Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae

Dispersal from Africa to the Neotropics was followed by multiple transitions across Neotropical biomes facilitated by frugivores

BACKGROUND AND AIM

Plant disjunctions have fascinated biogeographers and ecologists for a long time. We use tribe Bocageeae (Annonaceae), a predominantly Neotropical plant group distributed across several present-day Neotropical biomes and with an African-American disjunction, to investigate long-distance dispersal mediated by frugivorous animals at both intercontinental and intracontinental scales.

METHODS

We reconstructed a species-level phylogeny of tribe Bocageeae with a dataset composed of 116 nuclear markers. We sampled 70 % of Bocageeae species, covering their geographical range and representing all eight genera. We estimated divergence times using BEAST, inferred ancestral range distributions and reconstructed ancestral states for fruit traits related to long-distance dispersal in a Bayesian framework.

KEY RESULTS

The ancestral Bocageeae date to the Early Eocene and were inferred to occur in Africa and proto-Amazonia. Their ancestral fruits were large and dehiscent. The first lineage split gave rise to an exclusively Neotropical clade during the Middle Eocene, in proto-Amazonia. Range exchange between the Amazon and the Atlantic Forest occurred at least once during the Miocene, and from Amazonia to Central America and Mexico during the Early Miocene. Transitions in different sets of fruit morphologies were inferred to be related to dispersal events across South American regions/biomes.

CONCLUSIONS

In Bocageeae, mammals might have been responsible for long-distance dispersal through the Boreotropics. In the Neotropics, proto-Amazonia is proposed to be the source for dispersal to other tropical American biomes. Long-distance dispersal might have happened via a wide range of dispersal guilds, depending on frugivore radiations, diversity and abundance in particular time periods and places. Hence, inter- and intracontinental dispersal might not rely on a single dispersal syndrome or guild, but more on the availability of frugivorous lineages for seed dispersal.

'Out of Africa' origin of the pantropical staghorn fern genus Platycerium (Polypodiaceae) supported by plastid phylogenomics and biogeographical analysis

BACKGROUND AND AIMS

The staghorn fern genus Platycerium is one of the most commonly grown ornamental ferns, and it evolved to occupy a typical pantropical intercontinental disjunction. However, species-level relationships in the genus have not been well resolved, and the spatiotemporal evolutionary history of the genus also needs to be explored.

METHODS

Plastomes of all the 18 Platycerium species were newly sequenced. Using plastome data, we reconstructed the phylogenetic relationships among Polypodiaceae members with a focus on Platycerium species, and further conducted molecular dating and biogeographical analyses of the genus.

KEY RESULTS

The present analyses yielded a robustly supported phylogenetic hypothesis of Platycerium. Molecular dating results showed that Platycerium split from its sister genus Hovenkampia ~35.2 million years ago (Ma) near the Eocene-Oligocene boundary and began to diverge ~26.3 Ma during the late Oligocene, while multiple speciation events within Platycerium occurred during the middle to late Miocene. Biogeographical analysis suggested that Platycerium originated in tropical Africa and then dispersed eastward to southeast Asia-Australasia and westward to neotropical areas.

CONCLUSIONS

Our analyses using a plastid phylogenomic approach improved our understanding of the species-level relationships within Platycerium. The global climate changes of both the Late Oligocene Warming and the cooling following the mid-Miocene Climate Optimum may have promoted the speciation of Platycerium, and transoceanic long-distance dispersal is the most plausible explanation for the pantropical distribution of the genus today. Our study investigating the biogeographical history of Platycerium provides a case study not only for the formation of the pantropical intercontinental disjunction of this fern genus but also the 'out of Africa' origin of plant lineages.

Botany and geogenomics: Constraining geological hypotheses in the neotropics with large-scale genetic data derived from plants

Decades of empirical research have revealed how the geological history of our planet shaped plant evolution by establishing well-known patterns (e.g., how mountain uplift resulted in high rates of diversification and replicate radiations in montane plant taxa). This follows a traditional approach where botanical data are interpreted in light of geological events. In this synthesis, I instead describe how by integrating natural history, phylogenetics, and population genetics, botanical research can be applied alongside geology and paleontology to inform our understanding of past geological and climatic processes. This conceptual shift aligns with the goals of the emerging field of geogenomics. In the neotropics, plant geogenomics is a powerful tool for the reciprocal exploration of two long standing questions in biology and geology: how the dynamic landscape of the region came to be and how it shaped the evolution of the richest flora. Current challenges that are specific to analytical approaches for plant geogenomics are discussed. I describe the scale at which various geological questions can be addressed from biological data and what makes some groups of plants excellent model systems for geogenomics research. Although plant geogenomics is discussed with reference to the neotropics, the recommendations given here for approaches to plant geogenomics can and should be expanded to exploring long-standing questions on how the earth evolved with the use of plant DNA.

Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity

During 25 surveys of global Phytophthora diversity, conducted between 1998 and 2020, 43 new species were detected in natural ecosystems and, occasionally, in nurseries and outplantings in Europe, Southeast and East Asia and the Americas. Based on a multigene phylogeny of nine nuclear and four mitochondrial gene regions they were assigned to five of the six known subclades, 2a-c, e and f, of Phytophthora major Clade 2 and the new subclade 2g. The evolutionary history of the Clade appears to have involved the pre-Gondwanan divergence of three extant subclades, 2c, 2e and 2f, all having disjunct natural distributions on separate continents and comprising species with a soilborne and aquatic lifestyle and, in addition, a few partially aerial species in Clade 2c; and the post-Gondwanan evolution of subclades 2a and 2g in Southeast/East Asia and 2b in South America, respectively, from their common ancestor. Species in Clade 2g are soilborne whereas Clade 2b comprises both soil-inhabiting and aerial species. Clade 2a has evolved further towards an aerial lifestyle comprising only species which are predominantly or partially airborne. Based on high nuclear heterozygosity levels ca. 38 % of the taxa in Clades 2a and 2b could be some form of hybrid, and the hybridity may be favoured by an A1/A2 breeding system and an aerial life style. Circumstantial evidence suggests the now 93 described species and informally designated taxa in Clade 2 result from both allopatric non-adaptive and sympatric adaptive radiations. They represent most morphological and physiological characters, breeding systems, lifestyles and forms of host specialism found across the Phytophthora clades as a whole, demonstrating the strong biological cohesiveness of the genus. The finding of 43 previously unknown species from a single Phytophthora clade highlight a critical lack of information on the scale of the unknown pathogen threats to forests and natural ecosystems, underlining the risk of basing plant biosecurity protocols mainly on lists of named organisms. More surveys in natural ecosystems of yet unsurveyed regions in Africa, Asia, Central and South America are needed to unveil the full diversity of the clade and the factors driving diversity, speciation and adaptation in Phytophthora. Taxonomic novelties: New species: Phytophthora amamensis T. Jung, K. Kageyama, H. Masuya & S. Uematsu, Phytophthora angustata T. Jung, L. Garcia, B. Mendieta-Araica, & Y. Balci, Phytophthora balkanensis I. Milenković, Ž. Tomić, T. Jung & M. Horta Jung, Phytophthora borneensis T. Jung, A. Durán, M. Tarigan & M. Horta Jung, Phytophthora calidophila T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, Phytophthora catenulata T. Jung, T.-T. Chang, N.M. Chi & M. Horta Jung, Phytophthora celeris T. Jung, L. Oliveira, M. Tarigan & I. Milenković, Phytophthora curvata T. Jung, A. Hieno, H. Masuya & M. Horta Jung, Phytophthora distorta T. Jung, A. Durán, E. Sanfuentes von Stowasser & M. Horta Jung, Phytophthora excentrica T. Jung, S. Uematsu, K. Kageyama & C.M. Brasier, Phytophthora falcata T. Jung, K. Kageyama, S. Uematsu & M. Horta Jung, Phytophthora fansipanensis T. Jung, N.M. Chi, T. Corcobado & C.M. Brasier, Phytophthora frigidophila T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora furcata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora inclinata N.M. Chi, T. Jung, M. Horta Jung & I. Milenković, Phytophthora indonesiensis T. Jung, M. Tarigan, L. Oliveira & I. Milenković, Phytophthora japonensis T. Jung, A. Hieno, H. Masuya & J.F. Webber, Phytophthora limosa T. Corcobado, T. Majek, M. Ferreira & T. Jung, Phytophthora macroglobulosa H.-C. Zeng, H.-H. Ho, F.-C. Zheng & T. Jung, Phytophthora montana T. Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora multipapillata T. Jung, M. Tarigan, I. Milenković & M. Horta Jung, Phytophthora multiplex T. Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora nimia T. Jung, H. Masuya, A. Hieno & C.M. Brasier, Phytophthora oblonga T. Jung, S. Uematsu, K. Kageyama & C.M. Brasier, Phytophthora obovoidea T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, Phytophthora obturata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora penetrans T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora platani T. Jung, A. Pérez-Sierra, S.O. Cacciola & M. Horta Jung, Phytophthora proliferata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora pseudocapensis T. Jung, T.-T. Chang, I. Milenković & M. Horta Jung, Phytophthora pseudocitrophthora T. Jung, S.O. Cacciola, J. Bakonyi & M. Horta Jung, Phytophthora pseudofrigida T. Jung, A. Durán, M. Tarigan & M. Horta Jung, Phytophthora pseudoccultans T. Jung, T.-T. Chang, I. Milenković & M. Horta Jung, Phytophthora pyriformis T. Jung, Y. Balci, K.D. Boders & M. Horta Jung, Phytophthora sumatera T. Jung, M. Tarigan, M. Junaid & A. Durán, Phytophthora transposita T. Jung, K. Kageyama, C.M. Brasier & H. Masuya, Phytophthora vacuola T. Jung, H. Masuya, K. Kageyama & J.F. Webber, Phytophthora valdiviana T. Jung, E. Sanfuentes von Stowasser, A. Durán & M. Horta Jung, Phytophthora variepedicellata T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora vietnamensis T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora ×australasiatica T. Jung, N.M. Chi, M. Tarigan & M. Horta Jung, Phytophthora ×lusitanica T. Jung, M. Horta Jung, C. Maia & I. Milenković, Phytophthora ×taiwanensis T. Jung, T.-T. Chang, H.-S. Fu & M. Horta Jung. Citation: Jung T, Milenković I, Balci Y, Janoušek J, Kudláček T, Nagy ZÁ, Baharuddin B, Bakonyi J, Broders KD, Cacciola SO, Chang T-T, Chi NM, Corcobado T, Cravador A, Đorđević B, Durán A, Ferreira M, Fu C-H, Garcia L, Hieno A, Ho H-H, Hong C, Junaid M, Kageyama K, Kuswinanti T, Maia C, Májek T, Masuya H, Magnano di San Lio G, Mendieta-Araica B, Nasri N, Oliveira LSS, Pane A, Pérez-Sierra A, Rosmana A, Sanfuentes von Stowasser E, Scanu B, Singh R, Stanivuković Z, Tarigan M, Thu PQ, Tomić Z, Tomšovský M, Uematsu S, Webber JF, Zeng H-C, Zheng F-C, Brasier CM, Horta Jung M (2024). Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity. Studies in Mycology 107: 251-388. doi: 10.3114/sim.2024.107.04.

Diversity and functional roles of floral glands in Malpighiaceae: insights in Lophopterys floribunda W.R. Anderson & C. Davis

Lophopterys floribunda is a Neotropical species of Malpighiaceae endemic to Brazil, occurring in both the Amazon and Atlantic Forest. Instead of the typical bi-glandular sepals reported for Neotropical Malpighiaceae, this species presents a single, large gland on the lateral sepals. In addition, ant patrolling was observed at the apex of bracts and bracteoles during fieldwork. Thus, this work aimed to describe the sepalar gland of L. floribunda and other secretory structures in its flowers and inflorescence. Samples of bracts, bracteoles, sepals, petals, and anther were collected and submitted to usual anatomical techniques. Unexpected nectaries at the apex of bracts and bracteoles, not visible to the naked eye, were described and represent a new type of structure for the family due to both their position and size. Mutualistic ants consume the exudate produced by these tiny nectaries, and such structures enable a specific visitation pattern for Lophopterys. Typical epithelial elaiophores occur on the lateral sepals, formed by an invaginated epidermis, which predominantly produce lipid secretion. The petal marginal glands are anatomically similar to the standard type of colleter, which exude mucilaginous substances. The exudate produced by the petal marginal glands was considered to have an additional role of contributing to the maintenance of the closed bud during the beginning of development. The globose epidermal cells containing lipids, proteins, and polysaccharides observed in the connective may be responsible for the typical aroma emitted by these flowers. The diversity of secretory structures reported here has application in both systematic and ecological studies of Malpighiaceae.

A comprehensive genus-level phylogeny and biogeographical history of the Lythraceae based on whole plastome sequences

BACKGROUND AND AIMS

The Lythraceae are a mainly subtropical to tropical family of the order Myrtales with 28 currently accepted genera and approximately 600 species. There is currently no well-supported phylogenetic and biogeographical hypothesis of the Lythraceae incorporating all currently accepted genera, which we sought to provide.

METHODS

Plastomes of representative species of 18 distinct Lythraceae genera were sequenced and annotated. Together with existing sequences, plastomes of all 28 currently accepted genera in the Lythraceae were brought together for the first time. The plastomes were aligned and a Bayesian phylogenetic hypothesis was produced. We then conducted a time-calibrated Bayesian analysis and a biogeographical analysis.

KEY RESULTS

Plastome-based Bayesian and maximum-likelihood phylogenetic trees are generally congruent with recent nuclear phylogenomic data and resolve two deeply branching major clades in the Lythraceae. One major clade concentrates shrubby and arboreal South American and African genera that inhabit seasonally dry environments, with larger, often winged seeds, adapted to dispersal by the wind. The second major clade concentrates North American, Asian, African and several near-cosmopolitan herbaceous, shrubby and arboreal genera, often inhabiting humid or aquatic environments, with smaller seeds possessing structures that facilitate dispersal by water.

CONCLUSIONS

We hypothesize that the Lythraceae dispersed early in the Late Cretaceous from South American to North American continents, with subsequent expansion in the Late Cretaceous of a North American lineage through Laurasia to Africa via a boreotropical route. Two later expansions of South American clades to Africa in the Palaeocene and Eocene, respectively, are also hypothesized. Transoceanic dispersal in the family is possibly facilitated by adaptations to aquatic environments that are common to many extant genera of the Lythraceae, where long-distance dispersal and vicariance may be invoked to explain several remarkable disjunct distributions in Lythraceae clades.

A new species of Hiptage (Malpighiaceae) from northwest Yunnan (China) based on molecular and morphological data

Hiptagestenopterum K.Tan & M.X.Ren, a new species of Hiptage collected from a deep valley close to the Nujiang Gorge, northwest of Yunnan Province, China, is described and illustrated based on molecular and morphological data. The new species was found isolated in an entrenched valley of the Laowo River, a tributary of the Nujiang River, at the northern edge of the distribution range of the genus. H.stenopterum shares some morphological similarities with the narrowly endemic H.incurvatum and H.lushuiensis. However, H.stenopterum is easily distinguished by its oblanceolate lateral wing of winged mericarp, 10 to 12 calyx glands, and branchlets densely rusty tomentose. The new species status is also supported by molecular phylogenetic analyses based on nuclear ribosome internal transcribed spacer (nrITS), which showed distinct systematic boundaries from the most morphologically similar species, H.incurvatum and their morphological relatives, H.lushuiensis.

