Phylogenomic loci define the generic boundaries of Gochnatieae and improve resolution at the species level in Moquiniastrum (Compositae).

Understanding the evolution of the tribe Gochnatieae (Compositae) has been the subject of considerable effort in the past decade. This is due to the key position of this tribe in the phylogeny of the sunflower family and the corresponding implications for biogeographic and morphological evolution of Compositae. Previous studies have confirmed the monophyly of this tribe as well as most of the genera that belong to it. However, phylogenetic resolution of Gochnatieae at both the genus- and species-level has remained poor. A subset of new phylogenomic loci used in this study has proven effective and has improved phylogenetic resolution in this group. The results of this work demonstrate Gochnatieae is a well-supported clade comprised of nine genera (Anastraphia, Cnicothamnus, Cyclolepis, Gochnatia, Moquiniastrum, Nahuatlea, Pentaphorus, Richterago, Tehuasca). One recently described genus, Vickia, was not included in this study; but its placement in Gochnatieae as a tenth genus in the tribe is well-justified. The monospecific Cyclolepis, which had been circumscribed within the tribe since its inception but was subsequently removed and designated as incertae sedis since 2014, is also shown to belong to Gochnatieae. We confirmed the monophyletic Moquiniastrum with two well-supported subclades. Ancestral area reconstruction analyses show that Gochnatieae originated in Eastern South America about 53 my. Apparently, except for Cyclolepis and Richterago, the ancestors of the other genera of Gochnatieae originated about 44 my from an area that now corresponds to the central Andes. The presence of the genera in the Chaco phytogeographic province, central Chile, and Mexico-United States-Caribbean is a result of dispersal from the central Andes. The ancestral distribution of Moquiniastrum corresponds to a large area comprising Eastern South America and the current central Andes, about 32 my. Ancestral character state reconstruction that included four characters indicates several states associated with complex plant reproductive biology such as gynodioecy, gynomonoecy, and polygamodioecy are derived in Gochnatieae as are heterogamous capitula (in Moquiniastrum and Richterago), dimorphic and subdimorphic corollas (in Cnicothamnus, Moquiniastrum, and Richterago), and the presence of marginal female corollas (in Moquiniastrum and Richterago). Within Moquiniastrum, two subclades (Densicephalum and Polymorphum) exhibit divergent patterns of trait evolution associated with these reproductive characters which suggests this genus can serve as a model to understand the sexual system evolution in plants.

Author Correction: Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding.

DNA barcoding is a valuable tool to support species identification with broad applications from traditional taxonomy, ecology, forensics, food analysis, and environmental science. We introduce Microfluidic Enrichment Barcoding (MEBarcoding) for plant DNA Barcoding, a cost-effective method for high-throughput DNA barcoding. MEBarcoding uses the Fluidigm Access Array to simultaneously amplify targeted regions for 48 DNA samples and hundreds of PCR primer pairs (producing up to 23,040 PCR products) during a single thermal cycling protocol. As a proof of concept, we developed a microfluidic PCR workflow using the Fluidigm Access Array and Illumina MiSeq. We tested 96 samples for each of the four primary DNA barcode loci in plants: rbcL, matK, trnH-psbA, and ITS. This workflow was used to build a reference library for 78 families and 96 genera from all major plant lineages - many currently lacking in public databases. Our results show that this technique is an efficient alternative to traditional PCR and Sanger sequencing to generate large amounts of plant DNA barcodes and build more comprehensive barcode databases.

Two new species of the Andean genus Xenophyllum (Senecioneae, Compositae).

Two new species of Xenophyllum are described from the Andes, X. funkianum sp. nov. from Ecuador and X. lorochaqui sp. nov. from northwestern Argentina. Both species are compared with the morphologically closest taxa and useful characters for their proper identification are provided. Detailed illustrations and distribution maps are also presented, as well as pictures of living plants when available.

Two new species for Gochnatia Kunth (Asteraceae, Gochnatieae) and an extension of the tribal range into Ecuador.

Two new species are added to the narrowly delimited genus Gochnatia. Of these, G. lojaensis sp. nov. represents a northern extension of the genus and tribe into Ecuador and G. recticulifolia sp. nov. occurs in northern Peru. In addition to descriptions for the two new species, a key is provided for all known species in the genus Gochnatia and a pubescence character is noted that clearly separates Gochnatia from Moquiniastrum.

Phylogenomics Yields New Insight Into Relationships Within Vernonieae (Asteraceae).

