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Many dicotyledonous plants produce structures called leaf domatia. Approximately 28% of 290 families have species with leaf domatia. These structures are abundant within the Rubiaceae and Vitaceae. 26% and 16% out of 206 representative species cited in literature from 48 plant families belong to the Rubiaceae and Vitaceae respectively. Leaf domatia are usually associated with mites and often mediate mutualistic relationships with predacious mites. These structures are pockets found in the underside of the leaf, where the secondary vein axils meet the major vein. In the present study, we examine the anatomical structures of leaf domatia from three plant species (Gardenia thunbergia Thunb., Rothmannia capensis Thunb., Rothmannia globosa (Hochst.) Keay) from the Rubiaceae family in order to find out if their internal tissues differ. These plants were sectioned and viewed under a Light Microscope in order to document their internal anatomy. A Transmission Electron Microscope was used to search for the presence of cuticular folds in their epidermis, which are thought to assist plant to communicate with mites. Results from this study suggested that the main features of domatial anatomy are the presence of an extra layer of tissue in the lower epidermis, a cuticle, cuticular folds, trichomes and the presence of an invagination. Cuticular folds were present inside the domatia but were not restricted to the domatial lamina. Thus, we conclude that these structures do not assist plant in plant-mite communication. This study provides a better understating of the anatomy of leaf domatia of the Rubiaceae.

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Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. To our knowledge, this is the first study to use nuclear rRNA at this taxonomic level, presumably because this marker is assumed to evolve so slowly that it is only suitable for phylogenetics.   Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolves effectively clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a 'barcoding gap', estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

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This study investigates genetic diversity in three species of Ephemeroptera, one eurytopic and therefore widespread (Afroptilum sudafricanum) and two stenotopic and thus endemic (Demoreptus natalensis and Demoreptus capensis) species, all of which co-occur in the southern Great Escarpment, South Africa. Mitochondrial DNA was analysed to compare the genetic diversity between the habitat generalist and the two habitat specialists. Afroptilum sudafricanum showed no indication of population genetic structure due to geographic location, while both Demoreptus species revealed clear genetic differentiation between geographic localities and catchments, evident from phylogenetic analyses and high FST values from AMOVA. In addition, the phylogenetic analyses indicate some deeper haplotype divergences within A. sudafricanum and Demoreptus that merit taxonomic attention. These results give important insight into evolutionary processes occurring through habitat specialisation and population isolation. Further research and sampling across a wider geographic setting that includes both major mountain blocks of the Escarpment and lowland non-Escarpment sites will allow for refined understanding of biodiversity and associated habitat preferences, and illuminate comparative inferences into gene flow and cryptic speciation.

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Southern Africa is a biodiversity hotspot of patellid limpets, with three genera (Helcion, Cymbula and Scutellastra) identified and described in the region. Scutellastra is the most diverse and most frequently studied of these and, along with Cymbula, includes species with territorial and non-territorial foraging behaviours. We used three mitochondrial markers (12S rRNA, 16S rRNA and COI) and one nuclear marker (ATPSß intron) to assess evolutionary relationships among species of Cymbula and Scutellastra with these two foraging behaviours and to identify which foraging mode is the more ancient. Maximum Likelihood and Bayesian Inference phylogenetic analyses revealed that the species sharing a foraging type are monophyletic in both genera. Territoriality is a derived character, as the clades with this foraging type are nested within a tree that otherwise comprises non-territorial taxa. These include Helcion, which was recovered as sister to the Cymbula/Scutellastra clade, and the next basal genus, Patella, which is ancestral to all southern African patellogastropods. Deep genetic divergence between the two foraging traits reflects strong adaptive effects of resource partitioning in the evolution of southern African patellid limpets.