The evolutionary history of bees in time and space

Bees are the most significant pollinators of flowering plants. This partnership began ca. 120 million years ago, but the uncertainty of how and when bees spread across the planet has greatly obscured investigations of this key mutualism. We present a novel analysis of bee biogeography using extensive new genomic and fossil data to demonstrate that bees originated in Western Gondwana (Africa and South America). Bees likely originated in the Early Cretaceous, shortly before the breakup of Western Gondwana, and the early evolution of any major bee lineage is associated with either the South American or African land masses. Subsequently, bees colonized northern continents via a complex history of vicariance and dispersal. The notable early absences from large landmasses, particularly in Australia and India, have important implications for understanding the assembly of local floras and diverse modes of pollination. How bees spread around the world from their hypothesized Southern Hemisphere origin parallels the histories of numerous flowering plant clades, providing an essential step to studying the evolution of angiosperm pollination syndromes in space and time.

Cenozoic migration of a desert plant lineage across the North Atlantic

Previous paleobotanical work concluded that Paleogene elements of the sclerophyllous subhumid vegetation of western Eurasia and western North America were endemic to these disjunct regions, suggesting that the southern areas of the Holarctic flora were isolated at that time. Consequently, molecular studies invoked either parallel adaptation to dry climates from related ancestors, or long-distance dispersal in explaining disjunctions between the two regions, dismissing the contemporaneous migration of dry-adapted lineages via land bridges as unlikely. We report Vauquelinia (Rosaceae), currently endemic to western North America, in Cenozoic strata of western Eurasia. Revision of North American fossils previously assigned to Vauquelinia confirmed a single fossil-species of Vauquelinia and one of its close relative Kageneckia. We established taxonomic relationships of fossil-taxa using diagnostic character combinations shared with modern species and constructed a time-calibrated phylogeny. The fossil record suggests that Vauquelinia, currently endemic to arid and subdesert environments, originated under seasonally arid climates in the Eocene of western North America and subsequently crossed the Paleogene North Atlantic land bridge (NALB) to Europe. This pattern is replicated by other sclerophyllous, dry-adapted and warmth-loving plants, suggesting that several of these taxa potentially crossed the North Atlantic via the NALB during Eocene times.

Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene.

Deep vicariance and frequent transoceanic dispersal shape the evolutionary history of a globally distributed fern family

PREMISE

The historical biogeography of ferns is typically expected to be dominated by long-distance dispersal due to their minuscule spores. However, few studies have inferred the historical biogeography of a large and widely distributed group of ferns to test this hypothesis. Our aims were to determine the extent to which long-distance dispersal vs. vicariance have shaped the history of the fern family Blechnaceae, to explore ecological correlates of dispersal and diversification, and to determine whether these patterns differ between the northern and southern hemispheres.

METHODS

We used sequence data for three chloroplast loci to infer a time-calibrated phylogeny for 154 of 265 species of Blechnaceae, including representatives of all genera in the family. This tree was used to conduct ancestral range reconstruction and stochastic character mapping, estimate diversification rates, and identify ecological correlates of diversification.

RESULTS

Blechnaceae originated in Eurasia and began diversifying in the late Cretaceous. A lineage comprising most extant diversity diversified principally in the austral Pacific region around the Paleocene-Eocene Thermal Maximum. Land connections that existed near the poles during periods of warm climates likely facilitated migration of several lineages, with subsequent climate-mediated vicariance shaping current distributions. Long-distance dispersal is frequent and asymmetrical, with New Zealand/Pacific Islands, Australia, and tropical America being major source areas.

CONCLUSIONS

Ancient vicariance and extensive long-distance dispersal have shaped the history of Blechnaceae in both the northern and southern hemispheres. The exceptional diversity in austral regions appears to reflect rapid speciation in these areas; mechanisms underlying this evolutionary success remain uncertain.

Structural diversity of elaiophores in Argentine species of Malpighiaceae: morphology, anatomy, and interaction with pollinators

Most Neotropical Malpighiaceae species are characterized by having zygomorphic flowers and oil glands in the sepals called elaiophores; these floral characteristics are associated with a particular pollination syndrome through oil-collecting bees. This work proposes a study about the structural characteristics of elaiophores in 18 species of Malpighiaceae present in Argentina. The main objectives are to describe the morphology and anatomy of the elaiophores, to detect variation in the number of glands, to compare similarities or differences in elaiophores of species belonging to different lineages, and to know about the potential pollinators and their association with the structural traits of the elaiophores. The morphology and the anatomy were studied using traditional methods of scanning electron and bright-field microscopes. Field trips were carried out to capture oil-collecting bee species on flowers, in different natural populations. Different measurements were taken in the flowers, elaiophores, and oil-collecting bees and were statistically analyzed. Although elaiophores showed a common pattern, some particularities in number, morphology, and anatomy were detected; few of these seem to be restricted to some groups of species phylogenetically related. As regards pollinators, a positive tendency was observed between the size of the flowers, elaiophores, and oil-collecting bees. However, the thickness of the cuticle presented a negative association with the size of the elaiophore and consequently with the floral diameter, which could be presumably related to the foraging behavior and/or the structure of oil-collecting apparatus of the bee species.

Phloem wedges in Malpighiaceae: origin, structure, diversification, and systematic relevance

Background

Phloem wedges furrowing the wood are one of the most notorious, widespread types of cambial variants in Angiosperms. Many lianas in Malpighiaceae show these variations in the arrangement of the secondary tissues. Here we explore their ontogeny, structure, and evolution in Malpighiaceae, where phloem wedges appeared multiple times, showing how they have contributed to the anatomical diversification of the family. Using a broad sampling with 143 species from 50 genera, covering all major lineages in Malpighiaceae, we crossed data from ontogeny, stem anatomy, and phylogenetic comparative methods to determine ontogenetic trajectories, final anatomical architectures, and evolution within the most recent phylogeny for the family.

Results

Phloem wedges appeared exclusively in lianas and disappeared in shrub lineages nested within liana lineages. At the onset of development, the vascular cambium is regular, producing secondary tissues homogeneously across its girth, but soon, portions of the cambium in between the leaf insertions switch their activity producing less wood and more phloem, initially generating phloem arcs, which progress into phloem wedges. In the formation of these wedges, two ontogenetic trajectories were found, one that maintains the continuity of the cambium, and another where the cambium gets dissected. Phloem wedges frequently remain as the main cambial variant in several lineages, while in others there are additional steps toward more complex cambial variants, such as fissured stems, or included phloem wedges, the latter a novel type of interxylary phloem first described for the family.

Conclusions

Phloem wedges evolved exclusively in lianas, with two different ontogenies explaining the 10 independent origins of phloem wedges in Malpighiaceae. The presence of phloem wedges has favored the evolution of even more complex cambial variants such as fissured stems and interxylary phloem.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13227-022-00196-3.

Evolution of andrenine bees reveals a long and complex history of faunal interchanges through the Americas during the Mesozoic and Cenozoic

Bees are presumed to have arisen in the early to mid-Cretaceous coincident with the fragmentation of the southern continents and concurrently with the early diversification of the flowering plants. Here, we apply DNA sequences from multiple genes to recover a dated phylogeny and historical biogeographic of andrenine bees, a large group of 3000 species mainly distributed in arid areas of North America, South America, and the Palearctic region. Our results corroborate the monophyly of Andreninae and points toward a South America origin for the group during the Late Cretaceous. Overall, we provide strong evidence of amphitropical distributional pattern currently observed in the American continent as result of faunal interchange in at least three historical periods, much prior to the Panama Isthmus closure. The Palearctic diversity is shown to have arisen from North America during the Eocene and Miocene, and the Afrotropical lineages likely originated from the Palearctic region in the Miocene when the Sahara Desert was mostly vegetated. The incursions from South to North America and then onto the Old World are chronological congruent with periods when open-vegetation habitats were available for trans-continental dispersal and at the times when aridification and temperature decline offered favorable circumstances for bee diversification.

Dissecting the difference in tree species richness between Africa and South America

Our full-scale comparison of Africa and South America’s lowland tropical tree floras shows that both Africa and South America’s moist and dry tree floras are organized similarly: plant families that are rich in tree species on one continent are also rich in tree species on the other continent, and these patterns hold across moist and dry environments. Moreover, we confirm that there is an important difference in tree species richness between the two continents, which is linked to a few families that are exceptionally diverse in South American moist forests, although dry formations also contribute to this difference. Plant families only present on one of the two continents do not contribute substantially to differences in tree species richness.

