Systematics, biogeography, and character evolution of Sparganium (Typhaceae): diversification of a widespread, aquatic lineage

The evolution of Ericaceae flowers and their pollination syndromes at a global scale

PREMISE

Floral evolution in large clades is difficult to study not only because of the number of species involved, but also because they often are geographically widespread and include a diversity of outcrossing pollination systems. The cosmopolitan blueberry family (Ericaceae) is one such example, most notably pollinated by bees and multiple clades of nectarivorous birds.

METHODS

We combined data on floral traits, pollination ecology, and geography with a comprehensive phylogeny to examine the structuring of floral diversity across pollination systems and continents. We focused on ornithophilous systems to test the hypothesis that some Old World Ericaceae were pollinated by now-extinct hummingbirds.

RESULTS

Despite some support for floral differentiation at a continental scale, we found a large amount of variability within and among landmasses, due to both phylogenetic conservatism and parallel evolution. We found support for floral differentiation in anther and corolla traits across pollination systems, including among different ornithophilous systems. Corolla traits show inconclusive evidence that some Old World Ericaceae were pollinated by hummingbirds, while anther traits show stronger evidence. Some major shifts in floral traits are associated with changes in pollination system, but shifts within bee systems are likely also important.

CONCLUSIONS

Studying the floral evolution of large, morphologically diverse, and widespread clades is feasible. We demonstrate that continent-specific radiations have led to widespread parallel evolution of floral morphology. We show that traits outside of the perianth may hold important clues to the ecological history of lineages.

A reappraisal of the phylogeny and historical biogeography of Sparganium (Typhaceae) using complete chloroplast genomes

BACKGROUND

Sparganium (Typhaceae) is a widespread temperate genus of ecologically important aquatic plants. Previous reconstructions of the phylogenetic relationships among Sparganium species are incompletely resolved partly because they were based on molecular markers comprising < 7,000 bp. Here, we sequenced and assembled the complete chloroplast genomes from 19 Sparganium samples representing 15 putative species and three putative subspecies in order to explore chloroplast genome evolution in this genus, clarify taxonomic lineages, estimate the divergence times of Sparganium species, and reconstruct aspects of the biogeographic history of the genus.

RESULTS

The 19 chloroplast genomes shared a conserved genome structure, gene content, and gene order. Our phylogenomic analysis presented a well-resolved phylogeny with robust support for most clades. Non-monophyly was revealed in three species: S. erectum, S. eurycarpum, and S. stoloniferum. Divergence time estimates suggest that the two subgenera of Sparganium split from each other ca. 30.67 Ma in the middle Oligocene. The subgenus Xanthosparganium diversified in the late Oligocene and Miocene, while the subgenus Sparganium diversified in the late Pliocene and Pleistocene. Ancestral area reconstruction suggested that the two subgenera may have originated in East Eurasia and North America.

CONCLUSION

The non-monophyletic nature of three putative species underscores the necessity of taxonomic revision for Sparganium: S. stoloniferum subsp. choui may be more appropriately identified as S. choui, and subspecies of S. erectum may be in fact distinct species. The estimated diversification times of the two subgenera correspond to their species and nucleotide diversities. The likely ancestral area for most of subgenus Xanthosparganium was East Eurasia and North America from where it dispersed into West Eurasia and Australia. Most of subgenus Sparganium likely originated in North America and then dispersed into Eurasia. Our study demonstrates some of the ways in which complete chloroplast genome sequences can provide new insights into the evolution, phylogeny, and biogeography of the genus Sparganium.

Hybridization and diversity of aquatic macrophyte Sparganium L. (Typhaceae) as revealed by high-throughput nrDNA sequencing

Sparganium is an emergent aquatic macrophyte widely spread in temperate and subtropical zones. Taxa of this genus feature high phenotypic plasticity and can produce interspecific hybrids. By means of high-throughput sequencing of the internal transcribed spacer (ITS1) of 35S rDNA, the status of 15 Eurasian Sparganium species and subspecies was clarified and the role of hybridization events in the recent evolution of the genus was investigated. It has been shown that a number of species such as S. angustifolium, S. fallax and S. subglobosum have homogenized rDNA represented by one major ribotype. The rDNA of other taxa is represented by two or more major ribotypes. Species with high rDNA heterogeneity are apparently of hybrid origin. Based on the differences in rDNA patterns, intraspecific diversity was identified in S. probatovae and S. emersum. Thus, we have concluded that Sparganium has extensive interspecific hybridization at the subgenus level, and there may also be occasional hybridization between species from different subgenera.