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South Africa's 800 km-long southern Great Escarpment hosts numerous endemic plant species only known from their type specimens or from very few records. This is a legacy of a 100-150 year lag between the pioneer work of 19(th) century botanists and repeat fieldwork in the 21(st) century. As a result, population and ecological data are lacking for many local endemic species. Here we report on the rediscovery of Lotononis harveyi B.-E.van Wyk 147 years after its original description, and provide the first detailed ecological notes on the poorly known shrub Macowania revoluta Oliv. Both species are locally endemic to the Great Winterberg-Amatholes (Eastern Cape Province). With only six known individuals, Lotononis harveyi is recommended the conservation status of Critically Endangered, with fire (and potentially grazing) being the main population constraints. Macowania revoluta is locally abundant, and it is surprising that it has been so poorly collected in recent decades. It occupies an important local niche as a keystone montane wetland species, and its narrow distribution range - combined with pressure from woody alien invasive species - suggests that its conservation status should be Rare. The research further highlights the need for continued biodiversity field research along South Africa's poorly explored Great Escarpment.

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Two new species of Indigofera L. (Leguminosae) are described from the Sneeuberg Centre of Floristic Endemism on the southern Great Escarpment, Eastern and Western Cape Provinces, South Africa. Both species are localised high-altitude endemics. Indigoferamagnifica Schrire & V.R. Clark is confined to the summit plateau of the Toorberg-Koudeveldberg-Meelberg west of Graaff-Reinet, and complements other western Sneeuberg endemics such as Ericapasserinoides (Bolus) E.G.H. Oliv. and Faurearecondita Rourke & V.R. Clark. Indigoferaasantasanensis Schrire & V.R. Clark is confined to a small area east of Graaff-Reinet, and complements several other eastern Sneeuberg endemics such as Euryopsexsudans B. Nord & V.R. Clark and Euryopsproteoides B. Nord. & V.R. Clark. Based on morphology, both new species belong to the Cape Clade of Indigofera, supporting a biogeographical link between the Cape Floristic Region and the Sneeuberg, as well as with the rest of the eastern Great Escarpment.

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BACKGROUND AND AIMS: The ability of plant lineages to reach all continents contributes substantially to their evolutionary success. This is exemplified by the Poaceae, one of the most successful angiosperm families, in which most higher taxa (tribes, subfamilies) have global distributions. Due to the old age of the ocean basins relative to the major angiosperm radiations, this is only possible by means of long-distance dispersal (LDD), yet the attributes of lineages with successful LDD remain obscure. Polyploid species are over-represented in invasive floras and in the previously glaciated Arctic regions, and often have wider ecological tolerances than diploids; thus polyploidy is a candidate attribute of successful LDD. METHODS: The link between polyploidy and LDD was explored in the globally distributed grass subfamily Danthonioideae. An almost completely sampled and well-resolved species-level phylogeny of the danthonioids was used, and the available cytological information was assembled. The cytological evolution in the clade was inferred using maximum likelihood (ML) as implemented in ChromEvol. The biogeographical evolution in the clade was reconstructed using ML and Bayesian approaches. KEY RESULTS: Numerous increases in ploidy level are demonstrated. A Late Miocene-Pliocene cycle of polyploidy is associated with LDD, and in two cases (the Australian Rytidosperma and the American Danthonia) led to secondary polyploidy. While it is demonstrated that successful LDD is more likely in polyploid than in diploid lineages, a link between polyploidization events and LDD is not demonstrated. CONCLUSIONS: The results suggest that polyploids are more successful at LDD than diploids, and that the frequent polyploidy in the grasses might have facilitated the extensive dispersal among continents in the family, thus contributing to their evolutionary success.

