Phylogeny of Acridocarpus-Brachylophon (Malpighiaceae): implications for tertiary tropical floras and Afroasian biogeography

Evolutionary history of the Asplenium scolopendrium complex (Aspleniaceae), a relictual fern with a northern pan-temperate disjunct distribution

Asplenium scolopendrium is distributed in northern temperate forests with many global biogeographic disjunctions. The species complex of A. scolopendrium has been generated by spatial segregation coupled with divergent evolution. We elucidated the biogeographic history of the A. scolopendrium complex by exploring its origin, dispersal and evolution, thus providing insights into the evolutionary history of the Tertiary floras with northern pan-temperate disjunct distributions. The results revealed that all infraspecific taxa descended from a widely distributed common ancestor in the Northern Hemisphere. This pan-temperate ancestral population formed by unidirectional westward dispersal from European origins primarily during the Early Eocene when the Earth’s climate was much warmer than today. The splitting of European, American and East Asian lineages occurred during the Early Miocene due to geo-climatic vicariances. Polyploidy events in the American ancestral populations created additional reproductive barriers. The star-shaped haplotypes in each continent indicated that local disjunctions also led to derived genotypes with potential to diverge into different taxa. This intracontinental lineage splitting is likely related to latitudinal range shift and habitat fragmentation caused by glacial cycles and climate change during the Pleistocene. The evolutionary history of the A. scolopendrium complex supported the Boreotropical hypothesis exhibiting range expansion during the Early Eocene Climatic Optimum.

Evolutionary relationships, biogeography and morphological characters of Glinus (Molluginaceae), with special emphasis on the genus composition in Sub-Saharan Africa

Glinus is a small genus of Molluginaceae with 8-10 species mostly distributed in the tropics of the World. Its composition and evolutionary relationships were poorly studied. A new molecular phylogeny constructed here using nuclear (ITS) and chloroplast (rbcL, trnK-matK) markers confirmed the monophyly of the genus. Based on ITS analysis, the following well-supported lineages are present within Glinus: the G. bainesii lineage is recovered as sister to the remainder of the genus followed by G. oppositifolius. Three other clades are: G. hirtus with G. orygioides; G. radiatus and G. lotoides; the latter is represented by a sample from North America, and G. zambesiacus as sister to G. setiflorus + G. lotoides + G. dictamnoides. On the plastid gene tree, G. bainesii + G. oppositifolius form a sister clade to all other Glinus species. The next clade is formed by G. hirtus and G. orygioides followed by G. radiatus plus an American sample of G. lotoides. The next branch comprises G. setiflorus as sister to G. zambesiacus + G. lotoides + G. dictamnoides. Glinus seems to have originated from Africa around the Late Eocene or Early Miocene, with further radiations to Australia and the Americas during the Late Miocene or Late Pliocene. Compared with the previous limited character set used for the diagnostics, we have found ten new morphological and carpological traits distinguishing Glinus members. In both trees based on nuclear and plastid datasets, the major phylogenetic clades cannot be characterized by the peculiar morphological characters. Many shared character states leading to their contrasting pattern in the multivariate analysis model are interpreted as a high homoplasy in the phylogenetically distant species. We paid special attention to the composition of the genus in Sub-Saharan Africa, a region with the greatest species diversity. Our results provide new insight into the taxonomy of Glinus in this region. Glinus lotoides var. virens accepted in many previous works is a synonym of G. dictamnoides that is closely related to G. lotoides based on molecular analysis and morphological characters. The status of the American populations of G. lotoides needs further investigation due to different characters of the specimens from the Old and the New World. Many specimens previously identified as G. lotoides var. virens and as the intermediates G. lotoides × G. oppositifolius belong to G. zambesiacus sp. nov. and G. hirtus comb. nov. (≡ Mollugo hirta); the latter species is resurrected from synonymy after 200 years of unacceptance. In some African treatments, G. hirtus was known under the invalidly published name G. dahomensis. Glinus zambesiacus is distributed in the southern and eastern parts of tropical Africa, and G. hirtus previously assumed to be endemic to West Africa is indeed a species with a wide distribution across the tropical part of the continent. Glinus microphyllus previously accepted as endemic to West Tropical Africa together with other new synonyms (G. oppositifolius var. lanatus, G. herniarioides, Wycliffea rotundifolia) is considered here as G. oppositifolius var. keenaniicomb. nov. (≡ Mollugo hirta var. keenanii), a variety found across the entire distribution of G. oppositifolius (Australia, Asia, and Africa). The presence of the American G. radiatus in Africa is not confirmed, and all records of this species belong to G. hirtus. The lectotypes of some names (G. dictamnoides, G. herniarioides, Mollugo hirta, M. setiflora, Pharnaceum pentagynum, Wycliffea) as well as a neotype of G. trianthemoides are designated. A new key to the identification of all Glinus species in Sub-Saharan Africa is provided. A checklist is given of all accepted species in this region (G. bainesii, G. hirtus, G. lotoides, G. oppositifolius s.l., G. setiflorus, and G. zambesiacus) with their nomenclature, morphological description and geographical distribution.

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.

Biogeography of Stigmaphyllon (Malpighiaceae) and a Meta-Analysis of Vascular Plant Lineages Diversified in the Brazilian Atlantic Rainforests Point to the Late Eocene Origins of This Megadiverse Biome

We investigated the biogeography of Stigmaphyllon, the second-largest lianescent genus of Malpighiaceae, as a model genus to reconstruct the age and biogeographic history of the Brazilian Atlantic Rainforest (BAF). Few studies to date have focused on the tertiary diversification of plant lineages in the BAFs, especially on Stigmaphyllon. Phylogenetic relationships for 24 species of Stigmaphyllon (18 ssp. From the Atlantic forest (out of 31 spp.), three spp. from the Amazon Rainforest, two spp. from the Caatinga biome, and a single species from the Cerrado biome) were inferred based on one nuclear DNA (PHYC) and two ribosomal DNA (ETS, ITS) regions using parsimony and Bayesian methods. A time-calibrated phylogenetic tree for ancestral area reconstructions was additionally generated, coupled with a meta-analysis of vascular plant lineages diversified in the BAFs. Our results show that: (1) Stigmaphyllon is monophyletic, but its subgenera are paraphyletic; (2) the most recent common ancestor of Stigmaphyllon originated in the Brazilian Atlantic Rainforest/Caatinga region in Northeastern Brazil ca. 26.0 Mya; (3) the genus colonized the Amazon Rainforest at two different times (ca. 22.0 and 6.0 Mya), the Caatinga biome at least four other times (ca. 14.0, 9.0, 7.0, and 1.0 Mya), the Cerrado biome a single time (ca. 15.0 Mya), and the Southern Atlantic Rainforests five times (from 26.0 to 9.0 Mya); (4) a history of at least seven expansion events connecting the Brazilian Atlantic Rainforest to other biomes from 26.0 to 9.0 Mya, and (5) a single dispersion event from South America to Southeastern Asia and Oceania at 22.0 Mya via Antarctica was proposed. Compared to a meta-analysis of time-calibrated phylogenies for 64 lineages of vascular plants diversified in the Brazilian Atlantic Rainforests, our results point to a late Eocene origin for this megadiverse biome.

