The Adesmia clade comprises five genera, with Adesmia being the most diverse and speciose, and formerly containing 206 species and 37 varieties, distributed in two subgenera and 43 series. The genus inhabits almost exclusively the South American Arid Diagonal, which hosts some of the driest environments on Earth. Within Adesmia subgenus Adesmia, three series primarily inhabit the Pampa grasslands: series Muricatae, Bicolores, and Subnudae. These taxonomically complex series display overlapping morphological characters and geographical distribution ranges, and their monophyly has never been tested. We carried out a thorough systematic study of the three series, combining Maximum Likelihood and Bayesian analyses of 87 sequences of nrITS DNA of Adesmia. Beased on our phylogenetic results, we provide a taxonomic revision of the species in series Muricatae, Bicolores, and Subnudae. Series Subnudae and Bicolores are nested within series Muricatae, and synonymization of the first two under series Muricatae is here proposed. Three clades containing species with geographical and morphological coherence were unraveled inside Adesmia. Three varieties are elevated to species level, and another six were reduced to synonyms. Seven lectotypes and one neotype are proposed. We recognize 21 species in the new circumscription of Adesmia series Muricatae, and provide a species identification key, descriptions, illustrations, and maps, as well as comments on phenology, taxonomy, etymology, distribution, and habitat. We also present conservation assessments for the species of the series.

Elucidating how species accumulate in diversity hotspots is an ongoing debate in evolutionary biology. The páramo, in the Northern Andes, has remarkably high indices of plant diversity, endemicity, and diversification rates. A hypothesis for explaining such indices is that allopatric speciation is high in the páramo given its island-like distribution. An alternative hypothesis is that the altitudinal gradient of the Andean topography provides a variety of niches that drive vertical parapatric ecological speciation. A formal test for evaluating the relative roles of allopatric and parapatric ecological speciation is lacking. The main aim of our study is to test which kind of speciation is more common in an endemic páramo genus. We developed a framework incorporating phylogenetics, species’ distributions, and a morpho-ecological trait (leaf area) to compare sister species and infer whether allopatric or parapatric ecological divergence caused their speciation. We applied our framework to the species-rich genus Linochilus (63 spp.) and found that the majority of recent speciation events in it (12 events, 80%) have been driven by allopatric speciation, while a smaller fraction (one event, 6.7%) is attributed to parapatric ecological speciation; two pairs of sister species produced inconclusive results (13.3%). We conclude that páramo autochthonous (in-situ) diversification has been primarily driven by allopatric speciation.

Despite the fast pace of exploration of the patterns and processes influencing Neotropical plant hyperdiversity, the taxa explored are mostly from large groups that are widely distributed, morphologically diverse, or economically important. Vochysiaceae is an example of an undersampled taxon, providing an excellent system for investigating Neotropical biogeography. We present a phylogenomics-based hypothesis of species relationships in Vochysiaceae to investigate its evolutionary history through space and time.We inferred a phylogeny for 122 species from Vochysiaceae and seven other families of Myrtales. Fossils from four myrtalean families were used to estimate the divergence times within Vochysiaceae. Historical biogeography was estimated using ancestral range probabilities and stochastic mapping.Monophyly of all genera was supported except for Qualea, which was split by Ruizterania into two clades. Vochysiaceae originated ~100 mya, splitting into an Afrotropical and a Neotropical lineage ~50 mya, and its ancestral range is in the area currently occupied by the Cerrado.The most recent common ancestor of Vochysiaceae + Myrtaceae had a West Gondwanan distribution, supporting a South American + African ancestral range of Vochysiaceae. On a global scale, geographic range reduction was the principal biogeographic event. At a finer scale, initial range reduction was also important and the Cerrado region was the most ancestral area with multiple colonization events to the Amazon, Central America, and the Atlantic Forest. Colonization events occurred from open areas to forest vegetation, an unusual finding regarding the evolution of plants in the Neotropics.