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BACKGROUND: When genetic structure is identified using mitochondrial DNA (mtDNA), but no structure is identified using biparentally-inherited nuclear DNA, the discordance is often attributed to differences in dispersal potential between the sexes. RESULTS: We sampled the intertidal rocky shore mussel Perna perna in a South African bay and along the nearby open coast, and sequenced maternally-inherited mtDNA (there is no evidence for paternally-inherited mtDNA in this species) and a biparentally-inherited marker. By treating males and females as different populations, we identified significant genetic structure on the basis of mtDNA data in the females only. CONCLUSIONS: This is the first study to report sex-specific differences in genetic structure based on matrilineally-inherited mtDNA in a passively dispersing species that lacks social structure or sexual dimorphism. The observed pattern most likely stems from females being more vulnerable to selection in habitats from which they did not originate, which also manifests itself in a male-biased sex ratio. Our results have three important implications for the interpretation of population genetic data. First, even when mtDNA is inherited exclusively in the female line, it also contains information about males. For that reason, using it to identify sex-specific differences in genetic structure by contrasting it with biparentally-inherited markers is problematic. Second, the fact that sex-specific differences were found in a passively dispersing species in which sex-biased dispersal is unlikely highlights the fact that significant genetic structure is not necessarily a function of low dispersal potential or physical barriers. Third, even though mtDNA is typically used to study historical demographic processes, it also contains information about contemporary processes. Higher survival rates of males in non-native habitats can erase the genetic structure present in their mothers within a single generation.

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BACKGROUND: Baetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different geographic locations. It has been associated with a wide range of ecological conditions, including pH extremes of pH 2.9-10.0 in polluted waters. We present a molecular study of the genetic variation within B. harrisoni across 21 rivers in its distribution range in southern Africa. RESULTS: Four gene regions were examined, two mitochondrial (cytochrome c oxidase subunit I [COI] and small subunit ribosomal 16S rDNA [16S]) and two nuclear (elongation factor 1 alpha [EF1α] and phosphoenolpyruvate carboxykinase [PEPCK]). Bayesian and parsimony approaches to phylogeny reconstruction resulted in five well-supported major lineages, which were confirmed using a general mixed Yule-coalescent (GMYC) model. Results from the EF1α gene were significantly incongruent with both mitochondrial and nuclear (PEPCK) results, possibly due to incomplete lineage sorting of the EF1α gene. Mean between-clade distance estimated using the COI and PEPCK data was found to be an order of magnitude greater than the within-clade distance and comparable to that previously reported for other recognised Baetis species. Analysis of the Isolation by Distance (IBD) between all samples showed a small but significant effect of IBD. Within each lineage the contribution of IBD was minimal. Tentative dating analyses using an uncorrelated log-normal relaxed clock and two published estimates of COI mutation rates suggest that diversification within the group occurred throughout the Pliocene and mid-Miocene (~2.4-11.5 mya). CONCLUSIONS: The distinct lineages of B. harrisoni correspond to categorical environmental variation, with two lineages comprising samples from streams that flow through acidic Table Mountain Sandstone and three lineages with samples from neutral-to-alkaline streams found within eastern South Africa, Malawi and Zambia. The results of this study suggest that B. harrisoni as it is currently recognised is not a single species with a wide geographic range and pH-tolerance, but may comprise up to five species under the phylogenetic species concept, each with limited pH-tolerances, and that the B. harrisoni species group is thus in need of taxonomic review.

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UNLABELLED: Botanical work since 2008 on the Sleeping Giant section of the Kamdebooberge (Sneeuberg mountain complex, Eastern Cape, South Africa) has indicated that these mountains may be of significant conservation value. Accordingly, a precursory, rapid multi-disciplinary biodiversity assessment was undertaken in January 2011, focusing on plants, tetrapod vertebrates and leafhoppers. The botanical results confirm the Kamdebooberge as being of high botanical conservation value, hosting three strict endemics, healthy populations of five other Sneeuberg endemics, and fynbos communities comprising species not found elsewhere in the Sneeuberg. The Kamdebooberge are important for herpetofauna (excluding serpentoids) and mammals, hosting several range-restricted and regional endemics. The expedition uncovered three new leafhopper species, together with several species previously only known from the Cape Floristic Region. Further detailed faunal work may provide further interesting results from these mountains, which show a high conservation value unique to the southern Escarpment. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/2193-1801-1-56) contains supplementary material, which is available to authorized users.

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The name Albuca caudata Jacq. has been widely misunderstood or even ignored since its description in 1791. After studying herbarium specimens and living populations in South Africa, plants fitting Jacquin´s concept of that species are found to be widely distributed in the Eastern Cape, mainly in the Albany centre of Endemism. Furthermore, some divergent specimens matching Baker´s concept of Albuca caudata are described as a new related species: Albuca bakeri. Data on typification, morphology, ecology, and distribution are reported for both taxa. Affinities and divergences with other close allies are also discussed.

