A phylogeny of the evening primrose family (Onagraceae) using a target enrichment approach with 303 nuclear loci.

BACKGROUND: The evening primrose family (Onagraceae) includes 664 species (803 taxa) with a center of diversity in the Americas, especially western North America. Ongoing research in Onagraceae includes exploring striking variation in floral morphology, scent composition, and breeding system, as well as the role of these traits in driving diversity among plants and their interacting pollinators and herbivores. However, these efforts are limited by the lack of a comprehensive, well-resolved phylogeny. Previous phylogenetic studies based on a few loci strongly support the monophyly of the family and the sister relationship of the two largest tribes but fail to resolve several key relationships. RESULTS: We used a target enrichment approach to reconstruct the phylogeny of Onagraceae using 303 highly conserved, low-copy nuclear loci. We present a phylogeny for Onagraceae with 169 individuals representing 152 taxa sampled across the family, including extensive sampling within the largest tribe, Onagreae. Deep splits within the family are strongly supported, whereas relationships among closely related genera and species are characterized by extensive conflict among individual gene trees. CONCLUSIONS: This phylogenetic resource will augment current research projects focused throughout the family in genomics, ecology, coevolutionary dynamics, biogeography, and the evolution of characters driving diversification in the family.

New insights into polyploid evolution and dynamic nature of Ludwigia section Isnardia (Onagraceae).

BACKGROUND: While polyploids are common in plants, the evolutionary history and natural dynamics of most polyploid groups are still unclear. Owing to plentiful earlier systematic studies, Ludwigia sect. Isnardia (comprising 22 wetland taxa) is an ideal allopolyploid complex to investigate polyploid evolution and natural dynamics within and among taxa. With a considerable sampling, we concentrated on revisiting earlier phylogenies of Isnardia, reevaluating the earlier estimated age of the most recent common ancestor (TMRCA), exploring the correlation between infraspecific genetic diversity and ploidy levels, and inspecting interspecific gene flows among taxa. RESULTS: Phylogenetic trees and network concurred with earlier phylogenies and hypothesized genomes by incorporating 192 atpB-rbcL and ITS sequences representing 91% of Isnardia taxa. Moreover, we detected three multi-origin taxa. Our findings on L. repens and L. sphaerocarpa were consistent with earlier studies; L. arcuata was reported as a multi-origin taxon here, and an additional evolutionary scenario of L. sphaerocarpa was uncovered, both for the first time. Furthermore, estimated Isnardia TMRCA ages based on our data (5.9 or 8.9 million years ago) are in accordance with earlier estimates, although younger than fossil dates (Middle Miocene). Surprisingly, infraspecific genetic variations of Isnardia taxa did not increase with ploidy levels as anticipated from many other polyploid groups. In addition, the exuberant, low, and asymmetrical gene flows among Isnardia taxa indicated that the reproductive barriers may be weakened owing to allopolyploidization, which has rarely been reported. CONCLUSIONS: The present research gives new perceptions of the reticulate evolution and dynamic nature of Isnardia and points to gaps in current knowledge about allopolyploid evolution.

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set.

PREMISE: To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. METHODS: We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). RESULTS: Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. CONCLUSIONS: High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.

The End of Botany.

Biologists unable to recognize common plants, and a decline in botany students, faculty, courses, university departments, and herbaria, highlight the current erosion of botany. How did we reach this crisis, knowing that plants form the basis for life? What are the causes? What can we do to reverse it?

New Guinea has the world's richest island flora.

New Guinea is the world's largest tropical island and has fascinated naturalists for centuries1,2. Home to some of the best-preserved ecosystems on the planet3 and to intact ecological gradients-from mangroves to tropical alpine grasslands-that are unmatched in the Asia-Pacific region4,5, it is a globally recognized centre of biological and cultural diversity6,7. So far, however, there has been no attempt to critically catalogue the entire vascular plant diversity of New Guinea. Here we present the first, to our knowledge, expert-verified checklist of the vascular plants of mainland New Guinea and surrounding islands. Our publicly available checklist includes 13,634 species (68% endemic), 1,742 genera and 264 families-suggesting that New Guinea is the most floristically diverse island in the world. Expert knowledge is essential for building checklists in the digital era: reliance on online taxonomic resources alone would have inflated species counts by 22%. Species discovery shows no sign of levelling off, and we discuss steps to accelerate botanical research in the 'Last Unknown'8.

Nomenclatural changes in Onagraceae.

