Unmatched tempo of evolution in Southern African semi-desert ice plants

Estimating the age of fire in the Cape flora of South Africa from an orchid phylogeny

Fire may have been a crucial component in the evolution of the Cape flora of South Africa, a region characterized by outstanding levels of species richness and endemism. However, there is, to date, no critical assessment of the age of the modern fire regime in this biome. Here, we exploit the presence of two obligate post-fire flowering clades in the orchid genus Disa, in conjunction with a robust, well-sampled and dated molecular phylogeny, to estimate the age by which fire must have been present. Our results indicate that summer drought (winter rainfall), the fire regime and the fynbos vegetation are several million years older than currently suggested. Summer drought and the fynbos vegetation are estimated to date back to at least the Early Miocene (ca 19.5 Ma). The current fire regime may have been established during a period of global cooling that followed the mid-Miocene Climatic Optimum (ca 15 Ma), which led to the expansion of open habitats and increased aridification. The first appearance of Disa species in the grassland biome, as well as in the subalpine habitat, is in striking agreement with reliable geological and palaeontological evidence of the age of these ecosystems, thus corroborating the efficacy of our methods. These results change our understanding of the historical mechanisms underlying botanical evolution in southern Africa, and confirm the potential of using molecular phylogenies to date events for which other information is lacking or inconclusive.

Phylogenetics of Puya (Bromeliaceae): Placement, major lineages, and evolution of Chilean species

Puya (Bromeliaceae), a large genus of terrestrial bromeliads found throughout a range of elevations in the Andes and central Chile, is of great systematic, evolutionary, and biogeographical interest. This first molecular phylogenetic study of Puya and related bromeliads employs matK, trnS-trnG, rps16, and PHYC sequences. Chloroplast DNA, nuclear DNA, and combined DNA data all place Puya closest to subfamily Bromelioideae. Nuclear and combined data support Puya as monophyletic, and the two subgenera are nonmonophyletic. All data indicate that the Chilean species of Puya are early diverging within the genus, consistent with Chilean genera as the first-diverging members of subfamily Bromelioideae. Central Chile is identified as a key region for understanding the biogeographical history of Bromeliaceae, as is true with other South American plant groups. A complicated history involving early chloroplast capture and later secondary hybridization and/or introgression is seen in Chilean lineages. These events help explain the occurrence of sterile inflorescence tips, floral color and shape, and leaf indument. The ecological radiation of Puya appears coincident with the final, recent rise of the Andes and subsequent high-elevation habitat diversification. Additionally, geographical distribution, rather than moisture or elevational adaptations, correlates to species relationships. Evolution of CAM photosynthesis has occurred multiple times.

Unparalleled rates of species diversification in Europe

The most rapid species radiations have been reported from 'evolutionary laboratories', such as the Andes and the Cape of South Africa, leading to the prevailing view that diversification elsewhere has not been as dramatic. However, few studies have explicitly assessed rates of diversification in northern regions such as Europe. Here, we show that carnations (Dianthus, Caryophyllaceae), a well-known group of plants from temperate Eurasia, have diversified at the most rapid rate ever reported in plants or terrestrial vertebrates. Using phylogenetic methods, we found that the majority of species of carnations belong to a lineage that is remarkably species-rich in Europe, and arose at the rate of 2.2-7.6 species per million years. Unlike most previous studies that have inferred rates of diversification in young diverse groups, we use a conservative approach throughout that explicitly incorporates the uncertainties associated with phylogenetic inference, molecular dating and incomplete taxon sampling. We detected a shift in diversification rates of carnations coinciding with a period of increase in climatic aridity in the Pleistocene, suggesting a link between climate and biodiversity. This explosive radiation suggests that Europe, the continent with the world's best-studied flora, has been underestimated as a cradle of recent and rapid speciation.

Darwin as a plant scientist: a Southern Hemisphere perspective

Events around the world this year celebrate the bicentenary of the birth of Charles Darwin (1809-1882) and the sesquicentenary of publication of his most important work, The Origin of Species (Darwin 1859). The associated plethora of books and papers now appearing to commemorate Darwin's work continue the traditional emphasis on his zoological and geological contributions. There has been some recent attention directed towards Darwin's relatively unsung but significant accomplishments as a botanist. Here, we bring together a review of Darwin's botanical discoveries and experiments and relevant aspects of his geological investigations, with a focus on the Southern Hemisphere. This is a relatively unexplored aspect of Darwin's contributions that yields some new insights meriting future research.