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A new species of Psoralea is described. Psoralea margaretiflora C.H. Stirton & V.R. Clark is endemic to the Sneeuberg Centre of Floristic Endemism, Eastern Cape, South Africa. This resprouter is characterised by its small greenish-white flowers with a small trifid purple nectar patch and translucent veins; 5(-7)-pinnate leaflets; multi-branching erect short seasonal flowering shoots; and tall habit of many stiff bare stems with the seasonal shoots massed at the apex. It is most similar to Psoralea oligophylla Eckl. & Zeyh., a widespread species found in the Eastern Cape. The reseeder Psoralea oligophylla differs in its lax virgate spreading habit with numerous long glaucous seasonal shoots; single stem, 1(-3)- glaucous leaflets; more numerous white flowers; and standard petals with a purple ring surrounding a bright yellow nectar patch.

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PREMISE: The cosmopolitan and ecologically important grass subfamily Aristidoideae comprises the widely distributed genus Aristida (250-290 species), Stipagrostis (50 species, with an African-Asian distribution), and Sartidia (five species, Africa and Madagascar). The subfamily includes species with C(3) (Sartidia and a single species of Aristida) and C(4) photosynthetic pathways. Rigorous phylogenetic reconstructions of species relationships are required to explain the biogeographic, physiological, and ecological diversity within this subfamily. METHODS: Chloroplast (trnL-F, rpl16) and nuclear (ITS) DNA sequences were obtained from 198 accessions, and the combined data set was subjected to parsimony, maximum likelihood, and Bayesian inference analyses. Dating analyses calibrated using previously published node ages were conducted to determine the ages of major radiations. RESULTS: The C(3) Sartidia is sister to a monophyletic Stipagrostis, and the (Sartidia, Stipagrostis) clade is sister to Aristida. Within Aristida, the only known C(3) species, A. longifolia, is sister to the remainder of the genus. Infrageneric sections of Aristida were not supported, and there are no synapomorphic morphological characters for the clades retrieved. Within Aristida, monophyletic Australian, African, North American, and South American clades are retrieved. CONCLUSIONS: The subfamily dates back to the late Miocene, with the major lineages present by the Pliocene. With one exception, regional clades of Aristida evolved in the Pliocene. The C(3) photosynthetic pathway is hypothesized to be the pleisomorphic condition for the subfamily, wherein two independent C(4) pathways (each with unique anatomical and genetic features) evolved, one within Aristida and one in Stipagrostis.

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Genetic divergence among populations of marine broadcast spawners in the absence of past geological barriers presents an intriguing challenge to understanding speciation in the sea. To determine how differences in life history affect genetic divergence and demographic histories across incomplete dispersal barriers, we conducted a comparative phylogeographic study of three intertidal limpets (Siphonaria spp.) represented on either side of a biogeographic disjunction separating tropical and subtropical marine provinces in southeastern Africa. Using a combination of mitochondrial and nuclear sequence data, we identified two distinct evolutionary lineages each in both Siphonaria concinna (a planktonic disperser) and S. nigerrima (a direct developer), and panmixia in a second planktonic disperser, S. capensis. Although phylogeographic breaks were present in two species, how these became established differed depending on their life histories. In the direct developer, lack of gene flow following divergence, and demographic expansion from a small initial size in the species' subtropical population, point to a single colonisation event. In contrast, the evolutionary lineages of the planktonic disperser split into two genetic lineages with much larger initial population sizes and southward gene flow continued at least periodically, indicating that divergence in this species may have been driven by a combination of reduced larval dispersal and divergent selection. These findings help explain why the presence or absence of phylogeographic breaks often appears to be independent of species' dispersal potential.

