Melastomeae come full circle: biogeographic reconstruction and molecular clock dating

Balancing selection on an MYB transcription factor maintains the twig trichome color variation in Melastoma normale

BACKGROUND

The factors that maintain phenotypic and genetic variation within a population have received long-term attention in evolutionary biology. Here the genetic basis and evolution of the geographically widespread variation in twig trichome color (from red to white) in a shrub Melastoma normale was investigated using Pool-seq and evolutionary analyses.

RESULTS

The results show that the twig trichome coloration is under selection in different light environments and that a 6-kb region containing an R2R3 MYB transcription factor gene is the major region of divergence between the extreme red and white morphs. This gene has two highly divergent groups of alleles, one of which likely originated from introgression from another species in this genus and has risen to high frequency (> 0.6) within each of the three populations under investigation. In contrast, polymorphisms in other regions of the genome show no sign of differentiation between the two morphs, suggesting that genomic patterns of diversity have been shaped by homogenizing gene flow. Population genetics analysis reveals signals of balancing selection acting on this gene, and it is suggested that spatially varying selection is the most likely mechanism of balancing selection in this case.

CONCLUSIONS

This study demonstrate that polymorphisms on a single transcription factor gene largely confer the twig trichome color variation in M. normale, while also explaining how adaptive divergence can occur and be maintained in the face of gene flow.

Chromosomal-level genome assembly of Melastoma candidum provides insights into trichome evolution

Melastoma, consisting of ~100 species diversified in tropical Asia and Oceania in the past 1-2 million years, represents an excellent example of rapid speciation in flowering plants. Trichomes on hypanthia, twigs and leaves vary markedly among species of this genus and are the most important diagnostic traits for species identification. These traits also play critical roles in contributing to differential adaptation of these species to their own habitats. Here we sequenced the genome of M. candidum, a common, erect-growing species from southern China, with the aim to provide genomic insights into trichome evolution in this genus. We generated a high-quality, chromosome-level genome assembly of M. candidum, with the genome size of 256.2 Mb and protein-coding gene number of 40,938. The gene families specific to, and significantly expanded in Melastoma are enriched for GO terms related to trichome initiation and differentiation. We provide evidence that Melastoma and its sister genus Osbeckia have undergone two whole genome duplications (WGDs) after the triplication event (γ) shared by all core eudicots. Preferential retention of trichome development-related transcription factor genes such as C2H2, bHLH, HD-ZIP, WRKY, and MYB after both WGDs might provide raw materials for trichome evolution and thus contribute to rapid species diversification in Melastoma. Our study provides candidate transcription factor genes related to trichome evolution in Melastoma, which can be used to evolutionary and functional studies of trichome diversification among species of this genus.

Historical biogeography and diversification of ringless Amanita (section Vaginatae) support an African origin and suggest niche conservatism in the Americas

Ectomycorrhizal fungi (ECM) sustain nutrient recycling in most terrestrial ecosystems, yet we know little about what major biogeographical events gave rise to present-day diversity and distribution patterns. Given the strict relationship between some ECM lineages and their hosts, geographically well-sampled phylogenies are central to understanding major evolutionary processes of fungal biodiversity patterns. Here, we focus on Amanita sect. Vaginatae to address global diversity and distribution patterns. Ancestral-state-reconstruction based on a 4-gene timetree with over 200 species supports an African origin between the late Paleocene and the early Eocene (ca. 56 Ma). Major biogeographic "out-of-Africa" events include multiple dispersal events to Southeast Asia (ca. 45-21 Ma), Madagascar (ca. 18 Ma), and the current Amazonian basin (ca. 45-36 Ma), the last two likely trans-oceanic. Later events originating in Southeast Asia involve Nearctic dispersal to North America (ca. 20-5 Ma), Oceania (Australia and New Zealand; ca. 15 Ma), and Europe (ca. 10-5 Ma). Subsequent dispersals were also inferred from Southeast Asia to East Asia (ca. 4 Ma); from North America to East Asia (ca. 11-8 Ma), Southeast Asia (ca. 19-2 Ma), Northern Andes (ca. 15 Ma), and Europe (ca. 15-2 Ma), respectively; and from the Amazon to the Caribbean region (ca. 25-20 Ma). Finally, we detected a significant increase in the net diversification rates in the branch leading to most northern temperate species in addition to higher state-dependent diversification rates in temperate lineages, consistent with previous findings. These results suggest that species of sect. Vaginatae likely have higher dispersal ability and higher adaptability to new environments, in particular compared to those of its sister clade, sect. Caesareae. Overall, the much wider distribution of A. sect. Vaginatae, from pan-tropical to pan-arctic, provides a unique window to understanding niche conservatism across a species-rich clade of ECM fungi.

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.