Differences in species diversity over continental scales represent imprints of evolutionary, ecological, and biogeographic events. Here, we investigate whether the higher tree species richness in South America relative to Africa is due to higher richness in certain taxonomic clades, irrespective of vegetation type, or instead due to higher richness in specific biomes across all taxonomic clades. We used tree species inventory data to address this topic and began by clustering inventories from each continent based on species composition to derive comparable vegetation units. We found that moist forests in South America hold approximately four times more tree species than do moist forests in Africa, supporting previous studies. We also show that dry vegetation types in South America, such as tropical dry forests and savannas, hold twice as many tree species as do those in Africa, even though they cover a much larger area in Africa, at present and over geological time. Overall, we show that the marked species richness difference between South America and Africa is due primarily to a key group of families in the South American Amazon and Atlantic moist forests, which while present and speciose in Africa, are markedly less diverse there. Moreover, we demonstrate that both South American and African tree floras are organized similarly and that speciose families on one continent are likely speciose on the other. Future phylogenetic and functional trait work focusing on these key families should provide further insight into the processes leading to South America’s exceptional plant species diversity.

Predominantly Eastward Long-Distance Dispersal in Pantropical Ochnaceae Inferred From Ancestral Range Estimation and Phylogenomics

Ochnaceae is a pantropical family with multiple transoceanic disjunctions at deep and shallow levels. Earlier attempts to unravel the processes that led to such biogeographic patterns suffered from insufficient phylogenetic resolution and unclear delimitation of some of the genera. In the present study, we estimated divergence time and ancestral ranges based on a phylogenomic framework with a well-resolved phylogenetic backbone to tackle issues of the timing and direction of dispersal that may explain the modern global distribution of Ochnaceae. The nuclear data provided the more robust framework for divergence time estimation compared to the plastome-scale data, although differences in the inferred clade ages were mostly small. While Ochnaceae most likely originated in West Gondwana during the Late Cretaceous, all crown-group disjunctions are inferred as dispersal-based, most of them as transoceanic long-distance dispersal (LDD) during the Cenozoic. All LDDs occurred in an eastward direction except for the SE Asian clade of Sauvagesieae, which was founded by trans-Pacific dispersal from South America. The most species-rich clade by far, Ochninae, originated from either a widespread neotropical-African ancestor or a solely neotropical ancestor which then dispersed to Africa. The ancestors of this clade then diversified in Africa, followed by subsequent dispersal to the Malagasy region and tropical Asia on multiple instances in three genera during the Miocene-Pliocene. In particular, Ochna might have used the South Arabian land corridor to reach South Asia. Thus, the pantropical distribution of Ochnaceae is the result of LDD either transoceanic or via land bridges/corridors, whereas vicariance might have played a role only along the stem of the family.

A global phylogenetic regionalization of vascular plants reveals a deep split between Gondwanan and Laurasian biotas

Existing global regionalization schemes for plants consider the compositional affinities among biotas, but these have not explicitly considered phylogenetic information. Here, we present for the first time, a phytogeographical delineation of the global vascular flora based on species-level evolutionary relationships. We analysed 8737 820 geographical occurrence records for vascular plants together with a time-calibrated phylogeny including 67 269 species. We constructed a global phylogenetic regionalization by estimating species composition and phylogenetic beta diversity among 200 km × 200 km grid cells across the world. We identified de novo 16 phytogeographical units that are deeply split into two clusters: Laurasian and Gondwanan. Our regionalization broadly matches previous schemes, but also highlights the separation of the Gondwanan biota into an Holotropical cluster and an Australian-Neozealandic-Patagonian cluster. In contrast, no clear split among Laurasian and Gondwanan biotas was retrieved when omitting phylogenetic information. The integration of phylogenetic and geographical information provides new insights into the delineation of phytogeographical areas and their historical relationships, enabling the identification of three large, clearly differentiated biotas, here referred to as kingdoms: Holarctic, Holotropical, and Austral. Our results provide further evidence for delineating transition zones and show a clear latitudinal pattern of increasing evolutionary distinctiveness towards the poles.

Around the world in 40 million years: Phylogeny and biogeography of Tecomeae (Bignoniaceae)

Intercontinental disjunct distributions can arise from vicariance, long distance dispersal, or both. Tecomeae (Bignoniaceae) are a nearly cosmopolitan clade of flowering plants providing us with an excellent opportunity to investigate global distribution patterns. While the tribe contains only about 57 species, it has achieved a distribution that is not only pantropical, but also extends into the temperate zones in both the Northern and Southern hemispheres. This distribution is similar to the distribution of its sister group, a clade of about 750 spp. that includes most remaining taxa in Bignoniaceae. To infer temporal and spatial patterns of dispersal, we generated a phylogeny of Tecomeae by gathering sequence data from chloroplast and nuclear markers for 41 taxa. Fossil calibrations were used to determine divergence times, and ancestral states were reconstructed to infer its biogeographic history. We found support for a South American origin and a crown age of the tribe estimated at ca. 40 Ma. Two dispersal events seem to have happened during the Eocene-Oligocene, one from South America to the Old World, and another from South America to North America. Furthermore, two other dispersal events seem to have taken place during the Miocene, one from North America to Asia, and another from Australia to South America. We suggest that intercontinental dispersal via land bridges and island hopping, as well as sweepstakes of long distance dispersal from the Eocene to the present explain the global distribution of Tecomeae.

A dated molecular phylogeny and biogeographical analysis reveals the evolutionary history of the trans-pacifically disjunct tropical tree genus Ormosia (Fabaceae)

The papilionoid legume genus Ormosia (Fabaceae) comprises about 150 species of trees and exhibits a striking disjunct geographical distribution between the New World- and Asian and Australasian wet tropics and subtropics. Modern classifications of Ormosia are not grounded on a well-substantiated phylogenetic hypothesis and have been limited to just portions of the geographical range of the genus. The lack of an evolutionarily-based foundation for systematic studies has hindered taxonomic work on the genus and prevented the testing of biogeographical hypotheses related to the origin of the Old World/New World disjunction and the individual dispersal histories within both areas. Here, we present the most comprehensively sampled molecular phylogeny of Ormosia to date, based on analysis of both nuclear (ITS) and plastid (matK and trnL-F) DNA sequences from 82 species of the genus. Phylogenetically-based divergence times and ancestral range estimations are employed to test hypotheses related to the biogeographical history of the genus. We find strong support for the monophyly of Ormosia and the grouping of all sampled Asian species of the genus into two comparably sized clades, one of which is sister to another large clade containing all sampled New World species. Within the New World clade, additional resolution supports the grouping of most species into three mutually exclusive subordinate clades. The remaining New World species form a fourth well-supported clade in the analyses of plastid sequences, but that result is contradicted by the analysis of ITS. With few exceptions the supported clades have not been previously recognized as taxonomic groups. The biogeographical analysis suggests that Ormosia originated in continental Asia and dispersed to the New World in the Oligocene or early Miocene via long-distance trans-oceanic dispersal. We reject the hypothesis that the inter-hemispheric disjunction in Ormosia resulted from fragmentation of a more continuous "Boreotropical" distribution since the dispersal post-dates Eocene climatic maxima. Both of the Old World clades appear to have originated in mainland Asia and subsequently dispersed into the Malay Archipelago and beyond, at least two lineages dispersing across Wallace's Line as far as the Solomon Islands and northeastern Australia. In the New World, the major clades all originated in Amazonia. Dispersal from Amazonia into peripheral areas in Central America, the Caribbean, and Extra-Amazonian Brazil occurred multiple times over varying time scales, the earliest beginning in the late Miocene. In a few cases, these dispersals were followed by local diversification, but not by reverse migration back to Amazonia. Within each of the two main areas of distribution, multiple modest bouts of oceanic dispersal were required to achieve the modern distributions.