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BACKGROUND: Ecosystem engineers facilitate habitat formation and enhance biodiversity, but when they become invasive, they present a critical threat to native communities because they can drastically alter the receiving habitat. Management of such species thus needs to be a priority, but the poorly resolved taxonomy of many ecosystem engineers represents a major obstacle to correctly identifying them as being either native or introduced. We address this dilemma by studying the sea squirt Pyura stolonifera, an important ecosystem engineer that dominates coastal communities particularly in the southern hemisphere. Using DNA sequence data from four independently evolving loci, we aimed to determine levels of cryptic diversity, the invasive or native status of each regional population, and the most appropriate sampling design for identifying the geographic ranges of each evolutionary unit. RESULTS: Extensive sampling in Africa, Australasia and South America revealed the existence of "nested" levels of cryptic diversity, in which at least five distinct species can be further subdivided into smaller-scale genetic lineages. The ranges of several evolutionary units are limited by well-documented biogeographic disjunctions. Evidence for both cryptic native diversity and the existence of invasive populations allows us to considerably refine our view of the native versus introduced status of the evolutionary units within Pyura stolonifera in the different coastal communities they dominate. CONCLUSIONS: This study illustrates the degree of taxonomic complexity that can exist within widespread species for which there is little taxonomic expertise, and it highlights the challenges involved in distinguishing between indigenous and introduced populations. The fact that multiple genetic lineages can be native to a single geographic region indicates that it is imperative to obtain samples from as many different habitat types and biotic zones as possible when attempting to identify the source region of a putative invader. "Nested" cryptic diversity, and the difficulties in correctly identifying invasive species that arise from it, represent a major challenge for managing biodiversity.

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The snake family Lamprophiidae Fitzinger (Serpentes: Elapoidea) is a putatively Late Eocene radiation of nocturnal snakes endemic to the African continent. It incorporates many of the most characteristic and prolific of Africa's non-venomous snake species, including the widespread type genus Lamprophis Fitzinger, 1843 (house snakes). We used approximately 2500 bases of mitochondrial and nuclear DNA sequence data from 28 (41%) of the approximately 68 recognised lamprophiid species in nine of the eleven genera to investigate phylogenetic structure in the family and to inform taxonomy at the generic level. Cytochrome b, ND4 and tRNA gene sequences (mitochondrial) and c-mos sequences (nuclear) were analysed using Maximum Likelihood, Bayesian Inference and Maximum Parsimony methods. The genus Mehelya Csiki, 1903 was paraphyletic with respect to Gonionotophis Boulenger, 1893. To address this, the concept of Gonionotophis is expanded to include all current Mehelya species. The genus Lamprophis emerged polyphyletic: the enigmatic Lamprophis swazicus was sister to Hormonotus modestus from West Africa, and not closely related to its nominal congeners. It is moved to a new monotypic genus (Inyoka gen. nov.). The remaining Lamprophis species occur in three early-diverging lineages. (1) Lamprophis virgatus and the widely distributed Lamprophis fuliginosus species complex (which also includes Lamprophis lineatus and Lamprophis olivaceus) formed a clade for which the generic name Boaedon Duméril, Bibron & Duméril, 1854 is resurrected. (2) The water snakes (Lycodonomorphus) were nested within Lamprophis (sensu lato), sister to Lamprophis inornatus. We transfer this species to the genus Lycodonomorphus Fitzinger, 1843. (3) We restrict Lamprophis (sensu strictissimo) to a small clade of four species endemic to southern Africa: the type species of Lamprophis Fitzinger, 1843 (Lamprophis aurora) plus Lamprophis fiskii, Lamprophis fuscus and Lamprophis guttatus.