Duplication of the Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) gene precedes the explosive radiation of the Ruschioideae

The Mesembryanthemoideae and Ruschioideae subfamilies are a major component of the Greater Cape Floristic Region in southern Africa. The Ruschioideae show an astonishing diversity of leaf shape and growth forms. Although 1,585 species are recognised within the morphologically diverse Ruschioideae, these species show minimal variation in plastid DNA sequence. We have investigated whether changes in selected leaf development transcription factors underpin the recent, rapid diversification of this large group of succulent plants. Degenerate primers designed to conserved regions of Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) and the Class III HD-ZIP family of genes, were used to amplify sequences corresponding to these genes from several species within the Mesembryanthemoideae and Ruschioideae subfamilies. Two members of the Class III HD-ZIP family were identified in both the Mesembryanthemoideae and Ruschioideae, and were derived from an ancient gene duplication event that preceded the divergence of gymnosperms and angiosperms. While a single ARP orthologue was identified in the Mesembryanthemoideae, two paralogues, ARPa and ARPb, were identified in the Ruschioideae subfamily. ARPa was present in all species of Ruschioideae analysed in this study. ARPb has been lost from the Apatesieae and Dorotheantheae tribes, which form an early evolutionary branch from the Ruschieae tribe, as well as from selected species within the Ruschieae. The recent duplication and subsequent selected gene loss of the ARP transcription factor correlates with the rapid diversification of plant forms in the Ruschioideae.

Explosive Pleistocene diversification and hemispheric expansion of a "great speciator"

Factors that influence speciation rates among groups of organisms are integral to deciphering macroevolutionary processes; however, they remain poorly understood. Here, we use molecular phylogenetic data and divergence time estimates to reconstruct the pattern and tempo of speciation within a widespread and homogeneous bird family (white-eyes, Zosteropidae) that contains an archetypal "great speciator." Our analyses show that the majority of this species-rich family constitutes a clade that arose within the last 2 million years, yielding a per-lineage diversification rate among the highest reported for vertebrates (1.95-2.63 species per million years). However, unlike most rapid radiations reported to date, this burst of diversification was not limited in geographic scope, but instead spanned the entire Old World tropics, parts of temperate Asia, and numerous Atlantic, Pacific, and Indian Ocean archipelagos. The tempo and geographic breadth of this rapid radiation defy any single diversification paradigm, but implicate a prominent role for lineage-specific life-history traits (such as rapid evolutionary shifts in dispersal ability) that enabled white-eyes to respond rapidly and persistently to the geographic drivers of diversification.

Divergence and diversification in North American Psoraleeae (Fabaceae) due to climate change

Background

Past studies in the legume family (Fabaceae) have uncovered several evolutionary trends including differential mutation and diversification rates across varying taxonomic levels. The legume tribe Psoraleeae is shown herein to exemplify these trends at the generic and species levels. This group includes a sizable diversification within North America dated at approximately 6.3 million years ago with skewed species distribution to the most recently derived genus, Pediomelum, suggesting a diversification rate shift. We estimate divergence dates of North American (NAm) Psoraleeae using Bayesian MCMC sampling in BEAST based on eight DNA regions (ITS, waxy, matK, trnD-trnT, trnL-trnF, trnK, trnS-trnG, and rpoB-trnC). We also test the hypothesis of a diversification rate shift within NAm Psoraleeae using topological and temporal methods. We investigate the impact of climate change on diversification in this group by (1) testing the hypothesis that a shift from mesic to xeric habitats acted as a key innovation and (2) investigating diversification rate shifts along geologic time, discussing the impact of Quaternary climate oscillations on diversification.

Results

NAm Psoraleeae represents a recent, rapid radiation with several genera originating during the Pleistocene, 1 to 2 million years ago. A shift in diversification rate is supported by both methods with a 2.67-fold increase suggested around 2 million years ago followed by a 8.73-fold decrease 440,000 years ago. The hypothesis that a climate regime shift from mesic to xeric habitats drove increased diversification in affected taxa was not supported. Timing of the diversification rate increase supports the hypothesis that glaciation-induced climate changes during the Quaternary influenced diversification of the group. Nonrandom spatial diversification also exists, with greater species richness in the American Southwest.

