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The water‐lily clade represents the second earliest‐diverging branch of angiosperms. Most of its species belong to Nymphaeaceae, of which the "core Nymphaeaceae"—comprising the genera Euryale, Nymphaea and Victoria—is the most diverse clade. Despite previous molecular phylogenetic studies on the core Nymphaeaceae, various aspects of their evolutionary relationships have remained unresolved. The length‐variable introns and intergenic spacers are known to contain most of the sequence variability within the water‐lily plastomes. Despite the challenges with multiple sequence alignment, any new molecular phylogenetic investigation on the core Nymphaeaceae should focus on these noncoding plastome regions. For example, a new plastid phylogenomic study on the core Nymphaeaceae should generate DNA sequence alignments of all plastid introns and intergenic spacers based on the principle of conserved sequence motifs. In this investigation, we revisit the phylogenetic history of the core Nymphaeaceae by employing such an approach. Specifically, we use a plastid phylogenomic analysis strategy in which all coding and noncoding partitions are separated and then undergo software‐driven DNA sequence alignment, followed by a motif‐based alignment inspection and adjustment. This approach allows us to increase the reliability of the character base compared to the default practice of aligning complete plastomes through software algorithms alone. Our approach produces significantly different phylogenetic tree reconstructions for several of the plastome regions under study. The results of these reconstructions underscore that Nymphaea is paraphyletic in its current circumscription, that each of the five subgenera of Nymphaea is monophyletic, and that the subgenus Nymphaea is sister to all other subgenera of Nymphaea. Our results also clarify many evolutionary relationships within the Nymphaea subgenera Brachyceras, Hydrocallis and Nymphaea. In closing, we discuss whether the phylogenetic reconstructions obtained through our motif‐based alignment adjustments are in line with morphological evidence on water‐lily evolution. [ABSTRACT FROM AUTHOR]

DNA barcoding aids in rapidly identifying specimens in various contexts by comparing short stretches of DNA to a reference database. Barcoding initiatives generate large reference databases of carefully curated high‐quality sequences to maximize identification success.BarKeeper provides a flexible tool for barcoding initiatives and in the context of phylogenetic studies to foster shared work on large datasets of raw sequence and associated metadata. It is free, open‐source and available as a set of Docker containers for easy setup. After setting it up once, all project members can use it independently of their operating system or location.BarKeeper offers features to collect and manage data and metadata about specimens, taxa and DNA sequences from Sanger sequencing and high‐throughput sequencing (HTS) technologies. It provides excellent flexibility by not being restricted to specific markers or taxon groups. Users can view and edit records and associated metadata while the app assists them by trimming and assembling reads. It automatically checks the quality of generated barcodes with a taxonomy‐based tool and offers a wide range of options for data analysis. Extensive search features allow querying the database for specific groups of records and saving the search results in the user's profile or downloading them in various file formats.BarKeeper combines multiple tools to aid barcoding projects in every step, from a reference taxa list to finished barcode sequences, thereby minimizing the number of laborious, potentially error‐prone manual steps and enabling efficient collaborative workflows. [ABSTRACT FROM AUTHOR]

Using the genus Casearia, we assessed the status of nested singletons: individual specimens corresponding to accepted species but in molecular trees appearing nested within clades of closely related species. Normally, such cases would be left undecided, while on the other hand, timely taxonomic decisions are required. We argue that morphological, chorological, and ecological data can be informative to illuminate patterns of speciation. Their use can provide a first step in testing taxon concepts at species level. We focused on five cases of nested singletons in trees of the genus Casearia. We employed PCA and cluster analysis to assess phenotypic differentiation. Using geocoordinates, we calculated niche space differentiation based on 19 bioclim variables, by means of PCA and niche equivalency and similarity tests and generated dot maps. We found that the singletons were morphologically distinctive in two of the five cases (Casearia selloana and C. manausensis), relatively distinctive in two other cases (C. zizyphoides and C. mariquitensis), and partially overlapping in the last case (C. grandiflora). For two cases (C. mariquitensis and C. selloana), ecological niche space was broadly overlapping, in two cases it was found broadly nested (C. grandiflora and C. zizyphoides), and in one case narrowly nested (C. manausensis), but in no case niche differentiation was observed. Niche overlap, similarity and equivalency showed corresponding patterns. Given these data, one would interpret C. selloana and C. manausensis as presumably well‐distinguished taxa, their narrow distribution ranges suggesting recently emerging lineages. The other three cases are not clearcut. Morphological data would suggest particularly C. grandiflora conspecific with C. arborea, but differences in the distribution are intriguing. Our approach would reject the notion of potential synonymy based on nested phylogenetic placement for at least two of the five cases. The other case also shows no complete lack of differentiation which would support synonymy. [ABSTRACT FROM AUTHOR]