Evolution of Dispersal, Habit, and Pollination in Africa Pushed Apocynaceae Diversification After the Eocene-Oligocene Climate Transition

Apocynaceae (the dogbane and milkweed family) is one of the ten largest flowering plant families, with approximately 5,350 species and diverse morphology and ecology, ranging from large trees and lianas that are emblematic of tropical rainforests, to herbs in temperate grasslands, to succulents in dry, open landscapes, and to vines in a wide variety of habitats. Despite a specialized and conservative basic floral architecture, Apocynaceae are hyperdiverse in flower size, corolla shape, and especially derived floral morphological features. These are mainly associated with the development of corolline and/or staminal coronas and a spectrum of integration of floral structures culminating with the formation of a gynostegium and pollinaria—specialized pollen dispersal units. To date, no detailed analysis has been conducted to estimate the origin and diversification of this lineage in space and time. Here, we use the most comprehensive time-calibrated phylogeny of Apocynaceae, which includes approximately 20% of the species covering all major lineages, and information on species number and distributions obtained from the most up-to-date monograph of the family to investigate the biogeographical history of the lineage and its diversification dynamics. South America, Africa, and Southeast Asia (potentially including Oceania), were recovered as the most likely ancestral area of extant Apocynaceae diversity; this tropical climatic belt in the equatorial region retained the oldest extant lineages and these three tropical regions likely represent museums of the family. Africa was confirmed as the cradle of pollinia-bearing lineages and the main source of Apocynaceae intercontinental dispersals. We detected 12 shifts toward accelerated species diversification, of which 11 were in the APSA clade (apocynoids, Periplocoideae, Secamonoideae, and Asclepiadoideae), eight of these in the pollinia-bearing lineages and six within Asclepiadoideae. Wind-dispersed comose seeds, climbing growth form, and pollinia appeared sequentially within the APSA clade and probably work synergistically in the occupation of drier and cooler habitats. Overall, we hypothesize that temporal patterns in diversification of Apocynaceae was mainly shaped by a sequence of morphological innovations that conferred higher capacity to disperse and establish in seasonal, unstable, and open habitats, which have expanded since the Eocene-Oligocene climate transition.

Phylogenomics, floral evolution, and biogeography of Lithospermum L. (Boraginaceae)

Lithospermum (Boraginaceae), a geographically cosmopolitan medium-sized genus, includes diverse floral morphology, with variation in corolla size and shape and in breeding system. Over the past decade, multiple studies have examined the evolutionary history of Lithospermum, with most utilizing DNA regions from the plastid genome and/or the nuclear ribosomal internal transcribed spacer. These studies have, in general, not resulted in well-resolved and well-supported phylogenies. In the present study, 298 nuclear DNA regions, amplified via target sequence capture, were utilized for phylogenetic reconstruction for Lithospermum and relatives in Boraginaceae, and patterns of floral evolution, species diversification, and biogeography were examined. Based on multiple phylogenetic methods, Lithospermum is resolved as monophyletic, and the New World species of the genus are also monophyletic. While minimal phylogenetic incongruence is resolved within the nuclear genome, incongruence between the nuclear and plastid genomes is recovered. This is likely due to incomplete lineage sorting during early diversification of the genus in the Americas approximately 7.8 million years ago. At least four shifts to longer corollas are identified throughout Lithospermum, and this may be due to selection for hummingbird-pollinated flowers, particularly for species in Mexico and the southwestern United States. In the New World, one clade of species of the genus diversified primarily across the United States and Canada, and another radiated throughout the mountains of Mexico.

Phytogeographic history of the Tea family inferred through high-resolution phylogeny and fossils

The tea family (Theaceae) has a highly unusual amphi-Pacific disjunct distribution: most extant species in the family are restricted to subtropical evergreen broadleaf forests in East Asia, while a handful of species occur exclusively in the subtropical and tropical Americas. Here we used an approach that integrates the rich fossil evidence of this group with phylogenies in biogeographic analysis to study the processes behind this distribution pattern. We first combined genome-skimming sequencing with existing molecular data to build a robust species-level phylogeny for c.140 Theaceae species, resolving most important unclarified relationships. We then developed an empirical Bayesian method to incorporate distribution evidence from fossil specimens into historical biogeographic analyses and used this method to account for the spatiotemporal history of Theaceae fossils. We compared our method with an alternative Bayesian approach and show that it provides consistent results while significantly reduces computational demands which allows analyses of much larger datasets. Our analyses revealed a circumboreal distribution of the family from the early Cenozoic to the Miocene and inferred repeated expansions and retractions of the modelled distribution in the Northern Hemisphere, suggesting that the current Theaceae distribution could be the remnant of a larger continuous distribution associated with the boreotropical forest that has been hypothesized to occupy most of the northern latitudes in the early Cenozoic. These results contradict with studies that only considered current species distributions and showcase the necessity of integrating fossil and molecular data in phylogeny-based parametric biogeographic models to improve the reliability of inferred biogeographical events.

Early Oligocene Itea (Iteaceae) leaves from East Asia and their biogeographic implications

Compressed materials of fossil foliage described here as Itea polyneura sp. nov. (Iteaceae) were collected from the Oligocene of Wenshan, Yunnan Province, southwestern China. The identification is based on the following characters: eucamptodromous secondary veins, strict scalariform tertiary veins, irregular tooth with setaceous apex. The leaf morphology of all modern and fossil species was compared with the new species from Wenshan and show that I. polyneura is most similar to the extant East Asian species Itea omeiensis, which inhabits subtropical forests of southern China. This discovery represents the first unambiguous leaf fossil record of Itea in East Asia. Together with other species in the Wenshan flora and evidence from several other flora in southern China, these findings demonstrate that Itea from East Asia arose with the Paleogene modernization.

Comparative Plastomes and Phylogenetic Analysis of Cleistogenes and Closely Related Genera (Poaceae)

Cleistogenes (Orininae, Cynodonteae, Chloridoideae, Poaceae) is an ecologically important genus. The phylogenetic placement of Cleistogenes and phylogenetic relationships among Cleistogenes taxa remain controversial for a long time. To resolve the intra- and inter-generic relationships of Cleistogenes, the plastomes of 12 Cleistogenes taxa (including 8 species and 4 varieties), one Orinus species, 15 Triodia species, two Tripogon species, and two Aeluropus species were included in the present study. All the taxa showed a similar pattern in plastome structure, gene order, gene content, and IR boundaries. The number of simple sequence repeats ranged from 145 (O. kokonorica) to 161 (T. plurinervata and T. schinzii). Moreover, 1,687 repeats were identified in these taxa, including 1,012 forward, 650 palindromic, 24 reverse, and one complement. Codon usage analysis revealed that these plastomes contained 16,633 (T. stipoides) to 16,678 (T. tomentosa) codons. Sequence divergence analysis among Cleistogenes and closely related genera identified five non-coding regions (trnS-UGA-psbZ, rpl32-trnL-UAG, trnQ-UUG-psbK, trnD-GUC-psbM, trnT-GGU-trnE-UUC). Phylogenetic analysis of complete plastomes indicated that Cleistogenes is sister to a clade composed of Orinus and Triodia, whereas it did not support the sister relationship between the recently proposed subtribe Orininae (Cleistogenes and Orinus) and Triodia. The subtribe Orininae was not supported by our complete plastome data. The split between Cleistogenes and Orinus-Triodia clade go back to 14.01 Ma. Besides, our findings suggested that C. squarrosa and C. songorica are the successive early diverging groups in the phylogenetic analysis. The other 10 taxa are divided into two groups: a monophyletic group composed of Cleistogenes sp. nov. and C. caespitosa var. ramosa is sister to other eight Cleistogenes taxa. Cleistogenes was estimated to have experienced rapid divergence within a short period, which could be a major obstacle in resolving phylogenetic relationships within Cleistogenes. Collectively, our results provided valuable insights into the phylogenetic study of grass species.