Conclusion

This study outlines NAm Psoraleeae as a model example of a recent, rapid radiation. Diversification rate shifts in NAm Psoraleeae are not due to current climate regimes as represented by habitat, but instead to past global climate change resulting from Quaternary glaciations. NAm Psoraleeae diversification is a good example of how earthly dynamics including global climate change and topography work together to shape biodiversity.

Plant speciation in continental island floras as exemplified by Nigella in the Aegean Archipelago

Continental shelf island systems, created by rising sea levels, provide a premier setting for studying the effects of geographical isolation on non-adaptive radiation and allopatric speciation brought about by genetic drift. The Aegean Archipelago forms a highly fragmented complex of mostly continental shelf islands that have become disconnected from each other and the mainland in relatively recent geological times (ca <5.2 Ma). These ecologically fairly homogenous islands thus provide a suitable biogeographic context for assessing the relative influences of past range fragmentation, colonization, gene flow and drift on taxon diversification. Indeed, recent molecular biogeographic studies on the Aegean Nigella arvensis complex, combining phylogenetic, phylogeographic and population level approaches, exemplify the importance of allopatry and genetic drift coupled with restricted gene flow in driving plant speciation in this continental archipelago at different temporal and spatial scales. While the recent (Late Pleistocene) radiation of Aegean Nigella, as well as possible instances of incipient speciation (in the Cyclades), is shown to be strongly conditioned by (palaeo)geographic factors (including changes in sea level), shifts in breeding system (selfing) and associated isolating mechanisms have also contributed to this radiation. By contrast, founder event speciation has probably played only a minor role, perhaps reflecting a migratory situation typical for continental archipelagos characterized by niche pre-emption because of a long established resident flora. Overall, surveys of neutral molecular markers in Aegean Nigella have so far revealed population genetic processes that conform remarkably well to predictions raised by genetic drift theory. The challenge is now to gain more direct insights into the relative importance of the role of genetic drift, as opposed to natural selection, in the phenotypic and reproductive divergence among these Aegean plant species.

A broad review of commercially important southern African medicinal plants

AIMS OF THE STUDY

Commercially important indigenous medicinal plants of southern Africa are reviewed in the context of fundamental knowledge about their ethnobotany, phylogeny, genetics, taxonomy, biochemistry, chemical variation, reproductive biology and horticulture. The aim is to explore the rapidly increasing number of scientific publications and to investigate the need for further research.

MATERIALS AND METHODS

The Scopus (Elsevier) reference system was used to investigate trends in the number of scientific publications and patents in 38 medicinal plant species. Fifteen species of special commercial interest were chosen for more detailed reviews: Agathosma betulina, Aloe ferox, Artemisia afra, Aspalathus linearis, Cyclopia genistoides, Harpagophytum procumbens, Hoodia gordonii, Hypoxis hemerocallidea, Lippia javanica, Mesembryanthemum tortuosum, Pelargonium sidoides, Siphonochilus aethiopicus, Sutherlandia frutescens, Warburgia salutaris and Xysmalobium undulatum.

RESULTS

In recent years there has been an upsurge in research and development of new medicinal products and new medicinal crops, as is shown by a rapid increase in the number of scientific publications and patents. Despite the fact that an estimated 10% of the plant species of the world is found in southern Africa, only a few have been fully commercialized and basic scientific information is often not available.

CONCLUSIONS

The limited available information indicates that some of the plants display remarkable regional variation in morphological, genetic and chemical characters that should be more thoroughly investigated. Basic biological information is needed to guide the rapidly accelerating commercialization process, especially the selection of superior clones, the development of new cultivars and the standardization of raw materials.

Plant species radiations: where, when, why?