A new subspecies and two new combinations are proposed in Onagraceae. Ludwigia glandulosa Walter subsp. brachycarpa C.-I Peng, subsp. nov. is morphologically distinct from the typical subspecies, with smaller capsules and leaves, different seed coat, and a restricted distribution. Epilobium sect. Pachydium (Fischer & C. A. Meyer) Hoch & K. Gandhi, comb. nov. refers to a distinctive group of species formerly known as Boisduvalia Spach and as Epilobium sect. Boisduvalia (Spach) Hoch & P. H. Raven. And Chamaenerion speciosum (Decaisne) Hoch & K. Gandhi, comb. nov. is proposed for a distinctive Himalayan species originally described in Epilobium.

Genome skimming provides new insight into the relationships in Ludwigia section Macrocarpon, a polyploid complex.

PREMISE OF THE STUDY: Interpreting relationships within groups containing polyploids, which are frequent in angiosperms, can be greatly assisted by genomic techniques. In this study, we used a genome-skimming approach to investigate the evolutionary relationships and origins of polyploids in the monophyletic group, Ludwigia section Macrocarpon (Onagraceae), which includes diploid, tetraploid, and hexaploid taxa. METHODS: We sampled all known taxa and ploidy levels in the section and conducted shotgun sequencing. We assembled plastomes, mitochondrial sequences, and completed nuclear ribosomal regions, reconstructed phylogenies, and conducted comparative genomic analyses for plastomes to gain insights into the relationships among studied taxa. KEY RESULTS: Within the section, results showed that the South American diploid taxa L. bonariensis and L. lagunae were closely related. We reported the first chromosome count (2n = 4× = 32) for L. neograndiflora, which is closely related to the two South American diploid taxa, although its exact origin remains unclear. The samples of the widespread, polyploid taxon L. octovalvis do not form a monophyletic group. Both tetraploid and hexaploid L. octovalvis lineages have originated more than once. At least one tetraploid in the L. octovalvis lineage may have been involved in the origins of hexaploids. One or more extinct/unsampled intermediate tetraploids in the L. octovalvis lineages had also likely been involved in the origins of hexaploids. CONCLUSIONS: Genome skimming provided important insights into the complex evolutionary relationships within sect. Macrocarpon, but additional sampling and data from single-copy nuclear regions are necessary to further elucidate the origins of the polyploids in this section.

Complete Plastome Sequence of Ludwigia octovalvis (Onagraceae), a Globally Distributed Wetland Plant.

Here, we present the first plastome of Ludwigia octovalvis (Onagraceae, Myrtales) as well as the first plastome in the subfamily Ludwigioideae. This genome is notable for its contracted inverted repeat regions and an expanded small single-copy region compared to other species in the orders Myrtales and Geraniales.

The correct name in Oenothera for Gauradrummondii (Onagraceae).

In 2007, Wagner and Hoch proposed the new name Oenotheraxenogaura W.L.Wagner & Hoch for the species then known as Gauradrummondii (Spach) Torrey & A. Gray (non Oenotheradrummondii Hooker, 1834). However, the authors overlooked the availability of Gaurahispida Bentham (1840) for this species. Accordingly, we herewith make the appropriate new combination for this species, Oenotherahispida (Bentham) W.L.Wagner, Hoch & Zarucchi, and place Oenotheraxenogaura in synonymy.

The correct name for a section of Ludwigia L. (Onagraceae).

In 1953, Hara provided new combinations for many sectional and species names when he combined Jussiaea L. with Ludwigia L., and at the time, Ludwigiasect.Oligospermum (Micheli) H.Hara was the correct name for one well-defined section. However, subsequent changes to/clarifications of the botanical code have necessitated a change for that name in that now an autonym is treated as having priority over the name or names of the same date and rank that established it. Since Hara's combination was based on Jussiaeasect.Oligospermum Micheli, the correct name for this section is Ludwigiasect.Jussiaea (L.) Hoch, W.L.Wagner, & P.H.Raven.

Taxonomic changes in Oenothera sections Gaura and Calylophus (Onagraceae).

The long-recognized genus Gaura was shown recently to be deeply nested within one of two major clades of Oenothera. New molecular data indicate further taxonomic changes are necessary in Oenothera sect. Gaura. We make these changes here, including three new combinations, in advance of the Onagraceae treatment for the Flora of North America. The new phylogenetic studies show that several pairs of taxa treated as subspecies in the most recent revision by Raven and Gregory (1972) had independent origins within sect. Gaura, and are here elevated to species level (Oenothera nealleyi for Gaura suffulta subsp. nealleyi; Oenothera dodgeniana for Gaura neomexicana subsp. neomexicana; and Oenothera podocarpa for Gaura hexandra subsp. gracilis). Also, a nomenclatural problem in Oenothera sect. Calylophus is corrected by adopting the name Oenothera capillifolia Scheele for the species known previously, and nomenclaturally correct, as Calylophus berlandieri Spach. This problem necessitates a new combination Oenothera capillifolia subsp. berlandieri.

