Showing papers in "Taxon in 2008"
TL;DR: The current results corroborate previous studies that identify a monophyletic subfamily Solanoideae and the more inclusive "x = 12" clade, which includes Nicotiana and the Australian tribe Anthocercideae, and provide greater resolution among lineages within Solanoidesae.
Abstract: A phylogeny of Solanaceae is presented based on the chloroplast DNA regions ndhF and trnLF. With 89 genera and 190 species included, this represents a nearly comprehensive genus-level sampling and provides a framework phylogeny for the entire family that helps integrate many previously-published phylogenetic studies within Solanaceae. The four genera comprising the family Goetzeaceae and the monotypic families Duckeodendraceae, Nolanaceae, and Sclerophylaceae, often recognized in traditional classifications, are shown to be included in Solanaceae. The current results corroborate previous studies that identify a monophyletic subfamily Solanoideae and the more inclusive "x = 12" clade, which includes Nicotiana and the Australian tribe Anthocercideae. These results also provide greater resolution among lineages within Solanoideae, confirming Jaltomata as sister to Solanum and identifying a clade comprised primarily of tribes Capsiceae (Capsicum and Lycianthes) and Physaleae. Stronger evidence also is provided for the inclusion of Capsicum within a paraphyletic Lycianthes. Solanaceae are a predominantly New World group, with several lineages represented on other continents. Apart from events within Solanum (for which sampling in this study is inadequate for biogeographic interpretations) the Old World representatives of Solanaceae can be accounted for by eight or nine dispersal events.
405 citations
TL;DR: Progress to date suggests that neither broad distribution nor large numbers of species in a family are insurmountable problems in compiling working lists, and the major barrier to completion of Target 1 remains the availability of taxonomists to contribute to the target.
Abstract: Target 1 of the Global Strategy for Plant Conservation (GSPC) is, "a widely accessible working list of all known plant species, as a step towards a complete world Flora". This paper discusses the importance of the Target to the GSPC itself, to many sectors of science and society, and to decision makers. It then examines the progress made to date and prospects for the Target's completion. Good progress has been made in bryophytes, ferns and gymnosperms with widely accessible working lists either complete or almost so for these groups. Online working lists are available for around 50% of flowering plants. In all, Target 1 is around 53% complete. It is estimated that there are around 352,000 flowering plants and that the current gap in online coverage is around 177,000 species. The major families constituting the gap are identified, the four largest being Apocynaceae, Malvaceae, Ericaceae and Apiaceae. The large majority of families for which there is no working list available are either cosmopolitan or pantropical in distribution. However, progress to date suggests that neither broad distribution nor large numbers of species in a family are insurmountable problems in compiling working lists. The major barrier to completion of Target 1 remains the availability of taxonomists to contribute to the target. Completion of Target 1 by 2010 is possible if botanical institutions recognise the importance of the Target and collaborate, lever funding and prioritise activities appropriately.
150 citations
TL;DR: This work used CRABS CLAW, a single-copy nuclear gene, to generate over 2,900 base pairs of new sequence data, and combined it with previously collected molecular data to examine morphological evolution in the Fagaceae, and proposed a new hypothesis to explain the evolution of the unusual cupules of Asian Lithocarpus and Chrysolepis.