Phylotranscriptomics reveals the complex evolutionary and biogeographic history of the genus Tsuga with an East Asian-North American disjunct distribution

The disjunct distribution between East Asia and North America is one of the best established biogeographic patterns. A robust phylogeny is fundamental for understanding the biogeographic histories of taxa with this distribution pattern. Tsuga (hemlock) is a genus of Pinaceae with a typical intercontinental disjunct distribution in East Asia and eastern and western North America, and its phylogeny has not been completely reconstructed in previous studies. In this study, we reconstructed a highly resolved phylogeny of Tsuga using 881 nuclear genes, 60 chloroplast genes and 23 mitochondrial genes and explored its biogeographic and reticulate evolutionary history. The results of phylogenetic analysis, molecular dating and ancestral area reconstruction indicate that Tsuga very likely originated from North America in the late Oligocene and dispersed from America to East Asia via the Bering Land Bridge during the middle Miocene. In particular, we found complex reticulate evolutionary pattern among the East Asian hemlock species. T. sieboldii possibly originated from hybridization with the ancestor of T. chinensis from mainland China and T. forrestii as the paternal donor and the ancestor of T. diversifolia and T. ulleungensis as the maternal donor. T. chinensis (Taiwan) could have originated by hybridization together with T. sieboldii and then evolved independently after dispersal to the Taiwan Island, subsequently experiencing mitochondrial DNA introgression with T. chinensis from mainland China. Moreover, our study found that T. chinensis from western China is more closely related to T. forrestii than to T. chinensis from eastern China. The nonmonophyletic T. chinensis needs taxonomic reconsideration.

Lectotypification of the name Melastoma candidum f. albiflorum and its taxonomic status

A nomenclatural and taxonomic treatment of the name Melastoma candidum f. albiflorum (Melastomataceae) is presented. A lectotype is designated for this name, with an updated morphological description based on fresh material. The name Melastoma candidum f. albiflorum is proposed as a heterotypic synonym of Melastoma candidum.

A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae

PREMISE

Putatively single-copy nuclear (SCN) loci, which are identified using genomic resources of closely related species, are ideal for phylogenomic inference. However, suitable genomic resources are not available for many clades, including Melastomataceae. We introduce a versatile approach to identify SCN loci for clades with few genomic resources and use it to develop probes for target enrichment in the distantly related Memecylon and Tibouchina (Melastomataceae).

METHODS

We present a two-tiered pipeline. First, we identified putatively SCN loci using MarkerMiner and transcriptomes from distantly related species in Melastomataceae. Published loci and genes of functional significance were then added (384 total loci). Second, using HybPiper, we retrieved 689 homologous template sequences for these loci using genome-skimming data from within the focal clades.

RESULTS

We sequenced 193 loci common to Memecylon and Tibouchina. Probes designed from 56 template sequences successfully targeted sequences in both clades. Probes designed from genome-skimming data within a focal clade were more successful than probes designed from other sources.

DISCUSSION

Our pipeline successfully identified and targeted SCN loci in Memecylon and Tibouchina, enabling phylogenomic studies in both clades and potentially across Melastomataceae. This pipeline could be easily applied to other clades with few genomic resources.

Analyses of Plastome Sequences Improve Phylogenetic Resolution and Provide New Insight Into the Evolutionary History of Asian Sonerileae/Dissochaeteae

Sonerileae/Dissochaeteae (Melastomataceae) comprises ca. 50 genera, two thirds of which occur in Southeast Asia. Phylogenetic relationships within this clade remain largely unclear, which hampers our understanding of its origin, evolution, and biogeography. Here, we explored the use of chloroplast genomes in phylogenetic reconstruction of Sonerileae/Dissochaeteae, by sampling 138 species and 23 genera in this clade. A total of 151 complete plastid genomes were assembled for this study. Plastid genomic data provided better support for the backbone of the Sonerileae/Dissochaeteae phylogeny, and also for relationships among most closely related species, but failed to resolve the short internodes likely resulted from rapid radiation. Trees inferred from plastid genome and nrITS sequences were largely congruent regarding the major lineages of Sonerileae/Dissochaeteae. The present analyses recovered 15 major lineages well recognized in both nrITS and plastid phylogeny. Molecular dating and biogeographical analyses indicated a South American origin for Sonerileae/Dissochaeteae during late Eocene (stem age: 34.78 Mya). Two dispersal events from South America to the Old World were detected in late Eocene (33.96 Mya) and Mid Oligocene (28.33 Mya) respectively. The core Asian clade began to diversify around early Miocene in Indo-Burma and dispersed subsequently to Malesia and Sino-Japanese regions, possibly promoted by global temperature changes and East Asian monsoon activity. Our analyses supported previous hypothesis that Medinilla reached Madagascar by transoceanic dispersal in Miocene. In addition, generic limits of some genera concerned were discussed.

The re-sequencing and re-assembly of complete chloroplast genome of Melastoma dodecandrum (Melastomataceae) from Fujian, China

The plant genus Melastoma of the family Melastomataceae is comprised of nine species and one variety in China. Melastoma dodecandrum is the only creeping species of this genus. Previous study has reported the complete chloroplast genome of M. dodecandrum from Guangzhou, China, but there may be some differences between plant populations from different regions. Herein, we reported the complete chloroplast genome of M. dodecandrum from Fuzhou, China, which was assembled from Pacbio and whole genome data was sequenced. The sequence has a circular molecular length of 156,598 bp and contained 129 genes. Phylogenetic analysis indicated that M. dodecandrum was closely related to M. candidum in Melastomataceae. The study aims to provide insights for the future studies on the differences in molecular evolution level between plant populations of M. dodecandrum and taxonomy of Melastoma.