Casearia (Salicaceae) is a pantropical genus of circa 200 species, around half of which dwell in the Neotropics. Despite the availability of phylogenetic studies that suggest that Casearia sensu Sleumer is not monophyletic, a strong phylogenetic framework was still lacking for this genus. We tested the monophyly of Casearia and examined the relationships of its species to other taxa of the tribe Samydeae, including Laetia, Samyda and Zuelania, which recently have been sunk into Casearia, as well as Euceraea, Lunania, Neoptychocarpus, Ryania and Tetrathylacium. We further put a focus on the Neotropical taxa since Casearia and allies are speciose both on the Caribbean islands and adjacent mainlands, thus providing an interesting group to address the origin of the Caribbean and Cuban flora. Our phylogenetic analyses based on four combined rapidly evolving plastid regions (petD, rpl16, rps4‐trnT‐L‐F, trnK‐matK‐psbA) as well as nuclear ITS revealed Casearia as monophyletic with high support, including not only the former members of Laetia, Samyda and Zuelania but also Euceraea and Neoptychocarpus. Casearia is constituted by several major clades, mostly being entirely Neotropical, one of which exclusively comprises species endemic to the Caribbean islands. Another clade, which includes all Palaeotropical species, is nested among Neotropical lineages. Our divergence date estimates using the plastid dataset and fossil calibration points in Salicaceae indicate that the Casearia crown group started to diversify during the late Eocene, approximately 39 Ma. The stem of the Old World clade diverged from Neotropical ancestors around 27 Ma, in the Oligocene. We used BayesTraits to reconstruct the evolution of seven characters commonly used to define Casearia and allied genera. We found morphological characters, such as branched inflorescences (fasciculate, glomerulous, cymose) or uniseriate stamen series, that work well to circumscribe the genus, whereas dioecy, which was used to diagnose Neoptychocarpus, or higher stamen numbers (>12), found in Laetia and Zuelania, are homoplastic in Salicaceae, the latter character derived within Casearia from ancestors with 7–12 stamens. Pellucid dots appear to have evolved earlier than the divergence of the Casearia clade in Samydeae, and were lost in Ryania and Tetrathylacium, and thus are no synapomorphy for Casearia. In order to establish a monophyletic genus concept for Casearia, we propose to also merge Euceraea and Neoptychocarpus. Our reconstruction of ancestral areas using BioGeoBears indicate that South America is the ancestral area of Casearia. From there, multiple migrations occurred to Mesoamerica and the Caribbean islands. The Caribbean that comprises nearly all Caribbean endemics started to diversify around 9.5 Ma. Our trees depict C. corymbosa, which exhibits significant infraspecific phylogenetic structure for the sampled Mexican and Colombian individuals, as the sister to the Caribbean clade. The other clade, with Cuban endemics (C. ternstroemioides) but also Mesoamerican and South American taxa, is not sufficiently resolved internally, to allow biogeographic conclusions. The Old World clade of Casearia provides another example for a late Laurasian migration starting in the Neotropics. [ABSTRACT FROM AUTHOR]

Premise: The genus Gynoxys and relatives form a species‐rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it. Methods: We sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif‐based adjustments of automatic DNA sequence alignments on phylogenetic tree inference. Results: Our results indicate that the inclusion of all plastid genome partitions is needed to infer well‐supported phylogenetic trees of the Gynoxoid group. Whole plastome‐based tree inference suggests that the genera Gynoxys and Nordenstamia are polyphyletic and form the core clade of the Gynoxoid group. This clade is sister to a clade of Aequatorium and Paragynoxys and also includes some but not all representatives of Paracalia. Conclusions: The concatenation and combined analysis of all plastid genome partitions and the construction of manually‐curated, motif‐based DNA sequence alignments are found to be instrumental in the recovery of well‐supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome‐level plastid sequence data sets is crucial for subsequent phylogeny reconstruction and that the manual post‐processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa. [ABSTRACT FROM AUTHOR]

High Andean forests harbor a remarkably high biodiversity and play a key role in providing vital ecosystem services for neighboring cities and settlements. However, they are among the most fragmented and threatened ecosystems in the neotropics. To preserve their unique biodiversity, a deeper understanding of the effects of anthropogenic perturbations on them is urgently needed. Here, we characterized the plant communities of high Andean forest remnants in the hinterland of Bogotá in 32 0.04 ha plots. We assessed the woody vegetation and sampled the understory and epiphytic cover. We gathered data on compositional and structural parameters and compiled a broad array of variables related to anthropogenic disturbance, ranging from local to landscape‐wide metrics. We also assessed phylogenetic diversity and functional diversity. We employed nonmetric multidimensional scaling (NMDS) to select meaningful variables in a first step of the analysis. Then, we performed partial redundancy analysis (pRDA) and generalized linear models (GLMs) in order to test how selected environmental and anthropogenic variables are affecting the composition, diversity, and aboveground biomass of these forests. Identified woody vegetation and understory layer communities were characterized by differences in elevation, temperature, and relative humidity, but were also related to different levels of human influence. We found that the increase of human‐related disturbance resulted in less phylogenetic diversity and in the phylogenetic clustering of the woody vegetation and in lower aboveground biomass (AGB) values. As to the understory, disturbance was associated with a higher diversity, jointly with a higher phylogenetic dispersion. The most relevant disturbance predictors identified here were as follows: edge effect, proximity of cattle, minimum fragment age, and median patch size. Interestingly, AGB was efficiently predicted by the proportion of late successional species. We therefore recommend the use of AGB and abundance of late successional species as indicators of human disturbance on high Andean forests. [ABSTRACT FROM AUTHOR]