Abstract: Fagaceae include nine genera and ca. 900 species, making it one of the largest and economically important groups within Fagales. Phylogenetic relationships remain unresolved despite a long history of systematic study. We used CRABS CLAW, a single-copy nuclear gene, to generate over 2,900 base pairs of new sequence data, and combined it with previously collected molecular data to examine morphological evolution in the Fagaceae. We clarified the relationships of Chrysolepis, Lithocarpus and Quercus, and in this improved phylogenetic context we inferred morphological transformations of the cupule. Phylogenetic analyses supported an origin for Quercus from a castaneoid ancestor and a novel sister group relationship for Asian Lithocarpus and Chrysolepis; however the monophyly of both Lithocarpus and subfamily Castaneoideae was rejected. Our data suggest that North American Lithocarpus densiflorus is distantly related to Asian Lithocarpus and more closely related to Quercus, supporting the hypothesis that the uniflorous cupules ofL. densiflorus and Quercus are derived from dichasium cupules via loss of lateral flowers. The sister group relationship of Asian Lithocarpus and Chrysolepis is supported by the morphological synapomorphy that each fruit is surrounded by a cupule. A new hypothesis is proposed to explain the evolution of the unusual cupules of Asian Lithocarpus and Chrysolepis. In this model, every flower represents a reduced dichasium, and we interpret the cupules of these taxa to be compound in nature, formed by multiple single-flowered cupules.
119 citations
TL;DR: The results indicate that Graphidaceae and Thelotremataceae cannot be separated, but form several lineages within one strongly supported monophyletic lineage.
Abstract: Family concepts in lichen-forming fungi are poorly understood and were traditionally based on easily observable characters. An example is the family Thelotremataceae, a species-rich group ofcrustose, predominantly tropical lichens with over 1,000 described species. Its distinction from Graphidaceae is largely based on ascoma shape (round vs. lirelliform). Previous studies already indicated that the distinction of these families is doubtful. However, these studies only included a few taxa of Thelotremataceae. Hence we obtained 96 new partial sequences of nuclear and mitochondrial ribosomal DNA, mostly of Thelotremataceae. We performed maximum parsimony and Bayesian phylogenetic analyses of a combined dataset of 105 samples, representing 97 species. Our results indicate that Graphidaceae and Thelotremataceae cannot be separated, but form several lineages within one strongly supported monophyletic lineage. Monophyly of Graphidaceae and Thelotremataceae each in their present circumscription was rejected significantly using two independent alternative topology tests. Consequently, Thelotremataceae is reduced to synonymy with Graphidaceae. Further, numerous genera in Graphidaceae and Thelotremataceae were found to be para- or polyphyletic, including all genera currently placed in Thelotremataceae, with the sole exception of Diploschistes. In Graphidaceae, Graphis and Sarcographa are polyphyletic as currently circumscribed. However, since the topology within Graphidaceae s.1. largely lacks support and given the large number of species not yet studied, a thorough evaluation of the generic concept requires a larger dataset, including additional genes and taxa.
114 citations
TL;DR: 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.
Abstract: 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, Austrobaileyales 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.
93 citations
TL;DR: The Artemisia/Kaschgaria lineage probably originated from an ancestor with disciform capitula, central hermaphrodite florets and Artemisia pollen type, and character reconstruction reveals that discoid capitula and Anthemis pollen type are the ancestral condition in the subtribe.
Abstract: To better understand the evolutionary history of the genus Artemisia (Anthemideae, Asteraceae) and its relationships to other genera of the subtribes Artemisiinae, Leucantheminae and Tanacetinae, 63 sequences of the external and 10 of the internal transcribed spacer of nuclear ribosomal DNA (ETS and ITS) were newly generated. Analyses were performed on the combined dataset using maximum parsimony, maximum likelihood and Bayesian inference. The combined analysis supports that all Artemisiinae genera included plus Hippolytia (subtribe Tanacetinae) and Nipponanthemum (subtribe Leucantheminae) constitute a monophyletic group. Within this group, a successive branching shows three monophyletic groups: (I) Nipponanthemuml Hippolytia/Brachanthemum; (2) the Dendranthema group; and (3) the Artemisia/Kaschgaria group. Within the latter, a new sister-group relationship is found between the monophyletic genus Kaschgaria and the Artemisia group, which comprises two main evolutionary lineages: (i) the Dracunculus clade including various Artemisia species and four Asian genera: Filifolium, Mausolea, Neopallasia and Turaniphytum; and (ii) the remaining subgenera of Artemisia plus the two North American genera: Picrothamnus and Sphaeromeria. Within this phylogenetic framework the evolution of two important characters (capitula and pollen type) in the group was inferred. Character reconstruction reveals that discoid capitula and Anthemis pollen type are the ancestral condition in the subtribe. The Artemisia/Kaschgaria lineage probably originated from an ancestor with disciform capitula, central hermaphrodite florets and Artemisia pollen type. Molecular evidence of several biogeographical migration routes of the genus Artemisia is presented.