Seasonal variation in the availability of floral hosts or pollinators is a key factor influencing diversity in plant-pollinator communities. In seasonally dry Neotropical habitats, where month-long periods of extreme drought are followed by a long rainy season, flowering is often synchronized with the beginning of precipitation, when environmental conditions are most beneficial for plant reproduction. In the Brazilian Cerrado, a seasonally dry ecosystem considered one of the world's biodiversity hotspots for angiosperms, plants with shallow root systems flower predominantly during the rainy season. Foraging activity in social bees however, the major pollinators in this biome, is not restricted to any particular season because a constant supply of resources is necessary to sustain their perennial colonies. Despite the Cerrado's importance as a center of plant diversity, the influence of its extreme cycles of drought and precipitation on the dynamics and stability of plant-pollinator communities is not well understood. We sampled plant-pollinator interactions of a Cerrado community weekly for one year and used network analyses to characterize intra-annual seasonal variation in community structure. We also compared seasonal differences in community robustness to species loss by simulating extinctions of plants and pollinators. We find that the community shrinks significantly in size during the dry season, becoming more vulnerable to disturbance due to the smaller pool of floral hosts available to pollinators during this period. Major changes in plant species composition but not in pollinators has led to high levels of turnover in plant-pollinator associations across seasons, indicated by in interaction dissimilarity (<3% of shared interactions). Aseasonal pollinators, which mainly include social bees and some solitary specialized bees, functioned as keystone species, maintaining robustness during periods of drastic changes in climatic conditions.

The current classification of angiosperms is based primarily on concatenated plastid markers and maximum likelihood (ML) inference. This approach has been justified by the assumption that plastid DNA (ptDNA) is inherited as a single locus and that its individual genes produce congruent trees. However, structural and functional characteristics of ptDNA suggest that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces. To examine this idea, we produced new complete plastid genome (plastome) sequences of 27 species and combined these data with publicly available sequences to produce a final dataset that includes 78 plastid genes for 89 species of rosids and five outgroups. We used four data matrices (i.e., gene, exon, codon-aligned, and amino acid) to infer species and gene trees using ML and multispecies coalescent (MSC) methods. Rosids include about one third of all angiosperms and their two major clades, fabids and malvids, were recovered in almost all analyses. However, we detected incongruence between species trees inferred with different matrices and methods and previously published plastid and nuclear phylogenies. We visualized and tested the significance of incongruence between gene trees and species trees. We then measured the distribution of phylogenetic signal across sites and genes supporting alternative placements of five controversial nodes at different taxonomic levels. Gene trees inferred with plastid data often disagree with species trees inferred using both ML (with unpartitioned or partitioned data) and MSC. Species trees inferred with both methods produced alternative topologies for a few taxa. Our results show that, in a phylogenetic context, plastid protein-coding genes may not be fully linked and behaving as a single locus. Furthermore, concatenated matrices may produce highly supported phylogenies that are discordant with individual gene trees. We also show that phylogenies inferred with MSC are accurate. We therefore emphasize the importance of considering variation in phylogenetic signal across plastid genes and the exploration of plastome data to increase accuracy of estimating relationships. We also support the use of MSC with plastome matrices in future phylogenomic investigations.

The name Adesmia arborea Bertero has been considered a nomen nudum since Colla's assertation that all new names in Bertero's publication detailing his Chilean collections of 1828 were nomina nuda. Subsequent authors seeking to validate the name A. arborea have provided conflicting descriptions adding confusion about the identity of the species. These problems arose from equating this name with other new names published by Bertero in the same work and because material collected and annotated by Bertero as A. arborea represents two different taxa. Here I show that A. arborea was, in fact, validly published by Bertero, provide evidence as to the collection number from which type must be chosen, and designate a Lectotype and Isolectotypes.

Phylogenomics has become increasingly popular in recent years mostly due to the increased affordability of next generation sequencing techniques. Phylogenomics has sparked interest in multiple fields of research, including systematics, ecology, epidemiology, and even personalized medicine, agriculture and pharmacy. Despite this trend, it is usually difficult to learn and understand how the analyses were done, how the results were obtained, and most importantly, how to replicate the study. Here we present the data and all of the code utilized to perform phylogenomic inferences using plastome data: from raw data to extensive phylogenetic inference and accuracy assessment. The data presented here utilizes plastome sequences available on GenBank (accession numbers of 94 species are available below) and the code is also available at https://github.com/deisejpg/rosids. Gonçalves et al. is the research article associated with the data analyses presented here.