Biogeography and evolution of Asian Gesneriaceae based on updated taxonomy

Based on an updated taxonomy of Gesneriaceae, the biogeography and evolution of the Asian Gesneriaceae are outlined and discussed. Most of the Asian Gesneriaceae belongs to Didymocarpoideae, except Titanotrichum was recently moved into Gesnerioideae. Most basal taxa of the Asian Gesneriaceae are found in the Indian subcontinent and Indo-China Peninsula, suggesting Didymocarpoideae might originate in these regions. Four species diversification centers were recognized, i.e. Sino-Vietnam regions, Malay Peninsula, North Borneo and Northwest Yunnan (Hengduan Mountains). The first three regions are dominated by limestone landscapes, while the Northwest Yunnan is well-known for its numerous deep gorges and high mountains. The places with at least 25% species are neoendemics (newly evolved and narrowly endemic) which were determined as evolutionary hotspots, including Hengduan Mountains, boundary areas of Yunnan-Guizhou-Guangxi in Southwest China, North Borneo, Pahang and Terengganu in Malay Peninsula, and mountainous areas in North Thailand, North Sulawesi Island. Finally, the underlying mechanisms for biogeographical patterns and species diversification of the Asian Gesneriaceae are discussed.

An ancient tropical origin, dispersals via land bridges and Miocene diversification explain the subcosmopolitan disjunctions of the liverwort genus Lejeunea

Understanding the biogeographical and diversification processes explaining current diversity patterns of subcosmopolitan-distributed groups is challenging. We aimed at disentangling the historical biogeography of the subcosmopolitan liverwort genus Lejeunea with estimation of ancestral areas of origin and testing if sexual system and palaeotemperature variations can be factors of diversification. We assembled a dense taxon sampling for 120 species sampled throughout the geographical distribution of the genus. Lejeunea diverged from its sister group after the Paleocene-Eocene boundary (52.2 Ma, 95% credibility intervals 50.1-54.2 Ma), and the initial diversification of the crown group occurred in the early to middle Eocene (44.5 Ma, 95% credibility intervals 38.5-50.8 Ma). The DEC model indicated that (1) Lejeunea likely originated in an area composed of the Neotropics and the Nearctic, (2) dispersals through terrestrial land bridges in the late Oligocene and Miocene allowed Lejeunea to colonize the Old World, (3) the Boreotropical forest covering the northern regions until the late Eocene did not facilitate Lejeunea dispersals, and (4) a single long-distance dispersal event was inferred between the Neotropics and Africa. Biogeographical and diversification analyses show the Miocene was an important period when Lejeunea diversified globally. We found slight support for higher diversification rates of species with both male and female reproductive organs on the same individual (monoicy), and a moderate positive influence of palaeotemperatures on diversification. Our study shows that an ancient origin associated with a dispersal history facilitated by terrestrial land bridges and not long-distance dispersals are likely to explain the subcosmopolitan distribution of Lejeunea. By enhancing the diversification rates, monoicy likely favoured the colonisations of new areas, especially in the Miocene that was a key epoch shaping the worldwide distribution.

Plastome phylogenomics, systematics, and divergence time estimation of the Beilschmiedia group (Lauraceae)

Intergeneric relationships of the Beilschmiedia group (Lauraceae) remain unresolved, hindering our understanding of their classification and evolutionary diversification. To remedy this, we sequenced and assembled complete plastid genomes (plastomes) from 25 species representing five genera spanning most major clades of Beilschmiedia and close relatives. Our inferred phylogeny is robust and includes two major clades. The first includes a monophyletic Endiandra nested within a paraphyletic Australasian Beilschmiedia group. The second includes (i) a subclade of African Beilschmiedia plus Malagasy Potameia, (ii) a subclade of Asian species including Syndiclis and Sinopora, (iii) the lone Neotropical species B. immersinervis, (iv) a subclade of core Asian Beilschmiedia, sister to the Neotropical species B. brenesii, and v) two Asian species including B. turbinata and B. glauca. The rampant non-monophyly of Beilschmiedia we identify necessitates a major taxonomic realignment of the genus, including but not limited to the mergers of Brassiodendron and Sinopora into the genera Endiandra and Syndiclis, respectively. Along these lines, the high degree of continental, clade-wide endemism we identify suggests that geographical distribution may be a good proxy for delineating taxa within this group. Our molecular divergence time estimates indicate that stem Beilschmiedia group members date to the Early Eocene (~50 Ma); their crown age dates to the Eocene-Oligocene boundary (~34 Ma). These findings contradict older estimates of the group and support mounting evidence that the origin and diversification of many pantropical angiosperm clades are not easily attributed to strict western Gondwanan vicariance. Finally, our study highlights the phylogenetic utility of plastomes in Lauraceace, and lays a solid foundation for future phylogenomic and biogeographic investigations within the family.

Phylogeny and biogeography of Astraea with new insights into the evolutionary history of Crotoneae (Euphorbiaceae)

We investigated species relationships in Astraea, a primarily Neotropical genus of tribe Crotoneae centered in Brazil, using data from the nuclear ribosomal ITS, and the plastid trnL-trnF and psbA-trnH spacers. With all species of Astraea sampled, along with representatives from across Crotoneae, the evolutionary history of Astraea was interpreted in a broader framework, as well as divergence time estimates and reconstructions of ancestral areas and morphological character states for Crotoneae. Our results show that Astraea is monophyletic, consisting of three main clades, and that most of its diversification took place from the Oligocene to the Pliocene, coincident with the formation of the South American "dry diagonal". As for Crotoneae, our data show incongruent phylogenetic positions between the nuclear and chloroplast data for most of its genera, and that the ancestor of the tribe was probably arborescent and might have occupied the Amazon Basin, most likely in moist forest, from which it spread throughout South America in the early Eocene. Ancestral state reconstruction recovered deeply lobed leaves and staminate petals bearing moniliform trichomes as putative synapomorphies for Astraea, whereas the absence or strong reduction of pistillate petals is widespread in Crotoneae and may be a synapomorphy for the tribe.

Molecular phylogeny of Hiptage (Malpighiaceae) reveals a new species from Southwest China

Hiptage is an Asia-endemic genus of Malpighiaceae currently placed in the tetrapteroid clade, representing one of the seven inter-continent dispersions from New to Old World. A molecular phylogeny based on sequences of the internal transcribed spacer (ITS) region was recovered for the first time for the genus. Our results showed that the most recent common ancestor of Hiptage probably originated in the South Indo-China Peninsula and diversified in this region. Based on phylogenetic evidence and relevant morphological traits, we propose a new species; Hiptage incurvatum is characterised by mericarps with arcuate anterior lateral wings, two large glands on the dorsal sepals, and small glands on the remaining sepals. The new species is from Mt. Cangshan, Dali City (25°35'N, 100°02'E) in North Yunnan, Southwest China and is notable for its occurrence at high altitude, 1400 m (the highest distribution currently known for the genus). The implications of this unusual species for the dispersal and evolution of the genus are discussed.

Biogeography and early diversification of Tapinotaspidini oil-bees support presence of Paleocene savannas in South America

Worldwide distributed tropical savannas were established only in the Miocene, with climatic cooling and rise of C4 grasses. However, there is evidence for an earlier presence of savanna-like vegetation in southern parts of South America. Here we investigated the biogeographic history of a clade of solitary bees which have endemic groups in areas covered by savannas and other types of open vegetation as well as forested areas. We hypothesized that these bees originated in savanna-like biomes and that shifts to forested areas and floral host shifts increased species diversification along their evolutionary history. We reconstructed a comprehensive phylogeny for Tapinotaspidini bees based majorly on original DNA sequences. We then used macroevolutionary tools to estimate ancestral range area and reconstructed ancestral habitat (open versus forested) and host plant association to analyze the effects of shifts in vegetation type and flower hosts on their diversification. Tapinotaspidini bees originated in the Paleocene and in a savanna-type, Cerrado-like, which is reinforced by reconstruction of open vegetation as the most probable ancestral area, thus bringing additional evidence to a much earlier origin of this vegetation type in South America. Shifts to forested areas occurred at least three times in a period of 30 Ma and were responsible for slight increases in diversification rates. Malpighiaceae is the ancestral floral host; host broadening occurred only in the Miocene and at least in three occasions. Host shifts, i.e. from Malpighiaceae to other oil families, occurred in the Eocene and Miocene. Both host broadening and host shifts did not significantly alter diversification rates, however exploitation of other oil sources were important in occupying new habitats. The link between biomes and host plant shifts and changes in diversification rate brings us additional insights into the evolution of bees and associated flora in South America.