It is time to synthesize the knowledge that has been generated through more than 260 years of botanical exploration, taxonomic and, more recently, phylogenetic research throughout the world. The adoption of an updated Global Strategy for Plant Conservation (GSPC) in 2011 provided the essential impetus for the development of the World Flora Online (WFO) project. The project represents an international, coordinated effort by the botanical community to achieve GSPC Target 1, an electronic Flora of all plants. It will be a first‐ever unique and authoritative global source of information on the world's plant diversity, compiled, curated, moderated and updated by an expert and specialist‐based community (Taxonomic Expert Networks – "TENs" – covering a taxonomic group such as family or order) and actively managed by those who have compiled and contributed the data it includes. Full credit and acknowledgement will be given to the original sources, allowing users to refer back to the primary data. A strength of the project is that it is led and endorsed by a global consortium of more than 40 leading botanical institutions worldwide. A first milestone for producing the World Flora Online is to be accomplished by the end of 2020, but the WFO Consortium is committed to continuing the WFO programme beyond 2020 when it will develop its full impact as the authoritative source of information on the world's plant biodiversity. [ABSTRACT FROM AUTHOR]

Jurinea (Asteraceae: Cardueae) is a large Eurasian genus of about 180 species with centres of diversity in Central and Southwest Asia and the eastern Mediterranean. The genus includes many species with adaptations to xero‐ and chasmophytic habitats and comprises numerous endemics, especially in the Caucasus. Generic delimitations between Jurinea and closely related genera have been difficult to assess, as have the phylogenetic relationships with the genera Himalaiella, Jurinella and Lipschitziella, each of which has been suggested as congeneric with Jurinea. A molecular phylogenetic investigation at both the specific and the generic level to establish the generic delimitation of Jurinea and to evaluate the intergeneric relationships of the genus with other members of the Cardueae was hitherto lacking. In this study, we reconstruct the phylogenetic relationships between Jurinea and several closely related genera based on a representative taxon sampling using DNA sequence data of nuclear (ITS, ETS) and plastid DNA regions (trnK/matK, trnL‐F). We also evaluate the infrageneric classification of Jurinea. Our results indicate that Jurinea is polyphyletic in its current circumscription, as the species J. gedrosiaca and J. cartilaginea are placed within the subtribe Centaureineae of the Cardueae. The rest of Jurinea is monophyletic and split into two major clades corresponding to the western and eastern range of the distribution area of the genus. The sister clade of Jurinea is composed of Himalaiella and Lipschitziella. Jurinella, which was segregated from Jurinea based on achene morphology, is congeneric with Jurinea. Like in other speciose Eurasian genera, the currently recognised sections do not reflect natural groups, whereas most clades found through molecular phylogenetic inference correlate with geographic patterns. A clade that exclusively comprises Caucasian endemics, including the narrow endemics of J. sect. Neobellae, was found. This clade represents an interesting study group for possible radiation events of Jurinea in the Caucasus. [ABSTRACT FROM AUTHOR]

Iresine is a neotropical genus of the Amaranthaceae with most of the species diversity in Mexico and Mesoamerica. It has suffered a complex classification history with considerably diverging views on the genus concept. We have carried out a phylogenetic analysis of Iresine and allied genera using sequence data of combined plastid introns (including the matK CDS) and spacers as well as ITS, and a dense sampling of species. Trees depict a clade of Iresine with Irenella and Woehleria deeply nested. This clade is sister to the remainder of Gomphrenoideae including Hebanthe and Trommsdorffia (= Pedersenia). One of two maximally supported subclades of Iresine comprises mostly species restricted to the Mexican highlands and adjacent areas, whereas the other subclade is composed of more widespread Mexican-Mesoamerican taxa. Pollen grains of Iresine and relatives were examined using high-resolution SEM, which yielded a matrix of 15 pollen characters. Ancestral character state reconstruction shows dodecahedral grains (in I. angustifolia and I. nigra) to have evolved within the Iresine clade, not involving the complete suite of character shifts associated with metareticulate pollen but just an increase of aperture diameter and a slight decrease of mesoporia width. To the contrary, four character state transformations occurred in the common ancestor of core Gomphrenoideae that led to metareticulate pollen (shifts to a distal orientation of punctae and microspines, to a sunken position of apertures relative to the distal part of mesoporia resulting in narrow mesoporia higher then wide, and a reduction in the diameter of mesoporia). The Iresine clade is characterized by pollen with well-separated ektexinous aperture membrane bodies, rounded or triangular, and gradually tapering into a single spine. For the monophyletic genus Iresine, 35 species are currently accepted. We provide a taxonomic backbone (including one new combination, one new name and several lectotypifications) that also comments on the current understanding of species delimitation. [ABSTRACT FROM AUTHOR]