High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies.We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the causes of incongruence among datasets, including simulations and the detection of introgression using the D-statistic (ABBA-BABA test).We found significant incongruence among the nuclear, chloroplast, and mitochondrial phylogenies. The strong signal of hybridization found by simulations and the D-statistic among genera and inside the main clades of Diplostephium indicate reticulate evolution as a main cause of phylogenetic incongruence.Our results add evidence for a major role of reticulate evolution in events of rapid diversification. Hybridization and introgression confound chloroplast and mitochondrial phylogenies in relation to the species tree as a result of the uniparental inheritance of these genomic regions. Practical implications regarding the prevalence of hybridization are discussed in relation to the phylogenetic method.

Ranking with the great 18th and 19th century botanists, Kolreuter, Sprengel, and Muller, Stefan Vogel was the 20th century plant biologist who discovered and explored an entirely new pollination syndrome - oil flowers and oil-collecting bees. His work inspired us to work on oil flowers and their associated bees in regions he did not visit. Throughout our work we were continually impressed with the creativity and thoroughness with which he explored this novel plant-pollinator system. Yet, time and subsequent explorations have elaborated and expanded on his work. Here we summarize his contributions and bring up to date the story of the oil flower pollination system focusing primarily on oil bees. Specifically we point out: our increased knowledge about the numbers of plants and bees partnering in this syndrome, the unrealized flexibility in the system; new findings of the chemistry of the floral oils, the use of the oils among various oil-collecting bees and the chemical signals used by at least some oil bees for floral host recognition. We also discuss what is known of the pollen and nectar hosts of oil-collecting bees. (C) 2017 Elsevier GmbH. All rights reserved.

Background and AimsNatural enemies are known to be important in regulating plant populations and contributing to species coexistence (Janzen-Connell effects). The strength of Janzen-Connell effects (both distance- and density-effects) varies across species, but the life history traits that may mediate such a variation are not well understood. This study examined Janzen-Connell effects across the life stages (seed through adult stages) of two sympatric palm species with distinct phenologies and shade tolerances, two traits that may mediate the strength and timing of Janzen-Connell effects.MethodsPopulations of two common palm species, Attalea phalerata and Astrocaryum murumuru , were studied in Manu National Park, Peru. Seed predation experiments were conducted to assess Janzen-Connell effects at the seed stage. In the post-seed stages, spatial point pattern analyses of the distributions of individuals and biomass were used to infer the strength of distance- and density-effects.Key ResultsSeed predation was both negative distance- and density-dependent consistent with the Janzen-Connell effects. However, only seedling recruitment for asynchronously fruiting Attalea phalerata was depressed near adults while recruitment remained high for synchronously fruiting Astrocaryum murumuru , consistent with weak distance-effects. Negative density-effects were strong in the early stages for shade-intolerant Attalea phalerata but weak or absent in shade-tolerant Astrocaryum murumuru.ConclusionsDistance- and density-effects varied among the life stages of the two palm species in a manner that corresponded to their contrasting phenology and shade tolerance. Generalizing such connections across many species would provide a route to understanding how trait-mediated Janzen-Connell effects scale up to whole communities of species.

Meconopsis is an herbaceous genus native to the high altitude habitats across the Himalaya and adjacent plateau and mountain areas. Attractive Meconopsis flowers have spurred many European botanists to study the taxonomy of the genus resulting in numerous infrageneric classifications, dating from the first taxonomic revision in the late 19th century until the most recent monograph in 2014. All, however, were morphology- based treatments and largely inconsistent with one another. To investigate the incongruence among the previous taxonomic grouping strategies of the species in Meconopsis and settle the controversies, we employed a well-resolved molecular phylogeny built by analyzing four chloroplast markers (trnL-trnF intergenic spacer, matK, ndhF, and rbcL). We found that the evolutionary relationships revealed by our phylogeny disagreed to varying degrees with any infrageneric relationship suggested by previous authors. Therefore, we propose a revised classification based on our phylogenetic topology as well as the morphological and cytological patterns reflected by the phylogenetic structure. To achieve a practical and approachable system, we have tried to retain as much as possible of phylogenetically meaningful components from previous taxonomies for the genus. As a result, we used the four major clades of our Meconopsis phylogeny as the bases for infrageneric sections (Meconopsis sect. Meconopsis, M. sect. Aculeatae, M. sect. Primulinae, and M. sect. Grandes). A key to the sections is provided, followed by a description and composition of each.