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Crabs of the family Hymenosomatidae are common in coastal and shelf regions throughout much of the southern hemisphere. One of the genera in the family, Hymenosoma, is represented in Africa and the South Pacific (Australia and New Zealand). This distribution can be explained either by vicariance (presence of the genus on the Gondwanan supercontinent and divergence following its break-up) or more recent transoceanic dispersal from one region to the other. We tested these hypotheses by reconstructing phylogenetic relationships among the seven presently-accepted species in the genus, as well as examining their placement among other hymenosomatid crabs, using sequence data from two nuclear markers (Adenine Nucleotide Transporter [ANT] exon 2 and 18S rDNA) and three mitochondrial markers (COI, 12S and 16S rDNA). The five southern African representatives of the genus were recovered as a monophyletic lineage, and another southern African species, Neorhynchoplax bovis, was identified as their sister taxon. The two species of Hymenosoma from the South Pacific neither clustered with their African congeners, nor with each other, and should therefore both be placed into different genera. Molecular dating supports a post-Gondwanan origin of the Hymenosomatidae. While long-distance dispersal cannot be ruled out to explain the presence of the family Hymenosomatidae on the former Gondwanan land-masses and beyond, the evolutionary history of the African species of Hymenosoma indicates that a third means of speciation may be important in this group: gradual along-coast dispersal from tropical towards temperate regions, with range expansions into formerly inhospitable habitat during warm climatic phases, followed by adaptation and speciation during subsequent cooler phases.

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The angiosperm family Proteaceae is a distinct component of the Cape Floristic Region biodiversity hotspot with 330 endemic species. Phylogenetic analyses of subfamily Proteoideae using sequence data from one nuclear and six plastid loci show that most of this diversity is contained in two distinct Cape floral clades. Molecular dating analyses, using Bayesian and penalized likelihood methods and four phylogenetically supported fossil age constraints, reveal contrasting histories for these two clades. The genus Protea belongs to a lineage that may have been in Africa since the Late Cretaceous but began to diversify in the Cape only 5-18 Myr ago. In contrast, the Leucadendrinae clade presumably arrived in the region no earlier than 46 Myr ago by long-distance dispersal from an Australian ancestor and the extant members of this clade began to diversify in the Cape 22-39 Myr ago. These results join a growing number of case studies that challenge the commonly accepted view that most of the Cape flora radiated synchronously in the Late Miocene and Early Pliocene when a Mediterranean climate settled in the region.

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Dating the Tree of Life has now become central to relating patterns of biodiversity to key processes in Earth history such as plate tectonics and climate change. Regions with a Mediterranean climate have long been noted for their exceptional species richness and high endemism. How and when these biota assembled can only be answered with a good understanding of the sequence of divergence times for each of their components. A critical aspect of dating by using molecular sequence divergence is the incorporation of multiple suitable age constraints. Here, we show that only rigorous phylogenetic analysis of fossil taxa can lead to solid calibration and, in turn, stable age estimates, regardless of which of 3 relaxed clock-dating methods is used. We find that Proteaceae, a model plant group for the Mediterranean hotspots of the Southern Hemisphere with a very rich pollen fossil record, diversified under higher rates in the Cape Floristic Region and Southwest Australia than in any other area of their total distribution. Our results highlight key differences between Mediterranean hotspots and indicate that Southwest Australian biota are the most phylogenetically diverse but include numerous lineages with low diversification rates.

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We explore the potential impact of conflicting gene trees on inferences of evolutionary history above the species level. When conflict between gene trees is discovered, it is common practice either to analyze the data separately or to combine the data having excluded the conflicting taxa or data partitions for those taxa (which are then recoded as missing). We demonstrate an alternative approach, which involves duplicating conflicting taxa in the matrix, such that each duplicate is represented by one partition only. This allows the combination of all available data in standard phylogenetic analyses, despite reticulations. We show how interpretation of contradictory gene trees can lead to conflicting inferences of both morphological evolution and biogeographic history, using the example of the pampas grasses, Cortaderia. The characteristic morphological syndrome of Cortaderia can be inferred as having arisen multiple times (chloroplast DNA [cpDNA]) or just once (nuclear ribosomal DNA [nrDNA]). The distributions of species of Cortaderia and related genera in Australia/New Guinea, New Zealand, and South America can be explained by few (nrDNA) or several (cpDNA) dispersals between the southern continents. These contradictions can be explained by past hybridization events, which have linked gains of complex morphologies with unrelated chloroplast lineages and have erased evidence of dispersals from the nuclear genome. Given the discrepancies between inferences based on the gene trees individually, we urge the use of approaches such as ours that take multiple gene trees into account.

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