Premise of the Study: Philodendron is a large genus of ~560 species and among the most conspicuous epiphytic components of Neotropical forests, yet its phylogenetic relationships, timing of divergence, and diversification history have remained unclear. We present a comprehensive phylogenetic study for Philodendron and investigate its diversification, including divergence‐time estimates and diversification rate shift analyses. Methods: We performed the largest phylogenetic reconstruction for Philodendron to date, including 125 taxa with a combined dataset of three plastid regions (petD, rpl16, and trnK/matK). We estimated divergence times using Bayesian evolutionary analysis sampling trees and inferred shifts in diversification rates using Bayesian analysis of macroevolutionary mixtures. Key Results: We found that Philodendron, its three subgenera, and the closely related genus Adelonema are monophyletic. Within Philodendron subgenus Philodendron, 12 statistically well‐supported clades are recognized. The genus Philodendron originated ~25 mya and a diversification rate upshift was detected at the origin of subgenus Philodendron ~12 mya. Conclusions: Philodendron is a species‐rich Neotropical lineage that diverged from Adelonema during the late Oligocene. Within Philodendron, the three subgenera currently accepted are recovered in two lineages: one contains the subgenera Meconostigma and Pteromischum and the other contains subgenus Philodendron. The lineage containing subgenera Meconostigma and Pteromischum underwent a consistent diversification rate. By contrast, a diversification rate upshift occurred within subgenus Philodendron ~12 mya. This diversification rate upshift is associated with the species radiation of the most speciose subgenus within Philodendron. The sections accepted within subgenus Philodendron are not congruent with the clades recovered. Instead, the clades are geographically defined. [ABSTRACT FROM AUTHOR]

Aim Species-rich dry grasslands have declined drastically in recent decades leading to spatial isolation of associated species. This can disrupt gene flow leading to genetic erosion, inbreeding and increased differentiation. Using Scabiosa canescens as a case for a threatened central European species confined to dry grasslands, we investigate the genetic consequences of spatial and functional isolation. In particular, inbreeding and loss of genetic diversity are expected to be more pronounced in populations at the northern margin of the sampling area due to more intense agriculture, less suitable habitat and potential post-glacial colonization from the south. Location Germany. Methods We genotyped 563 individuals at 10 microsatellite loci from 22 populations across the species' range in Germany. We analyse spatial genetic structure and patterns of isolation by distance ( IBD) at multiple scales. Further, we identify latitudinal and altitudinal patterns of genetic diversity and inbreeding. Results We found strong population differentiation but no IBD up to at least 200 km. Levels of inbreeding were positively correlated with latitude and tended to decline with altitude. An integration of altitude and latitude into temperature-corrected altitude ( CA) was positively correlated with genetic diversity. Populations in the Upper Rhine Valley appear to have a distinct ancestry. Main conclusions We interpret the strong population differentiation combined with no IBD up to at least 200 km as a sign for disrupted extensive gene flow. A trend for reduced genetic diversity towards the northern populations occurring at lower altitudes is probably driven by more intense land use but cannot be conclusively distinguished from other potential factors such as a more recent colonization history. Apart from the distinct Upper Rhine Valley populations, our findings suggest that assisted gene flow up to 100 km would mitigate genetic differentiation, inbreeding and loss of genetic diversity caused by disrupted long-distance dispersal. [ABSTRACT FROM AUTHOR]

Abstract: With approximately 25 endemic species, the genus Pyrus (pears) is highly diverse in the Caucasus ecoregion. The majority of Caucasian pears inhabit xerophytic open woodlands or similar habitats, to which they display morphological adaptations, such as narrow leaves. The other species, both Caucasian and non‐Caucasian taxa, mainly inhabit mesophytic forests and display broad leaves. Using a representative taxon sampling of Pyrus from the Caucasus, Europe and Asia, we reconstruct phylogenetic relationships in the genus based on multiple plastid regions. We also estimate the divergence times of major clades in Pyrus, reconstruct the evolution of leaf shapes, and discuss the emergence of xeromorphic leaf traits. Our results confirm the monophyly of Pyrus and the existence of two major clades: (a) an E Asian clade with a crown group age of 15.7 (24.02–8.37 95% HPD) My, and (b) a W Eurasian clade that comprises species from Europe, SW Asia and the Caucasus and that displays a slightly younger crown group of 12.38 (19.02–6.41 95% HPD) My. The existing infrageneric classification of Pyrus was found partially incongruent with the inferred phylogenetic trees. Several currently accepted species were not recovered as monophyletic, indicating that current species limits require re‐evaluation. Ancestral character state reconstructions revealed several independent transitions from broad‐ to narrow‐shaped leaves in Pyrus, probably via intermediate‐shaped leaves. [ABSTRACT FROM AUTHOR]