87 citations
TL;DR: Opopanax and Smyrniopsis, traditionally treated in two tribes, are confirmed as monophyletic sister groups in the Apioid superclade.
Abstract: The flora of Iran is rich in endemic species of Apiaceae, many of which have been poorly investigated and whose phylogenetic relationships are unknown. We investigate the relationships within five genus groups of Apiaceae subfamily Apioideae native to the Flora Iranica region using nuclear ribosomal DNA ITS sequences. Supplementary comparative data come from morphology and, for one of these groups, petiole anatomy and palynology. These groups of Apioideae are circumscribed initially on the basis of morphological similarities and/or the results of previous molecular systematic investigations, then redefined and confirmed as monophyletic based on the results of maximum parsimony, maximum likelihood, and Bayesian analyses of ITS sequences from a broader sampling of species. These five redefined groups and their constituent genera include the Cachrys group (Alococarpum, Azilia, Bilacunaria, Cachrys, Diplotaenia, Eriocycla, Ferulago, Prangos), Cymbocarpum group (Cymbocarpum, Ducrosia, Kalakia), Ferula group (Dorema, Ferula, Leutea), Johrenia group (Holandrea, Johrenia, Johreniopsis), and Opopanax group (Opopanax, Smyrniopsis). Azilia eryngioides is a sister group to all other members of the Cachrys group, coincident with its highly unusual morphology. The monotypic Alococarpum may be transferred into Prangos pending further study. The Cymbocarpum group is contained within tribe Tordylieae, the latter now expanded to include Cymbocarpum, and the monotypic Kalakia is submerged within Cymbocarpum. Dorema and Leutea arise from within a paraphyletic Ferula in tribe Scandiceae; nomenclatural changes are suggested, but must await supporting evidence from chloroplast DNA. Neither Johrenia nor Johreniopsis of the Johrenia group (tribe Selineae) is monophyletic, with all examined species except Johrenia golestanica arising from within a paraphyletic Holandrea. Holandrea may be transferred into Johrenia and J. golestanica may constitute a new, monotypic genus pending confirmation from further investigations. Opopanax and Smyrniopsis, traditionally treated in two tribes, are confirmed as monophyletic sister groups in the Apioid superclade. They share similar morphological attributes and are closely allied to Petroedmondia, Magydaris, and Crenosciadium.
87 citations
TL;DR: It is argued that the efficacy of any particular plant DNA barcode selection should reflect the anticipated performance of the resulting barcode database in assignment of a query sequence to species, and a measure of barcode efficacy based on the rationale of database performance, "the probability of correct identification" (PCI).
Abstract: The selection of a DNA barcode in plants has been impeded in part due to the relatively low rates of nucleotide substitution observed at the most accessible plastid markers. However, the absence of consensus also reflects a lack of standards for comparing potential barcode markers. While many publications have suggested a host of plant DNA barcodes, the studies cannot be readily compared with each other through any quantitative or statistical parameter, partly because they put forward no single compelling rationale relevant to the adoption of a DNA barcode in plants. Here, we argue that the efficacy of any particular plant DNA barcode selection should reflect the anticipated performance of the resulting barcode database in assignment of a query sequence to species. While legitimate scientific disagreement exists over the criteria relevant to “database performance”, the notion gives a unifying rationale for prioritizing selection criteria. Accordingly, we suggest a measure of barcode efficacy based on the rationale of database performance, “the probability of correct identification” (PCI). Moreover, the definition of PCI is left flexible enough to handle most of the scientific disagreement over how to best evaluate DNA barcodes. Finally, we consider how different types of barcodes might require different methods of analysis and database design and indicate how the analysis might affect the selection of the most broadly effective barcode for land plants.
