Fire impacts bacterial composition in Protea repens (Proteaceae) infructescences.

The diverse bacterial communities in and around plants provide important benefits, such as protection against pathogens and cycling of essential minerals through decomposition of moribund plant biomass. Biodiverse fynbos landscapes generally have limited deadwood habitats due to the absence of large trees and frequent fire. In this study, we determined the effect of a fire disturbance on the bacterial communities in a fynbos landscape dominated by the shrub Protea repens using 16S ribosomal RNA amplicon sequencing. The bacterial community composition in newly formed fruiting structures (infructescences) and soil at a recently burnt site was different from that in an unburnt site. Bacteria inhabiting P. repens infructescences were similar to well-known taxa from decomposing wood and litter. This suggests a putative role for these aboveground plant structures as reservoirs for postfire decomposer bacteria. The results imply that inordinately frequent fires, which are commonplace in the Anthropocene, are a significant disturbance to bacterial communities and could affect the diversity of potentially important microbes from these landscapes.

Mismatches between demographic niches and geographic distributions are strongest in poorly dispersed and highly persistent plant species.

The ecological niche of a species describes the variation in population growth rates along environmental gradients that drives geographic range dynamics. Niches are thus central for understanding and forecasting species' geographic distributions. However, theory predicts that migration limitation, source-sink dynamics, and time-lagged local extinction can cause mismatches between niches and geographic distributions. It is still unclear how relevant these niche-distribution mismatches are for biodiversity dynamics and how they depend on species life-history traits. This is mainly due to a lack of the comprehensive, range-wide demographic data needed to directly infer ecological niches for multiple species. Here we quantify niches from extensive demographic measurements along environmental gradients across the geographic ranges of 26 plant species (Proteaceae; South Africa). We then test whether life history explains variation in species' niches and niche-distribution mismatches. Niches are generally wider for species with high seed dispersal or persistence abilities. Life-history traits also explain the considerable interspecific variation in niche-distribution mismatches: poorer dispersers are absent from larger parts of their potential geographic ranges, whereas species with higher persistence ability more frequently occupy environments outside their ecological niche. Our study thus identifies major demographic and functional determinants of species' niches and geographic distributions. It highlights that the inference of ecological niches from geographical distributions is most problematic for poorly dispersed and highly persistent species. We conclude that the direct quantification of ecological niches from demographic responses to environmental variation is a crucial step toward a better predictive understanding of biodiversity dynamics under environmental change.

Isolation by distance and isolation by environment contribute to population differentiation in Protea repens (Proteaceae L.), a widespread South African species.

PREMISE OF THE STUDY: The Cape Floristic Region (CFR) of South Africa is renowned for its botanical diversity, but the evolutionary origins of this diversity remain controversial. Both neutral and adaptive processes have been implicated in driving diversification, but population-level studies of plants in the CFR are rare. Here, we investigate the limits to gene flow and potential environmental drivers of selection in Protea repens L. (Proteaceae L.), a widespread CFR species. METHODS: We sampled 19 populations across the range of P. repens and used genotyping by sequencing to identify 2066 polymorphic loci in 663 individuals. We used a Bayesian FST outlier analysis to identify single-nucleotide polymorphisms (SNPs) marking genomic regions that may be under selection; we used those SNPs to identify potential drivers of selection and excluded them from analyses of gene flow and genetic structure. RESULTS: A pattern of isolation by distance suggested limited gene flow between nearby populations. The populations of P. repens fell naturally into two or three groupings, which corresponded to an east-west split. Differences in rainfall seasonality contributed to diversification in highly divergent loci, as do barriers to gene flow that have been identified in other species. CONCLUSIONS: The strong pattern of isolation by distance is in contrast to the findings in the only other widespread species in the CFR that has been similarly studied, while the effects of rainfall seasonality are consistent with well-known patterns. Assessing the generality of these results will require investigations of other CFR species.

Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.

PREMISE OF THE STUDY: Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa. METHODS: We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for a total of 163 individuals, and obtained sequences for 498 low-copy, orthologous nuclear loci using anchored phylogenomics. We compare several approaches for building species trees, and explore gene tree-species tree discrepancies to determine whether poor phylogenetic resolution reflects a lack of informative sites, incomplete lineage sorting, or hybridization. KEY RESULTS: Phylogenetic estimates from species tree approaches are similar to one another and recover previously well-supported clades within Protea, in addition to providing well-supported phylogenetic hypotheses for previously poorly resolved intrageneric relationships. Individual gene trees are markedly different from one another and from species trees. Nonetheless, analyses indicate that differences among gene trees occur primarily concerning clades supported by short branches. CONCLUSIONS: Species tree methods using hundreds of nuclear loci provided strong support for many previously unresolved relationships in the radiation of the genus Protea. In cases where support for particular relationships remains low, these appear to arise from few informative sites and lack of information rather than strongly supported disagreement among gene trees.