Structure and features of the complete chloroplast genome of Melastoma dodecandrum

Melastoma dodecandrum, the only creeping species in the Melastoma genus, serves as a medicinal herb in southeast China. It belongs to the huge family Melastomataceae, which contains over 5000 species worldwide. In this study, we used next-generation sequencing to determine the complete chloroplast genome sequences of M. dodecandrum, which is a circular molecule of 156,611 bp in length. After annotation, we identified 131 putative genes in total, comprised of 85 protein-coding genes, 38 transfer RNA genes and 8 ribosomal RNA genes. Genome structure, GC content, repeat sequences and codon usage were investigated to gain a comprehensive understanding of this genome. Furthermore, we conducted comparative genome analyses between the M. dodecandrum genome and that of four other Melastomataceae species. Additionally, a phylogenetic analysis was performed based on available chloroplast genomes of Melastomataceae species and several Myrtaceae species, revealing the taxonomic relationships between M. dodecandrum and related species. In conclusion, our study represents the first look into the complete chloroplast genome of M. dodecandrum, providing abundant information for further studies such as species identification, taxonomy and phylogenetic resolution of Melastomataceae species.

De novo Assembly and Characterization of the Floral Transcriptomes of Two Varieties of Melastoma malabathricum

Melastoma malabathricum is an important medicinal and landscape plant that is globally distributed in temperate and subtropical regions. However, available genomic information for the entire Melastomataceae family is notably limited. In view of the application potential of floral parts in secondary metabolite extraction, we characterized for the first time the floral transcriptomes of two key M. malabathricum varieties, purple variety and white variety. Our transcriptome assembly generated 52,498 and 49,380 unigenes with an N50 of 1,906 and 1,929 bases for the purple and white varieties, respectively. Comparative analysis of two transcriptomes demonstrated that they are highly similar but also highlighted genes that are presumably lineage specific, which explains the phenotypes of each variety. Additionally, a shared transcriptional signature across the floral developmental stages was identified in both M. malabathricum varieties; this signature included pathways related to secondary metabolite synthesis, plant hormone signaling and production, energy homeostasis and nutrient assimilation pathways, and cellular proliferation. The expression levels of flavonoid accumulation and candidate flavonoid biosynthesis-related genes in M. malabathricum flower development stages validated the transcriptome findings. The transcriptome data presented in this study will serve as a valuable resource for future work on the exploitation of M. malabathricum and other related species. The gene expression dynamics during flower development will facilitate the discovery of lineage-specific genes associated with phenotypic characteristics and will elucidate the mechanism of the ontogeny of individual flower types.

Molecular identification of natural hybridization between Melastoma malabathricum and Melastoama beccarianum in Sarawak, Malaysia

Hybridization is very common in flowering plants and it plays a significant role in plant evolution and adaptation. Melastoma L. (Melastomataceae) comprises about 80-90 species in tropical Asia and Oceania, among which 41 species occur in Borneo. Natural hybridization is frequently reported in Melastoma in China, but so far there have been no confirmed cases of hybridization in Southeast Asia (including Borneo), where most species occur. Here, we identified a case of natural hybridization between Melastoma malabathricum L. and Melastoma beccarianum Cogn. in Sarawak, Malaysia, by using sequence data of three nuclear genes and one chloroplast intergenic spacer. Melastoma malabathricum is the most widespread species of this genus, occurring in almost the whole range of this genus, while M. beccarianum is a local species endemic to northern Borneo. Our results showed that natural hybridization and introgression occur between M. malabathricum and M. beccarianum, and the introgression was asymmetrical, mainly from M. malabathricum to M. beccarianum. As adaptive traits can be transferred by introgression, our study suggests that natural hybridization should be a significant mechanism for the evolution and adaptation of Melastoma in Southeast Asia. However, introgression from the common species M. malabathricum to the relatively rare species M. beccarianum may cause the decline of M. beccarianum, incurring conservation concern. With a large number of species of Melastoma and almost year-around flowering in Southeast Asia, more cases of natural hybridization are expected to be found and identified in near future.

Comparative transcriptomics sheds light on differential adaptation and species diversification between two Melastoma species and their F1 hybrid

Variation in gene expression has been shown to promote adaptive divergence, and can lead to speciation. The plant genus Melastoma, thought to have diversified through adaptive radiation, provides an excellent model for the study of gene expressional changes during adaptive differentiation and following interspecific hybridization. In this study, we performed RNA-seq on M. candidum, M. sanguineum and their F1 hybrid, to investigate the role of gene expression in species diversification within the genus. Reference transcriptomes were assembled using combined data from both parental species, resulting in 50 519 and 48 120 transcripts for the leaf and flower petal, after removing redundancy. Differential expression analysis uncovered 3793 and 2116 differentially expressed (DE) transcripts, most of which are between M. candidum and M. sanguineum. Differential expression was observed for genes related to light responses, as well as genes that regulate the development of leaf trichomes, a trait that among others is thought to protect plants against sunlight, suggesting the differential adaptation of the species to sunlight intensity. The analysis of positively selected genes between the two species also revealed possible differential adaptation to other abiotic stresses such as drought and temperature. In the hybrid, almost all possible modes of expression were observed at the DE transcripts, although at most transcripts, the expression levels were similar to that of either parent instead of being intermediate. A small number of transgressively expressed transcripts that matched genes known to promote plant growth and adaptation to stresses in new environments were also found, possibly explaining the vigour observed in the hybrid. The findings in this study provided insights into the role of gene expression in the diversification of Melastoma, which we believe is an important example for more cross-taxa comparisons in the future.