83 citations
TL;DR: Overall, psbA-trnH, currently a candidate for plant barcoding, was the least discriminatory region in this study.
Abstract: The DNA barcode potential of three regions (the nuclear ribosomal ITS and the plastid psbA-trnH and trnT-trnL intergenic spacers) was investigated for the plant genus Aspalathus L. (Fabaceac: Crotalarieae). Aspalathus is a large genus (278 species) that revealed low levels of DNA variation in phylogenetic studies. In a 51-species dataset for the psbA-trnH and ITS regions, 45%, and 16% of sequences respectively were identical to the sequence of at least one other species, with two species undiscriminated even when the two regions were combined. In contrast, trnT-trnL, discriminated between all species in this dataset. In a larger ITS and trnT-trnL dataset. including a further 82 species. 7 species in five pairwise comparisons remained Undiscriminated when the two regions were combined. Four of the five pairs of species not discriminated by sequence data were readily distinguished using a combination of qualitative and quantitative morphological data. The difficulty of barcoding in this group is increased by the presence of intraspecific variation in all three regions studied. In the case of psbA-trnH, three intraspecific samples had a sequence identical to at least one other species. Overall, psbA-trnH. currently a candidate for plant barcoding, was the least discriminatory region in our study.
74 citations
TL;DR: The Hengduan Mountains of the Sino-Himalayas are rich in endemic species of Apiaceae subfamily Apioideae and to ascertain their higher-level phylogenetic placements within the subfamily, 106 accessions were examined including the Chinese endemic genera Changium, Cyclorhiza, Notopterygium, Nothosmyrnium, and Sinolimprichtia.
Abstract: The Hengduan Mountains of the Sino-Himalayas are rich in endemic species of Apiaceae subfamily Apioideae. To investigate relationships among these species and to ascertain their higher-level phylogenetic placements within the subfamily, we examined 106 accessions (representing 100 species from 52 genera) including the Chinese endemic genera Changium, Cyclorhiza, Notopterygium, Nothosmyrnium, and Sinolimprichtia. Sixty-three of these accessions were newly sequenced. Phylogenetic trees were inferred using maximum parsimony and Bayesian analyses of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences. The phylogenetic trees were highly consistent and revealed several major clades heretofore unrecognized in the subfamily. Changium and Cyclorhiza fall within the Komarovia clade of previous investigations and Nothosmyrnium allies with tribe Pimpinelleae. Notopterygium and Sinolimprichtia along with many other taxa of Sino-Himalayan distribution comprise a well-supported East Asia clade; Vicatia and Haplosphaera arise within a paraphyletic Notopterygium. Other newly recognized, well-supported major clades include the Chamaesium clade, sister group to all other examined Apioideae except tribe Bupleureae, and the Asian Acronema clade, sister group to tribe Scandiceae. The Chamaesium clade and Bupleureae may represent the earliest diverging lineages of Apioideae in Asia. Sinodielsia allies weakly with Pterocyclus or is a sister group to the clade of tribe Apieae plus Pterocyclus; Sinodielsia is distinct from Meeboldia and Vicatia. Genera whose boundaries are poorly defined and controversial on the basis of morphology (Ligusticum, Peucedanum, Physospermopsis, Pimpinella, Pleurospermum, Sinocarum, Tongoloa, Trachyspermum) are not monophyletic in the ITS-based phylogenies. Further study of these Chinese endemics is necessary to produce a comprehensive, modern classification of Apiaceae subfamily Apioideae.
TL;DR: The carpel morphology clearly differs from extant Cabombaceae so that Pluricarpellatia is considered to represent an extinct member of Nymphaeales, most likely branching off early in this lineage, and may thus be the most basal member of this clade described so far.