The spatial and temporal patterns of plant species radiations are largely unknown. I used a nonlinear regression to estimate speciation and extinction rates from all relevant dated clades. Both are surprisingly high. A high species richness can be the result of either little extinction, thus preserving the diversity that dates from older radiations (a 'mature radiation'), or a 'recent and rapid radiation'. The analysis of radiations from different regions (Andes, New Zealand, Australia, southwest Africa, tropics and Eurasia) revealed that the diversity of Australia may be largely the result of mature radiations. This is in sharp contrast to New Zealand, where the flora appears to be largely the result of recent and rapid radiations. Mature radiations are characteristic of regions that have been climatically and geologically stable throughout the Neogene, whereas recent and rapid radiations are more typical of younger (Pliocene) environments. The hyperdiverse Cape and Neotropical floras are the result of the combinations of mature as well as recent and rapid radiations. Both the areas contain stable environments (the Amazon basin and the Cape Fold Mountains) as well as dynamic landscapes (the Andes and the South African west coast). The evolution of diversity can only be understood in the context of the local environment.

Radiation of southern African daisies: biogeographic inferences for subtribe Arctotidinae (Asteraceae, Arctotideae)

The majority of the approximately 80-90 species in subtribe Arctotidinae occur in southern Africa with the centre of diversity in the winter-rainfall region. Three species are restricted to afromontane eastern Africa and three species are endemic to Australia. To investigate biogeographic and phylogenetic relationships within Arctotidinae, sequence data from four cpDNA regions (psbA-trnH, trnT-trnL and trnL-trnF spacers and trnL intron) and the ITS nrDNA region for 59 Arctotidinae species were analyzed with parsimony and Bayesian-inference approaches. Eight well-supported major lineages were resolved. The earliest-diverging extant lineages are afromontane or inhabit mesic habitats, whereas almost all sampled taxa from the winter-rainfall and semi-arid areas have diverged more recently. Molecular dating estimated that the major clades diverged during the Miocene and Pliocene, which is coincident with the trend of increasing rainfall seasonality, aridification and vegetation changes in southwestern Africa. Trans-oceanic dispersal to Australia was estimated to have occurred during the Pliocene.

Timing and tempo of early and successive adaptive radiations in Macaronesia

The flora of Macaronesia, which encompasses five Atlantic archipelagos (Azores, Canaries, Madeira, Cape Verde, and Salvage), is exceptionally rich and diverse.

Spectacular radiation of numerous endemic plant groups has made the Macaronesian islands an outstanding area for studies of evolution and speciation. Despite intensive investigation in the last 15 years, absolute age and rate of diversification are poorly known for the flora of Macaronesia. Here we report molecular divergence estimates and rates of diversification for five representative, putative rapid radiations of monophyletic endemic plant lineages across the core eudicot clade of flowering plants. Three discrete windows of colonization during the Miocene and early Pliocene are suggested for these lineages, all of which are inferred to have had a single colonization event followed by rapid radiation. Subsequent inter-archipelago dispersal events into Madeira and the Cape Verdes took place very recently during the late Pliocene and Pleistocene after initial diversification on the Canary Islands. The tempo of adaptive radiations differs among the groups, but is relatively rapid compared to continental and other island radiations. Our results demonstrate that opportunity for island colonization and successful radiation may have been constrained to discrete time periods of profound climatic and geological changes in northern African and the Mediterranean.

Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade

The disparity in species richness among groups of organisms is one of the most pervasive features of life on earth. A number of studies have addressed this pattern across higher taxa (e.g. 'beetles'), but we know much less about the generality and causal basis of the variation in diversity within evolutionary radiations at lower taxonomic scales. Here, we address the causes of variation in species richness among major lineages of Australia's most diverse vertebrate radiation, a clade of at least 232 species of scincid lizards. We use new mitochondrial and nuclear intron DNA sequences to test the extent of diversification rate variation in this group. We present an improved likelihood-based method for estimating per-lineage diversification rates from combined phylogenetic and taxonomic (species richness) data, and use the method in a hypothesis-testing framework to localize diversification rate shifts on phylogenetic trees. We soundly reject homogeneity of diversification rates among members of this radiation, and find evidence for a dramatic rate increase in the common ancestor of the genera Ctenotus and Lerista. Our results suggest that the evolution of traits associated with climate tolerance may have had a role in shaping patterns of diversity in this group.