Phylogeny, biogeography and systematics of the hyper-diverse blister beetle genus Hycleus (Coleoptera: Meloidae)

Hycleus is a hyper-diverse genus of blister beetles including ~500 species widely distributed in the Old World, currently divided into three "sections" and into 45 "phenetic" species groups according to morphological characters. Recently the monophyly of Hycleus was questioned pointing out its paraphyly with respect to the genera Ceroctis and Paractenodia. In this study, we built a time-calibrated phylogenetic tree based on DNA sequence data from mitochondrial and nuclear genes obtained from 125 species, to understand the phylogenetic relationships among the species of this genus, to infer the biogeographic processes behind their diversification, and to assess their taxonomy and classification. Our results identified four main lineages one of which included the species belonging to Ceroctis and Paractenodia; therefore, both taxa are now referred to Hycleus as new synonyms. The three described sections of Hycleus resulted polyphyletic and are rejected, whereas several species groups represented well supported clades. Hycleus likely originated in Africa during the Early Miocene (~20 Mya), and subsequently spread in Europe and western Asia. Later, in the Late Miocene (~6 Mya) a Saharo-Sindian group branched off from the Palaearctic lineage, whereas the Oriental Region was colonized following a dispersal event through the Arabian Peninsula from the Afrotropical Region (~5 Mya).

Functional role and evolutionary contributions of floral gland morphoanatomy in the Paleotropical genus Acridocarpus (Malpighiaceae)

The stereotyped floral morphology of Neotropical Malpighiaceae species—zygomorphic and calyx with oil glands—is correlated with oil-bee pollination. In contrast, the floral trends of the Paleotropical lineages are actinomorphy and lack of calyx glands, probably due to the absence of oil-collecting bees. The Paleotropical genus Acridocarpus is an exception because of its zygomorphic, gland-bearing flowers. Glands throughout Acridocarpus inflorescences were morphoanatomically evaluated to verify the occurrence of patterns related to species and geographic distribution. Herbarium (25 species) and fresh samples of A. longifolius were processed according to standard anatomical techniques. To verify the presence of glucose and protein, strip tests were applied to the exudate. Fresh samples were fixed and submitted to histochemical tests. Based on the occurrence, number and placement of glands, three distribution patterns were recognized on the bracteole and ten on the calyx. Bract, bracteole and sepal glands have a typical nectary structure with a palisade-like epidermis and vascularized parenchyma. Glands were classified as short-stalked, sessile or immersed. Histochemical tests performed on bract and sepal glands of A. longifolius were positive for proteins, polysaccharides and phenolic compounds, and negative for oil compounds. Glucose and protein were detected in the exudate. These results allow us to recognize the glands in Acridocarpus inflorescences as nectaries. This comprehensive morphoanatomical study helps to clarify the correlation between patterns of floral morphology and secretion consumers, as well as to better understand floral evolution in Malpighiaceae across their dispersal events.

Phylogeny, historical biogeography and characters evolution of the drought resistant fern Pyrrosia Mirbel (Polypodiaceae) inferred from plastid and nuclear markers

Pyrrosia s.l. comprises ca. 60 species with a disjunct Africa/Asia and Australia distribution. The infrageneric classification of Pyrrosia s.l. is controversial based on the phylogenetic analyses of chloroplast markers and morphology. Based on the expanded taxon sampling of Pyrrosia s.l. (51 species), we investigated its phylogeny, biogeography, character evolution and environmental adaptation by employing five chloroplastid markers (rbcL, matK, psbA-trnH, and rps4 + rps4-trnS) and one single (low)-copy nuclear gene, LEAFY. Pyrrosia s.l. was divided into six major clades and eight subclades. Reticulate evolution was revealed both among clades and among species in Pyrrosia s.l. Ancestral character state optimization revealed high levels of homoplastic evolution of the diagnostic characters in Pyrrosia s.l., while the crassulacean acid metabolism pathway seems to have an independent origin. Molecular dating and biogeographic diversification analyses suggested that Pyrrosia s.l. originated no later than the Oligocene and the main clades diversified during the Oligocene and Miocene, with southern Asia, the Indo-China Peninsula and southwestern and southern China as the most likely ancestral areas. Transoceanic long-distance dispersal, rather than vicariance, contributed to the intercontinental disjunction. Diversification scenarios of Pyrrosia s.l. under geological movements and climate fluctuation are also discussed.

Phylogeny and biogeography of the amphi-Pacific genus Aphananthe

Aphananthe is a small genus of five species showing an intriguing amphi-Pacific distribution in eastern, southern and southeastern Asia, Australia, and Mexico, also with one species in Madagascar. The phylogenetic relationships of Aphananthe were reconstructed with two nuclear (ITS & ETS) and two plastid (psbA-trnH & trnL-trnF) regions. Clade divergence times were estimated with a Bayesian approach, and the ancestral areas were inferred using the dispersal-extinction-cladogenesis and Bayesian Binary MCMC analyses. Aphananthe was supported to be monophyletic, with the eastern Asian A. aspera resolved as sister to a clade of the remaining four species. Aphananthe was inferred to have originated in the Late Cretaceous (71.5 mya, with 95% HPD: 66.6-81.3 mya), and the crown age of the genus was dated to be in the early Miocene (19.1 mya, with 95% HPD: 12.4-28.9 mya). The fossil record indicates that Aphananthe was present in the high latitude thermophilic forests in the early Tertiary, and experienced extinctions from the middle Tertiary onwards. Aphananthe originated in Europe based on the inference that included fossil and extant species, but eastern Asia was estimated to be the ancestral area of the clade of the extant species of Aphananthe. Both the West Gondwanan vicariance hypothesis and the boreotropics hypothesis could be excluded as explanation for its amphi-Pacific distribution. Long-distance dispersals out of eastern Asia into North America, southern and southeastern Asia and Australia, and Madagascar during the Miocene account for its wide intercontinental disjunct distribution.

The measure of success: geographic isolation promotes diversification in Pachydactylus geckos

Background

Geckos of the genus Pachydactylus and their close relatives comprise the most species-rich clade of lizards in sub-Saharan Africa. Many explanations have been offered to explain species richness patterns of clades. In the Pachydactylus group, one possible explanation is a history of diversification via geographic isolation. If geographic isolation has played a key role in facilitating diversification, then we expect species in more species-rich subclades to have smaller ranges than species in less diverse subclades. We also expect traits promoting geographic isolation to be correlated with small geographic ranges. In order to test these expectations, we performed phylogenetic analyses and tested for correlations among body size, habitat choice, range sizes, and diversification rates in the Pachydactylus group.

