dates to the Oligocene and early Miocene epochs.

Identifying genetic markers for a range of phylogenetic utility-From species to family level.

Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci.

Turnover of southern cypresses in the post-Gondwanan world: extinction, transoceanic dispersal, adaptation and rediversification.

Cupressaceae subfamily Callitroideae has been an important exemplar for vicariance biogeography, but its history is more than just disjunctions resulting from continental drift. We combine fossil and molecular data to better assess its extinction and, sometimes, rediversification after past global change. Key fossils were reassessed and their phylogenetic placement for calibration was determined using trait mapping and Bayes Factors.

Congruent biogeographical disjunctions at a continent-wide scale: Quantifying and clarifying the role of biogeographic barriers in the Australian tropics.

Aim: To test whether novel and previously hypothesized biogeogaphic barriers in the Australian Tropics represent significant disjunction points or hard barriers, or both, to the distribution of plants.

Location: Australian tropics: Australian Monsoon Tropics and Australian Wet Tropics.

Methods: The presence or absence of 6,861 plant species was scored across 13 putative biogeographic barriers in the Australian Tropics, including two that have not previously been recognised.

Australia lacks stem succulents but is it depauperate in plants with crassulacean acid metabolism (CAM)?

In the flora of Australia, the driest vegetated continent, crassulacean acid metabolism (CAM), the most water-use efficient form of photosynthesis, is documented in only 0.6% of native species. Most are epiphytes and only seven terrestrial.

Biogeographic calibrations for the molecular clock.

Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units.

Interpreting the modern distribution of Myrtaceae using a dated molecular phylogeny.

The angiosperm family Myrtaceae has extant and fossil taxa from all southern continents and is assumed to be of Gondwanan origin. Many modern groups contain sister taxa that have disjunct transoceanic distributions, which can be interpreted as a result of either vicariance or long-distance dispersal and establishment (LDDE). Further, some Myrtaceae groups occur on Pacific islands with enigmatic geological histories.

Phylogenetic diversity meets conservation policy: small areas are key to preserving eucalypt lineages.

Evolutionary and genetic knowledge is increasingly being valued in conservation theory, but is rarely considered in conservation planning and policy. Here, we integrate phylogenetic diversity (PD) with spatial reserve prioritization to evaluate how well the existing reserve system in Victoria, Australia captures the evolutionary lineages of eucalypts, which dominate forest canopies across the state. Forty-three per cent of remaining native woody vegetation in Victoria is located in protected areas (mostly national parks) representing 48% of the extant PD found in the state.

Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees.

Background: Estimating divergence times in phylogenies using a molecular clock depends on accurate modeling of nucleotide substitution rates in DNA sequences. Rate heterogeneity among lineages is likely to affect estimates, especially in lineages with long stems and short crowns ("broom" clades) and no internal calibration. We evaluate the performance of the random local clocks model (RLC) and the more routinely employed uncorrelated lognormal relaxed clock model (UCLN) in situations in which a significant rate shift occurs on the stem branch of a broom clade.

Three explanations for biodiversity hotspots: small range size, geographical overlap and time for species accumulation. An Australian case study.

To understand the generation and maintenance of biodiversity hotspots, we tested three major hypotheses: rates of diversification, ecological limits to diversity, and time for species accumulation. Using dated molecular phylogenies, measures of species' range size and geographical clade overlap, niche modelling, and lineages-through-time plots of Australian Fabaceae, we compared the southwest Australia Floristic Region (SWAFR; a global biodiversity hotspot) with a latitudinally equivalent non-hotspot, southeast Australia (SEA). Ranges of species (real and simulated) were smaller in the SWAFR than in SEA.

Evolutionary consequences of shifts to bird-pollination in the Australian pea-flowered legumes (Mirbelieae and Bossiaeeae).

Background: Interactions with pollinators are proposed to be one of the major drivers of diversity in angiosperms. Specialised interactions with pollinators can lead to specialised floral traits, which collectively are known as a pollination syndrome. While it is thought that specialisation to a pollinator can lead to either an increase in diversity or in some cases a dead end, it is not well understood how transitions among specialised pollinators contribute to changes in diversity.

Climate, not Aboriginal landscape burning, controlled the historical demography and distribution of fire-sensitive conifer populations across Australia.

