Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum.

PREMISE: Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants. METHODS: A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum (Angiosperms353 probe set). RESULTS: While the taxonomic framework of Solanum remained stable, gene tree conflicts and discordance between phylogenetic trees generated from the target-capture and plastome datasets were observed. The latter correspond to regions with short internodal branches, and network analysis and polytomy tests suggest the backbone is composed of three polytomies found at different evolutionary depths. The strongest area of discordance, near the crown node of Solanum, could potentially represent a hard polytomy. CONCLUSIONS: We argue that incomplete lineage sorting due to rapid diversification is the most likely cause for these polytomies, and that embracing the uncertainty that underlies them is crucial to understand the evolution of large and rapidly radiating lineages.

Phylogenetics and historical biogeography of Solanum section Brevantherum (Solanaceae).

Patterns of diversification in Neotropical plants have been studied intensively over the past decades. Most studies have focused on groups that migrated to and radiated into the Neotropics, however, with little focus on understanding diversification patterns in indigenous Neotropical groups. This study focuses on Solanum section Brevantherum Seithe (Solanaceae), a group of Neotropical nightshade shrubs or treelets defined mostly by terminal inflorescences with long peduncles, plurifoliate sympodial units and porrect-stellate, dendritic-echinoid, or lepidote trichomes. We generated sequences from two nuclear (ITS, waxy) and one plastid marker (trnT-F) to infer phylogenetic relationships under Bayesian and Maximum likelihood approaches. We reconstructed a time-calibrated tree to estimate both the ages of main splits and the ancestral ranges of the lineages. Finally, we carried out a biogeographic stochastic mapping (BSM) analysis to determine the main processes driving current distributions of the group. Results show the non-monophyly of the section as previously recognized and the homoplasy of morphological characters traditionally used to circumscribe it. Two main clades that encompass most species formerly recognized in section Brevantherum are recovered and named as the Erianthum and Abutiloides clades. Divergence time estimates suggest that the Erianthum and Abutiloides clades split around 5.7 Mya in the upper Miocene. Two main dispersal events from the Atlantic rainforest are supported in the Erianthum clade: one dispersal to Mesoamerica and a second dispersal to the Northern Andes. Within the Abutiloides clade, cladogenetic events were restricted to the Andean region. Our BSM analysis suggests within-area speciation and range expansion as the main processes shaping the extant distribution of species of both clades. As no putative morphological synapomorphies can yet be assigned to what could correspond to a new circumscription of Solanum section Brevantherum (with the exclusion of Solanum bullatum Vell. and inclusion of S. inelegans Rusby and four species described since the group last revision) we discourage the continued use of what would be an ambiguous sectional nomenclature.

An amazing new Capsicum (Solanaceae) species from the Andean-Amazonian Piedmont.

Capsicum regale Barboza & Bohs, sp. nov., a new species from the tropical wet forests of the eastern Andean slopes (Colombia, Ecuador, and Peru) is described and illustrated. This new species belongs to the Andean clade (all species 2n = 26) of Capsicum and is similar to C. longifolium Barboza & S.Leiva in its glabrescence, calyx morphology, and corolla and seed color but differs in its membranous and elliptic leaves, fleshy calyces, deeper stellate corollas, longer filaments, longer and purple fruiting pedicels, purple berries, and larger seeds. Its chromosome number was counted (2n = 26), a preliminary assessment of conservation status is given and discussed, and an updated identification key to the species of the Andean clade is provided.

A revision of the Morelloid Clade of Solanum L. (Solanaceae) in North and Central America and the Caribbean.

The Morelloid Clade, also known as the black nightshades or "Maurella" (Morella), is one of the 10 major clades within the mega-diverse genus Solanum L. The clade is most species rich in the central to southern Andes, but species occur around the tropics and subtropics, some extending well into the temperate zone. Plants of the group are herbaceous or short-lived perennials, with small white or purplish white flowers, and small juicy berries. Due to the complex morphological variation and weedy nature of these plants, coupled with the large number of published synonyms (especially for European taxa), our understanding of species limits and diversity in the Morelloid Clade has lagged behind that of other major groups in Solanum. Here we provide the second in a three-part series of revisions of the morelloid solanums treating the species occurring in North and Central America and the Caribbean (for the Old World see "PhytoKeys 106", the third part will treat species of South America). Synonymy, morphological descriptions, distribution maps, and common names and uses are provided for all 18 species occurring in this region. We treat 10 of these species as native, and eight as putatively naturalised, introduced and/or invasive in the region. We provide complete descriptions with nomenclatural details, including lecto- and neotypifications, for all species. Keys to all species occurring in the whole region and for each area within it (i.e., North America, Central America and Mexico, and the islands of the Caribbean), illustrations to aid identification both in herbaria and in the field, and distribution maps are provided. Preliminary conservation assessments are provided for all species. Details of all specimens examined are provided in three Supplementary materials sections.