Campanula s.l. is one of the most speciose flowering plant lineages of the Holarctic (ca. 600 species). In the present study we sequenced three regions of the plastid genome ( petD, rpl16 and trnK/ matK) across a broad sample of Campanula s.l., which markedly improved phylogenetic resolution and statistical support compared to previous studies. Based on this robust phylogenetic hypothesis we estimated divergence times using BEAST, diversification rate shifts using Bayesian Analysis of Macroevolutionary Mixture ( BAMM) and TreePar, and ancestral ranges using Biogeography with Bayesian (and likelihood) Evolutionary Analyses in R . Campanula s.l. is estimated to have originated during the Early Eocene but the major diversification events occurred between the Late Oligocene and Middle Miocene. Two upward diversification rate shifts were revealed by BAMM, specific to the crown nodes of two Campanula clades: CAM17, a mostly South European- SW Asian lineage originating during the Middle Miocene and containing nearly half of all known Campanula species; and CAM15B, a SW Asian-Sino-Himalayan lineage of nine species originating in the early Pleistocene. The dynamic diversification history of Campanula and the inferred rate shifts are discussed in a geo-historical context. [ABSTRACT FROM AUTHOR]

Limonium (Plumbaginaceae) is a nearly cosmopolitan halophytic genus with ca. 350 species, a large number of which occurs in the Mediterranean region. We have generated a sequence dataset of several plastid (trnK intron including the matK gene, petD intron with the petB-petD spacer, trnL intron with the trnL-trnF spacer) and one nuclear region (nrITS), spanning the major lineages within the genus (102 accessions representing 76 species of Limonium) and related genera. Bayesian inference, maximum likelihood and maximum parsimony analyses converge on a Limonium clade that includes the genera Afrolimon, Eremolimon and Linczevskia. Plastid and nuclear trees congruently depict a number of major clades, most of them with a characteristic vegetative morphology and growing in specific habitats. Although the position of Afrolimon is incongruently resolved as the sister of a subclade comprising Limonium vulgare and relatives in the plastid trees versus being the sister to a Limonium sogdianum--L. bellidifolium--L. aureum clade in the nrITS tree, both genomic compartments show that Afrolimon is deeply nested in Limonium. Eremolimon is resolved as a close relative of L. sogdianum and L. ferganense based on plastid and nuclear genomic compartments. Our phylogenetic analysis resulted in an improved picture of internal relationships. Apart from the monophyletic subgenera Limonium subg. Limonium and L. subg. Pteroclados, nine wellsupported clades of L. subg. Limonium are evident, several of which are predominantly constituted by species of a certain geographic range. A subclade of IranoTuranian species (L. iranicum, L. suffruticosum and relatives) is shown to be unrelated to a L. axillare subclade, indicating an independent origin of the woody habit in these two lineages. Limonium sect. Iranolimon sect. nov. is described for the IranoTuranian woody lineage. The new combination L. sect. Circinaria comb. nov., is established for taxa sometimes included in Afrolimon. [ABSTRACT FROM AUTHOR]

Aim Using the Acalyphoideae, we explore the origin and diversification of the Caribbean flora. This lineage of flowering plants constitutes an important component of the flora of the Caribbean islands with many endemics. Furthermore, because it is also diverse in adjacent Mexico, Mesoamerica and South America, it allows a representative analysis of possible migration routes into the Caribbean. Location Neotropics, Cuba, Hispaniola and the Caribbean region, Mexico and Mesoamerica. Methods We generated a well-resolved and dated phylogenetic hypothesis based on a dense sampling, in particular of the New World taxa but also representing all remaining Acalyphoideae, and combined datasets of chloroplast spacers and introns. Bayesian divergence-time estimation was applied to determine node ages. Ancestral states of distributional areas were reconstructed in a Bayesian framework to determine the geographical origin of the Caribbean ancestors. Results A Neotropical clade started to diversify 59.29 [50.41-68.44 95% highest posterior density ( HPD)] Ma within the Acalyphoideae. The Caribbean islands then were reached several times independently from the Miocene onwards. The exclusively Caribbean Leucocroton- Lasiocroton- Garciadelia [9.1 (6.3-12.3 95% HPD) Ma] and Acidoton- Platygyna [9.3 (5.2-15.4 95% HPD) Ma] clades exhibit one of the most successful plant radiations in the region, and Caribbean subclades of Acalypha and Bernardia just date back to the Pliocene and Pleistocene, respectively. Main conclusions Our data show that Mexico and Mesoamerica have played a key role as a source for today's Caribbean Acalyphoideae. Their ancestors arrived from the mainland to the Caribbean islands during the Miocene when Caribbean land masses were completely separated and then diversified in situ. We postulate long-distance dispersal to have played a major role for colonizing the Caribbean. [ABSTRACT FROM AUTHOR]