The specific status of Melastoma kudoi (Melastomataceae, Melastomeae)

BACKGROUND

Melastoma has undergone rapid species radiation during the last one million years, and circumscription of some species in the genus has remained controversial. Melastoma kudoi, an erect species narrowly endemic to central Taiwan was previously treated as a synonym of M. intermedium, a semicreeping hybrid between the erect species M. candidum and the creeping M. dodecandrum, making its identity questionable. We addressed this question based on molecular and morphological data.

RESULTS

Phylogenetic analyses based on nrITS sequence data revealed that M. kudoi is most closely related to M. dodecandrum. Further analyses of six nuclear genes (cam, chi, gapC, gbss, tpi and vr) and two chloroplast markers (trnL-trnF and psbA) showed that M. kudoi is well diverged from its close relatives. Morphologically, it is also easily distinguished from related species by its erect habit, center-positioned stigma, and spreading, basally enlarged hairs on the hypanthium.

CONCLUSIONS

Both molecular phylogenetic and morphological data suggest that M. kudoi is well separated from M. intermedium, M. dodecandrum, and O. scaberrima, and should be treated as a distinct species. Taxonomic treatment and detailed description of M. kudoi are provided.

Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species

BACKGROUND

Plukenetia is a small pantropical genus of lianas and vines with variably sized edible oil-rich seeds that presents an ideal system to investigate neotropical and pantropical diversification patterns and seed size evolution. We assessed the biogeography and seed evolution of Plukenetia through phylogenetic analyses of a 5069 character molecular dataset comprising five nuclear and two plastid markers for 86 terminals in subtribe Plukenetiinae (representing 20 of ~ 23 Plukenetia species). Two nuclear genes, KEA1 and TEB, were used for phylogenetic reconstruction for the first time. Our goals were: (1) produce a robust, time-dependent evolutionary framework for Plukenetia using BEAST; (2) reconstruct its biogeographical history with ancestral range estimation in BIOGEOBEARS; (3) define seed size categories; (4) identify patterns of seed size evolution using ancestral state estimation; and (5) conduct regression analyses with putative drivers of seed size using the threshold model.

RESULTS

Plukenetia was resolved into two major groups, which we refer to as the pinnately- and palmately-veined clades. Our analyses suggest Plukenetia originated in the Amazon or Atlantic Forest of Brazil during the Oligocene (28.7 Mya) and migrated/dispersed between those regions and Central America/Mexico throughout the Miocene. Trans-oceanic dispersals explain the pantropical distribution of Plukenetia, including from the Amazon to Africa in the Early Miocene (17.4 Mya), followed by Africa to Madagascar and Africa to Southeast Asia in the Late Miocene (9.4 Mya) and Pliocene (4.5 Mya), respectively. We infer a single origin of large seeds in the ancestor of Plukenetia. Seed size fits a Brownian motion model of trait evolution and is moderately to strongly associated with plant size, fruit type/dispersal syndrome, and seedling ecology. Biome shifts were not drivers of seed size, although there was a weak association with a transition to fire prone semi-arid savannas.

CONCLUSIONS

The major relationships among the species of Plukenetia are now well-resolved. Our biogeographical analyses support growing evidence that many pantropical distributions developed by periodic trans-oceanic dispersals throughout the Miocene and Pliocene. Selection on a combination of traits contributed to seed size variation, while movement between forest edge/light gap and canopy niches likely contributed to the seed size extremes in Plukenetia.

Using an integrated approach to identify cryptic species, divergence patterns and hybrid species in Asian ladies' tresses orchids (Spiranthes, Orchidaceae)

Spiranthes (∼36 species, Orchidaceae) is a small genus with a global distribution. It has a center of diversity in North America with only a few species occurring in Asia. This study focuses on the Asian Spiranthes with an emphasis on understanding their biogeographic relationships and species delimitations using molecular markers. Our phylogenetic trees based on nuclear (ITS) and chloroplast (trnL-trnLF, matK and trnS-G) sequences from samples across their range in Asia revealed the Asian Spiranthes are monophyletic. Ancestral area optimization suggested that North America forms the ancestral region for the Asian Spiranthes rather than Europe suggesting that they originated from a single long-distance dispersal event. Our study also revealed the presence of a cryptic species S. himalayensis, which was discovered based on molecular data thus emphasizing the importance of wide geographical sampling in phylogenetic studies. Sequences of cloned ITS provided support for the hypothesis that natural hybridization between S. sinensis and the newly described S. himalayensis resulted in the allotetraploid S. hongkongensis, with S. himalayensis as the paternal parent. One of the species complexes known in Asia is the S. sinensis complex, which shows a wide occurrence and is known for local geographical variants. Some of these variants have been described as new species in Australia and New Zealand. Our studies show that all the sampled variants including the Australian and New Zealand species show monophyly despite having long branches. This suggests that there may be high rates of gene flow between the geographically distinct forms resulting in lack of species resolution within the S. sinensis complex.