Comparative transcriptomics and genomic patterns of discordance in Capsiceae (Solanaceae).

The integration of genomics and phylogenetics allows new insight into the structure of gene tree discordance, the relationships among gene position, gene history, and rate of evolution, as well as the correspondence of gene function, positive selection, and gene ontology enrichment across lineages. We explore these issues using the tribe Capsiceae (Solanaceae), which is comprised of the genera Lycianthes and Capsicum (peppers). In combining the annotated genomes of Capsicum with newly sequenced transcriptomes of four species of Lycianthes and Capsicum, we develop phylogenies for 6747 genes, and construct a backbone species tree using both concordance and explicit phylogenetic network approaches. We quantify phylogenetic discordance among individual gene trees, measure their rates of synonymous and nonsynonymous substitution, and test whether they were positively selected along any branch of the phylogeny. We then map these genes onto the annotated Capsicum genome and test whether rates of evolution, gene history, and gene ontology vary significantly with gene position. We observed substantial discordance among gene trees. A bifurcating species tree placing Capsicum within a paraphyletic Lycianthes was supported over all phylogenetic networks. Rates of synonymous and nonsynonymous substitution varied 41-fold and 130-fold among genes, respectively, and were significantly lower in pericentromeric regions. We found that results of concordance tree analyses vary depending on the subset of genes used, and that genes within the pericentromeric regions only capture a portion of the observed discordance. We identified 787 genes that have been positively selected throughout the diversification history of Capsiceae, and discuss the importance of these genes as targets for investigation of economically important traits in the domesticated peppers.

A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree.

BACKGROUND: The Solanaceae is a plant family of great economic importance. Despite a wealth of phylogenetic work on individual clades and a deep knowledge of particular cultivated species such as tomato and potato, a robust evolutionary framework with a dated molecular phylogeny for the family is still lacking. Here we investigate molecular divergence times for Solanaceae using a densely-sampled species-level phylogeny. We also review the fossil record of the family to derive robust calibration points, and estimate a chronogram using an uncorrelated relaxed molecular clock. RESULTS: Our densely-sampled phylogeny shows strong support for all previously identified clades of Solanaceae and strongly supported relationships between the major clades, particularly within Solanum. The Tomato clade is shown to be sister to section Petota, and the Regmandra clade is the first branching member of the Potato clade. The minimum age estimates for major splits within the family provided here correspond well with results from previous studies, indicating splits between tomato and potato around 8 Million years ago (Ma) with a 95% highest posterior density (HPD) 7-10 Ma, Solanum and Capsicum c. 19 Ma (95% HPD 17-21), and Solanum and Nicotiana c. 24 Ma (95% HPD 23-26). CONCLUSIONS: Our large time-calibrated phylogeny provides a significant step towards completing a fully sampled species-level phylogeny for Solanaceae, and provides age estimates for the whole family. The chronogram now includes 40% of known species and all but two monotypic genera, and is one of the best sampled angiosperm family phylogenies both in terms of taxon sampling and resolution published thus far. The increased resolution in the chronogram combined with the large increase in species sampling will provide much needed data for the examination of many biological questions using Solanaceae as a model system.

A new species of Solanum named for Jeanne Baret, an overlooked contributor to the history of botany.

We describe Solanum baretiaesp. nov., a new species of Solanum section Anarrhichomenum, named in honor of Jeanne Baret, who sailed as the assistant to botanist Philibert Commerson on Louis Antoine de Bougainville's global circumnavigation (1766-1769). The species is similar to Solanum chimborazense, but differs in having larger flowers, more flowers per inflorescence, and different patterns of pubescence on the filaments (pubescent adaxially and glabrous abaxially) and style (papillose to sparsely pubescent). A description, illustration, photos, and comparisons to similar species are included. Also included is a preliminary conservation assessment, along with a brief account of the important role played by Baret during the expedition. The new species appears to be restricted to the Amotape-Huancabamba zone, an area of southern Ecuador and northern Peru known for its exceptional biodiversity.

An explosive innovation: Phylogenetic relationships of Solanum section Gonatotrichum (Solanaceae).