* Premise of the study: The Caucasus represents one of the world's biodiversity hotspots and includes the climatic refugia Hyrcan on the southern coast of the Caspian Sea and Colchis on the eastern coast of the Black Sea, where different species survived during the Quaternary climatic oscillations. We evaluated the genetic diversity of the relict tree Zelkova carpinifolia shared between the two refugia and distributed throughout the Caucasus and adjacent areas. * Methods: Specimens were collected from 30 geographical sites in Azerbaijan, Georgia, Iran, and Turkey and screened for variability at eight nuclear microsatellite loci. The genetic diversity among and within populations was assessed using a set of statistical measures. * Key results: We detected 379 different genotypes from a total of 495 individuals with varying degrees of clonal reproduction at the different sites. Low to intermediate levels of genetic diversity were observed at all sites, and strong differentiation between sampling sites was absent. In addition, we observed no clear genetic differentiation between the Colchis and Hyrcan. Bayesian clustering of the genotypes revealed three populations with high levels of admixture between the sampling sites. * Conclusions: The lack of strong genetic structure of studied populations of Z. carpinifolia contrasts with a previous study based on chloroplast markers and suggests that long-distance pollen dispersal is an important factor of gene flow among populations of Z. carpinifolia. The present study does not reveal any particular site with particularly isolated genotypes that would deserve more attention for conservation purposes than others, although some sites should be considered for further investigation. [ABSTRACT FROM AUTHOR]

Recent phylogenetic analyses revealed a grade with Ranunculales, Sabiales, Proteales, Trochodendrales, and Buxales as first branching eudicots, with the respective positions of Proteales and Sabiales still lacking statistical confidence. As previous analyses of conserved plastid genes remain inconclusive, we aimed to use and evaluate a representative set of plastid introns (group I: trnL; group II: petD, rpl16, trnK) and intergenic spacers ( trnL-F, petB-petD, atpB-rbcL, rps3-rpl16) in comparison to the rapidly evolving matK and slowly evolving atpB and rbcL genes. Overall patterns of microstructural mutations converged across genomic regions, underscoring the existence of a general mutational pattern throughout the plastid genome. Phylogenetic signal differed strongly between functionally and structurally different genomic regions and was highest in matK, followed by spacers, then group II and group I introns. The more conserved atpB and rbcL coding regions showed distinctly lower phylogenetic information content. Parsimony, maximum likelihood, and Bayesian phylogenetic analyses based on the combined dataset of non-coding and rapidly evolving regions (>14 000 aligned characters) converged to a backbone topology of eudicots with Ranunculales branching first, a Proteales-Sabiales clade second, followed by Trochodendrales and Buxales. Gunnerales generally appeared as sister to all remaining core eudicots with maximum support. Our results show that a small number of intron and spacer sequences allow similar insights into phylogenetic relationships of eudicots compared to datasets of many combined genes. The non-coding proportion of the plastid genome thus can be considered an important information source for plastid phylogenomics. [ABSTRACT FROM AUTHOR]

• Premise of the study: The Cactaceae are a major New World plant family and popular in horticulture. Still, taxonomic units and species limits have been difficult to define, and molecular phylogenetic studies so far have yielded largely unresolved trees, so relationships within Cactaceae remain insufficiently understood. This study focuses on the predominantly epiphytic tribe Rhipsalideae and evaluates the utility of a spectrum of plastid genomic regions. • Methods: We present a phylogenetic study including 52 of the 53 Rhipsalideae species and all the infraspecific taxa. Seven regions ( trnK intron, matK , rbcL , rps3 - rpl16 , rpl16 intron, psbA-trnH , trnQ-rps16 ), ca. 5600 nucleotides (nt) were sequenced per sample. The regions used were evaluated for their phylogenetic performance and performance in DNA-based species recognition based on operational taxonomic units (OTUs) defined beforehand. • Key results: The Rhipsalideae are monophyletic and contain five clades that correspond to the genera Rhipsalis , Lepismium , Schlumbergera , Hatiora , and Rhipsalidopsis . The species-level tree was well resolved and supported; the rpl16 and trnK introns yielded the best phylogenetic signal. Although the psbA-trnH and trnQ-rps16 spacers were the most successful individual regions for OTU identification, their success rate did not significantly exceed 70%. The highest OTU identification rate of 97% was found using the combination of psbA-trnH, rps3-rpl16, trnK intron, and trnQ-rps16 as a minimum possible marker length (ca. 1660 nt). • Conclusions : The phylogenetic performance of a marker is not determined by the level of sequence variability, and species discrimination power does not necessarily correlate with phylogenetic utility. [ABSTRACT FROM AUTHOR]