Spatial, Phylogenetic, Environmental and Biological Components of Variation in Extinction Risk: A Case Study Using Banksia.

Comparative analyses of extinction risk routinely apply methods that account for phylogenetic non-independence, but few analyses of extinction risk have addressed the possibility of spatial non-independence. We explored patterns of extinction risk in Banksia, a plant genus largely endemic to Australia's southwest biodiversity hotspot, using methods to partition the variance in two response variables (threat status and range size) into phylogenetic, spatial, and independent components. We then estimated the effects of a number of biological and external predictors on extinction risk independently of phylogeny and space. The models explained up to 34.2% of the variation in range size and up to 9.7% of the variation in threat status, nearly all of which was accounted for by the predictors, not by phylogeny or space. In the case of Banksia, therefore, high extinction risk can be clearly linked with biological syndromes (such as a brief flowering period) or geographic indicators of human impact (such as extensive habitat loss), but cannot be predicted from phylogenetic relatedness or geographic proximity.

Fossil evidence for open, Proteaceae-dominated heathlands and fire in the Late Cretaceous of Australia.

PREMISE OF THE STUDY: The origin of biomes is of great interest globally. Molecular phylogenetic and pollen evidence suggest that several plant lineages that now characterize open, burnt habitats of the sclerophyll biome, became established during the Late Cretaceous of Australia. However, whether this biome itself dates to that time is problematic, fundamentally because of the near-absence of relevant, appropriately aged, terrestrial plant macro- or mesofossils. METHODS: We recovered, identified, and interpreted the ecological significance of fossil pollen, foliar and other remains from a section of core drilled in central Australia, which we dated as Late Campanian-Maastrichtian. KEY RESULTS: The sediments contain plant fossils that indicate nutrient-limited, open, sclerophyllous vegetation and abundant charcoal as evidence of fire. Most interestingly, >30 pollen taxa and at least 12 foliage taxa are attributable to the important Gondwanan family Proteaceae, including several minute, amphistomatic, and sclerophyllous foliage forms consistent with subfamily Proteoideae. Microfossils, including an abundance of Sphagnales and other wetland taxa, provided strong evidence of a fenland setting. The local vegetation also included diverse Ericaceae and Liliales, as well as a range of ferns and gymnosperms. CONCLUSIONS: The fossils provide strong evidence in support of hypotheses of great antiquity for fire and open vegetation in Australia, point to extraordinary persistence of Proteaceae that are now emblematic of the Mediterranean-type climate southwestern Australian biodiversity hotspot and raise the profile of open habitats as centers of ancient lineages.

Kinase domain-targeted isolation of defense-related receptor-like kinases (RLK/Pelle) in Platanus×acerifolia: phylogenetic and structural analysis.

BACKGROUND: Plant receptor-like kinase (RLK/Pelle) family regulates growth and developmental processes and interaction with pathogens and symbionts.Platanaceae is one of the earliest branches of Eudicots temporally located before the split which gave rise to Rosids and Asterids. Thus investigations into the RLK family in Platanus can provide information on the evolution of this gene family in the land plants.Moreover RLKs are good candidates for finding genes that are able to confer resistance to Platanus pathogens. RESULTS: Degenerate oligonucleotide primers targeting the kinase domain of stress-related RLKs were used to isolate for the first time 111 RLK gene fragments in Platanus×acerifolia. Sequences were classified as candidates of the following subfamilies: CrRLK1L, LRR XII, WAK-like, and LRR X-BRI1 group. All the structural features typical of the RLK kinase domain were identified, including the non-RD motif which marks potential pathogen recognition receptors (PRRs). The LRR XII candidates, whose counterpart in Arabidopsis and rice comprises non-RD PRRs, were mostly non-RD kinases, suggesting a group of PRRs. Region-specific signatures of a relaxed purifying selection in the LRR XII candidates were also found, which is novel for plant RLK kinase domain and further supports the role of LRR XII candidates as PRRs. As we obtained CrRLK1L candidates using primers designed on Pto of tomato, we analysed the phylogenetic relationship between CrRLK1L and Pto-like of plant species. We thus classified all non-solanaceous Pto-like genes as CrRLK1L and highlighted for the first time the close phylogenetic vicinity between CrRLK1L and Pto group. The origins of Pto from CrRLK1L is proposed as an evolutionary mechanism. CONCLUSIONS: The signatures of relaxed purifying selection highlight that a group of RLKs might have been involved in the expression of phenotypic plasticity and is thus a good candidate for investigations into pathogen resistance.Search of Pto-like genes in Platanus highlighted the close relationship between CrRLK1L and Pto group. It will be exciting to verify if sensu strictu Pto are present in taxonomic groups other than Solanaceae, in order to further clarify the evolutionary link with CrRLK1L.We obtained a first valuable resource useful for an in-depth study on stress perception systems.