The complete chloroplast genome of Sparganium angustifolium (Typhaceae)

The complete chloroplast (cp) genome of Sparganium angustifolium was sequenced and annotated in the present study. The circular genome is 161,720 bp in length and exhibits a typical quadripartite structure with a large single-copy (LSC, 88,981 bp) and small single-copy (SSC, 18,731 bp) regions, separated by a pair of inverted repeats (IRs, 27,004 bp). The cp genome contains 114 unique genes, including 80 protein-coding, 30 tRNA, and four rRNA genes. The phylogenetic analysis of Typhaceae strongly supported the monophyly of Sparganium and resolved two clades that represented newly revised two subgenera. S. angustifolia has the closest relationship with S. emersum in the present sampling extent.

Molecular confirmation of the hybrid origin of Sparganium longifolium (Typhaceae)

Sparganium longifolium was reported as a hybrid between S. emersum and S. gramineum based on its intermediate type or the common characteristics of its parent species. Its hybrid origin needs to be confirmed using molecular technology. We investigated the origin of S. longifolium based on 10 populations of S. emersum, S. gramineum and S. longifolium from five lakes in European Russia, using sequences of six nuclear loci and one chloroplast DNA fragment. Haplotype network, principal coordinate analysis and genetic clustering based on data of nuclear loci confirmed that S. longifolium is the hybrid between S. emersum and S. gramineum. We found that the natural hybridization between S. emersum and S. gramineum is bidirectional but asymmetrical, and the latter mainly acts as maternal species. We also found that all samples of S. longifolium were F1 generations, and thus hypothesized that S. emersum and S. gramineum could likely maintain their species boundary through the post-zygote reproductive isolation mechanism of F1 generation sterility.

Characterization of the complete chloroplast genome of Sparganium glomeratum (Typhaceae) from Jilin Province, China and phylogenetic analysis

The complete chloroplast genome of Sparganium glomeratum was sequenced and assembled in this study. The circular genome is 160,391 bp in length and exhibits a typical quadripartite structure with a large single-copy (LSC, 87,660 bp) and small single-copy (SSC, 18,721 bp) regions, separated by a pair of inverted repeats (IRs, 27,005 bp). The cp genome contains 113 unique genes, including 79 protein-coding, 30 tRNA, and four rRNA genes. The phylogenetic analysis within the Poales showed that Sparganium is monophyletic and most closely related to Typha. Within Sparganium, S. glomeratum is sister to the clade of S. stoloniferum and S. euricarpum. The work reported here will provide useful information for the evolutionary studies on the genus of Sparganium.

The complete chloroplast genome of Sparganium fallax (Typhaceae)

Sparganium fallax is an aquatic perennial herb distributed in eastern Asia. The complete chloroplast genome of S. fallax was sequenced and assembled. The genome size was 161,838 bp in length with 36.8% GC content. Its quadripartite structure consisted of the large single copy (LSC, 89,042 bp) and small single copy (SSC, 18,774bp) regions, separated by a pair of inverted repeats (IRS) of 27,011bp. The genome contained 114 genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis within order Poales including three Sparganium species showed that Sparganium is monophyletic and most closely related to Typha.