Climate and fire are the key environmental factors that shape the distribution and demography of plant populations in Australia. Because of limited palaeoecological records in this arid continent, however, it is unclear as to which factor impacted vegetation more strongly, and what were the roles of fire regime changes owing to human activity and megafaunal extinction (since ca 50 kya). To address these questions, we analysed historical genetic, demographic and distributional changes in a widespread conifer species complex that paradoxically grows in fire-prone regions, yet is very sensitive to fire.

The impact of multiple biogeographic barriers and hybridization on species-level differentiation.

Premise Of The Study: The glacial cycles of the Quaternary did not impact Australia in the same way as Europe and North America. Here we investigate the history of population isolation, species differentiation, and hybridization in the southeastern Australian landscape, using five species of Lomatia (Proteaceae). We use a chloroplast DNA phylogeography to assess chloroplast haplotype (chlorotype) sharing among these species and whether species with shared distributions have been affected by shared biogeographic barriers.

Phylogenetic niche conservatism: what are the underlying evolutionary and ecological causes?

Phylogenetic niche conservatism (PNC) is the tendency of lineages to retain their niche-related traits through speciation events. A recent surge in the availability of well-sampled molecular phylogenies has stimulated phylogenetic approaches to understanding ecological processes at large geographical scales and through macroevolutionary time. We stress that PNC is a pattern, not a process, and is found only in some traits and some lineages.

Not an ancient relic: the endemic Livistona palms of arid central Australia could have been introduced by humans.

Livistona mariae is an endemic palm localized in arid central Australia. This species is separated by about 1000 km from its congener L. rigida, which grows distantly in the Roper River and Nicholson-Gregory River catchments in northern Australia.

Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae.

The identification and application of reliable fossil calibrations represents a key component of many molecular studies of evolutionary timescales. In studies of plants, most paleontological calibrations are associated with macrofossils. However, the pollen record can also inform age calibrations if fossils matching extant pollen groups are found.

Isolation and characterization of 52 polymorphic EST-SSR markers for Callitris columellaris (Cupressaceae).

Premise Of The Study: We developed simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) for Callitris columellaris sensu lato (s.l.) to elucidate population genetic structure and detect outlier loci by genome scan.

Cenozoic extinctions account for the low diversity of extant gymnosperms compared with angiosperms.

We test the widely held notion that living gymnosperms are 'ancient' and 'living fossils' by comparing them with their sister group, the angiosperms. This perception derives partly from the lack of gross morphological differences between some Mesozoic gymnosperm fossils and their living relatives (e.g.

Flammable biomes dominated by eucalypts originated at the Cretaceous-Palaeogene boundary.

Fire is a major modifier of communities, but the evolutionary origins of its prevalent role in shaping current biomes are uncertain. Australia is among the most fire-prone continents, with most of the landmass occupied by the fire-dependent sclerophyll and savanna biomes. In contrast to biomes with similar climates in other continents, Australia has a tree flora dominated by a single genus, Eucalyptus, and related Myrtaceae.

Hypothesis testing in biogeography.

Often, biogeography is applied only as a narrative addition to phylogenetic studies and lacks scientific rigour. However, if research questions are framed as hypotheses, biogeographical scenarios become testable. In this review, we explain some problems with narrative biogeography and show how the use of explicit hypotheses is changing understanding of how organisms came to be distributed as they are.

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.

Livistona palms in Australia: ancient relics or opportunistic immigrants?

Eighteen of the 34 species of the fan palm genus Livistona (Arecaceae) are restricted to Australia and southern New Guinea, east of Wallace's Line, an ancient biogeographic boundary between the former supercontinents Laurasia and Gondwana. The remaining species extend from SE Asia to Africa, west of Wallace's Line. Competing hypotheses contend that Livistona is (a) ancient, its current distribution a relict of the supercontinents, or (b) a Miocene immigrant from the north into Australia as it drifted towards Asia.

Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history.

We present a new, broadly applicable measure of the spatial restriction of phylogenetic diversity, termed phylogenetic endemism (PE). PE combines the widely used phylogenetic diversity and weighted endemism measures to identify areas where substantial components of phylogenetic diversity are restricted. Such areas are likely to be of considerable importance for conservation.

Explosive radiation or cryptic mass extinction? Interpreting signatures in molecular phylogenies.

How biodiversity is generated and maintained underlies many major questions in evolutionary biology, particularly relating to the tempo and pattern of diversification through time. Molecular phylogenies and new analytical methods provide additional tools to help interpret evolutionary processes. Evolutionary rates in lineages sometimes appear punctuated, and such "explosive" radiations are commonly interpreted as adaptive, leading to causative key innovations being sought.