Convergent and correlated evolution of major life-history traits in the angiosperm genus Leucadendron (Proteaceae).

Natural selection is expected to cause convergence of life histories among taxa as well as correlated evolution of different life-history traits. Here, we quantify the extent of convergence of five key life-history traits (adult fire survival, seed storage, degree of sexual dimorphism, pollination mode, and seed-dispersal mode) and test hypotheses about their correlated evolution in the genus Leucadendron (Proteaceae) from the fire-prone South African fynbos. We reconstructed a new molecular phylogeny of this highly diverse genus that involves more taxa and molecular markers than previously. This reconstruction identifies new clades that were not detected by previous molecular study and morphological classifications. Using this new phylogeny and robust methods that account for phylogenetic uncertainty, we show that the five life-history traits studied were labile during the evolutionary history of the genus. This diversity allowed us to tackle major questions about the correlated evolution of life-history strategies. We found that species with longer seed-dispersal distances tended to evolve lower pollen-dispersal distance, that insect-pollinated species evolved decreased sexual dimorphism, and that species with a persistent soil seed-bank evolved toward reduced fire-survival ability of adults.

What has molecular systematics contributed to our knowledge of the plant family Proteaceae?

Molecular systematics has revolutionized our understanding of the evolution of the Proteaceae. Phylogenetic relationships have been reconstructed down to generic level and below from alignments of chloroplast and nuclear DNA sequences. These trees have enabled the monophyly of all subfamilies, tribes, and subtribes to be rigorously tested and the construction of a new classification of the family at these ranks. Molecular data have also played a major part in testing the monophyly of genera and infrageneric taxa, some of which have been recircumscribed as a result. Molecular trees and chronograms have been used to test numerous previously postulated biogeographic and evolutionary hypotheses, some of which have been modified or abandoned as a result. Hypotheses that have been supported by molecular phylogenetic trees and chronograms include the following: that the proteaceous pattern of repeated disjunct distributions across the southern hemisphere is partly the result of long-distance dispersal; that high proteaceous diversity in south-western Australia and the Cape Floristic Region of South Africa is due to high diversification rates in some clades but is not an evolutionary response to Mediterranean climates; that the sclerophyllous leaves of many shrubby members of the family are not adaptations to dry environments but for protecting mesophyll in brightly illuminated habitats; that deeply encrypted foliar stomata are adaptations for minimizing water loss in dry environments; and that Protea originated in the Cape Floristic Region of South Africa and that one of its subclades has greatly expanded its distribution into tropical savannas. Reconstructing phylogeny down to species level is now the main goal of molecular systematists of the Proteaceae. The biggest challenge in achieving this task will be resolving species trees from numerous gene trees in complexes of closely related species.

Evolution of a hotspot genus: geographic variation in speciation and extinction rates in Banksia (Proteaceae).

BACKGROUND: Hotspots of angiosperm species richness and endemism in Mediterranean-climate regions are among the most striking, but least well-understood, geographic patterns of biodiversity. Recent studies have emphasized the importance of rapid diversification within hotspots, compared to non-hotspot regions, as a major contributor to these patterns. We constructed the first near-complete phylogeny of Banksia (Proteaceae) to test whether diversification rates have differed between lineages confined to the southwest Australian hotspot and those found throughout southern, eastern and northern Australia. We then tested for variation in diversification rates among the bioclimatic zones within the southwest hotspot itself. RESULTS: Although Banksia species richness in the southwest is ten times that of the rest of the continent, we find little evidence for more rapid diversification in the southwest, although this result is inconclusive. However, we find firmer support for substantial rate variation within the southwest hotspot, with more rapid diversification in the semi-arid heaths and shrublands, compared to the high-rainfall forests. Most of the Banksia diversity of the southwest appears to be generated in the heaths and shrublands, with a high migration rate out of this zone boosting diversity of the adjacent forest zone. CONCLUSIONS: The geographic pattern of diversification in Banksia appears more complex than can be characterized by a simple hotspot vs. non-hotspot comparison, but in general, these findings contrast with the view that the high diversity of Mediterranean hotspots is underpinned by rapid radiations. Steady accumulation of species at unexceptional rates, but over long periods of time, may also have contributed substantially to the great botanical richness of these regions.