Abstract: A fossil herbaceous angiosperm, Pluricarpellatia peltata gen. et sp. nov., is described from the Lower Cretaceous Crato Formation of northeastern Brazil. The description is based on several nearly complete specimens with roots, cordate, excentrically peltate to centrally peltate leaves, and flowering structures with in situ seeds. The seeds are smooth to verrucate and have the micropyle and hilum close together and have laminar placentation. Pluricarpellatia shares several characters with extant Nymphaeales, such as a rhizomatous growth form and simple, petiolate, peltate leaves, and laminar placentation. Similarities to Cabombaceae include an apocarpous gynoecium. However, the carpel morphology clearly differs from extant Cabombaceae so that Pluricarpellatia is considered to represent an extinct member of Nymphaeales, most likely branching off early in this lineage, and may thus be the most basal member of this clade described so far. In addition to Pluricarpellatia an unnamed nymphaealean plant (Taxon A), possibly belonging to the Nymphaeaceae, is described. During the late Aptian to earliest Albian representatives of Nymphaeales may have already developed a moderate diversity.
TL;DR: The phylogenetic hypothesis is in conflict with the primary classification of Mathew into subgenera and sections, most notably by placing the highly morphologically deviant C. banaticus not as sister group to subgenus Crocus but imbedded within it.
Abstract: For the first time a phylogenetic analysis of the genus Crocus is presented. The phylogeny includes all but two of the currently 88 recognized species of the genus. The analysis is based on a total of 222 phylogenetically informative characters derived from nucleotide sequence data from three protein-coding (ndhF, accD, rpoC1) and two non-coding (trnH-pshA, rpl36-rps8) plastid regions. The phylogenetic hypothesis is in conflict with the primary classification of Mathew into subgenera and sections, most notably by placing the highly morphologically deviant C. banaticus (subgenus Crociris) not as sister group to subgenus Crocus but imbedded within it. The grouping of the taxa into series is better supported, though not entirely. Of the fifteen series recognized by Mathew, eight are confirmed as being monophyletic, monophyly of one more remains a possibility, and monophyly of a further two series is only violated by one taxon. Not unexpectedly, the two most species-rich groups, series Reticulati and series Biflori encompassing almost 1/3 of all species, are clearly non-monophyletic, but the present data do not satisfactorily solve their phylogenetic relationships.
TL;DR: The recent reclassification of Veronica to include the Southern Hemisphere Hebe-complex, North American Synthyris and Besseya, and the Eurasian Pseudolysimachion necessitated numerous nomenclatural changes including 24 new combinations in the latter presented here.
Abstract: The genus Veronica and its previous segregates have become one focus of the debate on whether to include paraphyletic taxa in classifications. The recent reclassification of Veronica to include the Southern Hemisphere Hebe-complex, North American Synthyris and Besseya, and the Eurasian Pseudolysimachion necessitated numerous nomenclatural changes including 24 new combinations in the latter presented here. The example of Pseudolysimachion demonstrates well the problems of paraphyletic taxa in classifications and therefore can serve as an exemplar.
TL;DR: Calcareous dinoflagellates are considered to be a monophyletic group of peridinoid taxa that have the potential to produce calcified exoskeletal structures during the life cycle, or that derive fro the fossil record through “cell reprograming”.
Abstract: Calcareous dinoflagellates are considered to be a monophyletic group of peridinoid taxa that have the potential to produce calcified exoskeletal structures during the life cycle, or that derive fro ...
TL;DR: The phylogenetic hypothesis presented here helps to resolve outstanding nomenclatural issues and provides a basis for examining character evolution within this diverse, desert-adapted clade of ferns.