Pectis is a genus of ±90 xeric adapted New World species. Previous molecular phylogenetic studies showed Pectis closely related to Porophyllum, and one analysis resolved Porophyllum species nested within Pectis. Some Pectis species are known to use C4 photosynthesis. Here we investigate the phylogeny of Pectis and Porophyllum, examine the ploidy levels and geographical distribution of Pectis species in light of its phylogeny, and infer the origin and extent of C4 photosynthesis in both genera. Chloroplast and ITS data from 78 Pectis and 22 Porophyllum species were used to test the monophyly of Pectis and its previously described sections. Carbon isotope data were obtained to infer the photosynthetic pathway of 80 species, and the results mapped on the inferred phylogenies to determine the timing and pattern of evolution of the C4 pathway. The ITS dataset supports a monophyletic Pectis sister to a monophyletic Porophyllum, while the chloroplast dataset places two Porophyllum species sister to a combined Pectis Porophyllum clade. Five well-supported lineages are recovered in Pectis. All Pectis sampled have ∂13C values consistent with C4 photosynthesis, and all Porophyllum species sampled have ∂13C values consistent with C3 photosynthesis. We conclude that Pectis is monophyletic but only two of its recognized sections are monophyletic. Porophyllum is monophyletic but its sections are not. Porophyllum amplexicaule and Pr. scoparium should be treated as members of a new genus. The switch to the C4 pathway in Pectis happened in the late Miocene, probably in north/central Mexico, at or after the divergence of Pectis and Porophyllum. This location and timing is consistent with the evolution of C4 photosynthesis in other North American eudicot lineages, suggesting similar environmental conditions may underlie the switch to C4 photosynthesis.

Meconopsis is a genus native to the high elevation habitats that range from the western Himalaya eastward to the Hengduan Mountains (China). The genus has been the subject of several taxonomic treatments and monographs by generations of botanists, which has led to a long and confusing taxonomic history with inconsistent species concepts and conflicting interpretations of relationships among named taxa. In the present study, we reconstructed the evolutionary history of Meconopsis utilizing four chloroplast markers (rbcL, matK, ndhF and the trnL-trnF intergenic spacer) and the nuclear ribosomal internal transcribed spacer (nrITS). Incongruence found between the cpDNA and nrITS trees was investigated to detect reticulate evolution, using the approximately unbiased (AU) method. Based on the evolutionary patterns revealed by our resultant phylogenies, we evaluated the species delimitations of the two most controversial “species” (Meconopsis horridula and Meconopsis napaulensis) in the genus and the inconsistency among their previously published treatments. As a result, we provide taxonomic suggestions for these species that include the proposal of a M. horridula species complex.

Abstract An updated inventory of Brazilian seed plants is presented and offers important insights into the country's biodiversity. This work started in 2010, with the publication of the Plants and Fungi Catalogue, and has been updated since by more than 430 specialists working online. Brazil is home to 32,086 native Angiosperms and 23 native Gymnosperms, showing an increase of 3% in its species richness in relation to 2010. The Amazon Rainforest is the richest Brazilian biome for Gymnosperms, while the Atlantic Rainforest is the richest one for Angiosperms. There was a considerable increment in the number of species and endemism rates for biomes, except for the Amazon that showed a decrease of 2.5% of recorded endemics. However, well over half of Brazillian seed plant species (57.4%) is endemic to this territory. The proportion of life-forms varies among different biomes: trees are more expressive in the Amazon and Atlantic Rainforest biomes while herbs predominate in the Pampa, and lianas are more expressive in the Amazon, Atlantic Rainforest, and Pantanal. This compilation serves not only to quantify Brazilian biodiversity, but also to highlight areas where there information is lacking and to provide a framework for the challenge faced in conserving Brazil's unique and diverse flora.