Asteraceae, or the sunflower family, is the largest family of flowering plants and is usually considered difficult to work with, not only due to its size, but also because of the abundant cases of polyploidy and ancient whole-genome duplications. Traditional molecular systematics studies were often impaired by the low levels of variation found in chloroplast markers and the high paralogy of traditional nuclear markers like ITS. Next-generation sequencing and novel phylogenomics methods, such as target capture and Hyb-Seq, have provided new ways of studying the phylogeny of the family with great success. While the resolution of the backbone of the family is in progress with some results already published, smaller studies focusing on internal clades of the phylogeny are important to increase sampling and allow morphological, biogeography, and diversification analyses, as well as serving as basis to test the current infrafamilial classification. Vernonieae is one of the largest tribes in the family, accounting for approximately 1,500 species. From the 1970s to the 1990s, the tribe went through several reappraisals, mainly due to the splitting of the mega genus Vernonia into several smaller segregates. Only three phylogenetic studies focusing on the Vernonieae have been published to date, both using a few molecular markers, overall presenting low resolution and support in deepest nodes, and presenting conflicting topologies when compared. In this study, we present the first attempt at studying the phylogeny of Vernonieae using phylogenomics. Even though our sampling includes only around 4% of the diversity of the tribe, we achieved complete resolution of the phylogeny with high support recovering approximately 700 nuclear markers obtained through target capture. We also analyzed the effect of missing data using two different matrices with different number of markers and the difference between concatenated and gene tree analysis.

An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae.

PREMISE: Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. METHODS: Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. RESULTS: Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. DISCUSSION: The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.

New combinations and synonyms in discoid caespitose Andean Senecio (Senecioneae, Compositae).

The names Werneria melanandra and W. pygmophylla are transferred to the genus Senecio. They belong to the group of the discoid caespitose Andean Senecio, specifically to the subgroup with blackish anthers and style branches and whitish corollas. The recognition of S. digitatus as a distinct species is also discussed. Within the framework of the mentioned group, the names S. casapaltensis and S. macrorrhizus are lectotypified, S. humillimus var. melanolepis is neotypified, an epitype is designated for the name W. melanandra, and nine new synonyms are proposed. An updated comprehensive dichotomous key including all discoid caespitose Senecio species from Bolivia and Peru is provided.

A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae.

The sunflower family, Asteraceae, comprises 10% of all flowering plant species and displays an incredible diversity of form. Asteraceae are clearly monophyletic, yet resolving phylogenetic relationships within the family has proven difficult, hindering our ability to understand its origin and diversification. Recent molecular clock dating has suggested a Cretaceous origin, but the lack of deep sampling of many genes and representative taxa from across the family has impeded the resolution of migration routes and diversifications that led to its global distribution and tremendous diversity. Here we use genomic data from 256 terminals to estimate evolutionary relationships, timing of diversification(s), and biogeographic patterns. Our study places the origin of Asteraceae at ∼83 MYA in the late Cretaceous and reveals that the family underwent a series of explosive radiations during the Eocene which were accompanied by accelerations in diversification rates. The lineages that gave rise to nearly 95% of extant species originated and began diversifying during the middle Eocene, coincident with the ensuing marked cooling during this period. Phylogenetic and biogeographic analyses support a South American origin of the family with subsequent dispersals into North America and then to Asia and Africa, later followed by multiple worldwide dispersals in many directions. The rapid mid-Eocene diversification is aligned with the biogeographic range shift to Africa where many of the modern-day tribes appear to have originated. Our robust phylogeny provides a framework for future studies aimed at understanding the role of the macroevolutionary patterns and processes that generated the enormous species diversity of Asteraceae.

VernoniasubgenusAustrovernonia, a new subgenus from South America (Compositae, Vernonieae, Vernoniinae).

Vernoniaincana Less. and V.echioides Less. are two semi-aquatic species from southern South American that are referred to as "the semi-aquatic Vernonia of South America" and they have been, until now, retained as members of Vernonia mostly because each had some unusual characters that made them hard to place. Based on an ongoing molecular study, we can now say that V.incana is the sister taxon to all true Vernonia and can therefore be responsibly left in Vernonia but, because of its morphological and geographic differences, it is now assigned to its own subgenus: Vernonia subg. Austrovernonia. Vernoniaechioides is not closely related to V.incana and is now part of a separate investigation. This placement of V.incana as sister to the true Vernonia species brings up the possibility of a South American root for the Vernonia clade and perhaps indicates a propensity in the lineage for growing in or near water. The species V.incana is lectotypified.

Home at Last II: Gerbera hieracioides (Kunth) Zardini (Mutisieae, Asteraceae) is really a Chaptalia.

Gerbera hieracioides (Kunth) Zardini of the Gerbera-complex (Mutisieae, Asteraceae/Compositae) is distributed in Ecuador and Peru. This perennial herb was first named as Onoseris hieracioides Kunth and was later recognised as Trichocline hieracioides (Kunth) Ferreyra. Now it is generally treated as Gerbera hieracioides (Kunth) Zardini but it has never been included in any section of Gerbera. In this study, the position of Gerbera hieracioides is assessed based on morphology and a molecular phylogeny that includes G. hieracioides and 28 other species from the Gerbera-complex. Morphologically, G. hieracioides bears leaves with the adaxial epidermal surface without stomates but with soft thin trichomes, bracteate scapes, trimorphic capitula and inner ray florets with the corolla shorter than the style. These characters suggest that the species is most closely related to Chaptalia rather than to Gerbera or Trichocline. Furthermore, the phylogenetic results based on two nuclear (ITS and ETS) and two chloroplast (trnL-trnF and trnL-rpl32) sequences strongly support the placement of G. hieracioides nested within Chaptalia. As both morphological characters and the molecular phylogenetic results support the transfer of G. hieracioides to Chaptalia, this enigmatic taxon is recognised as Chaptalia hieracioides (Kunth) X.-D. Xu & W. Zheng.