Abstract: Cheilanthoid ferns (Pteridaceae) are a diverse and ecologically important clade, unusual among ferns for their ability to colonize and diversify within xeric habitats. These extreme habitats are thought to drive the extensive evolutionary convergence, and thus morphological homoplasy, that has long thwarted a natural classification of cheilanthoid ferns. Here we present the first multigene phylogeny to focus on taxa traditionally assigned to the large genus Notholaena. New World taxa (Notholaena sensu Tryon) are only distantly related to species occurring in the Old World (Notholaena sensu Pichi Sermolli). The circumscription of Notholaena adopted in recent American floras is shown to be paraphyletic, with species usually assigned to Cheilanthes and Cheiloplecton nested within it. The position of Cheiloplecton is particularly surprising-given its well-developed false indusium and non-farinose blade, it is morphologically anomalous within the "notholaenoids". In addition to clarifying natural relationships, the phylogenetic hypothesis presented here helps to resolve outstanding nomenclatural issues and provides a basis for examining character evolution within this diverse, desert-adapted clade.
TL;DR: A single genus of Hydatel-laceae, Trithuria, is distinguished, which consists of one species in New Zealand, ten species in Australia and two species in India, and is hypothesize that two south-western Australian endemics known as Hydatella dioica and Trithia occidentalis represent male and female individuals, respectively, of the same biological species.
Abstract: Hydatellaceae was traditionally circumscribed as a family of two genera, Hydatella and Trithuria. We place Hydatella in synonymy of Trithuria. We describe three new species of Hydatellaceae from northern Australia and one new species from south-western Western Australia. Thus, we distinguish a single genus of Hydatel-laceae, Trithuria, which consists of one species in New Zealand, ten species in Australia and one species in India. Two main characters were formerly used to distinguish between Hydatella and Trithuria: (1) reproductive units unisexual (homogamous) vs. bisexual (heterogamous) and (2) fruits with three prominent ribs, typically dehiscent vs. without prominent ribs, indehiscent. New evidence shows that the type of reproductive unit does not correlate with fruit morphology in Hydatellaceae. We hypothesize that two south-western Australian endemics known as Hydatella dioica and Trithuria occidentalis represent male and female individuals, respectively, of the same biological species. All four dioecious species of Hydatellaceae show similar sexual dimorphism. Male plants have reproductive units with longer and fewer involucral bracts than female ones. Anthers are much longer in dioecious species than in the morphologically closest cosexual species. The evolutionary significance of dioecy in Hydatellaceae is discussed.
TL;DR: These analyses support the monophyly of the four major clades and the relationships among them, andAsterales are inferred to be sister to a clade containing Apiales and Dipsacales, which is consistent with more weakly supported results from previous studies.
Abstract: Broad-scale phylogenetic analyses of the angiosperms and of the Asteridae have failed to confidently resolve relationships among the major lineages of the campanulid Asteridae (i.e., the euasterid II ofAPG II, 2003). To address this problem we assembled presently available sequences for a core set of 50 taxa, representing the diversity of the four largest lineages (Apiales, Aquifoliales, Asterales, Dipsacales) as well as the smaller "unplaced" groups (e.g., Bruniaceae, Paracryphiaceae, Columelliaceae). We constructed four data matrices for phylogenetic analysis: a chloroplast coding matrix (atpB, matK, ndhF, rbcL), a chloroplast non-coding matrix (rpsl6 intron, trnT-F region, trnV-atpE IGS), a combined chloroplast dataset (all seven chloroplast regions), and a combined genome matrix (seven chloroplast regions plus 18S and 26S rDNA). Bayesian analyses of these datasets using mixed substitution models produced often well-resolved and supported trees. Consistent with more weakly supported results from previous studies, our analyses support the monophyly of the four major clades and the relationships among them. Most importantly, Asterales are inferred to be sister to a clade containing Apiales and Dipsacales. Paracryphiaceae is consistently placed sister to the Dipsacales. However, the exact relationships of Bruniaceae, Columelliaceae, and an Escallonia clade depended upon the dataset. Areas of poor resolution in combined analyses may be partly explained by conflict between the coding and non-coding data partitions. We discuss the implications of these results for our understanding of campanulid phylogeny and evolution, paying special attention to how our findings bear on character evolution and biogeography in Dipsacales.