Diversification of Lupinus (Leguminosae) in the western New World: derived evolution of perennial life history and colonization of montane habitats

Previous phylogenetic studies of Lupinus (Leguminosae) based on nuclear DNA have shown that the western New World taxa form a monophyletic group representing the majority of species in the genus, with evidence for high rates of recent diversification in South America following final uplift of the Andes 2-4 million years ago (Mya). For this study, three regions of rapidly evolving non-coding chloroplast DNA (trnL intron, trnS-trnG, and trnT-trnL) were examined to estimate the timing and rates of diversification in the western New World, and to infer ancestral states for geographic range, life history, and maximum elevation. The western New World species (5.0-9.3Mya, 0.6-1.1 spp./My) comprise a basally branching assemblage of annual plants endemic to the lower elevations of western North America, from which two species-rich clades are recently derived: (i) the western North American perennials from the Rocky Mountains, Great Basin, and Pacific Slope (0.7-2.1Mya, 2.0-5.9 spp./My) and (ii) the predominantly perennial species from the Andes Mountains of South America and highlands of Mexico (0.8-3.4Mya, 1.4-5.7spp./My). Bayesian posterior predictive tests for association between life history and maximum elevation demonstrate that perennials are positively correlated with higher elevations. These results are consistent with a series of one or more recent radiations in the western New World, and indicate that rapid diversification of Lupinus coincides with the derived evolution of perennial life history, colonization of montane habitats, and range expansion from North America to South America.

DO REEFS DRIVE DIVERSIFICATION IN MARINE TELEOSTS? EVIDENCE FROM THE PUFFERFISH AND THEIR ALLIES (ORDER TETRAODONTIFORMES)

A major challenge in evolutionary biology lies in explaining patterns of high species numbers found in biodiversity hot spots. Tropical coral reefs underlie most marine hot spots and reef-associated fish faunas represent some of the most diverse assemblages of vertebrates on the planet. Although the standing diversity of modern reef fish clades is usually attributed to their ecological association with corals, untangling temporal patterns of codiversification has traditionally proved difficult. In addition, owing to uncertainty in higher-level relationships among acanthomorph fish, there have been few opportunities to test the assumption that reef-association itself leads to higher rates of diversification compared to other habitats. Here we use relaxed-clock methods in conjunction with statistical measures of species accumulation and phylogenetic comparative methods to clarify the temporal pattern of diversification in reef and nonreef-associated lineages of tetraodontiforms, a morphologically diverse order of teleost fish. We incorporate 11 fossil calibrations distributed across the tetraodontiform tree to infer divergence times and compare results from models of autocorrelated and uncorrelated evolutionary rates. All major tetraodontiform reef crown groups have significantly higher rates of diversification than the order as a whole. None of the nonreef-associated families show this pattern with the exception of the aracanid boxfish. Independent contrasts analysis also reveals a significantly positive relationship between diversification rate and proportion of reef-associated species within each family when aracanids are excluded. Reef association appears to have increased diversification rate within tetraodontiforms. We suggest that both intrinsic factors of reef habitat and extrinsic factors relating to the provincialization and regionalization of the marine biota during the Miocene (about 23-5 MY) played a role in shaping these patterns of diversity.

Living with the genetic signature of Miocene induced change: evidence from the phylogeographic structure of the endemic angulate tortoise Chersina angulata

The phylogeographic structure of the monotypic endemic southern African angulate tortoise Chersina angulata was investigated throughout its distribution with the use of partial sequences from three mtDNA loci (COI, cyt b and ND4). Phylogeographic and phylogenetic structuring obtained for the three mtDNA markers were highly congruent and suggested the presence of two genetically distinct, reciprocally monophyletic evolutionary lineages. Group one contained two subclades with haplotypes from the north-western Cape and south-western Cape, respectively, while haplotypes from the southern Cape comprised group two. The two major clades were separated by nine and eight mutational steps for COI and ND4, respectively. Of the three mtDNA gene regions examined, the ND4 partial sequence contained the most phylogenetic signal. Haplotype diversity was generally low and we recovered 34 haplotypes for the 125 animals sequenced for the ND4 subunit. Nested clade analyses performed on the variable ND4 partial sequences suggested the presence of two major refugial areas for this species. The demographic history of the taxon was characterised by range expansion and prolonged historical fragmentation. Divergence time estimates suggest that the temporal and spatial distribution of the taxon was sculpted by changes in temperature and rainfall patterns since the late Miocene. Corroborative evidence from other reptiles is also suggestive of a late Miocene divergence, indicating that this was a major epoch for cladogenesis in southern Africa. Apart from the genetic differences between the two major clades, we also note morphometric and behavioural differences, alluding to the presence of two putative taxa nested within C. angulata.