Low rate of between-population seed dispersal restricts genetic connectivity and metapopulation dynamics in a clonal shrub.

Clonal species normally have low seed production, low recruitment rates and long lifespans, and it is expected that the rates of long-distance dispersal (LDD) of seeds will be low as well. Banksia candolleana is a clonal shrub in Mediterranean-type, fire-prone sclerophyll shrublands of southwestern Australia, whose reproductive biology and population dynamics contrast with those of co-occurring nonclonal congeneric species, all of which are restricted to a mosaic of sand dunes set within a matrix of inhospitable swales. Using microsatellite markers, we genotyped 499 plants in all 15 populations of B. candolleana within a 12-km(2) area, assessed population genetic differentiation, and quantified the effective rate of interpopulation seed dispersal through genetic assignment of individuals to populations. We measured life history, reproductive and demographic attributes, and compared these with two co-occurring Banksia species, a non-clonal resprouter and a nonsprouter. B. candolleana has much higher levels of population genetic differentiation, and one-third the rate of interpopulation seed migration, as the other two species (2.2% vs 5.5-6.8% of genotyped plants inferred to be immigrants), though distances reached by LDD are comparable (0.3-2.3 km). The low rate of interpopulation dispersal was supported by an analysis of the age structure of three populations that suggests a mean interdune migration rate of <800 m in 200 years, and 60% of suitable dunes remain uninhabited. Thus, B. candolleana has poor properties for promoting long-distance dispersal. It is unclear if these are idiosyncratic to this species or whether such properties are to be expected of clonal species in general where LDD is less critical for species survival.

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.

Fire-adapted Gondwanan Angiosperm floras evolved in the Cretaceous.

BACKGROUND: Fires have been widespread over the last 250 million years, peaking 60-125 million years ago (Ma), and might therefore have played a key role in the evolution of Angiosperms. Yet it is commonly believed that fireprone communities existed only after the global climate became more arid and seasonal 15 Ma. Recent molecular-based studies point to much earlier origins of fireprone Angiosperm floras in Australia and South Africa (to 60 Ma, Paleocene) but even these were constrained by the ages of the clades examined. RESULTS: Using a molecular-dated phylogeny for the great Gondwanan family Proteaceae, with a 113-million-year evolutionary history, we show that the ancestors of many of its characteristic sclerophyll genera, such as Protea, Conospermum, Leucadendron, Petrophile, Adenanthos and Leucospermum (all subfamily Proteoideae), occurred in fireprone habitats from 88 Ma (83-94, 95% HPD, Mid-Upper Cretaceous). This coincided with the highest atmospheric oxygen (combustibility) levels experienced over the past 150 million years. Migration from non-fireprone (essentially rainforest-climate-type) environments was accompanied by the evolution of highly speciose clades with a range of seed storage traits and fire-cued seed release or germination mechanisms that was diagnostic for each clade by 71 Ma, though the ant-dispersed lineage (as a soil seed-storage subclade) was delayed until 45 Ma. CONCLUSIONS: Focusing on the widespread 113-million-year-old family Proteaceae, fireproneness among Gondwanan Angiosperm floras can now be traced back almost 90 million years into the fiery Cretaceous. The associated evolution of on-plant (serotiny) and soil seed storage, and later ant dispersal, affirms them as ancient adaptations to fire among flowering plants.

The phylogenetic signal of species co-occurrence in high-diversity shrublands: different patterns for fire-killed and fire-resistant species.