Sequence data from the matK gene, the trnK group II intron, the trnL group I intron and the trnL-F spacer were analysed for a broad sampling of the rosids and other eudicots. For the first time all putative genera of Dipentodontaceae and Tapisciaceae (Dipentodon, Huertea, Perrottetia, Tapiscia), as well as the recently described Gerrardinaceae were included in a molecular phylogenetic dataset. All genera were found in a well supported Huerteales clade. Moreover, with the rapidly evolving and non-coding plastid sequence data we were able to resolve the Huerteales clade to branch after Sapindales, and to be sister to a Brassicales-Malvales clade. Increased resolution and support among the malvids underscore the potential of plastid introns and spacers as well as the matK gene as phylogenetic markers in rosids. [ABSTRACT FROM AUTHOR]

With the present study we attempt to elucidate the history of the order Nymphaeales water-lilies and relatives-in time and space. On the basis of a dense taxon sampling that covers all genera of Cabombaceae and Nymphaeaceae and all subgenera of the genus Nymphaea, and on the basis of well-supported phylogenetic hypotheses, we estimate divergence times in Nymphaeales. Distribution data for all species are used to reconstruct ancestral ranges and to identify possible dispersal events in the biogeographic history of Nymphaeales. Considering the fossil record for the clade as well as geologic history, a plausible historical scenario can be drawn. The assessment of extant biogeography shows that there are several centres of species diversity for Nymphaeales, i.e., northern South America, Central America, the Zambezian region of Africa and northern Australia. However, the diversification of the Nymphaeales started in the Northern Hemisphere when the northern landmasses were covered by tropical vegetation, except for the very high latitudes. The estimation of divergence times depicted two distinct radiation events, a rapid first differentiation into three major lineages during the Paleocene (Cabonibaceae, Nuphar, remaining Nymphaeaceae and the radiation of core Nymphaeaceae (Victoria, Euryale, Nymphaea incl. Ondinea) from the Late Oligocene to Middle Miocene. The second radiation probably started in the Northern Hemisphere. We hypothesize that subsequent spatial separation and southward relocation of the descendants led to the disjunct distribution of extant sister lineages in core Nymphaeaceae, e.g., Euryale-Victoria or Nymphaea subgg. Hydrocallis and Lotos. [ABSTRACT FROM AUTHOR]

The Nymphaeales (water lilies) clade has diverged as the second branch in the tree of angiosperms and is composed of the three families Cabombaceae, Nymphaeaceae and Hydatellaceae. Extant species diversity is constituted by 82 species, about half of which belong to the nearly globally distributed genus Nymphaea. DNA sequence datasets of multiple non-coding and rapidly evolving regions from all three genomic compartments (ca. 8 kb of sequence per taxon) for a dense sampling of Nymphaeales, Austrobai leyales and Amborella were examined. In an attempt to review the literature on water lilies of the past decades a matrix comprising 62 morphological characters was generated. The crown group of extant Nymphaeales is supported by a series of synapomorphies, several of which have evolved in line with the acquisition of herbaceous habits and adaptations to an aquatic lifestyle such as the loss of cambium and sclerenchyma. Further innovations evolved subsequently within the diversification of the water lily crown group such as hydropotes, or an aril as floating device for the seeds in core Nymphaeaceae that have evolved fruits ripening under water. Both Hydatellaceae and Cabombaceae exhibit many derived features that in part may be explained as adaptations to anemophily. The Nymphaeaceae are supported as monophyletic by most character partitions, including morphology, as are Nuphar and Barclaya as successive sisters to the core Nymphaeacae (Nymphaea, Ondinea, Euryale, Victoria). Parsimony analysis of the morphological dataset alone yielded a well resolved and statistically supported tree. Ondinea appears as a close relative of the Australian subg. Anecphya clade within Nymphaea by all genomic compartments and morphology. Earlier hypotheses of Nymphaea being paraphyletic to the Euryale-Victoria clade are inferred in nuclear trees, albeit with low support. Different morphological characters equivocally support a position of the Euryale-Victoria clade as sister to the subg. Hydrocallis-Lotus clade within Nymphaea or as sister to all species of Nymphaea. The diversification of the water lily clade is further characterized by a trend towards increased complexity in floral architecture. [ABSTRACT FROM AUTHOR]