Results

Both body size and habitat use are inferred to have shifted multiple times across the phylogeny of the Pachydactylus group, with large size and generalist habitat use being ancestral for the group. Geographic range size is correlated with both of these traits. Small-bodied species have more restricted ranges than large-bodied species, and rock-dwelling species have more restricted ranges than either terrestrial or generalist species. Rock-dwelling and small body size are also associated with higher rates of diversification, and subclades retaining ancestral conditions for these traits are less species rich than subclades in which shifts to small body size and rocky habitat use have occurred. The phylogeny also illustrates inadequacies of the current taxonomy of the group.

Conclusions

The results are consistent with a model in which lineages more likely to become geographically isolated diversify to a greater extent, although some patterns also resemble those expected of an adaptive radiation in which ecological divergence acts as a driver of speciation. Therefore, the Pachydactylus group may represent an intermediate between clades in which radiation is adaptive versus those in which it is non-adaptive.

Phylogeny of Elatinaceae and the Tropical Gondwanan Origin of the Centroplacaceae(Malpighiaceae, Elatinaceae) Clade

The flowering plant family Elatinaceae is a widespread aquatic lineage inhabiting temperate and tropical latitudes, including ∼35(-50) species. Its phylogeny remains largely unknown, compromising our understanding of its systematics. Moreover, this group is particularly in need of attention because the biogeography of most aquatic plant clades has yet to be investigated, resulting in uncertainty about whether aquatic plants show histories that deviate from terrestrial plants. We inferred the phylogeny of Elatinaceae from four DNA regions spanning 59 accessions across the family. An expanded sampling was used for molecular divergence time estimation and ancestral area reconstruction to infer the biogeography of Elatinaceae and their closest terrestrial relatives, Malpighiaceae and Centroplacaceae. The two genera of Elatinaceae, Bergia and Elatine, are monophyletic, but several traditionally recognized groups within the family are non-monophyletic. Our results suggest two ancient biogeographic events in the Centroplacaceae(Malpighiaceae, Elatinaceae) clade involving western Gondwana, while Elatinaceae shows a more complicated biogeographic history with a high degree of continental endemicity. Our results indicate the need for further taxonomic investigation of Elatinaceae. Further, our study is one of few to implicate ancient Gondwanan biogeography in extant angiosperms, especially significant given the Centroplacaceae(Malpighiaceae, Elatinaceae) clade's largely tropical distribution. Finally, Elatinaceae demonstrates long-term continental in situ diversification, which argues against recent dispersal as a universal explanation commonly invoked for aquatic plant distributions.

Phylogenetic relationships, character evolution and biogeographic diversification of Pogostemon s.l. (Lamiaceae)

Pogostemon (Lamiaceae; Lamioideae) sensu lato is a large genus consisting of about 80 species with a disjunct African/Asian distribution. The infrageneric taxonomy of the genus has historically been troublesome due to morphological variability and putative convergent evolution within the genus. Notably, some species of Pogostemon are obligately aquatic, perhaps the only Lamiaceae taxa which exhibit this trait. Phylogenetic analyses using the nuclear ribosomal internal transcribed spacer (ITS) and five plastid regions (matK, rbcL, rps16, trnH-psbA, trnL-F), confirmed the monophyly of Pogostemon and its sister relationship with the genus Anisomeles. Pogostemon was resolved into two major clades, and none of the three morphologically defined subgenera of Pogostemon were supported as monophyletic. Inflorescence type (spikes with more than two lateral branches vs. a single terminal spike, or rarely with two lateral branches) is phylogenetically informative and consistent with the two main clades we recovered. Accordingly, a new infrageneric classification of Pogostemon consisting of two subgenera is proposed. Molecular dating and biogeographic diversification analyses suggest that Pogostemon split from its sister genus in southern and southeast Asia in the early Miocene. The early strengthening of the Asia monsoon system that was triggered by the uplifting of the Qinghai-Tibetan Plateau may have played an important role in the subsequent diversification of the genus. In addition, our results suggest that transoceanic long-distance dispersal of Pogostemon from Asia to Africa occurred at least twice, once in the late Miocene and again during the late-Miocene/early-Pliocene.

Living on the edge: timing of Rand Flora disjunctions congruent with ongoing aridification in Africa

The Rand Flora is a well-known floristic pattern in which unrelated plant lineages show similar disjunct distributions in the continental margins of Africa and adjacent islands—Macaronesia-northwest Africa, Horn of Africa-Southern Arabia, Eastern Africa, and Southern Africa. These lineages are now separated by environmental barriers such as the arid regions of the Sahara and Kalahari Deserts or the tropical lowlands of Central Africa. Alternative explanations for the Rand Flora pattern range from vicariance and climate-driven extinction of a widespread pan-African flora to independent dispersal events and speciation in situ. To provide a temporal framework for this pattern, we used published data from nuclear and chloroplast DNA to estimate the age of disjunction of 17 lineages that span 12 families and nine orders of angiosperms. We further used these estimates to infer diversification rates for Rand Flora disjunct clades in relation to their higher-level encompassing lineages. Our results indicate that most disjunctions fall within the Miocene and Pliocene periods, coinciding with the onset of a major aridification trend, still ongoing, in Africa. Age of disjunctions seemed to be related to the climatic affinities of each Rand Flora lineage, with sub-humid taxa dated earlier (e.g., Sideroxylon) and those with more xeric affinities (e.g., Campylanthus) diverging later. We did not find support for significant decreases in diversification rates in most groups, with the exception of older subtropical lineages (e.g., Sideroxylon, Hypericum, or Canarina), but some lineages (e.g., Cicer, Campylanthus) showed a long temporal gap between stem and crown ages, suggestive of extinction. In all, the Rand Flora pattern seems to fit the definition of biogeographic pseudocongruence, with the pattern arising at different times in response to the increasing aridity of the African continent, with interspersed periods of humidity allowing range expansions.

The establishment of Central American migratory corridors and the biogeographic origins of seasonally dry tropical forests in Mexico

Biogeography and community ecology can mutually illuminate the formation of a regional species pool or biome. Here, we apply phylogenetic methods to a large and diverse plant clade, Malpighiaceae, to characterize the formation of its species pool in Mexico, and its occupancy of the seasonally dry tropical forest (SDTF) biome that occurs there. We find that the ~162 species of Mexican Malpighiaceae represent ~33 dispersals from South America beginning in the Eocene and continuing until the Pliocene (~46.4-3.8 Myr). Furthermore, dispersal rates between South America and Mexico show a significant six-fold increase during the mid-Miocene (~23.9 Myr). We hypothesize that this increase marked the availability of Central America as an important corridor for Neotropical plant migration. We additionally demonstrate that this high rate of dispersal contributed substantially more to the phylogenetic diversity of Malpighiaceae in Mexico than in situ diversification. Finally, we show that most lineages arrived in Mexico pre-adapted with regard to one key SDTF trait, total annual precipitation. In contrast, these lineages adapted to a second key trait, precipitation seasonality, in situ as mountain building in the region gave rise to the abiotic parameters of extant SDTF. The timing of this in situ adaptation to seasonal precipitation suggests that SDTF likely originated its modern characteristics by the late Oligocene, but was geographically more restricted until its expansion in the mid-Miocene. These results highlight the complex interplay of dispersal, adaptation, and in situ diversification in the formation of tropical biomes. Our results additionally demonstrate that these processes are not static, and their relevance can change markedly over evolutionary time. This has important implications for understanding the origin of SDTF in Mexico, but also for understanding the temporal and spatial origin of biomes and regional species pools more broadly.