Outcomes of the 2011 Botanical Nomenclature Section at the XVIII International Botanical Congress.

The Nomenclature Section held just before the 18th International Botanical Congress in Melbourne, Australia in July 2011 saw sweeping changes to the way scientists name new plants, algae, and fungi. The changes begin on the cover: the title was broadened to make explicit that the Code applies not only to plants, but also to algae and fungi. The new title will now be the International Code of Nomenclature of algae, fungi, and plants. For the first time in history the Code will allow for the electronic publication of names of new taxa. In an effort to make the publication of new names more accurate and efficient, the requirement for a Latin validating diagnosis or description was changed to allow either English or Latin for these essential components of the publication of a new name. Both of these latter changes will take effect on 1 January 2012. The nomenclatural rules for fungi will see several important changes, the most important of which is probably the adoption of the principle of "one fungus, one name." Paleobotanists will also see changes with the elimination of the concept of "morphotaxa" from the Code.

Family-level relationships of Onagraceae based on chloroplast rbcL and ndhF data.

Despite intensive morphological and molecular studies of Onagraceae, relationships within the family are not fully understood. One drawback of previous analyses is limited sampling within the large tribe Onagreae. In addition, the monophyly of two species-rich genera in Onagreae, Camissonia and Oenothera, has never been adequately tested. To understand relationships within Onagraceae, test the monophyly of these two genera, and ascertain the affinities of the newly discovered genus Megacorax, we conducted parsimony and maximum likelihood analyses with rbcL and ndhF sequence data for 24 taxa representing all 17 Onagraceae genera and two outgroup Lythraceae. Results strongly support a monophyletic Onagraceae, with Ludwigia as the basal lineage and a sister-taxon relationship between Megacorax and Lopezia. Gongylocarpus is supported as sister to Epilobieae plus the rest of Onagreae, although relationships within the latter clade have limited resolution. Thus, we advocate placement of Gongylocarpus in a monogeneric tribe, Gongylocarpeae. Most relationships within Onagreae are weakly resolved, suggesting a rapid diversification of this group in western North America. Neither Camissonia nor Oenothera appears to be monophyletic; however, increased taxon sampling is needed to clarify those relationships. Morphological characters generally agree with the molecular data, providing further support for relationships.

A CLADISTIC ANALYSIS OF CIRCAEA (ONAGRACEAE).

Abstract- Circaea (Onagraceae), a genus of seven species from the northern hemisphere, forms a monophylctic group defined by the following synapomorphies: two stamens (opposite the sepals), fruits indehiscent capsules, hooked hairs on the fruits, and perianth parts reduced to two. A cladistic analysis of the genus was performed using 22 characters from morphology, anatomy and palynology. The seven species and seven additional subspecies were considered the terminal taxa. Polarity of the characters is based on the outgroup comparison method. Eighteen equally parsimonious cladograms were produced, each with 32 steps and a consistency index of 0.75. A successive weighting procedure was applied, resulting in six cladograms with a consistency index of 0.95. All 24 cladograms share the following seven monophylctic groups: (1) all species except C. cordala and C. glabrescens (stipules deciduous); (2) the group of C. mollis, the three subspecies of C. lutetiana and C. erubescens (exsertcd nectary); (3) C. repens and all six subspecies of C. alpina (single-seeded fruits, stolons terminated by tubers, and viscin threads reduced or absent); (4) the six subspecies of C. alpina (unilocular ovaries with no trace of a second loculc and tardily opening perianth); (5) C. alpina subspecies alpina, micrantha, pacifica, and imaicola (flowers opening on ascending to erect pedicels); (6) C. alpina subspecies alpina, micrantha, and pacifica (translucent leaves); (7) C. alpina subspecies alpina and murantha (glabrous stems). Results of the cladistic analysis support most of the current systematic classification of the genus, except for the relationships among the three subspecies of C. lutetiana.

Nectar resource use by Colias butterflies : Chemical and visual aspects.

Nectar foraging preferences of Colias butterflies in two different mountain ecosystems are examined with respect to plant distribution, nectar quantity, carbohydrate (and amino acid) content of nectar, and visual pattern of the plants utilized and avoided. Colias, and apparently numerous other small, ectothermic, low-energy-demand pollinators, "patronize" plants producing relatively dilute nectars containing a high proportion of monosaccharide sugars and significant amounts of polar, nitrogen-rich amino acids. These plants also converge on a common "target" flower pattern in ultraviolet and human-visible light. High-energy demand, endothermic pollinators, by contrast, appear to require higher concentration nectars and/or higher proportions of di- and oligosaccharide sugars. These results are discussed in the light of water balance and energy budget demands of different pollinator classes. Questions are also raised concerning behavioral aspects of pollinator search for resources and the pertinence of these data to the concept of floral mimicry.