Intracellular DNA transfer events restricted to the genus Convallaria within the Asparagaceae family: Possible mechanisms and potential as genetic markers for biographical studies

Intracellular gene transfer among plant genomes is a common phenomenon. Due to their high conservation and high plastid membrane integrity, chloroplast (cp) genomes incorporate foreign genetic material very rarely. Convallaria is a small monocotyledonous genus consisting of C. keiskei, C. majalis and C. montana. Here, we characterized, analyzed and identified 3.3 and 3.7 kb of mitochondrial DNA sequences in the plastome (MCP) of C. majalis and C. montana, respectively. We identified 6 bp and 23 bp direct repeats and mitochondrial pseudogenes, with rps3, rps19 and rpl10 identified in the MCP region. Additionally, we developed novel plastid molecular genetic markers to differentiate Convallaria spp. based on 21 populations. BEAST and biogeographical analyses suggested that Convallaria separated into Eurasian and North American lineages during the middle Pliocene and originated in East Asia. Vicariance in the genus was followed by dispersal into Europe and southeastern North America. These analyses indicate that the MCP event was restricted to the genus Convallaria of Asparagaceae, in contrast to similar events that occurred in its common ancestors with other families of land plants. However, further mitochondrial and population studies are necessary to understand the integration of the MCP region and gene flow in the genus Convallaria.

Expansin gene loss is a common occurrence during adaptation to an aquatic environment

Expansins comprise a superfamily of plant cell wall loosening proteins that can be divided into four individual families (EXPA, EXPB, EXLA and EXLB). Aside from inferred roles in a variety of plant growth and developmental traits, little is known regarding the function of specific expansin clades, for which there are at least 16 in flowering plants (angiosperms); however, there is evidence to suggest that some expansins have cell-specific functions, in root hair and pollen tube development, for example. Recently, two duckweed genomes have been sequenced (Spirodela polyrhiza strains 7498 and 9509), revealing significantly reduced superfamily sizes. We hypothesized that there would be a correlation between expansin loss and morphological reductions seen among highly adapted aquatic species. In order to provide an answer to this question, we characterized the expansin superfamilies of the greater duckweed Spirodela, the marine eelgrass Zostera marina and the bladderwort Utricularia gibba. We discovered rampant expansin gene and clade loss among the three, including a complete absence of the EXLB family and EXPA-VII. The most convincing correlation between morphological reduction and expansin loss was seen for Utricularia and Spirodela, which both lack root hairs and the root hair expansin clade EXPA-X. Contrary to the pattern observed in other species, four Utricularia expansins failed to branch within any clade, suggesting that they may be the result of neofunctionalization. Last, an expansin clade previously discovered only in eudicots was identified in Spirodela, allowing us to conclude that the last common ancestor of monocots and eudicots contained a minimum of 17 expansins.

Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

PREMISE OF THE STUDY

A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species-rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega-genus Salvia.

METHODS

A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared.

KEY RESULTS

A well-resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade.

CONCLUSIONS

Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.

Ontogenesis of the genets and ramets of some European species of the genus Sparganium subgenus Xanthosparganium

Representatives of the Sparganium L. genus belong to an ecological group of short grass helophytes which live in the shoreline area of different water bodies. Despite the fact that most representatives of the genus exhibit notable polymorphism (depending on the level regime of a water body, they can form various ecological forms), characteristic of all of them is presence of only one living form – vegetative mobile clear polycentric long-rhizomatous pseudoannual polycarpic plant with racemose root system. The objective of the article was to study the ontogenesis of genets and ramets on the example of representatives of the Xanthosparganium subgenus (S. emersum Rehm., S. glomeratum (Laest. ex Beurl.) Neum., S. gramineum Georgi and S. natans L.). The research was conducted using the ontogenetic approach. In the study, we analyzed ontogenesis of genet (from generative diaspore) and ontogenesis of ramets (from vegetative diaspores – tuber-like structures and axillary buds of vegetative-generative monocarpic and vegetative rosette shoots). We demonstrated that ontogenesis of genets and ramets (on the basis of tuber-like structures) in laboratory conditions is abrupt. It was found that the model species of Sparganium are characteristic in combining of incomplete and special ontogenesis, which is related to the omission of phases of the post-generative period. Such peculiarity is conditioned by increase in tempi of ontogenetic development. On the basis of specific ontogenesis, a variant of shortened ontogenesis is possible, during which the virginile ontogenetic condition is omitted. This feature could be characterized as dynamic polyvariance of ontogenesis, whereas bud initiation and development of shoots throughout the vegetative season, characterized as heterochrony, has been formed over the process of natural selection. Heterochrony (on the basis of iterative branching without periods of rest) includes a property of formation of vegetative-generative shoots which develop on the basis of sylleptic shoots of subsequent orders of branching. The main course of ontogenesis in natural conditions corresponds to D-type which occurs in order of generations of individuals of vegetative origin.