Patterns of diversification amongst tropical regions compared: a case study in Sapotaceae

Species diversity is unequally distributed across the globe, with the greatest concentration occurring in the tropics. Even within the tropics, there are significant differences in the numbers of taxa found in each continental region. Manilkara is a pantropical genus of trees in the Sapotaceae comprising c. 78 species. Its distribution allows for biogeographic investigation and testing of whether rates of diversification differ amongst tropical regions. The age and geographical origin of Manilkara are inferred to determine whether Gondwanan break-up, boreotropical migration or long distance dispersal have shaped its current disjunct distribution. Diversification rates through time are also analyzed to determine whether the timing and tempo of speciation on each continent coincides with geoclimatic events. Bayesian analyses of nuclear (ITS) and plastid (rpl32-trnL, rps16-trnK, and trnS-trnFM) sequences were used to reconstruct a species level phylogeny of Manilkara and related genera in the tribe Mimusopeae. Analyses of the nuclear data using a fossil-calibrated relaxed molecular clock indicate that Manilkara evolved 32-29 million years ago (Mya) in Africa. Lineages within the genus dispersed to the Neotropics 26-18 Mya and to Asia 28-15 Mya. Higher speciation rates are found in the Neotropical Manilkara clade than in either African or Asian clades. Dating of regional diversification correlates with known palaeoclimatic events. In South America, the divergence between Atlantic coastal forest and Amazonian clades coincides with the formation of drier Cerrado and Caatinga habitats between them. In Africa diversification coincides with Tertiary cycles of aridification and uplift of the east African plateaux. In Southeast Asia dispersal may have been limited by the relatively recent emergence of land in New Guinea and islands further east c. 10 Mya.

Phylogeny and historical biogeography of Isodon (Lamiaceae): rapid radiation in south-west China and Miocene overland dispersal into Africa

Rapid organismal radiations occurring on the Qinghai-Tibetan Plateau (QTP) and the mechanisms underlying Asia-Africa intercontinental disjunctions have both attracted much attention from evolutionary biologists. Here we use the genus Isodon (Lamiaceae), a primarily East Asian lineage with disjunct species in central and southern Africa, as a case study to shed light upon these processes. The molecular phylogeny and biogeographic history of Isodon were reconstructed using sequences of three plastid markers, the nuclear ribosomal internal transcribed spacer (nrITS), and a low-copy nuclear gene (LEAFY intron II). The evolution of chromosome numbers in this genus was also investigated using probabilistic models. Our results support a monophyletic Isodon that includes the two disjunct African species, both of which likely formed through allopolyploidy. An overland migration from Asia to Africa through Arabia during the early Miocene is proposed as the most likely explanation for the present disjunct distribution of Isodon. The opening of the Red Sea in the middle Miocene may appear to have had a major role in disrupting floristic exchange between Asia and Africa. In addition, a rapid radiation of Isodon was suggested to occur in the late Miocene. It corresponds with one of the major uplifts of the QTP and subsequent aridification events. Our results support the hypothesis that geological and climatic events play important roles in driving biological diversification of organisms distributed in the QTP area.

Long-term morphological stasis maintained by a plant-pollinator mutualism

Many major branches in the Tree of Life are marked by stereotyped body plans that have been maintained over long periods of time. One possible explanation for this stasis is that there are genetic or developmental constraints that restrict the origin of novel body plans. An alternative is that basic body plans are potentially quite labile, but are actively maintained by natural selection. We present evidence that the conserved floral morphology of a species-rich flowering plant clade, Malpighiaceae, has been actively maintained for tens of millions of years via stabilizing selection imposed by their specialist New World oil-bee pollinators. Nine clades that have lost their primary oil-bee pollinators show major evolutionary shifts in specific floral traits associated with oil-bee pollination, demonstrating that developmental constraint is not the primary cause of morphological stasis in Malpighiaceae. Interestingly, Malpighiaceae show a burst in species diversification coinciding with the origin of this plant-pollinator mutualism. One hypothesis to account for radiation despite morphological stasis is that although selection on pollinator efficiency explains the origin of this unique and conserved floral morphology, tight pollinator specificity subsequently permitted greatly enhanced diversification in this system.

Multimillion-year climatic effects on palm species diversity in Africa

Past climatic changes have caused extinction, speciation, and range dynamics, but assessing the influence of past multimillion-year climatic imprints on present-day biodiversity patterns remains challenging. We analyzed a new continental-scale data set to examine the importance of paleoclimatic effects on current gradients in African palm richness patterns. Using climate reconstructions from the late Miocene (-10 mya), the Pliocene (-3 mya), and the Last Glacial Maximum (0.021 mya), we found that African palm diversity patterns exhibit pronounced historical legacies related to long-term climate change. Notably, pre-Pleistocene paleoprecipitation variables differentially affected current diversity patterns of palms grouped by contrasting habitat requirements. Accounting for present-day environment, rain forest palms exhibit greater species richness in localities where Pliocene precipitation was relatively high, whereas open-habitat palms show higher species richness in areas of relatively low precipitation during the Miocene Epoch. Our results demonstrate that diversity-climate relationships among African palm species include multimillion-year lagged dynamics, i.e., with historical legacies persisting across much longer time periods than commonly recognized.

Radiation and repeated transoceanic dispersal of Schoeneae (Cyperaceae) through the southern hemisphere

PREMISE OF THE STUDY

The broad austral distribution of Schoeneae is almost certainly a product of long-distance dispersal. Owing to the inadequacies of existing phylogenetic data and a lack of rigorous biogeographic analysis, relationships within the tribe remain poorly resolved and its pattern of radiation and dispersal uncertain. We employed an expanded sampling of taxa and markers and a rigorous analytic approach to address these limitations. We evaluated the roles of geography and ecology in stimulating the initial radiation of the group and its subsequent dispersal across the southern hemisphere.

METHODS

A dated tree was reconstructed using reversible-jump Markov chain Monte Carlo (MCMC) with a polytomy prior and molecular dating, applied to data from two nuclear and three cpDNA regions. Ancestral areas and habitats were inferred using dispersal-extinction-cladogenesis models.