The complete chloroplast genome sequence of Melastoma candidum (Melastomataceae)

The plant genus Melastoma is comprised of members estimated to have formed through recent species radiation. Natural hybridization among member species further complicates taxonomy within the genus. Herein, we report the complete chloroplast genome of M. candidum, assembled from partial data obtained from a parallel whole-genome Illumina paired-end sequencing effort on the species. The chloroplast genome was 156,682 bp in length, with a large single-copy (LSC) region of 86,084 bp, a small single-copy (SSC) region of 17,094 bp, separated by two inverted repeat (IR) regions of 26,752 bp each. It was predicted to contain a total of 129 genes, with an overall GC content of 37.17%. Phylogenetic analysis placed M. candidum in the same clade as species within the Melastomeae tribe of Melastomataceae.

Similar Morphologies but Different Origins: Hybrid Status of Two More Semi-creeping Taxa of Melastoma

Inferring the origins of hybrid taxa based on morphology alone is difficult because morphologically similar hybrids can arise from hybridization between different populations of the same parental species or be produced by hybridization of different parental species. In this study, we investigated the origins of two semi-creeping taxa in Melastoma, which are morphologically similar to a natural hybrid, M. intermedium, by sequencing a chloroplast intergenic spacer, nuclear ribosomal internal transcribed spacer and two low-copy nuclear genes (tpi and cam) in these taxa and their putative parental species. Our sequence analysis provides compelling evidence for the hybrid status of the two semi-creeping taxa: one originating from hybridization between M. dodecandrum and M. malabathricum, and the other between M. dodecandrum and M. normale. The origins of these hybrids are therefore clearly different from M. intermedium, and morphological similarity for the three hybrids is most likely due to their origins from hybridization between the same creeping species M. dodecandrum and a different erect species in each of the three cases. We also observed low rate of introgression from M. normale to M. dodecandrum, and genetic exchange between them may transfer adaptive traits to M. dodecandrum. Rare occurrence of these two hybrids may be due to small range overlaps between parental species in one case, and different flowering periods between parental species in the other.

Post-Boreotropical dispersals explain the pantropical disjunction in Paederia (Rubiaceae)

BACKGROUND AND AIMS

Pantropical intercontinental disjunction is a common biogeographical pattern in flowering plants exhibiting a discontinuous distribution primarily in tropical Asia, Africa and the Americas. Only a few plant groups with this pattern have been investigated at the generic level with molecular phylogenetic and biogeographical methods. Paederia (Rubiaceae) is a pantropical genus of 31 species of woody lianas, with the greatest species diversity in continental Asia and Madagascar and only two species from tropical America. The aim of this study was to reconstruct the biogeographical history of Paederia based on phylogenetic analyses to explore how the genus attained its pantropical distribution.

METHODS

Maximum parsimony and Bayesian inference were used for phylogenetic analyses using sequences of five plastid markers (the rbcL gene, rps16 intron, trnT-F region, atpB-rbcL spacer and psbA-trnH spacer). Biogeographical inferences were based on a Bayesian uncorrelated lognormal relaxed molecular clock together with both Bayesian and likelihood ancestral area reconstructions.

KEY RESULTS

The data suggest an early diverged Asian lineage sister to the clade of the remaining species consisting of a predominantly Asian sub-clade and a primarily Malagasy sub-clade. Paederia is inferred to have originated in the Oligocene in tropical continental Asia. It then reached Africa in the early to middle Miocene, most probably via long-distance dispersal across the Indian Ocean. The two Neotropical species are inferred to have derived independently in the late Miocene from ancestors of Asia and East Africa, respectively.

CONCLUSIONS

The results demonstrate the importance of post-Boreotropical long-distance dispersals (across three major oceans) in shaping the global pantropical disjunction in some plants, such as Paederia, with small, winged diaspores adapted to long-distance dispersal by various agents including wind, ocean currents or birds. Overland migration is less likely to explain its palaeotropical disjunction between Asia and Africa.

Inferences of biogeographical histories within subfamily Hyacinthoideae using S-DIVA and Bayesian binary MCMC analysis implemented in RASP (Reconstruct Ancestral State in Phylogenies)

BACKGROUND AND AIMS

Subfamily Hyacinthoideae (Hyacinthaceae) comprises more than 400 species. Members are distributed in sub-Saharan Africa, Madagascar, India, eastern Asia, the Mediterranean region and Eurasia. Hyacinthoideae, like many other plant lineages, show disjunct distribution patterns. The aim of this study was to reconstruct the biogeographical history of Hyacinthoideae based on phylogenetic analyses, to find the possible ancestral range of Hyacinthoideae and to identify factors responsible for the current disjunct distribution pattern.

METHODS

Parsimony and Bayesian approaches were applied to obtain phylogenetic trees, based on sequences of the trnL-F region. Biogeographical inferences were obtained by applying statistical dispersal-vicariance analysis (S-DIVA) and Bayesian binary MCMC (BBM) analysis implemented in RASP (Reconstruct Ancestral State in Phylogenies).

KEY RESULTS

S-DIVA and BBM analyses suggest that the Hyacinthoideae clade seem to have originated in sub-Saharan Africa. Dispersal and vicariance played vital roles in creating the disjunct distribution pattern. Results also suggest an early dispersal to the Mediterranean region, and thus the northward route (from sub-Saharan Africa to Mediterranean) of dispersal is plausible for members of subfamily Hyacinthoideae.