C4 photosynthesis evolved multiple times in the Amaranthaceae s.s., but the C4 evolutionary lineages are unclear because the photosynthetic pathway is unknown for most species of the family. To clarify the distribution of C4 photosynthesis in the Amaranthaceae, we determined carbon isotope ratios of 607 species and mapped these onto a phylogeny determined from matK/trnK sequences. Approximately 28% of the Amaranthaceae species use the C4 pathway. C4 species occur in 10 genera—Aerva, Amaranthus, Blutaparon, Alternanthera, Froelichia, Lithophila, Guillerninea, Gomphrena, Gossypianthus, and Tidestromia. Aerva, Alternanthera, and Goniphrena contain both C3 and C4 species. In Aerva, 25% of the sampled species are C4. In Alternanthera, 19.5% are C4, while 89% of the Goniphrena species are C4. Integration of isotope and matK/trnK data indicated C4 photosynthesis evolved five times in the Amaranthaceae, specifically in Aerva, Alternanthera, Amaranthus, Tidestrornia, and a lineage containing Froelichia, Blutaparon, Guilleminea, Gomphrena pro parte, and Lithophila. Aerva and Gomphrena are both polyphyletic with C3 and C4 species belonging to distinct clades. Alternanthera appears to be monophyletic with C4 photosynthesis originating in a terminal sublineage of procumbent herbs. Alpine C4 species were also identified in Alternanthera, Amaran thus, and Gornphrena, including one species (Gomphrena meyeniana) from 4600 m a.s.l. [ABSTRACT FROM AUTHOR]

The genus Pinguicula is one of the three genera of the carnivorous Lentibulariaceae, comprising approximately 80 species. Phylogeny inference using nucleotide sequences of the chloroplast gene matK and the trnK group II intron, as well as a set of 32 morphological characters revealed five well-supported, major lineages within the genus. These lineages largely reflect radiations in clearly defined geographic regions, whereas most previously recognized sections of the genus are shown to be para- or polyphyletic. A species-rich Mexican-Central American-Caribbean clade has the Eurasian P. alpina and an East Asian clade as successive sisters. All three are characterized by a production of flower buds on winter-resting plants, a specific corolla hair structure and a very large corolla lower central lobe. Another diverse clade is composed of species with primarily European distribution including the widespread type species P. vulgaris. For this clade, vegetative reproduction during dormancy is synapomorphic. Species native to SE North America and the South American Andes and a group of Mediterranean and NE Atlantic coast species together appear in a fifth well-supported clade, that is characterized by a tropical-type growth habit. It is the only clade that has reached temperate zones of the southern hemisphere. [ABSTRACT FROM AUTHOR]

Plastid matK gene sequences for 374 genera representing all angiosperm orders and 12 genera of gymnosperms were analyzed using parsimony (MP) and Bayesian inference (BI) approaches. Traditionally, slowly evolving genomic regions have been preferred for deep-level phylogenetic inference in angiosperms. The matK gene evolves approximately three times faster than the widely used plastid genes rbcL and atpB. The MP and BI trees are highly congruent. The robustness of the strict consensus tree supercedes all individual gene analyses and is comparable only to multigene-based phylogenies. Of the 385 nodes resolved, 79% are supported by high jackknife values, averaging 88%. Amborella is sister to the remaining angiosperms, followed by a grade of Nymphaeaceae and Austrobaileyales. Bayesian inference resolves Amborella + Nymphaeaceae as sister to the rest, but with weak (0.42) posterior probability. The MP analysis shows a trichotomy sister to the Austrobaileyales representing eumagnoliids, monocots + Chloranthales, and Ceratophyllum + eudicots. The mark gene produces the highest internal support yet for basal eudicots and, within core eudicots, resolves a crown group comprising Berberidopsidaceae/Aextoxicaceae, Santalales, and Caryophyllales + asterids. Moreover, matK sequences provide good resolution within many angiosperm orders. Combined analyses of mark and other rapidly evolving DNA regions with available multigene data sets have strong potential to enhance resolution and internal support in deep level angiosperm phylogenetics and provide additional insights into angiosperm evolution. Key words: angiosperms; Bayesian inference; matK; phylogeny; systematics. [ABSTRACT FROM AUTHOR]

Information about the Caryophyllales 2015 conference held at the Botanic Garden and Botanical Museum in Berlin, Germany from September 13-18, 2015 is presented. Topics include expanding the international Caryophyllales network, plant morphology, classifications and phylogeny, species diversity in angiosperm order Caryophyllales, and workshops introducing biodiversity informatics tools.

The article discusses highlights of a nymphaeales symposium that was held at the XVII International Botanical Congress in Vienna, Austria. An analysis provided an overview of the current understanding of evolutionary relationships in Nymphaeales based on sequence data of all three genomic compartments and morphology. A research explored leaf characters that are diverse and show phylogenetic information potential in Nymphaeales.