KEY RESULTS

Schoeneae originated in Australia in the Paleocene. The existence of a "hard" polytomy at the base of the clade reflects the rapid divergence of six principal lineages ca. 50 Ma, within Australia. From this ancestral area, Schoeneae have traversed the austral oceans with remarkable frequency, a total of 29 distinct dispersal events being reported here. Dispersal rates between landmasses are not explicable in terms of the geographical distances separating them. Transoceanic dispersal generally involved habitat stasis.

CONCLUSIONS

Although the role of dispersal in explaining global distribution patterns is now widely accepted, the apparent ease with which such dispersal may occur has perhaps been under-appreciated. In Schoeneae, transoceanic dispersal has been remarkably frequent, with ecological opportunity, rather than geography, being most important in dictating dispersal patterns.

Evolutionary history of the Afro-Madagascan Ixora species (Rubiaceae): species diversification and distribution of key morphological traits inferred from dated molecular phylogenetic trees

BACKGROUND AND AIMS

Previous work on the pantropical genus Ixora has revealed an Afro-Madagascan clade, but as yet no study has focused in detail on the evolutionary history and morphological trends in this group. Here the evolutionary history of Afro-Madagascan Ixora spp. (a clade of approx. 80 taxa) is investigated and the phylogenetic trees compared with several key morphological traits in taxa occurring in Madagascar.

METHODS

Phylogenetic relationships of Afro-Madagascan Ixora are assessed using sequence data from four plastid regions (petD, rps16, rpoB-trnC and trnL-trnF) and nuclear ribosomal external transcribed spacer (ETS) and internal transcribed spacer (ITS) regions. The phylogenetic distribution of key morphological characters is assessed. Bayesian inference (implemented in BEAST) is used to estimate the temporal origin of Ixora based on fossil evidence.

KEY RESULTS

Two separate lineages of Madagascan taxa are recovered, one of which is nested in a group of East African taxa. Divergence in Ixora is estimated to have commenced during the mid Miocene, with extensive cladogenesis occurring in the Afro-Madagascan clade during the Pliocene onwards.

CONCLUSIONS

Both lineages of Madagascan Ixora exhibit morphological innovations that are rare throughout the rest of the genus, including a trend towards pauciflorous inflorescences and a trend towards extreme corolla tube length, suggesting that the same ecological and selective pressures are acting upon taxa from both Madagascan lineages. Novel ecological opportunities resulting from climate-induced habitat fragmentation and corolla tube length diversification are likely to have facilitated species radiation on Madagascar.

Integrated fossil and molecular data reveal the biogeographic diversification of the eastern Asian-eastern North American disjunct hickory genus (Carya Nutt.)

The hickory genus (Carya) contains ca. 17 species distributed in subtropical and tropical regions of eastern Asia and subtropical to temperate regions of eastern North America. Previously, the phylogenetic relationships between eastern Asian and eastern North American species of Carya were not fully confirmed even with an extensive sampling, biogeographic and diversification patterns had thus never been investigated in a phylogenetic context. We sampled 17 species of Carya and 15 species representing all other genera of the Juglandaceae as outgroups, with eight nuclear and plastid loci to reconstruct the phylogeny of Carya. The phylogenetic positions of seven extinct genera of the Juglandaceae were inferred using morphological characters and the molecular phylogeny as a backbone constraint. Divergence times within Carya were estimated with relaxed Bayesian dating. Biogeographic analyses were performed in DIVA and LAGRANGE. Diversification rates were inferred by LASER and APE packages. Our results support two major clades within Carya, corresponding to the lineages of eastern Asia and eastern North America. The split between the two disjunct clades is estimated to be 21.58 (95% HPD 11.07-35.51) Ma. Genus-level DIVA and LAGRANGE analyses incorporating both extant and extinct genera of the Juglandaceae suggested that Carya originated in North America, and migrated to Eurasia during the early Tertiary via the North Atlantic land bridge. Fragmentation of the distribution caused by global cooling in the late Tertiary resulted in the current disjunction. The diversification rate of hickories in eastern North America appeared to be higher than that in eastern Asia, which is ascribed to greater ecological opportunities, key morphological innovations, and polyploidy.

Phylogeny, biogeography and divergence times in Passiflora (Passifloraceae)

As part of a long-term investigation on the evolution of Passiflora L., we investigated the divergence ages of the genus and diversification of its subgenera, relating them with biogeographical and/or historical events, and other characteristics of this taxon. The main aim of the present work was to evaluate the biogeographic distribution of this genus to better understand its evolutionary history. This is the first time that representatives from South American and Old World Passifloraceae genera have been studied as a group comprising a total of 106 widely distributed species, with representative samples of the four suggested subgenera. Seven DNA regions were studied, comprising 7,431 nucleotides from plastidial, mitochondrial and nuclear genomes. Divergence time estimates were obtained by using a Bayesian Markov Chain Monte Carlo method and a random local clock model for each partition. Three major subgenera have been shown to be monophyletic and here we are proposing to include another subgenus in the Passiflora infrageneric classification. In general, divergence among the four subgenera in Passiflora is very ancient, ranging from ∼32 to ∼38 Mya, and Passifloraceae seems to follow a biogeographic scenario proposed for several plant groups, originating in Africa, crossing to Europe/Asia and arriving in the New World by way of land bridges. Our results indicated that Passiflora ancestors arrived in Central America and diversified quickly from there, with many long distance dispersion events.

Burseraceae: a model for studying the Amazon flora

A well-studied group of plants can serve as a model for addressing issues in conservation, evolution, and biogeography, making it possible to assign conservation status with confidence and detecting not only those taxa that are most threatened but also those that represent basal, unique, and/or relictual members of entire lineages. Clarified higher-level phylogenetic relationships open the door to more refined systematics of clades without having to worry if they are para- or polyphyletic. A well-studied group can also be an excellent testing ground for new or under-utilized tools and independent data sets. Research on the Burseraceae, with over 100 taxa in the Amazon, is rapidly arriving at the point where the family can be used effectively both as a tool for conservation and as a model for studying the processes influencing the origin and maintenance of high diversity in the Amazonian flora. First, we are resolving higher-level phylogenies as well as species-level taxonomy in various clades, allowing comparative approaches. Second, the family occurs throughout Amazonia and is well-represented in most habitats overall, but most of the taxa are restricted in their distributions and/or habitats; this makes it possible to test the relative importance of geographic barriers vs. habitat diversity in the speciation process. The family is sufficiently large to provide adequate statistical power for hypothesis testing and yet small enough to achieve the necessary sampling intensity, allowing us to assess the relative impacts of morphological innovation, ecological opportunity, and biogeographic events on the diversification of Burseraceae and related groups.