CONCLUSIONS

Biogeographical analyses reveal that subfamily Hyacinthoideae has originated in sub-Saharan Africa. S-DIVA indicates an early dispersal event to the Mediterranean region followed by a vicariance event, which resulted in Hyacintheae and Massonieae tribes. By contrast, BBM analysis favours dispersal to the Mediterranean region, eastern Asia and Europe. Biogeographical analysis suggests that sub-Saharan Africa and the Mediterranean region have played vital roles as centres of diversification and radiation within subfamily Hyacinthoideae. In this bimodal distribution pattern, sub-Saharan Africa is the primary centre of diversity and the Mediterranean region is the secondary centre of diversity. Sub-Saharan Africa was the source area for radiation toward Madagascar, the Mediterranean region and India. Radiations occurred from the Mediterranean region to eastern Asia, Europe, western Asia and India.

Phylogeny, adaptive radiation, and historical biogeography in Bromeliaceae: insights from an eight-locus plastid phylogeny

PREMISE

Bromeliaceae form a large, ecologically diverse family of angiosperms native to the New World. We use a bromeliad phylogeny based on eight plastid regions to analyze relationships within the family, test a new, eight-subfamily classification, infer the chronology of bromeliad evolution and invasion of different regions, and provide the basis for future analyses of trait evolution and rates of diversification.

METHODS

We employed maximum-parsimony, maximum-likelihood, and Bayesian approaches to analyze 9341 aligned bases for four outgroups and 90 bromeliad species representing 46 of 58 described genera. We calibrate the resulting phylogeny against time using penalized likelihood applied to a monocot-wide tree based on plastid ndhF sequences and use it to analyze patterns of geographic spread using parsimony, Bayesian inference, and the program S-DIVA.

RESULTS

Bromeliad subfamilies are related to each other as follows: (Brocchinioideae, (Lindmanioideae, (Tillandsioideae, (Hechtioideae, (Navioideae, (Pitcairnioideae, (Puyoideae, Bromelioideae))))))). Bromeliads arose in the Guayana Shield ca. 100 million years ago (Ma), spread centrifugally in the New World beginning ca. 16-13 Ma, and dispersed to West Africa ca. 9.3 Ma. Modern lineages began to diverge from each other roughly 19 Ma.

CONCLUSIONS

Nearly two-thirds of extant bromeliads belong to two large radiations: the core tillandsioids, originating in the Andes ca. 14.2 Ma, and the Brazilian Shield bromelioids, originating in the Serro do Mar and adjacent regions ca. 9.1 Ma.

Biogeography of cedrela (meliaceae, sapindales) in central and South america

Dated phylogenies have helped clarify the complex history of many plant families that today are restricted to the world's tropical forests, but that have Eocene, Oligocene, and Miocene fossils from the northern hemisphere. One such family is the Meliaceae. Here we infer the history of the neotropical Meliaceae genus Cedrela (17 species), the sister clade of which today is restricted to tropical Asia. Sequences from the nuclear ribosomal spacer region and five plastid loci obtained for all ingroup species and relevant outgroups were used to infer species relationships and for molecular-clock dating under two Bayesian relaxed clock models. The clock models differed in their handling of rate autocorrelation and sets of fossil constraints. Results suggest that (1) crown group diversification in Cedrela started in the Oligocene/Early Miocene and intensified in the Late Miocene and Early Pliocene, and (2) Central American Cedrela species do not form a clade, implying reentry into Central America after the closure of the Panamanian Isthmus. At present, Cedrela is distributed in both dry and humid habitats, but morphological features suggest an origin in dry forest under seasonal climates, fitting with Miocene and Pliocene Cedrela fossils from deciduous forests.

Phylogeny and biogeography of Alangiaceae (Cornales) inferred from DNA sequences, morphology, and fossils

Alangiaceae, in the basal Asterid clade Cornales, consists of only one genus, Alangium. The genus has approximately 24 species distributed mainly in tropical and subtropical regions of the Old World and is well represented in the Tertiary fossil record of the northern hemisphere. We conducted phylogenetic and biogeographic analyses for Alangium by integrating data from DNA sequences, morphology, and fossils to evaluate systematic and biogeographic hypotheses. The results largely agree with the traditional classification of four sections within the genus, and suggest sects. Conostigma and Rhytidandra are successive sister taxa to a clade containing sects. Marlea and Alangium. Our results also indicate that the widespread species A. chinense consists of at least two lineages meriting recognition as distinct species. Biogeographic analysis using DIVA and divergence time dating with the Bayesian method (MULTIDIVTIME) resolved the ancestor of Alangium as being in S.E. Asia in the Late Cretaceous. Several intercontinental migrations involving the margin of the Tethys seaway (TESW), the North Atlantic land bridge (NALB) or the Bering land bridge (BLB), and long-distance dispersals are suggested. The results support TESW for plant migration of thermophilic (including evergreen) taxa in the early Tertiary.