TL;DR: A critical reevaluation of carpological characters traditionally used to delimit Lithodora corroborates the results of the molecular analysis and indicates that the cupulate areole and the mericarpid appendage found in the genus are homoplasious.
Abstract: Lithodora (Boraginaceae tribe Lithospermeae) comprises nine species of often narrowly endemic dwarf shrubs and shrubs. The genus shows a Mediterranean distribution with the centre of diversity in the western Mediterranean region. Lithodora is distinguished from its allies in Lithospermeae by a shrubby habit, the absence of both faucal scales and an annulus, and a very unusual mericarpid morphology, and it has therefore been regarded as a natural group in the past. Phylogenetic relationships of Lithodora were investigated with nuclear ribosomal ITS1 and chloroplast trnL UAA intron sequences using parsimony and likelihood analyses. The results strongly indicate a polyphyly of Lithodora, which falls into two clades: The majority of species forms a monophyletic group ("Lithodora II") in a well supported clade together with a Lithospermum s.1. clade (including the New World genera Onosmodium and Macromeria) and our sample of Buglossoides species. A smaller number of species ("Lithodora I") falls into a second well supported clade including the monotypic genera Mairetis, Paramoltkia and Halacsya. A critical reevaluation of carpological characters traditionally used to delimit Lithodora corroborates the results of the molecular analysis and indicates that the cupulate areole and the mericarpid appendage found in the genus are homoplasious. The polyphyly of Lithodora is formally recognised by removing "Lithodora II" as a newly established genus, Glandora. The seven newly required combinations in the genus are provided.
Journal Article•
TL;DR: This study presents the first phylogenetic study of Edraianthus based on multiple plastid DNA sequences derived from a wide taxonomic sampling and geographic range and strongly supports its monophyly as currently circumscribed.
Abstract: The Balkan Peninsula is known as an ice-age refugium and an area with high rates of speciation and diversification. Only a few genera have their centers of distribution in the Balkans and the endemic genus Edraianthus is one of its most prominent groups. As such, Edraianthus is an excellent model not only for studying speciation processes and genetic diversity but also for testing hypotheses regarding biogeography, identification and characterization of refugia, as well as post-glacial colonization and migration dynamics in SE Europe. The genus comprises 10 to 28 species and was traditionally divided into three sections: E. sect. Edraianthus, E. sect. Uniflori, and E. sect. Spathulati. We present here the first phylogenetic study of Edraianthus based on multiple plastid DNA sequences (trnL-F region and rbcL-atpB spacer) derived from a wide taxonomic sampling and geographic range. While the sister-group to Edraianthus could not be ascertained, the results strongly support its monophyly as currently circumscribed. The phylogentic relationships among Edraianthus and its closely related genera Halacsyella, Petkovia, Muehlbergella, and Protoedraianthus are discussed and their respective taxonomical standings are reevaluated based on molecular evidence. Our study identified several distinct monophyletic groups within Edraianthus, some of which correspond closely to previously established taxonomic treatments and some of which are first identified here. Morphologic, taxonomic, and biogeographic implications of these relationships are also discussed.
TL;DR: This work critically discusses the most recent taxonomic and systematic conclusions in the light of a worldwide screening of genetic diversity within the genus Arabidopsis and defines gaps of knowledge to focus and stimulate future research activities.