Spatial scale of local adaptation and population genetic structure in a miniature succulent, Argyroderma pearsonii

Explicit understanding of the spatial scale of evolutionary processes is required in order to set targets for their effective conservation. Here, we explore the spatial context of neutral and adaptive divergence in the species-rich Knersvlakte region of South Africa. Specifically, we aimed to assess the importance of erosional drainage basins as spatial units of evolutionary process. We used amplified fragment length polymorphism (AFLP) and reciprocal transplants to investigate genetic differentiation in Argyroderma pearsonii, sampled from sparse and dense quartz habitats within each of three drainage basins. This design allowed assessment of differentiation at two distinct spatial scales; between habitats within basins, and between basins. We found near-perfect concordance between genetic clusters and basin occupancy, suggesting restricted interbasin gene flow. In addition, transplants reveal adaptive divergence between basins on the dense quartz habitat. We have shown that neutral and adaptive differentiation occurs between basins, but not between habitats within basins, suggesting that conservation plans aimed at conserving multiple interconnected drainage basins will capture an important axis of evolutionary process on the Knersvlakte.

The distribution of species diversity across a flora's component lineages: dating the Cape's 'relicts'

The Cape Floristic Region is exceptionally species-rich both for its area and latitude, and this diversity is highly unevenly distributed among genera. The modern flora is hypothesized to result largely from recent (post-Oligocene) speciation, and it has long been speculated that particular species-poor lineages pre-date this burst of speciation. Here, we employ molecular phylogenetic data in combination with fossil calibrations to estimate the minimum duration of Cape occupation by 14 unrelated putative relicts. Estimates vary widely between lineages (7-101 Myr ago), and when compared with the estimated timing of onset of the modern flora's radiation, it is clear that many, but possibly not all, of these lineages pre-date its establishment. Statistical comparisons of diversities with lineage age show that low species diversity of many of the putative relicts results from a lower rate of diversification than in dated Cape radiations. In other putative relicts, however, we cannot reject the possibility that they diversify at the same underlying rate as the radiations, but have been present in the Cape for insufficient time to accumulate higher diversity. Although the extremes in diversity of currently dated Cape lineages fall outside expectations under a constant underlying diversification rate, sampling of all Cape lineages would be required to reject this null hypothesis.

Wide-band tracheids in genera of Portulacaceae: novel, non-xylary tracheids possibly evolved as an adaptation to water stress

Wide-band tracheids (WBTs) are novel tracheids with wide, lignified secondary walls that intrude deeply into the cell lumen when viewed in transverse sections. These tracheids are found in a few genera in related families in the order Caryophyllales: Aizoaceae, Cactaceae, and Portulacaceae. WBTs in these three families vary in (1) systematic occurrence (found in more highly derived genera in each family), (2) location in plant organs, and (3) structure and dimensions. In addition, an analysis was conducted of WBT cell walls to test the hypothesis that WBTs evolved as an adaptation to water stress (i.e., the wide secondary walls should prevent collapse of the primary wall during water stress). The cell wall data show that primary cell walls in WBTs cannot inwardly collapse to occlusion, thus providing support for the water stress hypothesis of WBT evolution. With consideration of their systematic occurrence, the molecular phylogenetic data, and data here showing support for a water stress adaptive origin, it is logical to assume that WBTs evolved in genera that were adapting to environments undergoing a rapid trend toward aridification.