History and Geography of Neotropical Tree Diversity

Early botanical explorers invoked biogeographic history to explain the remarkable tree diversity of Neotropical forests. In this context, we review the history of Neotropical tree diversity over the past 100 million years, focusing on biomes with significant tree diversity. We evaluate hypotheses for rain forest origins, intercontinental disjunctions, and models of Neotropical tree diversification. To assess the impact of biotic interchange on the Amazon tree flora, we examined biogeographic histories of trees in Ecuador's Yasuní Forest, which suggest that nearly 50% of its species descend from immigrant lineages that colonized South America during the Cenozoic. Long-distance and intercontinental dispersal, combined with trait filtering and niche evolution, are important factors in the community assembly of Neotropical forests. We evaluate the role of pre-Columbian people on Neotropical tree diversity and discuss the future of Neotropical forests in the Anthropocene.

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.

DNA barcoding and TLC as tools to properly identify natural populations of the Mexican medicinal species Galphimia glauca Cav

Galphimia glauca is a plant that is endemic to Mexico and has been commonly used since pre-Hispanic times to treat various illnesses, including central nervous system disorders and inflammation. The first studies investigating a natural population of G. glauca in Mexico showed that the plant has anxiolytic and sedative activities in mice and humans. The plant's bioactive compounds were isolated and identified, and they belong to a family of nor-secofriedelanes called galphimines. The integration of DNA barcoding and thin-layer chromatography analysis was performed to clarify whether the botanical classification of the populations in the study, which were collected in different regions of Mexico, as G. glauca was correct or if the populations consist of more than one species of the genus Galphimia. We employed six DNA barcodes (matK, rbcL, rpoC1, psbA-trnH, ITS1 and ITS2) that were analyzed individually and in combination and then compared each other, to indicate differences among the studied populations. In the phylogenetic analysis, ITS1 and ITS2 markers as well as the combination of all DNA regions were the most efficient for discriminating the population studied. The thin-layer chromatography analysis exhibited four principal chemical profiles, one of which corresponded to the populations that produced galphimines. DNA barcoding was consistent and enabled us to differentiate the populations that produce galphimines from those that do not. The results of this investigation suggest that the studied populations belong to at least four different species of the genus Galphimia. The phylogenetic analysis and the thin-layer chromatography chemical profiles were convenient tools for establishing a strong relationship between the genotype and phenotype of the studied populations and could be used for quality control purposes to prepare herbal medicines from plants of the genus Galphimia.

Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species)

PREMISE OF THE STUDY

This investigation establishes the first DNA-sequence-based phylogenetic hypothesis of species relationships in the coca family (Erythroxylaceae) and presents its implications for the intrageneric taxonomy and neotropical biogeography of Erythroxylum. We also identify the closest wild relatives and evolutionary relationships of the cultivated coca taxa.

METHODS

We focused our phylogenomic inference on the largest taxonomic section in the genus Erythroxylum (Archerythroxylum O.E.Schulz) using concatenation and gene tree reconciliation methods from hybridization-based target capture of 427 genes.

KEY RESULTS

We show that neotropical Erythroxylum are monophyletic within the paleotropical lineages, yet Archerythroxylum and all of the other taxonomic sections from which we sampled multiple species lack monophyly. We mapped phytogeographic states onto the tree and found some concordance between these regions and clades. The wild species E. gracilipes and E. cataractarum are most closely related to the cultivated E. coca and E. novogranatense, but relationships within this "coca" clade remain equivocal.

CONCLUSIONS

Our results point to the difficulty of morphology-based intrageneric classification in this clade and highlight the importance of integrative taxonomy in future systematic revisions. We can confidently identify E. gracilipes and E. cataractarum as the closest wild relatives of the coca taxa, but understanding the domestication history of this crop will require more thorough phylogeographic analysis.

Is the East Asian flora ancient or not?

The East Asian flora (EAF) is a key biodiversity hotspot for understanding the origin and evolution of Northern Hemisphere floras, but there is an ongoing debate on whether it is a museum or a cradle for seed plants. Within the EAF, two main floras, the Sino-Himalayan Flora (mainly the Rhododendron Flora) and the Sino-Japanese Flora (mainly the Metasequoia Flora), have been recognized. Previous studies suggested that the EAF is ancient and the Metasequoia Flora is older than the Rhododendron Flora. To test this hypothesis, we synthesized molecular as well as fossil data on seed plants, focusing on the biogeographical origins and historical evolution of the EAF. We compared the ages of its two constituent floras, and examined the impact of the Asian monsoon and other environmental changes on the development of EAF through meta-analysis. Our results suggest that the EAF might be relatively young, with most of its clades originating since the Miocene. The Rhododendron Flora and the Metasequoia Flora are probably of a similar age. The formation and development of the Asian monsoon might have been the main factors that have driven the evolution of EAF. In the Rhododendron Flora, the north-south mountain chains increased the concentration of species and reduced extinction, and the barriers between the east and west have resulted in species differentiation, which triggered it to become a diversity center. The EAF appears to have multiple biogeographical origins, having closely affiliated not only with other floras in the Northern Hemisphere, but also with Gondwanan floras.

Evolution in the Amphi-Atlantic tropical genus Guibourtia (Fabaceae, Detarioideae), combining NGS phylogeny and morphology

Tropical rain forests support a remarkable diversity of tree species, questioning how and when this diversity arose. The genus Guibourtia (Fabaceae, Detarioideae), characterized by two South American and 13 African tree species growing in various tropical biomes, is an interesting model to address the role of biogeographic processes and adaptation to contrasted environments on species diversification. Combining whole plastid genome sequencing and morphological characters analysis, we studied the timing of speciation and diversification processes in Guibourtia through molecular dating and ancestral habitats reconstruction. All species except G. demeusei and G. copallifera appear monophyletic. Dispersal from Africa to America across the Atlantic Ocean is the most plausible hypothesis to explain the occurrence of Neotropical Guibourtia species, which diverged ca. 11.8 Ma from their closest African relatives. The diversification of the three main clades of African Guibourtia is concomitant to Miocene global climate changes, highlighting pre-Quaternary speciation events. These clades differ by their reproductive characters, which validates the three subgenera previously described: Pseudocopaiva, Guibourtia and Gorskia. Within most monophyletic species, plastid lineages start diverging from each other during the Pliocene or early Pleistocene, suggesting that these species already arose during this period. The multiple transitions between rain forests and dry forests/savannahs inferred here through the plastid phylogeny in each Guibourtia subgenus address thus new questions about the role of phylogenetic relationships in shaping ecological niche and morphological similarity among taxa.

Insights on the evolutionary origin of Detarioideae, a clade of ecologically dominant tropical African trees

African tropical forests are generally considered less diverse than their Neotropical and Asian counterparts. By contrast, the Detarioideae is much more diverse in Africa than in South America and Asia. To better understand the evolution of this contrasting diversity pattern, we investigated the biogeographical and ecological origin of this subfamily, testing whether they originated in dry biomes surrounding the Tethys Seaway as currently hypothesized for many groups of Leguminosae. We constructed the largest time-calibrated phylogeny for the subfamily to date, reconstructed ancestral states for geography and biome/habitat, estimated diversification and extinction rates, and evaluated biome/habitat and geographic shifts in Detarioideae. The ancestral habitat of Detarioideae is postulated to be a primary forest (terra firme) originated in Africa-South America, in the early Palaeocene, after which several biome/habitat and geographic shifts occurred. The origin of Detarioideae is older than previous estimates, which postulated a dry (succulent) biome origin according to the Tethys Seaway hypothesis, and instead we reveal a post Gondwana and terra firme origin for this early branching clade of legumes. Detarioideae include some of the most dominant trees in evergreen forests and have likely played a pivotal role in shaping continental African forest diversity.