BACKGROUND: Using phylogenies in community ecology is now commonplace, but typically, studies assume and test for a single common phylogenetic signal for all species in a community, at a given scale. A possibility that remains little-explored is that species differing in demographic or ecological attributes, or facing different selective pressures, show different community phylogenetic patterns, even within the same communities. Here I compare community phylogenetic patterns for fire-killed and fire-resistant Banksia species in the fire-prone shrublands of southwest Australia. RESULTS: Using new Bayesian phylogenies of Banksia, together with ecological trait data and abundance data from 24 field sites, I find that fire regeneration mode influences the phylogenetic and phenotypic signal of species co-occurrence patterns. Fire-killed species (reseeders) show patterns of phylogenetic and phenotypic repulsion consistent with competition-driven niche differentiation, but there are no such patterns for fire-resistant species (resprouters). For pairs of species that differ in fire response, co-occurrence is mediated by environmental filtering based on similarity in edaphic preferences. CONCLUSIONS: These results suggest that it may be simplistic to characterize an entire community by a single structuring process, such as competition or environmental filtering. For this reason, community analyses based on pairwise species co-occurrence patterns may be more informative than those based on whole-community structure metrics.

Genetic structure and bio-climatic modeling support allopatric over parapatric speciation along a latitudinal gradient.

BACKGROUND: Four of the five species of Telopea (Proteaceae) are distributed in a latitudinal replacement pattern on the south-eastern Australian mainland. In similar circumstances, a simple allopatric speciation model that identifies the origins of genetic isolation within temporal geographic separation is considered as the default model. However, secondary contact between differentiated lineages can result in similar distributional patterns to those arising from a process of parapatric speciation (where gene flow between lineages remains uninterrupted during differentiation). Our aim was to use the characteristic distributional patterns in Telopea to test whether it reflected the evolutionary models of allopatric or parapatric speciation. Using a combination of genetic evidence and environmental niche modelling, we focused on three main questions: do currently described geographic borders coincide with genetic and environmental boundaries; are there hybrid zones in areas of secondary contact between closely related species; did species distributions contract during the last glacial maximum resulting in distributional gaps even where overlap and hybridisation currently occur? RESULTS: Total genomic DNA was extracted from 619 individuals sampled from 36 populations representing the four species. Seven nuclear microsatellites (nSSR) and six chloroplast microsatellites (cpSSR) were amplified across all populations. Genetic structure and the signature of admixture in overlap zones was described using the Bayesian clustering methods implemented in STUCTURE and NewHybrids respectively. Relationships between chlorotypes were reconstructed as a median-joining network. Environmental niche models were produced for all species using environmental parameters from both the present day and the last glacial maximum (LGM).The nSSR loci amplified a total of 154 alleles, while data for the cpSSR loci produced a network of six chlorotypes. STRUCTURE revealed an optimum number of five clusters corresponding to the four recognised species with the additional division of T. speciosissima into populations north and south of the Shoalhaven River valley. Unexpectedly, the northern disjunct population of T. oreades grouped with T. mongaensis and was identified as a hybrid swarm by the Bayesian assignment test implemented in NewHybrids. Present day and LGM environmental niche models differed dramatically, suggesting that distributions of all species had repeatedly expanded and contracted in response to Pleistocene climatic oscillations and confirming strongly marked historical distributional gaps among taxes. CONCLUSIONS: Genetic structure and bio-climatic modeling results are more consistent with a history of allopatric speciation followed by repeated episodes of secondary contact and localised hybridisation, rather than with parapatric speciation. This study on Telopea shows that the evidence for temporal exclusion of gene flow can be found even outside obvious geographical contexts, and that it is possible to make significant progress towards excluding parapatric speciation as a contributing evolutionary process.

Time-calibrated phylogeny of the woody Australian genus Hakea (Proteaceae) supports multiple origins of insect-pollination among bird-pollinated ancestors.

PREMISE OF THE STUDY: A past study based on morphological data alone showed that the means by which plants of the Australian genus Hakea reduce florivory is related to the evolution of bird pollination. For example, bird pollination was shown to have arisen only in insect-pollinated lineages that already produced greater amounts of floral cyanide, a feature that reduces florivory. We examine a central conclusion of that study, and a common assumption in the literature, that bird pollination arose in insect-pollinated lineages, rather than the reverse. METHODS: We combined morphological and DNA data to infer the phylogeny and age of the Australian genus Hakea, using 9.2 kilobases of plastid and nuclear DNA and 46 morphological characters from a taxonomically even sampling of 55 of the 149 species. KEY RESULTS: Hakea is rooted confidently in a position that has not been suggested before. The phylogeny implies that bird pollination is primitive in Hakea and that multiple shifts to insect pollination have occurred. The unexpectedly young age of Hakea (a crown age of ca. 10 Ma) makes it coincident with its primary bird pollinators (honeyeaters) throughout its history. CONCLUSIONS: Our study demonstrates that Hakea is an exception to the more commonly described shift from insect to bird pollination. However, we note that only one previous phylogenetic study involved Australian plants and their honeyeater pollinators and that our finding might prove to be more common on that continent.

