AusTraits, a curated plant trait database for the Australian flora.

We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.

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. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies.

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. Five vicariance hypotheses were tested by comparing molecular divergence times with the timing of tectonic rifting. The role of adaptation to fire (serotiny) in its spread across a drying Australia was tested for Callitris. Our findings suggest that three transoceanic disjunctions within the Callitroideae probably arose from long-distance dispersal. A signature of extinction, centred on the end-Eocene global climatic chilling and drying, is evident in lineages-through-time plots and in the fossil record. Callitris, the most diverse extant callitroid genus, suffered extinctions but surviving lineages adapted and re-radiated into dry, fire-prone biomes that expanded in the Neogene. Serotiny, a key adaptation to fire, likely evolved in Callitris coincident with the biome shift. Both extinction and adaptive shifts have probably played major roles in this chronicle of turnover and renewal, but better understanding of biogeographical history requires improved taxonomy of fossils.

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. Randomizations of these data were used to test whether more species showed disjunctions (gaps in distribution) or likely barriers (range limits) at these points than expected by chance. RESULTS: Two novel disjunctions in the Australian Tropics flora are identified in addition to eleven putative barriers previously recognized for animals. Of these, eleven disjunction points (all within the Australian Monsoon Tropics) were found to correspond to range-ending barriers to a significant number of species, while neither of the two disjunctions found within the Australian Wet Tropics limited a significant number of species' ranges. MAIN CONCLUSIONS: Biogeographic barriers present significant distributional limits to native plant species in the Australian Monsoon Tropics but not in the Australian Wet Tropics.

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. However, much of Australia is unsurveyed, and carbon isotope signature, commonly used to assess photosynthetic pathway diversity, does not distinguish between plants with low-levels of CAM and C3 plants. We provide the first census of CAM for the Australian flora and suggest that the real frequency of CAM in the flora is double that currently known, with the number of terrestrial CAM species probably 10-fold greater. Still unresolved is the question why the large stem-succulent life - form is absent from the native Australian flora even though exotic large cacti have successfully invaded and established in Australia.

Ploidy and domestication are associated with genome size variation in Palms.

PREMISE OF THE STUDY: The genome size of a species (C-value) is associated with growth, development and adaptation to environmental changes. Angiosperm C-values range 1200-fold and frequently vary within species, although little is known about the impacts of domestication on genome size. Genome size variation among related species of palms is of evolutionary significance because changes characterize clades and may be associated with polyploidy, transposon amplifications, deletions, or rearrangements. Further knowledge of genome size will provide crucial information needed for planning of whole genome sequencing and accurate annotations. We studied the genome size of Cocos nucifera and its variation among cultivars, and compared it to values for related palms from the Attaleinae subtribe. METHODS: Flow cytometric analysis of isolated nuclei from young palm leaves was used to estimate genome sizes of 23 coconut cultivars (Talls, Dwarfs, and hybrids) worldwide and 17 Cocoseae species. Ancestral genome size was reconstructed on a maximum likelihood phylogeny of Attaleinae from seven WRKY loci. KEY RESULTS: The coconut genome is large-averaging 5.966 pg-and shows intraspecific variation associated with domestication. Variation among Tall coconuts was significantly greater than among Dwarfs. Attaleinae genomes showed moderate size variation across genera, except polyploids Jubaeopsis caffra, Voanioala gerardii, Beccariophoenix alfredii, and Allagoptera caudescens, which had larger genomes. CONCLUSIONS: Our results contribute to the understanding of the relationship between domestication and genome size in long-lived tree crops and provide a basis for whole-genome sequencing of the coconut and other domesticated plants. Polyploidy evolved independently in two clades within Attaleinae.

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. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses.

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. We tested hypotheses of vicariance and LDDE by estimating divergence times using a relaxed molecular clock calibrated with 12 fossils. In total, 88 genera and 202 species were sampled, representing both subfamilies and all tribes of Myrtaceae. We reconstructed the family as Gondwanan in origin. Of the 22 geographically disjunct sister groups in our study, up to six are potentially explained as the product of vicariance, three resulting from overland dispersal via new land connections, and 13 due to LDDE events. Nine of the 13 hypothesized LDDE events occurred in fleshy-fruited taxa. Our results indicate that most of the transoceanic distribution patterns in Myrtaceae have occurred since the Miocene due to LDDE, whereas inferred vicariance events all occurred before the Late Eocene. There are many instances of sister relationships between species-poor and species-rich groups in Myrtaceae, and at least three occurrences of geographically isolated taxa on long branches of the phylogeny (Arillastrum, Myrtus, and Tepualia), whose modern-day distributions are difficult to explain without additional fossil or geological evidence.