Solanum is one of the largest plant genera and exhibits a wide range of morphological diversity. Solanum section Gonatotrichum, the focus of this study, is unique within the genus because of its fruits that swell with turgor pressure and explosively dehisce to disperse the seeds. We infer phylogenetic relationships within section Gonatotrichum using DNA sequence data from two nuclear regions (ITS and the granule-bound starch synthase gene [GBSSI or waxy]) and the chloroplast region trnT-F. The resulting phylogenetic trees support the monophyly of the section with the inclusion of Solanum lignescens, a species not previously thought to belong to the group due to the presence of stellate hairs. This inclusion of this species in section Gonatotrichum suggests that the simple, often geniculate hairs of species in the group may represent reduced stellate hairs. The presence of heterantherous flowers appears to be derived in the section, but this character is largely lost in Solanum parcistrigosum.

Keeping it simple: flowering plants tend to retain, and revert to, simple leaves.

• A wide range of factors (developmental, physiological, ecological) with unpredictable interactions control variation in leaf form. Here, we examined the distribution of leaf morphologies (simple and complex forms) across angiosperms in a phylogenetic context to detect patterns in the directions of changes in leaf shape. • Seven datasets (diverse angiosperms and six nested clades, Sapindales, Apiales, Papaveraceae, Fabaceae, Lepidium, Solanum) were analysed using maximum likelihood and parsimony methods to estimate asymmetries in rates of change among character states. • Simple leaves are most frequent among angiosperm lineages today, were inferred to be ancestral in angiosperms and tended to be retained in evolution (stasis). Complex leaves slowly originated ('gains') and quickly reverted to simple leaves ('losses') multiple times, with a significantly greater rate of losses than gains. Lobed leaves may be a labile intermediate step between different forms. The nested clades showed mixed trends; Solanum, like the angiosperms in general, had higher rates of losses than gains, but the other clades had higher rates of gains than losses. • The angiosperm-wide pattern could be taken as a null model to test leaf evolution patterns in particular clades, in which patterns of variation suggest clade-specific processes that have yet to be investigated fully.

Multiple recent horizontal transfers of the cox1 intron in Solanaceae and extended co-conversion of flanking exons.

BACKGROUND: The most frequent case of horizontal transfer in plants involves a group I intron in the mitochondrial gene cox1, which has been acquired via some 80 separate plant-to-plant transfer events among 833 diverse angiosperms examined. This homing intron encodes an endonuclease thought to promote the intron's promiscuous behavior. A promising experimental approach to study endonuclease activity and intron transmission involves somatic cell hybridization, which in plants leads to mitochondrial fusion and genome recombination. However, the cox1 intron has not yet been found in the ideal group for plant somatic genetics - the Solanaceae. We therefore undertook an extensive survey of this family to find members with the intron and to learn more about the evolutionary history of this exceptionally mobile genetic element. RESULTS: Although 409 of the 426 species of Solanaceae examined lack the cox1 intron, it is uniformly present in three phylogenetically disjunct clades. Despite strong overall incongruence of cox1 intron phylogeny with angiosperm phylogeny, two of these clades possess nearly identical intron sequences and are monophyletic in intron phylogeny. These two clades, and possibly the third also, contain a co-conversion tract (CCT) downstream of the intron that is extended relative to all previously recognized CCTs in angiosperm cox1. Re-examination of all published cox1 genes uncovered additional cases of extended co-conversion and identified a rare case of putative intron loss, accompanied by full retention of the CCT. CONCLUSIONS: We infer that the cox1 intron was separately and recently acquired by at least three different lineages of Solanaceae. The striking identity of the intron and CCT from two of these lineages suggests that one of these three intron captures may have occurred by a within-family transfer event. This is consistent with previous evidence that horizontal transfer in plants is biased towards phylogenetically local events. The discovery of extended co-conversion suggests that other cox1 conversions may be longer than realized but obscured by the exceptional conservation of plant mitochondrial sequences. Our findings provide further support for the rampant-transfer model of cox1 intron evolution and recommend the Solanaceae as a model system for the experimental analysis of cox1 intron transfer in plants.

A 10-gene phylogeny of Solanum section Herpystichum (Solanaceae) and a comparison of phylogenetic methods.