Banksia born to burn.

• Historical evidence of recurrent fire in many of the world's biomes suggests that fire may have had profound evolutionary influences on their extant floras. However, the role of fire as a selective force in the origin and evolution of plant traits remains controversial. • Using Bayesian Monte-Carlo-Markov-Chain procedures and calibration points from the fossil record, we generated a dated phylogeny for the iconic Australian genus Banksia, and reconstructed the evolutionary/chronological position of five putatively fire-related traits. • The fire-dependent trait, on-plant seed storage (serotiny), and associated fire-enhancing trait, dead floret retention, co-originated with the first appearance of Banksia 60.8 million yr ago (Palaeocene). Whether nonsprouting or resprouting is ancestral was indeterminable, but the first banksias were nonclonal. Derived traits, such as dead leaf retention (fire-enhancing) and clonality (underground budbanks; fire-avoiding), first appeared 26-16 million yr ago (Miocene) with the onset of seasonal drought and thus more frequent fire, and culminated in dead florets/bracts completely covering the persistent fruits in some species. • Thus, fire may have been a selective force in the very origin of Banksia 40 million yr before the onset of climate seasonality in the Miocene, and continued to have an impact on the direction of evolution, favouring traits consistent with adaptation to an increasingly (sometimes less) fire-prone environment.

Causes of plant diversification in the Cape biodiversity hotspot of South Africa.

The Cape region of South Africa is one of the most remarkable hotspots of biodiversity with a flora comprising more than 9000 plant species, almost 70% of which are endemic, within an area of only ± 90,000 km2. Much of the diversity is due to an exceptionally large contribution of just a few clades that radiated substantially within this region, but little is known about the causes of these radiations. Here, we present a comprehensive analysis of plant diversification, using near complete species-level phylogenies of four major Cape clades (more than 470 species): the genus Protea, a tribe of legumes (Podalyrieae) and two speciose genera within the iris family (Babiana and Moraea), representing three of the seven largest plant families in this biodiversity hotspot. Combining these molecular phylogenetic data with ecological and biogeographical information, we tested key hypotheses that have been proposed to explain the radiation of the Cape flora. Our results show that the radiations started throughout the Oligocene and Miocene and that net diversification rates have remained constant through time at globally moderate rates. Furthermore, using sister-species comparisons to assess the impact of different factors on speciation, we identified soil type shifts as the most important cause of speciation in Babiana, Moraea, and Protea, whereas shifts in fire-survival strategy is the most important factor for Podalyrieae. Contrary to previous findings in other groups, such as orchids, pollination syndromes show a high degree of phylogenetic conservatism, including groups with a large number of specialized pollination syndromes like Moraea. We conclude that the combination of complex environmental conditions together with relative climatic stability promoted high speciation and/or low extinction rates as the most likely scenario leading to present-day patterns of hyperdiversity in the Cape.

Plant responses to climate in the Cape Floristic Region of South Africa: evidence for adaptive differentiation in the Proteaceae.

Local adaptation along environmental gradients may drive plant species radiation within the Cape Floristic Region (CFR), yet few studies examine the role of ecologically based divergent selection within CFR clades. In this study, we ask whether populations within the monophyletic white protea clade (Protea section Exsertae, Proteaceae) differ in key functional traits along environmental gradients and whether differences are consistent with local adaptation. Using seven taxa, we measured trait-environment associations and selection gradients across 35 populations of wild adults and their offspring grown in two common gardens. Focal traits were leaf size and shape, specific leaf area (SLA), stomatal density, growth, and photosynthetic rate. Analyses on wild and common garden plants revealed heritable trait differences that were associated with gradients in rainfall seasonality, drought stress, cold stress, and less frequently, soil fertility. Divergent selection between gardens generally matched trait-environment correlations and literature-based predictions, yet variation in selection regimes among wild populations generally did not. Thus, selection via seedling survival may promote gradient-wide differences in SLA and leaf area more than does selection via adult fecundity. By focusing on the traits, life stages, and environmental clines that drive divergent selection, our study uniquely demonstrates adaptive differentiation among plant populations in the CFR.