Climate niches of milkweeds with plesiomorphic traits (Secamonoideae; Apocynaceae) and the milkweed sister group link ancient African climates and floral evolution

PREMISE OF THE STUDY

Climate change that increases mortality of plants and pollinators can create mate-finding Allee effects and thus act as a strong selective force on floral morphology. Milkweeds (Secamonoideae and Asclepiadoideae; Apocynaceae) are typically small plants of seasonally dry habitats, with pollinia and high pollen-transfer efficiency. Their sister group (tribe Baisseeae and Dewevrella) is mostly comprised of giant lianas of African rainforests, with pollen in monads. Comparison of the two groups motivated a new hypothesis: milkweeds evolved in the context of African aridification and the shifting of rainforest to dry forest. Pollinia and high pollen-transfer efficiency may have been adaptations that alleviated mate-finding Allee effects generated by high mortality during droughts. We formally tested whether milkweeds have a drier climate niche by comparing milkweeds with plesiomorphic traits (Secamonoideae) and the milkweed sister group in continental Africa.

METHODS

We georeferenced specimens of the milkweed sister group and Secamonoideae in continental Africa, extracted 19 climatic variables from the Worldclim model, conducted factor analysis to identify correlated suites of variables, and compared the frequency distributions of the two lineages relative to each factor.

KEY RESULTS

The distributions of Secamonoideae and the milkweed sister group differed significantly relative to four factors, each correlated with a distinct suite of climate parameters: (1) air temperature (Secamonoideae: cooler), (2) total and (3) summer precipitation (Secamonoideae: drier), and (4) temperature seasonality and isothermality (Secamonoideae: more seasonal and less isothermal).

CONCLUSIONS

Secamonoideae in continental Africa inhabit drier, cooler sites than do the milkweed sister group, consistent with a shift from rainforests to dry forests in a cooling climate.

Little ecological divergence associated with speciation in two African rain forest tree genera

BACKGROUND

The tropical rain forests (TRF) of Africa are the second largest block of this biome after the Amazon and exhibit high levels of plant endemism and diversity. Two main hypotheses have been advanced to explain speciation processes that have led to this high level of biodiversity: allopatric speciation linked to geographic isolation and ecological speciation linked to ecological gradients. Both these hypotheses rely on ecology: in the former conservation of ecological niches through time is implied, while in the latter adaptation via selection to alternative ecological niches would be a prerequisite. Here, we investigate the role of ecology in explaining present day species diversity in African TRF using a species level phylogeny and ecological niche modeling of two predominantly restricted TRF tree genera, Isolona and Monodora (Annonaceae). Both these genera, with 20 and 14 species, respectively, are widely distributed in African TRFs, with a few species occurring in slightly less humid regions such as in East Africa.

RESULTS

A total of 11 sister species pairs were identified most of them occurring in allopatry or with little geographical overlap. Our results provide a mixed answer on the role of ecology in speciation. Although no sister species have identical niches, just under half of the tests suggest that sister species do have more similar niches than expected by chance. PCA analyses also support little ecological differences between sister species. Most speciation events within both genera predate the Pleistocene, occurring during the Late Miocene and Pliocene periods.

CONCLUSIONS

Ecology is almost always involved in speciation, however, it would seem to have had a little role in species generation within Isolona and Monodora at the scale analyzed here. This is consistent with the geographical speciation model for TRF diversification. These results contrast to other studies for non-TRF plant species where ecological speciation was found to be an important factor of diversification. The Pliocene period appears to be a vital time in the generation of African TRF diversity, whereas Pleistocene climatic fluctuations have had a smaller role on speciation than previously thought.Ecological niche modeling, species level phylogeny, ecological speciation, African tropics, Isolona, Monodora, Annonaceae.

A dated phylogeny and collection records reveal repeated biome shifts in the African genus Coccinia (Cucurbitaceae)

BACKGROUND

Conservatism in climatic tolerance may limit geographic range expansion and should enhance the effects of habitat fragmentation on population subdivision. Here we study the effects of historical climate change, and the associated habitat fragmentation, on diversification in the mostly sub-Saharan cucurbit genus Coccinia, which has 27 species in a broad range of biota from semi-arid habitats to mist forests. Species limits were inferred from morphology, and nuclear and plastid DNA sequence data, using multiple individuals for the widespread species. Climatic tolerances were assessed from the occurrences of 1189 geo-referenced collections and WorldClim variables.

RESULTS

Nuclear and plastid gene trees included 35 or 65 accessions, representing up to 25 species. The data revealed four species groups, one in southern Africa, one in Central and West African rain forest, one widespread but absent from Central and West African rain forest, and one that occurs from East Africa to southern Africa. A few individuals are differently placed in the plastid and nuclear (LFY) trees or contain two ITS sequence types, indicating hybridization. A molecular clock suggests that the diversification of Coccinia began about 6.9 Ma ago, with most of the extant species diversity dating to the Pliocene. Ancestral biome reconstruction reveals six switches between semi-arid habitats, woodland, and forest, and members of several species pairs differ significantly in their tolerance of different precipitation regimes.

CONCLUSIONS

The most surprising findings of this study are the frequent biome shifts (in a relatively small clade) over just 6 - 7 million years and the limited diversification during and since the Pleistocene. Pleistocene climate oscillations may have been too rapid or too shallow for full reproductive barriers to develop among fragmented populations of Coccinia, which would explain the apparently still ongoing hybridization between certain species. Steeper ecological gradients in East Africa and South Africa appear to have resulted in more advanced allopatric speciation there.

A complete generic phylogeny of Malpighiaceae inferred from nucleotide sequence data and morphology

PREMISE OF THE STUDY

The Malpighiaceae include ∼1300 tropical flowering plant species in which generic definitions and intergeneric relationships have long been problematic. The goals of our study were to resolve relationships among the 11 generic segregates from the New World genus Mascagnia, test the monophyly of the largest remaining Malpighiaceae genera, and clarify the placement of Old World Malpighiaceae. •

METHODS

We combined DNA sequence data for four genes (plastid ndhF, matK, and rbcL and nuclear PHYC) from 338 ingroup accessions that represented all 77 currently recognized genera with morphological data from 144 ingroup species to produce a complete generic phylogeny of the family. •

KEY RESULTS AND CONCLUSIONS

The genera are distributed among 14 mostly well-supported clades. The interrelationships of these major subclades have strong support, except for the clade comprising the wing-fruited genera (i.e., the malpighioid+Amorimia, Ectopopterys, hiraeoid, stigmaphylloid, and tetrapteroid clades). These results resolve numerous systematic problems, while others have emerged and constitute opportunities for future study. Malpighiaceae migrated from the New to Old World nine times, with two of those migrants being very recent arrivals from the New World. The seven other Old World clades dispersed much earlier, likely during the Tertiary. Comparison of floral morphology in Old World Malpighiaceae with their closest New World relatives suggests that morphological stasis in the New World likely results from selection by neotropical oil-bee pollinators and that the morphological diversity found in Old World flowers has evolved following their release from selection by those bees.