PREMISE OF THE STUDY: Solanum section Herpystichum is a lineage that comprises both widespread and very narrowly distributed species. This study investigates the phylogenetic relationships of sect. Herpystichum and evaluates several phylogenetic methods for analysis of multiple sequences. METHODS: Sequence data from seven nuclear (ITS, GBSSI, and five COSII) and three plastid (psbA-trnH, trnT-trnF, and trnS-trnG) regions were concatenated and analyzed under maximum parsimony and Bayesian criteria. In addition, we used two analytical methods that take into account differences in topologies resulting from the analyses of the individual markers: Bayesian Estimation of Species Trees (BEST) and supertree analysis. KEY RESULTS: The monophyletic Solanum sect. Herpystichum was resolved with moderate support in the concatenated maximum parsimony and Bayesian analyses and the supertree analysis, and relationships within the section were well-resolved and strongly supported. The BEST topology, however, was poorly resolved. Also, because of how BEST deals with missing sequences, >25% of our accessions, including two species, had to be excluded from the analyses. Our results indicate a progenitor-descendent relationship with two species nested within the widespread S. evolvulifolium. CONCLUSIONS: Analytical methods that consider individual topologies are important for studies based on multiple molecular markers. On the basis of analyses in this study, BEST had the serious shortcoming that taxa with missing sequences must be removed from the analysis or they can produce spurious topologies. Supertree analysis provided a good alternative for our data by allowing the inclusion of all 10 species of sect. Herpystichum.

Molecular delimitation of clades within New World species of the "spiny solanums" (Solanum subg. Leptostemonum).

Solanum subg. Leptostemonum contains approximately 350-450 species, including the cultivated eggplant, S. melongena. Most species placed in this subgenus form a monophyletic group, the Leptostemonum clade, characterized by the presence of stellate hairs and prickles, leading to the common name of "spiny solanums". Here we present a phylogenetic analysis that circumscribes the major clades within the spiny solanums and examines the relationships among them, with an emphasis on New World species. Of particular interest is the clarification of the clade limits and species composition of groups that have not been well-sampled. We also increase sampling of taxa that have been previously analyzed in molecular studies, namely those in the Torva, Micracantha, and Erythrotrichum clades. These groups have convergent morphological characteristics that have challenged taxonomists, making classification difficult. Results from our study delimit 14 clades within the spiny solanums, including the newly designated Asterophorum, Gardneri, Sisymbriifolium, and Thomasiifolium clades. We also establish the placement of species not previously sampled, especially those endemic to Brazil. These results give an increased understanding of the evolution of the Leptostemonum clade by defining monophyletic groups within it and identify areas of the phylogenetic tree that remain unresolved and require further taxon sampling.

Two new species of Solanum (Solanaceae) from the Amotape-Huancabamba Zone of southern Ecuador and northern Peru.

Two new species of Solanum subgenus Leptostemonum from southern Ecuador and northern Peru are described here. Solanum rubicaule S. Stern, sp. nov., is a member of sect. Torva and is characterized by a festooning, scandent growth form and fruits held horizontally on recurved pedicels. Solanum achorum S. Stern, sp. nov., is a member of sect. Erythrotrichum and is characterized by 4-12-flowered inflorescences, small seeds, and a small calyx. Both species are distributed in the Amotape-Huancabamba Zone of the Andes in northern Peru and southern Ecuador.

Two new South American species of Solanum section Crinitum (Solanaceae).

Two new species of Solanum section Crinitum are described here. Solanum falciforme Farruggia, sp. nov., closely resembles Solanum crinitum and Solanum lycocarpum, but differs by the presence of falcate trichomes on the young growth. It is endemic to the cerrado and adjacent woodlands of Distrito Federal, Bahia, Goiás and Minas Gerais, Brazil. The other species, Solanum pseudosycophanta Farruggia, sp.nov., has close affinities to Solanum sycophanta butdiffers from the latter in having prominent long-stalked stellate hairs along the stem, calyx, petiole and the adaxial surface of the leaf, in contrast to Solanum sycophanta which is glabrous or pubescent with sessile to short-stalked multangulate hairs. This species is narrowly distributed in tropical montane forests of northern Peru and southern Ecuador.

A 15-Myr-old genetic bottleneck.

Balancing selection preserves variation at the self-incompatibility locus (S-locus) of flowering plants for tens of millions of years, making it possible to detect demographic events that occurred prior to the origin of extant species. In contrast to other Solanaceae examined, SI species in the sister genera Physalis and Witheringia share restricted variation at the S-locus. This restriction is indicative of an ancient bottleneck that occurred in a common ancestor. We sequenced 14 S-alleles from the subtribe Iochrominae, a group that is sister to the clade containing Physalis and Witheringia. At least 6 ancient S-allele lineages are represented among these alleles, demonstrating that the Iochrominae taxa do not share the restriction in S-locus diversity. Therefore, the bottleneck occurred after the divergence of the Iochrominae from the lineage leading to the most recent common ancestor of Physalis and Witheringia. Using cpDNA sequences, 3 fossil dates, and a Bayesian-relaxed molecular clock approach, the crown group of Solanaceae was estimated to be 51 Myr old and the restriction of variation at the S-locus occurred 14.0-18.4 Myr before present. These results confirm the great age of polymorphism at the S-locus and the utility of loci under balancing selection for deep historical inference.