Home at last III: Transferring Uechtritzia and Asian Gerbera species into Oreoseris (Compositae, Mutisieae).

Recently the Asian Gerbera species were shown to form a clade that was not the sister group of the African Gerbera. In this study, the position of the Asian Gerbera species was further assessed based on morphology and molecular phylogenetic analyses that included six Asian Gerbera and 26 other species from the Gerbera-complex. Morphological results showed that the six Asian Gerbera species, which were sampled, bear leaves with the adaxial epidermal surface lacking stomates, possess bracteate scapes and lack inner ray florets. These characters suggest that the Asian Gerbera species are most closely related to the species of Uechtritzia, which also share similar pollen grain size and shape with the Asian Gerbera, rather than to the African Gerbera. Furthermore, the phylogenetic results based on two nuclear (ITS and ETS) and three chloroplast (trnL-trnF, trnL-rpl32 and trnC-petN) sequences strongly support the Asian Gerbera and Uechtritzia forming a clade, with the latter nested within the Asian Gerbera species. Both morphological and molecular phylogenetic data thus confirmed the taxonomic identity of the Asian Gerbera and Uechtritzia. The authors herein formally treat the nine species of the Asian Gerbera and the three species of Uechtritzia as members of the genus Oreoseris, which is the earliest generic name of this lineage and has the nomenclatural priority.

Applications of deep convolutional neural networks to digitized natural history collections.

Natural history collections contain data that are critical for many scientific endeavors. Recent efforts in mass digitization are generating large datasets from these collections that can provide unprecedented insight. Here, we present examples of how deep convolutional neural networks can be applied in analyses of imaged herbarium specimens. We first demonstrate that a convolutional neural network can detect mercury-stained specimens across a collection with 90% accuracy. We then show that such a network can correctly distinguish two morphologically similar plant families 96% of the time. Discarding the most challenging specimen images increases accuracy to 94% and 99%, respectively. These results highlight the importance of mass digitization and deep learning approaches and reveal how they can together deliver powerful new investigative tools.

Data Release: DNA barcodes of plant species collected for the Global Genome Initiative for Gardens Program, National Museum of Natural History, Smithsonian Institution.

The Global Genome Initiative has sequenced and released 1961 DNA barcodes for genetic samples obtained as part of the Global Genome Initiative for Gardens Program. The dataset includes barcodes for 29 plant families and 309 genera that did not have sequences flagged as barcodes in GenBank and sequences from officially recognized barcoding genetic markers meet the data standard of the Consortium for the Barcode of Life. The genetic samples were deposited in the Smithsonian Institution's National Museum of Natural History Biorepository and their records were made public through the Global Genome Biodiversity Network's portal. The DNA barcodes are now available on GenBank.

Amazon plant diversity revealed by a taxonomically verified species list.

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.

Nine species from Madagascar are moved from Vernonia to Distephanus (Compositae, Vernonieae).

The genus Distephanus is native to Madagascar, the Mauritius, central and southern Africa, Yemen (Socotra Island), and China. The majority of the diversity is found in Madagascar. Here we provide new combinations for nine species of Vernonia that belong in Distephanus, all from Madagascar. All of the species were formerly placed in the large genus Vernonia, now greatly reduced.

An analysis of Echinacea chloroplast genomes: Implications for future botanical identification.

Echinacea is a common botanical used in dietary supplements, primarily to treat upper respiratory tract infections and to support immune function. There are currently thought to be nine species in the genus Echinacea. Due to very low molecular divergence among sister species, traditional DNA barcoding has not been successful for differentiation of Echinacea species. Here, we present the use of full chloroplast genomes to distinguish between all 9 reported species. Total DNA was extracted from specimens stored at the National Museum of Natural History, Smithsonian Institution, which had been collected from the wild with species identification documented by experts in the field. We used Next Generation Sequencing (NGS) and CLC Genomics Workbench to assemble complete chloroplast genomes for all nine species. Full chloroplasts unambiguously differentiated all nine species, compared with the very few single nucleotide polymorphisms (SNPs) available with core DNA barcoding markers. SNPs for any two Echinacea chloroplast genomes ranged from 181 to 910, and provided robust data for unambiguous species delimitation. Implications for DNA-based species identification assays derived from chloroplast genome sequences are discussed in light of product safety, adulteration and quality issues.