The root of the East African cichlid radiations

BACKGROUND

For decades cichlid fishes (Perciformes: Cichlidae) of the East African cichlid radiations (Teleostei: Cichlidae) have served as natural experimental subjects for the study of speciation processes and the search for potential speciation key factors. Despite numerous phylogenetic studies dealing with their intragroup relationships, surprisingly little is known about the phylogenetic placement and time of origin of this enigmatic group. We used multilocus DNA-sequence data from five nuclear and four mitochondrial genes and refined divergence time estimates to fill this knowledge gap.

RESULTS

In concordance with previous studies, the root of the East African cichlid radiations is nested within the so called "Tilapias", which is a paraphyletic assemblage. For the first time, we clarified tilapiine intragroup relationships and established three new monophyletic groups:"Oreochromini", "Boreotilapiini" and a group with a distribution center in East/Central Africa, the "Austrotilapiini". The latter is the founder lineage of the East African radiations and emerged at the Miocene/Oligocene boundary at about 14 to 26 mya.

CONCLUSION

Our results provide the first resolved hypothesis for the phylogenetic placement of the megadiverse East African cichlid radiations as well as for the world's second most important aquaculture species, the Nile Tilapia, Oreochromis niloticus. Our analyses constitute not only a robust basis for African cichlid phylogenetics and systematics, but provide a valid and necessary framework for upcoming comparative phylogenomic studies in evolutionary biology and aquaculture.

Molecular phylogenetics reveal multiple tertiary vicariance origins of the African rain forest trees

Background

Tropical rain forests are the most diverse terrestrial ecosystems on the planet. How this diversity evolved remains largely unexplained. In Africa, rain forests are situated in two geographically isolated regions: the West-Central Guineo-Congolian region and the coastal and montane regions of East Africa. These regions have strong floristic affinities with each other, suggesting a former connection via an Eocene pan-African rain forest. High levels of endemism observed in both regions have been hypothesized to be the result of either 1) a single break-up followed by a long isolation or 2) multiple fragmentation and reconnection since the Oligocene. To test these hypotheses the evolutionary history of endemic taxa within a rain forest restricted African lineage of the plant family Annonaceae was studied. Molecular phylogenies and divergence dates were estimated using a Bayesian relaxed uncorrelated molecular clock assumption accounting for both calibration and phylogenetic uncertainties.

Results

Our results provide strong evidence that East African endemic lineages of Annonaceae have multiple origins dated to significantly different times spanning the Oligocene and Miocene epochs. Moreover, these successive origins (c. 33, 16 and 8 million years – Myr) coincide with known periods of aridification and geological activity in Africa that would have recurrently isolated the Guineo-Congolian rain forest from the East African one. All East African taxa were found to have diversified prior to Pleistocene times.

Conclusion

Molecular phylogenetic dating analyses of this large pan-African clade of Annonaceae unravels an interesting pattern of diversification for rain forest restricted trees co-occurring in West/Central and East African rain forests. Our results suggest that repeated reconnections between the West/Central and East African rain forest blocks allowed for biotic exchange while the break-ups induced speciation via vicariance, enhancing the levels of endemicity. These results provide an explanation for present day distribution patterns and origins of endemicity for African rain forest trees. Moreover, given the pre-Pleistocene origins of all the studied endemic East African genera and species, these results also offer important insights for setting conservation priorities in these highly diversified but threatened ecosystems.

Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited

The family Brassicaceae comprises 3710 species in 338 genera, 25 recently delimited tribes, and three major lineages based on phylogenetic results from the chloroplast gene ndhF. To assess the credibility of the lineages and newly delimited tribes, we sequenced an approximately 1.8-kb region of the nuclear phytochrome A (PHYA) gene for taxa previously sampled for the chloroplast gene ndhF. Using parsimony, likelihood, and Bayesian methods, we reconstructed the phylogeny of the gene and used the approximately unbiased (AU) test to compare phylogenetic results from PHYA with findings from ndhF. We also combined ndhF and PHYA data and used a Bayesian mixed model approach to infer phylogeny. PHYA and combined analyses recovered the same three large lineages as those recovered in ndhF trees, increasing confidence in these lineages. The combined tree confirms the monophyly of most of the recently delimited tribes (only Alysseae, Anchonieae, and Descurainieae are not monophyletic), while 13 of the 23 sampled tribes are monophyletic in PHYA trees. In addition to phylogenetic results, we documented the trichome branching morphology of species across the phylogeny and explored the evolution of different trichome morphologies using the AU test. Our results indicate that dendritic, medifixed, and stellate trichomes likely evolved independently several times in the Brassicaceae.

A rapid diversification of rainforest trees (Guatteria; Annonaceae) following dispersal from Central into South America

Several recent studies have suggested that a substantial portion of today's plant diversity in the Neotropics has resulted from the dispersal of taxa into that region rather than vicariance, but more data are needed to substantiate this claim. Guatteria (Annonaceae) is, with 265 species, the third largest genus of Neotropical trees after Inga (Fabaceae) and Ocotea (Lauraceae), and its widespread distribution and frequent occurrence makes the genus an excellent model taxon to study diversification patterns. This study reconstructed the phylogeny of Guatteria and inferred three major biogeographical events in the history of the genus: (1) a trans-oceanic Miocene migration from Central into South America before the closing of the Isthmus of Panama; (2) a major diversification of the lineage within South America; and (3) several migrations of South American lineages back into Central America via the closed Panamanian land bridge. Therefore, Guatteria is not an Amazonian centred-genus sensu Gentry but a major Miocene diversification that followed its dispersal into South America. This study provides further evidence that migration into the Neotropics was an important factor in the historical assembly of its biodiversity. Furthermore, it is shown that phylogenetic patterns are comparable to those found in Ocotea and Inga and that a closer comparison of these genera is desirable.

Phylogenetic systematics and tempo of evolution of the Viverrinae (Mammalia, Carnivora, Viverridae) within feliformians: Implications for faunal exchanges between Asia and Africa