A phylogeny of the oil bee tribe Ctenoplectrini (Hymenoptera: Anthophila) based on mitochondrial and nuclear data: evidence for early Eocene divergence and repeated out-of-Africa dispersal

The bee tribe Ctenoplectrini, with two genera, comprises nine species in tropical Africa and ten in Asia and Australia. Most of them collect floral oil, pollen, and nectar from Cucurbitaceae, but three species are thought to be cleptoparasites. The unusual morphology of Ctenoplectrini has made it difficult to infer their closest relatives, in turn preventing an understanding of these bees' geographic and temporal origin. We used two mitochondrial and two nuclear markers (4741 nucleotides) generated for most of the species to test the monophyly of the tribe, its relationships to other Apidae, and its biogeographic history. Ctenoplectrini are strongly supported as monophyletic and closest to the Long-horned bees, Eucerini. The presumably cleptoparasitic species form a clade (Ctenoplectrina) that is sister to the remaining species (Ctenoplectra), confirming the independent evolution of cleptoparasitism in this tribe. Tree topology and molecular dating together suggest that Ctenoplectrini originated in Africa in the Early Eocene and that Ctenoplectra dispersed twice from Africa to Asia, sometime in the Late Eocene, 30-40 my ago, from where one species reached the Australian continent via Indonesia and New Guinea in the mid-Miocene, c. 13 my ago. Dry and cool mid-Miocene climates also coincide with the divergence between Ctenoplectra bequaerti from West Africa and Ctenoplectra terminalis from East and South Africa, perhaps related to fragmentation of the equatorial African rainforest belt.

Extreme long-distance dispersal of the lowland tropical rainforest tree Ceiba pentandra L. (Malvaceae) in Africa and the Neotropics

Many tropical tree species occupy continental expanses of rainforest and flank dispersal barriers such as oceans and mountains. The role of long-distance dispersal in establishing the range of such species is poorly understood. In this study, we test vicariance hypotheses for range disjunctions in the rainforest tree Ceiba pentandra, which is naturally widespread across equatorial Africa and the Neotropics. Approximate molecular clocks were applied to nuclear ribosomal [ITS (internal transcribed spacer)] and chloroplast (psbB-psbF) spacer DNA sampled from 12 Neotropical and five West African populations. The ITS (N=5) and psbB-psbF (N=2) haplotypes exhibited few nucleotide differences, and ITS and psbB-psbF haplotypes were shared by populations on both continents. The low levels of nucleotide divergence falsify vicariance explanations for transatlantic and cross-Andean range disjunctions. The study shows how extreme long-distance dispersal, via wind or marine currents, creates taxonomic similarities in the plant communities of Africa and the Neotropics.

Assessing Calibration Uncertainty in Molecular Dating: The Assignment of Fossils to Alternative Calibration Points

Although recent methodological advances have allowed the incorporation of rate variation in molecular dating analyses, the calibration procedure, performed mainly through fossils, remains resistant to improvements. One source of uncertainty pertains to the assignment of fossils to specific nodes in a phylogeny, especially when alternative possibilities exist that can be equally justified on morphological grounds. Here we expand on a recently developed fossil cross-validation method to evaluate whether alternative nodal assignments of multiple fossils produce calibration sets that differ in their internal consistency. We use an enlarged Crypteroniaceae-centered phylogeny of Myrtales, six fossils, and 72 combinations of calibration points, termed calibration sets, to identify (i) the fossil assignments that produce the most internally consistent calibration sets and (ii) the mean ages, derived from these calibration sets, for the split of the Southeast Asian Crypteroniaceae from their West Gondwanan sister clade (node X). We found that a correlation exists between s values, devised to measure the consistency among the calibration points of a calibration set (Near and Sanderson, 2004), and nodal distances among calibration points. By ranking all sets according to the percent deviation of s from the regression line with nodal distance, we identified the sets with the highest level of corrected calibration-set consistency. These sets generated lower standard deviations associated with the ages of node X than sets characterized by lower corrected consistency. The three calibration sets with the highest corrected consistencies produced mean age estimates for node X of 79.70, 79.14, and 78.15 My. These timeframes are most compatible with the hypothesis that the Crypteroniaceae stem lineage dispersed from Africa to the Deccan plate as it drifted northward during the Late Cretaceous.

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.

EVOLUTIONARY DIVERSIFICATION AND THE ORIGIN OF THE DIVERSITY–ENVIRONMENT RELATIONSHIP

Global patterns in species richness have resisted explanation since they first caught the attention of ecologists in the 1960s. The failure of ecology to fully integrate the diversity issue into its core of accepted wisdom derives from an inappropriate concept of community and the rejection of history and region as formative contexts for ecological systems. Traditionally, ecologists have held that the pervasive relationship between species richness and conditions of the physical environment reflects the influence of environment on the ability of populations to coexist locally. However, many ecologists now recognize that this relationship can also develop historically from the evolutionary diversification of lineages within and between ecological zones. To assess the relative roles of local ecological constraint vs. regional and historical unfolding of diversity-environment relationships, we must abandon localized concepts of the community and adopt historical (particularly phylogenetic) and geographic methods to evaluate the evolution of diversity within large regions and its influence on diversity at local scales. This integrated perspective opens new research directions for ecologists to explore the formation of species, adaptive diversification, and the adjustment of ecological distributions of species on regional scales.

Relaxed molecular clocks for dating historical plant dispersal events

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

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.