Ancient polymorphism reveals unidirectional breeding system shifts.

Loss of complex characters is thought to be irreversible (Dollo's law). However, hypotheses of irreversible evolution are remarkably difficult to test, especially when character transitions are frequent. In such cases, inference of ancestral states, in the absence of fossil evidence, is uncertain and represents the single greatest constraint for reconstructing the evolutionary history of characters. Breeding system character transitions are of particular interest because they affect the amount and distribution of genetic variation within species. Transitions from obligate outcrossing to partial or predominant self-fertilization are thought to represent one of the most common trends in flowering plants. We use the unique molecular genetic properties (manifested as deep persistent polymorphisms) of the locus that enforces outcrossing to demonstrate that its loss is irreversible in the plant family Solanaceae. We argue that current phylogenetic methods of reconstruction are potentially inadequate in cases where ancestral state information is inferred by using only the phylogeny and the distribution of character states in extant taxa. This study shows in a statistical framework that a particular character transition is irreversible, consistent with Dollo's law.

A four-gene study of evolutionary relationships in Solanum section Acanthophora.

The "spiny solanums," Solanum subgenus Leptostemonum (Solanaceae), comprise a large lineage with over 350 species and include the cultivated eggplant, Solanum melongena. Despite the importance of this subgenus, phylogenetic relationships among these taxa are currently unclear. The present research contributes to this understanding while focusing on Solanum section Acanthophora, a group of ca. 19 species defined by the presence of simple hairs, rather than the stellate hairs common across the rest of subgenus Leptostemonum. In this study we inferred phylogenetic relationships among 29 Solanum taxa, including 14 species of section Acanthophora, using DNA sequence data from two nuclear regions (ITS and the granule-bound starch synthase gene [GBSSI or waxy]) and two chloroplast regions (trnT-trnF and trnS-trnG). This combination of gene regions resulted in a well resolved phylogenetic hypothesis, with results strongly suggesting that Solanum sect. Acanthophora is not monophyletic, although the majority of taxa comprise a monophyletic lineage that is sister to Solanum section Lasiocarpa. Of the four gene regions, waxy was especially useful for phylogenetic inference, with both a high percentage of parsimony-informative sites as well as a low level of homoplasy. Further studies in progress will help elucidate relationships of sect. Acanthophora with respect to other members of subgenus Leptostemonum.

Solanaceae--a model for linking genomics with biodiversity.

Recent progress in understanding the phylogeny of the economically important plant family Solanaceae makes this an ideal time to develop models for linking the new data on plant genomics with the huge diversity of naturally occurring species in the family. Phylogenetics provides the framework with which to investigate these linkages but, critically, good species-level descriptive resources for the Solanaceae community are currently missing. Phylogeny in the family as a whole is briefly reviewed, and the new NSF Planetary Biodiversity Inventories project 'PBI: Solanum-a worldwide treatment' is described. The aims of this project are to provide species-level information across the global scope of the genus Solanum and to make this available over the Internet. The project is in its infancy, but will make available nomenclatural information, descriptions, keys and illustrative material for all of the approximately 1500 species of Solanum. With this project, the opportunity of linking valid, up-to-date taxonomic information about wild species of Solanum with the genomic information being generated about the economically important species of the genus (potato, tomato and eggplant) can be realized. The phylogenetic framework in which the PBI project is set is also of enormous potential benefit to other workers on Solanum. The community of biologists working with Solanaceae has a unique opportunity to effectively link genomics and taxonomy for better understanding of this important family, taking plant biology to a new level for the next century.

An ITS phylogeny of Balsamorhiza and Wyethia (Asteraceae: Heliantheae).

The relationships among the species of Balsamorhiza and Wyethia (Asteraceae: Heliantheae) were examined using data from the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA. The ITS sequences were obtained from nine species of Balsamorhiza and 14 species of Wyethia as well as seven outgroup genera. Five of the outgroup genera were members of the subtribe Engelmanniinae of the tribe Heliantheae, the subtribe that includes Balsamorhiza and Wyethia. The resulting trees show that Balsamorhiza and Wyethia together form a monophyletic group. Balsamorhiza alone is monophyletic, but neither of its two sections is monophyletic. Wyethia is paraphyletic. One group of Wyethia species, including all members of sections Alarconia and Wyethia as well as W. bolanderi from section Agnorhiza, is monophyletic and sister to Balsamorhiza. The other species of Wyethia (all placed in section Agnorhiza) are part of a polytomy along with the clade composed of Balsamorhiza plus the rest of Wyethia.