We reconstructed the phylogeny of the subfamily Viverrinae (Mammalia, Carnivora, Viverridae) using a approximately 3kb data set in order to reassess timing and patterns of faunal exchanges between Asia and Africa. Maximum parsimony, maximum likelihood, and Bayesian analyses of separated and combined matrices (cytochrome b, transthyretin intron I and IRBP exon 1 [IRBP1]) recovered all the well-supported relationships within feliformian lineages. In addition, IRBP1 supported paraphyly of genus Herpestes and contributed to the resolution of equivocal hypotheses within Viverridae, including (1) the monophyly of Viverrinae, and (2) Viverricula sister-group of the other terrestrial civets (Civettictis and Viverra). The combined analysis yielded a robust phylogeny, recovering monophyly of Prionodontidae and yielding high posterior probabilities for nodes (1) (Prionodontidae, Felidae) and (2) ((Felidae, Prionodontidae), ((Hyaenidae, (Herpestidae, Eupleridae)), Viverridae)). Using a fossil cross-validation method, we estimated the emergence of Viverridae at 34.29Myr, with a separation between the three traditional subfamilies Hemigalinae, Paradoxurinae, and Viverrinae during the Late Oligocene-Early Miocene. The terrestrial civets and the splits between (1) Civettictis and Viverra and (2) Poiana and Genetta were estimated to appear during the Middle Miocene. Parsimony- and maximum likelihood-based methods yielded unambiguous ancestral area reconstructions, including the Asian origin of the family Viverridae, the subfamily Viverrinae, the terrestrial civets and the clade (Civettictis, Viverra). On the grounds of genetic distances, morphological divergence, and divergence time estimates, we propose the erection of the subfamily Genettinae (including Genetta and Poiana). Our analyses suggested two independent migration events from Asia to Africa, during the Middle Miocene (Civettictis) and between the Late Oligocene and Middle Miocene (Genettinae). These results are in agreement with the hypothesis of Miocene routes from Asia to Africa-via the Arabian microplate-that would have involved several independent events of migrations. Couched in the context of the viverrid fossil record, our study calls for a revision of the paleontological data in order to fully appreciate the complexity of Afro-Asian faunal exchanges.

Phylogeny of the parasitic plant family Orobanchaceae inferred from phytochrome A

Partial sequences of the nuclear gene encoding the photoreceptor phytochrome A (PHYA) are used to reconstruct relationships within Orobanchaceae, the largest of the parasitic angiosperm families. The monophyly of Orobanchaceae, including nonphotosynthetic holoparasites, hemiparasites, and nonparasitic Lindenbergia is strongly supported. Phytochrome A data resolve six well-supported lineages that contain all of the sampled genera except Brandisia, which is sister to the major radiation of hemiparasites. In contrast to previous plastid and ITS trees, relationships among these major clades also are generally well supported. Thus, the robust phylogenetic hypothesis inferred from the PHYA data provides a much better context in which to evaluate the evolution of parasitism within the group. Ninety-eight species of Orobanchaceae, representing 43 genera, are included and Brandisia, Bungea, Cymbaria, Esterhazya, Nesogenes, Phtheirospermum, Radamaea, Siphonostegia, and Xylocalyx are confirmed as members of Orobanchaceae. The earliest diverging lineage of hemiparasites is identified for the first time; it contains Bungea, Cymbaria, Monochasma, Siphonostegia, and the monotypic Schwalbea, which is federally endangered. This basal clade is marked by the presence of two novel introns. A second, apparently independent gain of one of these introns marks a clade of largely European taxa. There is significant rate heterogeneity among PHYA sequences, and the presence of multiple PHYA in some taxa is consistent with observed ploidy levels.

Insights into the historical construction of species-rich biomes from dated plant phylogenies, neutral ecological theory and phylogenetic community structure

Analytical methods are now available that can date all nodes in a molecular phylogenetic tree with one calibration, and which correct for variable rates of DNA substitution in different lineages. Although these techniques are approximate, they offer a new tool to investigate the historical construction of species-rich biomes. Dated phylogenies of globally distributed plant families often indicate that dispersal, even across oceans, rather than plate tectonics, has generated their wide distributions. By contrast, there are indications that animal lineages have undergone less long distance dispersal. Dating the origin of biome-specific plant groups offers a means of estimating the age of the biomes they characterize. However, rather than a simple emphasis on biome age, we stress the importance of studies that seek to unravel the processes that have led to the accumulation of large numbers of species in some biomes. The synthesis of biological inventory, systematics and evolutionary biology offered by the frameworks of neutral ecological theory and phylogenetic community structure offers a promising route for future work.

The phylogenetic history and biogeography of the frankincense and myrrh family (Burseraceae) based on nuclear and chloroplast sequence data

Generalized hypotheses for the vicariant, Gondwanan origin of pantropically distributed eudicotyledon families must be refined to accommodate recently revised dates that indicate major continental rifting events predate the evolution of many tricolpate angiosperm clades. Here, we use molecular phylogenies of an eudicotyledon family previously hypothesized to have a Gondwanan origin, the Burseraceae, to test this and other alternative biogeographical hypotheses in light of recalibrated geological events. Phylogenies based on nuclear and chloroplast data were reconstructed for 13 of the 18 genera (50 spp. total) of Burseraceae using parsimony, maximum likelihood, and Bayesian methods. Ages of all lineages were estimated using penalized likelihood and semiparametric rate smoothing [Bioinformatics 2003 (19) 301], which allows the user to calibrate phylogenies based on non-clock-like DNA sequence data with fossil information. Biogeographical hypotheses were tested by comparing ages of species and more inclusive lineages with their extant and most parsimonious ancestral distributions. Our data support a North American Paleocene origin for the Burseraceae followed by dispersal of ancestral lineages to eastern Laurasia and Southern Hemisphere continents.

Phylogeny and biogeography of exacum (gentianaceae): a disjunctive distribution in the Indian ocean basin resulted from long distance dispersal and extensive radiation

Disjunctive distributions across paleotropical regions in the Indian Ocean Basin (IOB) often invoke dispersal/vicariance debates. Exacum (Gentianaceae, tribe Exaceae) species are spread around the IOB, in Africa, Madagascar, Socotra, the Arabian peninsula, Sri Lanka, India, the Himalayas, mainland Southeast Asia including southern China and Malaysia, and northern Australia. The distribution of this genus was suggested to be a typical example of vicariance resulting from the breakup of the Gondwanan supercontinent. The molecular phylogeny of Exacum is in principle congruent with morphological conclusions and shows a pattern that resembles a vicariance scenario with rapid divergence among lineages, but our molecular dating analysis demonstrates that the radiation is too recent to be associated with the Gondwanan continental breakup. We used our dating analysis to test the results of DIVA and found that the program predicted impossible vicariance events. Ancestral area reconstruction suggests that Exacum originated in Madagascar, and divergence dating suggests its origin was not before the Eocene. The Madagascan progenitor, the most recent common ancestor of Exacum, colonized Sri Lanka and southern India via long-distance dispersals. This colonizer underwent an extensive range expansion and spread to Socotra-Arabia, northern India, and mainland Southeast Asia in the northern IOB when it was warm and humid in these regions. This widespread common ancestor retreated subsequently from most parts of these regions and survived in isolation in Socotra-Arabia, southern India-Sri Lanka, and perhaps mainland Southeast Asia, possibly as a consequence of drastic climatic changes, particularly the spreading drought during the Neogene. Secondary diversification from these surviving centers and Madagascar resulted in the extant main lineages of the genus. The vicariance-like pattern shown by the phylogeny appears to have resulted from long-distance dispersals followed by extensive range expansion and subsequent fragmentation. The extant African species E. oldenlandioides is confirmed to be recently dispersed from Madagascar.