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. A modest expansion in protected areas of 5% (less than 1% of the state area) would increase protected PD by 33% over current levels. In a recent policy change, portions of the national parks were opened for development. These tourism development zones hold over half the PD found in national parks with some species and clades falling entirely outside of protected zones within the national parks. This approach of using PD in spatial prioritization could be extended to any clade or area that has spatial and phylogenetic data. Our results demonstrate the relevance of PD to regional conservation policy by highlighting that small but strategically located areas disproportionally impact the preservation of evolutionary lineages.

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. Geographical overlap of clades was significantly greater for Daviesia in the SWAFR than in SEA, but the inverse for Bossiaea. Lineage diversification rates over the past 10 Myr did not differ between the SWAFR and SEA in either genus. Interaction of multiple factors probably explains the differences in measured diversity between the two regions. Steeper climatic gradients in the SWAFR probably explain the smaller geographical ranges of both genera there. Greater geographical overlap of clades in the SWAFR, combined with a longer time in the region, can explain why Daviesia is far more species-rich there than in SEA. Our results indicate that the time for speciation and ecological limits hypotheses, in concert, can explain the differences in biodiversity.

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. We compare the results of simulations to empirical results from analyses of a real rate-heterogeneous taxon - Australian grass trees (Xanthorrhoea) - whose substitution rate is slower than in its sister groups, as determined by relative rate tests. RESULTS: In the simulated datasets, the RLC model performed much better than UCLN: RLC correctly estimated the age of the crown node of slow-rate broom clades, whereas UCLN estimates were consistently too young. Similarly, in the Xanthorrhoea dataset, UCLN returned significantly younger crown ages than RLC (mean estimates respectively 3-6 Ma versus 25-35 Ma). In both real and simulated datasets, Bayes Factor tests strongly favored the RLC model over the UCLN model. CONCLUSIONS: The choice of an unsuitable molecular clock model can strongly bias divergence time estimates. In particular, for data predicted to have more rate variation among than within clades, dating with RLC is much more likely to be accurate than with UCLN. The choice of clocks should be informed by the biology of the study group (e.g., life-form) or assessed with relative rate tests and post-hoc model comparisons.

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. Here, we use evolutionary trait reconstruction of bee-pollination and bird-pollination syndromes in Australian egg-and-bacon peas (Mirbelieae and Bossiaeeae) to test whether transitions between pollination syndromes is correlated with changes in species diversity. We also test for directionality in transitions that might be caused by selection by pollinators or by an evolutionary ratchet in which reversals to the original pollination syndrome are not possible. RESULTS: Trait reconstructions of Australian egg-and-bacon peas suggest that bee-pollination syndrome is the ancestral form and that there has been replicated evolution of bird-pollination syndromes. Reconstructions indicate potential reversals from bird- to bee-pollination syndromes but this is not consistent with morphology. Species diversity of bird-pollination syndrome clades is lower than that of their bee-pollination syndrome sisters.We estimated the earliest transitions from bee- to bird-pollination syndrome occurred between 30.8 Ma and 10.4 Ma. Geographical structuring of pollination syndromes was found; there were fewer bird-pollination species in the Australian southeast temperate region compared to other regions of Australia. CONCLUSIONS: A consistent decrease in diversification rate coincident with switches to bird pollination might be explained if greater dispersal by bird pollinators results in higher levels of connectivity among populations and reduced chances of allopatric speciation.The earliest transitions overlap with the early diversification of Australian honeyeaters - the major lineage of pollinating birds in Australia. Our findings are consistent with the idea that environment and availability of pollinators are important in the evolution of pollination syndromes. Changes in flower traits as a result of transitions to bird-pollination syndrome might also limit reversals to a bee-pollination syndrome.

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. Genetic demographic analysis showed that the arid populations experienced strong bottlenecks, consistent with range contractions during the Last Glacial Maximum (ca 20 kya) predicted by species distribution models. In southern temperate regions, the population sizes were estimated to have been mostly stable, followed by some expansion coinciding with climate amelioration at the end of the last glacial period. By contrast, in the flammable tropical savannahs, where fire risk is the highest, demographic analysis failed to detect significant population bottlenecks. Collectively, these results suggest that the impact of climate change overwhelmed any modifications to fire regimes by Aboriginal landscape burning and megafaunal extinction, a finding that probably also applies to other fire-prone vegetation across Australia.

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. • METHODS: We used six chloroplast DNA simple sequence repeats (cpSSR) across five species of Lomatia, sampled across their entire distributional range in southeastern Australia. Resulting size data were combined, presented as a network, and visualized on a map. Biogeographical barriers were tested using AMOVA. To explore hypotheses of chlorotype origin, we converted the network into a cladogram and reconciled with all possible species trees using parsimony-based tree mapping. • KEY RESULTS: Some chlorotypes were shared across multiple species of Lomatia in the study, including between morphologically differentiated species. Chlorotypes were either widespread in distribution or geographically restricted to specific regions. Biogeographical structure was identified across the range of Lomatia. The most parsimonious reconciled tree incorporated horizontal transfer of chlorotypes. • CONCLUSIONS: Lomatia shows evidence of both incomplete lineage sorting and extensive hybridization between co-occurring species. Although the species in the study appear to have responded to a number of biogeographic barriers to varying degrees, our findings identified the Hunter River Valley as the most important long-term biogeographic barrier for the genus in southeastern Australia.