Geographical structure, narrow species ranges, and Cenozoic diversification in a pantropical clade of epiphyllous leafy liverworts

The evolutionary history and classification of epiphyllous cryptogams are still poorly known. Leptolejeunea is a largely epiphyllous pantropical liverwort genus with about 25 species characterized by deeply bilobed underleaves, elliptic to narrowly obovate leaf lobes, the presence of ocelli, and vegetative reproduction by cladia. Sequences of three chloroplast regions (rbcL, trnL-F, psbA) and the nuclear ribosomal ITS region were obtained for 66 accessions of Leptolejeunea and six outgroup species to explore the phylogeny, divergence times, and ancestral areas of this genus. The phylogeny was estimated using maximum-likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method. Leptolejeunea likely originated in Asia or the Neotropics within a time interval from the Early Eocene to the Late Cretaceous (67.9 Ma, 95% highest posterior density [HPD]: 47.9-93.7). Diversification of the crown group initiated in the Eocene or early Oligocene (38.4 Ma, 95% HPD: 27.2-52.6). Most species clades were established in the Miocene. Leptolejeunea epiphylla and L. schiffneri originated in Asia and colonized African islands during the Plio-Pleistocene. Accessions of supposedly pantropical species are placed in different main clades. Several monophyletic morphospecies exhibit considerable sequence variation related to a geographical pattern. The clear geographic structure of the Leptolejeunea crown group points to evolutionary processes including rare long-distance dispersal and subsequent speciation. Leptolejeunea may have benefitted from the large-scale distribution of humid tropical angiosperm forests in the Eocene.

Evolution: Velvet Worm Biogeography

The present-day distribution of velvet worms corresponds neatly to the ancient supercontinent Gondwana - except for a puzzling outpost in southeast Asia. Jaw-dropping new fossil material now establishes when and how peripatid onychophorans reached this isolated spot.

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.

Unraveling the biogeographical history of Chrysobalanaceae from plastid genomes

PREMISE OF THE STUDY

The complex geological and climatic history of the Neotropics has had major implications on the diversification of plant lineages. Chrysobalanaceae is a pantropical family of trees and shrubs with 75% of its 531 species found in the Neotropics, and a time-calibrated phylogeny of this family should shed light on the tempo of diversification in the Neotropical flora. Previously published phylogenetic hypotheses of this family were poorly supported, and its biogeography remains unclear.

METHODS

We assembled the complete plastid genome of 51 Chrysobalanaceae species, and increased taxon sampling by Sanger-sequencing of five plastid regions for an additional 88 species. We generated a time-calibrated tree including all 139 Chrsyobalanaceae species and 23 outgroups. We then conducted an ancestral area reconstruction analysis and estimated diversification rates in the family.

KEY RESULTS

The tree generated with the plastid genome alignment was almost fully resolved. It supports the polyphyly of Licania and Hirtella. The family has diversified starting around the Eocene-Oligocene transition. An ancestral area reconstruction confirms a Paleotropical origin for Chrysobalanaceae with several transoceanic dispersal events. The main Neotropical clade likely resulted from a single migration event from Africa around 28 mya ago, which subsequently underwent rapid diversification.

CONCLUSIONS

Given the diverse ecologies exhibited by extant species, we hypothesize that the rapid diversification of Chrysobalanaceae following the colonization of the Neotropics was triggered by habitat specialization during the complex geological and paleoclimatic history of the Neotropics.

Molecular evidence supports ancient long-distance dispersal for the amphi-Atlantic disjunction in the giant yellow shrimp plant (Barleria oenotheroides)

PREMISE OF THE STUDY

Barleria is a large, pantropical genus of ca. 265 species mainly distributed in the Old World with only one species, B. oenotheroides, extending to the neotropics. This amphi-Atlantic disjunction, frequently displayed by pantropical taxa, has been traditionally explained with vicariance or geodispersal hypotheses and increasingly with long-distance dispersal. The native status of this species in the New World is controversial.

METHODS

A molecular phylogeographic study based on the nuclear ribosomal ITS region and plastid trnL-F, rps16, and trnS-G sequences was done to clarify the origin of this tropical intercontinental disjunction. Divergence times were estimated with various analytical approaches, including different markers and primary calibration points.

KEY RESULTS

Divergence ages estimated for Barleria lineages disagree with vicariance or geodispersal hypotheses. Genetic differentiation of American vs. African populations of B. oenotheroides does not support a recent anthropogenic introduction to the New World. Our data suggest ancient long-distance dispersal from the Old to the New World probably during the Pliocene or Upper Miocene. The number of dispersal events remains unclear.

CONCLUSIONS

Our study demonstrates the native status of Barleria in the New World, resolving one of only three presumed natural Old World-New World disjunctions at the species level among Acanthaceae. This case constitutes a further documented example of the "out-of-Africa" pattern in the family, despite their lack of documented assisted-dispersal syndromes, and highlights the importance of long-distance dispersal to explain pantropical distributions in many families.

Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant clade

PREMISE OF THE STUDY

The clusioid clade (Malpighiales) has an ancient fossil record (∼90 Ma) and extant representatives exhibit a pantropical distribution represented on all former Gondwanan landmasses (Africa, Australia, India, Madagascar, and South America) except Antarctica. Several biogeographers have hypothesized that the clusioid distribution is an example of Gondwanan vicariance. Our aim is to test the hypothesis that the modern distribution of the clusioid clade is largely explained by Gondwanan fragmentation.

METHODS

Using a four gene, 207-taxon data set we simultaneously estimated the phylogeny and divergence times of the clusioid clade using a Bayesian Markov chain Monte Carlo approach. Ancestral Area Reconstructions (AARs) were then conducted on a distribution of 1000 trees and summarized on a reduced phylogeny.

KEY RESULTS

Divergence time estimates and AARs revealed only two or four cladogenic events that are potentially consistent with Gondwanan vicariance, depending on the placement of the ancient fossil Paleoclusia. In contrast, dispersal occurred on > 25% of the branches, indicating the current distribution of the clade likely reflects extensive recent dispersal during the Cenozoic (< 65 Ma), most of which occurred after the beginning of the Eocene (∼56 Ma).

CONCLUSIONS

These results support growing evidence that suggests many traditionally recognized angiosperm clades (families and genera) are too young for their distributions to have been influenced strictly by Gondwanan fragmentation. Instead, it appears that corridors of dispersal may be the best explanation for numerous angiosperm clades with Gondwanan distributions.

Roles of Clonal Integration in both Heterogeneous and Homogeneous Habitats

Many studies have shown that clonal integration can promote the performance of clonal plants in heterogeneous habitats, but the roles of clonal integration in both heterogeneous and homogeneous habitats were rarely studied simultaneously. Ramet pairs of Alternanthera philoxeroides (Mart.) Griseb were placed in two habitats either heterogeneous or homogeneous in soil nutrient availability, with stolon connections left intact or severed. Total biomass, total length of stolons, and number of new ramets of distal (relatively young) ramets located in low-nutrient environments were significantly greater when the distal ramets were connected to than when they were disconnected from proximal (relatively old) ramets located in high-nutrient environments. Total length of stolons of proximal ramets growing in low-nutrient environments was significantly higher when the proximal ramets were connected to than when they were disconnected from the distal ramets growing in high-nutrient environments, but stolon connection did not affect total biomass or number of new ramets of the proximal ramets. Stolon severing also did not affect the growth of the whole ramet pairs in heterogeneous environments. In homogeneous high-nutrient environments stolon severing promoted the growth of the proximal ramets and the ramet pairs, but in homogeneous low-nutrient environments it did not affect the growth of the proximal or distal ramets. Hence, for A. philoxeroides, clonal fragmentation appears to be more advantageous than clonal integration in resource-rich homogeneous habitats, and clonal integration becomes beneficial in heterogeneous habitats. Our study contributes to revealing roles of clonal integration in both heterogeneous and homogeneous habitats and expansion patterns of invasive clonal plants such as A. philoxeroides in multifarious habitats.