Multiple Miocene Melastomataceae dispersal between Madagascar, Africa and India

Melastomataceae sensu stricto (excluding Memecylaceae) comprise some 3000 species in the neotropics, 1000 in Asia, 240 in Africa, and 230 in Madagascar. Previous family-wide morphological and DNA analyses have shown that the Madagascan species belong to at least three unrelated lineages, which were hypothesized to have arrived by trans-oceanic dispersal. An alternative hypothesis posits that the ancestors of Madagascan, as well as Indian, Melastomataceae arrived from Africa in the Late Cretaceous. This study tests these hypotheses in a Bayesian framework, using three combined sequence datasets analysed under a relaxed clock and simultaneously calibrated with fossils, some not previously used. The new fossil calibration comes from a re-dated possibly Middle or Upper Eocene Brazilian fossil of Melastomeae. Tectonic events were also tentatively used as constraints because of concerns that some of the family's fossils are difficult to assign to nodes in the phylogeny. Regardless of how the data were calibrated, the estimated divergence times of Madagascan and Indian lineages were too young for Cretaceous explanations to hold. This was true even of the oldest ages within the 95% credibility interval around each estimate. Madagascar's Melastomeae appear to have arrived from Africa during the Miocene. Medinilla, with some 70 species in Madagascar and two in Africa, too, arrived during the Miocene, but from Asia. Gravesia, with 100 species in Madagascar and four in east and west Africa, also appears to date to the Miocene, but its monophyly has not been tested. The study afforded an opportunity to compare divergence time estimates obtained earlier with strict clocks and single calibrations, with estimates based on relaxed clocks and different multiple calibrations and taxon sampling.

Molecular evidence on plant divergence times

Estimation of divergence times from sequence data has become increasingly feasible in recent years. Conflicts between fossil evidence and molecular dates have sparked the development of new methods for inferring divergence times, further encouraging these efforts. In this paper, available methods for estimating divergence times are reviewed, especially those geared toward handling the widespread variation in rates of molecular evolution observed among lineages. The assumptions, strengths, and weaknesses of local clock, Bayesian, and rate smoothing methods are described. The rapidly growing literature applying these methods to key divergence times in plant evolutionary history is also reviewed. These include the crown group ages of green plants, land plants, seed plants, angiosperms, and major subclades of angiosperms. Finally, attempts to infer divergence times are described in the context of two very different temporal settings: recent adaptive radiations and much more ancient biogeographic patterns.

Phylogeny and circumscription of the near-endemic Brazilian tribe Microlicieae (Melastomataceae)

The members of tribe Microlicieae in the flowering plant family Melastomataceae are nearly all endemic to the cerrado biome of Brazil. Traditional classifications of the Melastomataceae have attributed between 15 and 17 genera to the Microlicieae, but subsequent revisions have circumscribed the tribe more narrowly. The monophyly and intergeneric relationships of the Microlicieae were evaluated through phylogenetic analyses with molecular and morphological data sets. Incorporation of DNA sequences from the intron of the chloroplast gene rpl16 into a previously generated family-wide data set yielded a clade comprising Chaetostoma, Lavoisiera, Microlicia, Rhynchanthera, Stenodon, and Trembleya ("core Microlicieae"), with Rhynchanthera as the first-diverging lineage. The other four genera of Microlicieae sampled are placed in other clades: Eriocnema with Miconieae; Siphanthera with Aciotis, Nepsera, and Acisanthera of Melastomeae; Castratella as sister to Monochaetum of Melastomeae; and Cambessedesia as part of an unresolved polytomy in a large clade that includes most Melastomataceae. Analyses of the chloroplast genes rbcL and ndhF that included three core genera produced similar results, as did the combined analysis of all three data sets. Combined parsimony analyses of DNA sequences from rpl16 and the nuclear ribosomal intercistronic transcribed spacer (ITS) region of 22 species of core Microlicieae yielded generally low internal support values. Lavoisiera, recently redefined on the basis of several morphological characters, was strongly supported as monophyletic. A morphological phylogenetic analysis of the Microlicieae based on 10 parsimony-informative characters recovered a monophyletic core Microlicieae but provided no further resolution among genera. Penalized likelihood analysis with two calibration time windows produced an age estimate of 3.7 million years for the time of initial divergence of strictly Brazilian core Microlicieae. This date is in general agreement with the estimated age of the most active stage of development of cerrado vegetation and implies an adaptive shift from hydric to seasonally dry habitats during the early evolution of this group.

Missing fossils, molecular clocks, and the origin of the Melastomataceae

In a recent analysis of the historical biogeography of Melastomataceae, Renner, Clausing, and Meyer (2001; American Journal of Botany 88(7): 1290-1300) rejected the hypothesis of a Gondwana origin. Using a fossil-calibrated chloroplast DNA (ndhF) phylogeny, they placed the early diversification of Melastomataceae in Laurasia at the Paleocene/Eocene boundary (ca. 55 Ma) and suggested that long-distance oceanic dispersals in the Oligocene and Miocene (34 to 5 Ma) account for its range expansion into South America, Africa, and Madagascar. Their critical assumption-that oldest northern mid-latitude melastome fossils reflect tribal ages and their geographic origins-may be erroneous, however, because of the sparse fossil record in the tropics. We show that rates of synonymous nucleotide substitutions derived by the Renner et al. (2001) model are up to three times faster than most published rates. Under a Gondwana-origin model advocated here, which includes dispersals from Africa to Southeast Asia via the "Indian ark" and emphasizes filter rather than either sweepstakes dispersal or strict vicariance, rates of nucleotide substitution fall within the range of published rates. We suggest that biogeographic reconstructions need to consider the paucity of Gondwanan fossils and that frequently overlooked interplate dispersal routes provide alternatives to vicariance, boreotropical dispersal, and long-distance oceanic dispersal as explanations for the amphi-oceanic disjunctions of many tropical rain forest plants.