The evolutionary history of Melianthus (Melianthaceae)

The evolutionary origins of the morphological and taxonomic diversity of angiosperms is poorly known. We used the genus Melianthus to explore the diversification of the southern African flora. Melianthus comprises eight species, and a phylogeny based on one nuclear and two plastid genes, as well as a morphological data set, confirmed that the genus is monophyletic. The two earliest diverging lineages are found in relatively mesic habitats, whereas the two terminal clades (an eastern and a western clade), each with three species, favor more arid habitats. The eastern clade is largely restricted to the summer-rainfall parts of southern Africa, and the western clade is found in winter-rainfall region. Molecular dating indicates a mid-Tertiary origin of the genus, with diversification of the eastern and western clades coincident with the Late Miocene-Pliocene uplift of the Escarpment mountains and the establishment of summer aridity along the west coast. The remarkably complex flowers are indicative of sunbird pollination, but many smaller birds can also visit. Speciation may be the consequence of allopatric divergence into edaphic-climatic niches. Divergence in flower and inflorescence morphology might be in response to the divergent pressures for nectar conservation in arid regions coupled with the need for signaling to avian pollinators in generally shrubby vegetation.

Island radiation on a continental scale: exceptional rates of plant diversification after uplift of the Andes

Species radiations provide unique insights into evolutionary processes underlying species diversification and patterns of biodiversity. To compare plant diversification over a similar time period to the recent cichlid fish radiations, which are an order of magnitude faster than documented bird, arthropod, and plant radiations, we focus on the high-altitude flora of the Andes, which is the most species-rich of any tropical mountains. Because of the recent uplift of the northern Andes, the upland environments where much of this rich endemic flora is found have been available for colonization only since the late Pliocene or Pleistocene, 2-4 million years (Myr) ago. Using DNA sequence data we identify a monophyletic group within the genus Lupinus representing 81 species endemic to the Andes. The age of this clade is estimated to be 1.18-1.76 Myr, implying a diversification rate of 2.49-3.72 species per Myr. This exceeds previous estimates for plants, providing the most spectacular example of explosive plant species diversification documented to date. Furthermore, it suggests that the high cichlid diversification rates are not unique. Lack of key innovations associated with the Andean Lupinus clade suggests that diversification was driven by ecological opportunities afforded by the emergence of island-like habitats after Andean uplift. Data from other genera indicate that lupines are one of a set of similarly rapid Andean plant radiations, continental in scale and island-like in stimulus, suggesting that the high-elevation Andean flora provides a system that rivals other groups, including cichlids, for understanding rapid species diversification.

How much evolutionary history in a 10 x 10 m plot?

We use a fully dated phylogenetic tree of the angiosperm families to calculate phylogenetic diversity (PD) in four South African vegetation types with distinct evolutionary histories. Since the branch length values are in this case represented by the ages of plant lineages, PD becomes the cumulative evolutionary age (CEA) of assemblages. Unsurprisingly, total CEA increases with family and with species diversity and observed values are the same as expected from random sampling of family lists. However, when random sampling is done from species lists, observed CEAs are generally lower than expected. In vegetation types which have undergone recent diversification-grassland, fynbos and Nama-karoo-co-occurring species are more closely related than expected, but in subtropical thicket the observed CEAs are well described by random sampling. The use of CEA has great potential for assessing the age of biotic assemblages, particularly as the dating of genus and species-level phylogenies become more accurate.

Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon)

Adaptive radiations have served as model systems for quantifying the build-up of species richness. Few studies have quantified the tempo of diversification in species-rich clades that contain negligible adaptive disparity, making the macroevolutionary consequences of different modes of evolutionary radiation difficult to assess. We use mitochondrial-DNA sequence data and recently developed phylogenetic methodologies to explore the tempo of diversification of eastern North American Plethodon, a species-rich clade of woodland salamanders exhibiting only limited phenotypic disparity. Lineage-through-time analysis reveals a high rate of lineage accumulation, 0.8 species per million years, occurring 11-8 million years ago in the P. glutinosus species group, followed by decreasing rates. This high rate of lineage accumulation is exceptional, comparable to the most rapid of adaptive radiations. In contrast to classic models of adaptive radiation where ecological niche divergence is linked to the origin of species, we propose that phylogenetic niche conservatism contributes to the rapid accumulation of P. glutinosus-group lineages by promoting vicariant isolation and multiplication of species across a spatially and temporally fluctuating environment. These closely related and ecologically similar lineages persist through long-periods of evolutionary time and form strong barriers to the geographic spread of their neighbours, producing a subsequent decline in lineage accumulation. Rapid diversification among lineages exhibiting long-term maintenance of their bioclimatic niche requirements is an under-appreciated phenomenon driving the build-up of species richness.