Revised phylogeny and historical biogeography of the cosmopolitan aquatic plant genus Typha (Typhaceae)

Typha is a cosmopolitan aquatic plant genus that includes species with widespread distributions. It is a relatively ancient genus with an abundant fossil record dating back to the Paleogene. However, the details of its biogeographic history have remained unclear until now. In this study, we present a revised molecular phylogeny using sequences of seven chloroplast DNA markers from nine species sampled from various regions in order to infer the biogeographic history of the genus. Two clades were recovered with robust support. Typha minima and T. elephantina comprised one clade, and the other clade included the remaining seven species, which represented a polytomy of four robustly supported subclades. Two widespread species, T. angustifolia and T. domingensis, were revealed to be paraphyletic, indicating the need for taxonomic revision. Divergence time estimation suggested that Typha had a mid-Eocene crown origin, and its diversification occurred in the Middle and Late Miocene. Ancestral area reconstruction showed that Typha possibly originated from eastern Eurasia. Both dispersal via the Beringian Land Bridge and recent transoceanic dispersal may have influenced the intercontinental distribution of Typha species.

Amphitropical disjunctions in New World Menthinae: Three Pliocene dispersals to South America following late Miocene dispersal to North America from the Old World

PREMISE OF THE STUDY

The subtribe Menthinae (Lamiaceae), with 35 genera and 750 species, is among the largest and most economically important subtribes within the mint family. Most genera of Menthinae are found exclusively in the New World, where the group has a virtually continuous distribution ranging from temperate North America to southern South America. In this study, we explored the presence, timing, and origin of amphitropical disjuncts within Menthinae.

METHODS

Our analyses were based on a data set consisting of 89 taxa and the nuclear ribosomal DNA markers ITS and ETS. Phylogenetic relationships were determined under maximum likelihood and Bayesian criteria, divergence times were estimated with the program BEAST, and ancestral range estimated with BioGeoBEARS.

KEY RESULTS

A North Atlantic Land Bridge migration event at about 10.6 Ma is inferred from western Eurasia to North America. New World Menthinae spread rapidly across North America, and then into Central and South America. Several of the large speciose genera are not monophyletic with nuclear rDNA, a finding mirrored with previous chloroplast DNA results. Three amphitropical disjunctions involving North and southern South America clades, one including a southeastern South American clade with several genera, were inferred to have occurred within the past 5 Myr.

CONCLUSIONS

Although three New World Menthinae genera occur in both North and South America, none exhibit an amphitropical disjunction. However, three clades exhibit amphitropical disjunctions, all dating to the early Pliocene, and all involve jump dispersals to either southeastern or southwestern South America from southeastern North America.

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.