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. At the simplest level, a pattern of PNC is an inevitable consequence of evolution - descent with modification and divergence of lineages - but several intrinsic causes, including physicochemical, developmental and genetic constraints, can lead directly to a marked pattern of PNC. A pattern of PNC can also be caused indirectly, as a by-product of other causes, such as extinction, dispersal limitation, competition and predation. Recognition of patterns of PNC can contribute to understanding macroevolutionary processes: for example, release from constraint in traits has been hypothesized to trigger adaptive radiations such as that of the angiosperms. Given the multiple causes of patterns of PNC, tests should address explicit questions about hypothesized processes. We conclude that PNC is a scientifically useful concept with applications to the practice of ecological research.

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. Such an isolated distribution of L. mariae has been assumed to have resulted from contraction of ancestral populations as Australia aridified from the Mid-Miocene (ca 15 Ma). To test this hypothesis at the population level, we examined the genetic relationships among 14 populations of L. mariae and L. rigida using eight nuclear microsatellite loci. Our population tree and Bayesian clustering revealed that these populations comprised two genetically distinct groups that did not correspond to the current classification at species rank, and L. mariae showed closest affinity with L. rigida from Roper River. Furthermore, coalescent divergence-time estimations suggested that the disjunction between the northern populations (within L. rigida) could have originated by intermittent colonization along an ancient river that has been drowned repeatedly by marine transgression. During that time, L. mariae populations could have been established by opportunistic immigrants from Roper River about 15 000 years ago, concurrently with the settlement of indigenous Australians in central Australia, who are thus plausible vectors. Thus, our results rule out the ancient relic hypothesis for the origin of L. mariae.

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. Recent work has shown that pollen of the myrtle family, Myrtaceae, can be classified into a number of morphological groups that are synapomorphic with molecular groups. By assembling a data matrix of pollen morphological characters from extant and fossil Myrtaceae, we were able to measure the fit of 26 pollen fossils to a molecular phylogenetic tree using parsimony optimisation of characters. We identified eight Myrtaceidites fossils as appropriate for calibration based on the most parsimonious placements of these fossils on the tree. These fossils were used to inform age constraints in a Bayesian phylogenetic analysis of a sequence alignment comprising two sequences from the chloroplast genome (matK and ndhF) and one nuclear locus (ITS), sampled from 106 taxa representing 80 genera. Three additional analyses were calibrated by placing pollen fossils using geographic and morphological information (eight calibrations), macrofossils (five calibrations), and macrofossils and pollen fossils in combination (12 calibrations). The addition of new fossil pollen calibrations led to older crown ages than have previously been found for tribes such as Eucalypteae and Myrteae. Estimates of rate variation among lineages were affected by the choice of calibrations, suggesting that the use of multiple calibrations can improve estimates of rate heterogeneity among lineages. This study illustrates the potential of including pollen-based calibrations in molecular studies of divergence times.

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. METHODS AND RESULTS: mRNA from an individual seedling was subjected to cDNA synthesis and then de novo pyrosequencing. Two hundred and nineteen primer pairs bordering sequence regions were designed from the obtained sequence data. In total, 52 showed polymorphism within 16 individuals representative of the species' entire range, with the number of alleles per locus and expected heterozygosity ranging from two to 10 and 0.06 to 0.84, respectively. CONCLUSIONS: The EST-SSR markers developed in this study will be useful for evaluating the range-wide genetic structure of C. columellaris s.l. and detecting outlier loci under selection, as well as providing useful markers to investigate the conservation genetics and reproductive ecology of the species.

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. Ginkgo, cycads and dawn redwood), suggesting that the rate of evolution of gymnosperms has been slow. We estimated the ages and diversification rates of gymnosperm lineages using Bayesian relaxed molecular clock dating calibrated with 21 fossils, based on the phylogenetic analysis of alignments of matK chloroplast DNA (cpDNA) and 26S nuclear ribosomal DNA (nrDNA) sequences, and compared these with published estimates for angiosperms. Gymnosperm crown groups of Cenozoic age are significantly younger than their angiosperm counterparts (median age: 32 Ma vs 50 Ma) and have long unbranched stems, indicating major extinctions in the Cenozoic, in contrast with angiosperms. Surviving gymnosperm genera have diversified more slowly than angiosperms during the Neogene as a result of their higher extinction rate. Compared with angiosperms, living gymnosperm groups are not ancient. The fossil record also indicates that gymnosperms suffered major extinctions when climate changed in the Oligocene and Miocene. Extant gymnosperm groups occupy diverse habitats and some probably survived after making adaptive shifts.