Molecular evidence for the age, origin, and evolutionary history of the American desert plant genus Tiquilia (Boraginaceae)

Although the deserts of North America are of very recent origin, their characteristic arid-adapted endemic plant lineages have been suggested to be much older. Earlier researchers have hypothesized that the ancestors of many of these modern desert lineages first adapted to aridity in highly localized arid or semi-arid sites as early as the late Cretaceous or early Tertiary, and that these lineages subsequently spread and diversified as global climate became increasingly arid during the Cenozoic. No study has explicitly examined these hypotheses for any North American arid-adapted plant group. The current paper tests these hypotheses using the genus Tiquilia (Boraginaceae), a diverse North American desert plant group. A strongly supported phylogeny of the genus is estimated using combined sequence data from three chloroplast markers (matK, ndhF, and rps16) and two nuclear markers (ITS and waxy). Ages of divergence events within the genus are estimated using penalized likelihood and a molecular clock approach on the ndhF tree for Tiquilia and representative outgroups, including most of the major lineages of Boraginales. The dating analysis suggests that the stem lineage of Tiquilia split from its nearest extant relative in the Paleocene or Eocene ( approximately 59-48 Ma). This was followed by a relatively long period before the first divergence in the crown group near the Eocene/Oligocene boundary ( approximately 33-29 Ma), shortly after the greatest Cenozoic episode of rapid aridification. Divergence of seven major lineages of Tiquilia is dated to the early-to-mid Miocene ( approximately 23-13 Ma). Several major lineages show a marked increase in diversification concomitant with the onset of more widespread semi-arid and then arid conditions beginning in the late Miocene ( approximately 7 Ma). This sequence of divergence events in Tiquilia agrees well with earlier researchers' ideas concerning North American desert flora assembly.

The South African and Namibian Populations of the Resurrection Plant Myrothamnus flabellifolius are Genetically Distinct and Display Variation in Their Galloylquinic Acid Composition

The polyphenol contents and compositions in desiccated leaves of Myrothamnus flabellifolius plants collected in various locations in Namibia and South Africa were analyzed using UV spectroscopy and high-performance liquid chromatography-mass spectrometry. A study of the genetic relatedness of these populations was also performed by determination of the DNA sequence of the intergenic spacer region between the psbA and the trnH genes in the chloroplast genome. Namibian M. flabellifolius plants contained significantly more polyphenols than South African plants. Namibian plants essentially contained a single polyphenol, 3,4,5-tri-O-galloylquinic acid, whereas South African plants contained a variety of galloylquinic acids including 3,4,5-tri-O-galloylquinic acid together with higher molecular weight galloylquinic acids. Sequence analysis revealed a 1.4% divergence between Namibian and South African plants corresponding to the separation of these populations of approximately 4 x 10(6) years. The significance of the poly-phenol content and composition to the desiccation tolerance of the two populations is discussed.

Relaxed molecular clocks for dating historical plant dispersal events

Age estimation from molecular sequences has emerged as a powerful tool for inferring when a plant lineage arrived in a particular area. Knowing the tenure of lineages within a region is key to understanding the evolution of traits, the evolution of biotic interactions, and the evolution of floras. New analytical methods model change in substitution rates along individual branches of a phylogenetic tree by combining molecular data with time constraints, usually from fossils. These "relaxed clock" approaches can be applied to several gene regions that need not all have the same substitution rates, and they can also incorporate multiple simultaneous fossil calibrations. Since 1995, at least 100 plant biogeographic studies have used molecular-clock dating, and about a fifth has used relaxed clocks. Many of these report evidence of long-distance dispersal. Meta-analyses of studies from the same geographic region can identify directional biases because of prevailing wind or water currents and the relative position and size of landmasses.

Evolution of diversity: the Cape flora

Although the environmental correlates of plant species richness have long received attention, research into the genesis of this diversity is in its infancy. The recent development of molecular dating methods and the inference of robust phylogenetic hypotheses have made it possible to investigate this problem. I use the Cape flora as a model to show that much modern diversity could be the result of recruiting diverse lineages over the entire Cenozoic into this flora, followed by in situ diversification (thus increasing species richness) of at least some of these lineages over a long period in an environmentally heterogeneous area.