Biogeography and diversification of Brassicales: A 103million year tale

Brassicales is a diverse order perhaps most famous because it houses Brassicaceae and, its premier member, Arabidopsis thaliana. This widely distributed and species-rich lineage has been overlooked as a promising system to investigate patterns of disjunct distributions and diversification rates. We analyzed plastid and mitochondrial sequence data from five gene regions (>8000bp) across 151 taxa to: (1) produce a chronogram for major lineages in Brassicales, including Brassicaceae and Arabidopsis, based on greater taxon sampling across the order and previously overlooked fossil evidence, (2) examine biogeographical ancestral range estimations and disjunct distributions in BioGeoBEARS, and (3) determine where shifts in species diversification occur using BAMM. The evolution and radiation of the Brassicales began 103Mya and was linked to a series of inter-continental vicariant, long-distance dispersal, and land bridge migration events. North America appears to be a significant area for early stem lineages in the order. Shifts to Australia then African are evident at nodes near the core Brassicales, which diverged 68.5Mya (HPD=75.6-62.0). This estimated age combined with fossil evidence, indicates that some New World clades embedded amongst Old World relatives (e.g., New World capparoids) are the result of different long distance dispersal events, whereas others may be best explained by land bridge migration (e.g., Forchhammeria). Based on these analyses, the Brassicaceae crown group diverged in Europe/Northern Africa in the Eocene, circa 43.4Mya (HPD=46.6-40.3) and Arabidopsis separated from close congeners circa 10.4Mya. These ages fall between divergent dates that were previously published, suggesting we are slowly converging on a robust age estimate for the family. Three significant shifts in species diversification are observed in the order: (1) 58Mya at the crown of Capparaceae, Cleomaceae and Brassicaceae, (2) 38Mya at the crown of Resedaceae+Stixis clade, and (3) 21Mya at the crown of the tribes Brassiceae and Sisymbrieae within Brassicaceae.

Divergence times, historical biogeography, and shifts in speciation rates of Myrtales

We examine the eudicot order Myrtales, a clade with strong Gondwanan representation for most of its families. Although previous phylogenetic studies greatly improved our understanding of intergeneric and interspecific relationships within the order, our understanding of inter-familial relationships still remains unresolved; hence, we also lack a robust time-calibrated chronogram to address hypotheses (e.g., biogeography and diversification rates) that have implicit time assumptions. Six loci (rbcL, ndhF, matK, matR, 18S, and 26S) were amplified and sequenced for 102 taxa across Myrtales for phylogenetic reconstruction and ten fossil priors were utilized to produce a chronogram in BEAST. Combretaceae is identified as the sister clade to all remaining families with moderate support, and within the latter clade, two strongly supported groups are seen: (1) Onagraceae+Lythraceae, and (2) Melastomataceae+the Crypteroniaceae, Alzateaceae, Penaeaceae clade along with Myrtaceae+Vochysiaceae. Divergence time estimates suggest Myrtales diverged from Geraniales ∼124Mya during the Aptian of the Early Cretaceous. The crown date for Myrtales is estimated at ∼116Mya (Albian-Aptian). BioGeoBEARS showed significant improvement in the likelihood score when the "jump dispersal" parameter was added. South America and/or Africa are implicated as important ancestral areas in all deeper nodes. BAMM analyses indicate that the best configuration included three significant shifts in diversification rates within Myrtales: near the crown of Melastomataceae (∼67-64Mya), along the stem of subfamily Myrtoideae (Myrtaceae; ∼75Mya), and along the stem of tribe Combreteae (Combretaceae; ∼50-45Mya). Issues with conducting diversification analyses more generally are examined in the context of scale, taxon sampling, and larger sets of phylogenetic trees.

Calibrated birth-death phylogenetic time-tree priors for bayesian inference

Here we introduce a general class of multiple calibration birth-death tree priors for use in Bayesian phylogenetic inference. All tree priors in this class separate ancestral node heights into a set of "calibrated nodes" and "uncalibrated nodes" such that the marginal distribution of the calibrated nodes is user-specified whereas the density ratio of the birth-death prior is retained for trees with equal values for the calibrated nodes. We describe two formulations, one in which the calibration information informs the prior on ranked tree topologies, through the (conditional) prior, and the other which factorizes the prior on divergence times and ranked topologies, thus allowing uniform, or any arbitrary prior distribution on ranked topologies. Although the first of these formulations has some attractive properties, the algorithm we present for computing its prior density is computationally intensive. However, the second formulation is always faster and computationally efficient for up to six calibrations. We demonstrate the utility of the new class of multiple-calibration tree priors using both small simulations and a real-world analysis and compare the results to existing schemes. The two new calibrated tree priors described in this article offer greater flexibility and control of prior specification in calibrated time-tree inference and divergence time dating, and will remove the need for indirect approaches to the assessment of the combined effect of calibration densities and tree priors in Bayesian phylogenetic inference.