Abstract: Since the introduction of Arabidopsis thaliana, the Thale Cress, to a broader scientific community in 1965, nearly 40 years passed until the phylogenetic position of this species was resolved and its closest relatives were characterized. More and more molecular data is available for Arabidopsis thaliana and it has become the most important model system among dicotyledonous plants. However, Arabidopsis thaliana provides only a limited set of traits and characters. We are now in the position that scientists move into the more diverse relatives of Arabidopsis, transferring knowledge from the model plant to these species. Hereby past taxonomy and phylogenetic concepts may lead to misunderstanding and confusion. Consequently there is much need to provide a comprehensive overview on current knowledge of systematics, evolution and diversity of Arabidopsis and its relatives, despite the several actual reviews focusing on various aspects of its taxonomy, ecology, and importance as model system considering also the closest wild relatives. Herein, we aim to critically discuss the most recent taxonomic and systematic conclusions in the light of a worldwide screening of genetic diversity within the genus Arabidopsis. We also define gaps of knowledge to focus and stimulate future research activities.
TL;DR: It is hypothesized 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.
Abstract: 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 ofCabombaceae 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 (Cabombaceae, 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.
TL;DR: The results of maximum parsimony analysis of 125 nuclear rDNA ITS sequences representing all tribes and major clades of the apioid superclade and closely related outgroups support the separation of the African group of genera from that of Eurasian Peucedanum.
Abstract: The African species currently residing in Peucedanum L. and associated platyspermous genera are not related to the Eurasian Peucedanum species. As the type of the genus is P. officinale L., which is part of the Eurasian group, a new generic classification is proposed for the African group. The affinities and circumscriptions of two previously enigmatic monotypic genera, Afroligusticum C. Norman and Erythroselinum Chiov., are clarified. The former is expanded, while the latter is subsumed into Lefebvrea A. Rich. along with six Peucedanum species. New combinations are formalized for 49 of the 58 species recognised, which are accommodated in six genera, as follows: Afroligusticum (13 spp.), Afrosciadium P.J.D. Winter gen. nov. (18 spp.), Cynorhiza Eckl. & Zeyh. (3 spp.), Lefebvrea (10 spp.), Nanobubon A.R. Magee gen. nov. (2 spp.), and Notobubon B.-E. van Wyk gen. nov. (12 spp.). Ten new synonyms are presented, in Cynorhiza (2), Lefebvrea (6) and Notobubon (2). Diagnostic characters include habit (woody shrubs, perennial herbs or monocarpic herbs), seasonality (evergreen or deciduous), leaf texture and arrangement, inflorescence structure, fruit morphology (size, shape and wing configuration) and fruit anatomy. The results of maximum parsimony analysis of 125 nuclear rDNA ITS sequences representing all tribes and major clades of the apioid superclade and closely related outgroups support the separation of the African group of genera from that of Eurasian Peucedanum.
TL;DR: The molecular data does not support Babcock's sectional delimitation of Crepis L.str which is mainly based on his hypotheses about karyotype evolution, so morphological and karyological characters are re-assessed with regard to the molecular phylogeny.
Abstract: In 1947 Babcock published his widely acknowledged monograph of the genus Crepis L. including a sectional classification of the species as well as extensive hypotheses about character evolution. To reinvestigate Babcock's evolutionary hypotheses and the generic delimitation of Crepis L. a phylogenetic analysis was conducted using ITS and chloroplast matK sequence data. The results revealed Crepis L. to be polyphyletic. A monophyletic clade including Central Asian and North American species of Crepis sect. Ixeridopsis is clearly isolated from Crepis s.str. and, as also supported by additional morphological evidence, needs to be transferred to the genus Askellia Weber (1984). A second clade comprising the genera Lapsana L. and Rhagadiolus Juss. as well as a statistically strongly supported clade of several Crepis species is sister to a third clade: the monophyletic Crepis s.str. Within Crepis s.str. the molecular data does not support Babcock's sectional delimitation which is mainly based on his hypotheses about karyotype evolution. Hence, morphological and karyological characters are re-assessed with regard to the molecular phylogeny.
TL;DR: A simple and reliable method for the extraction of nuclear DNA from grains of herbarium specimens ofmer wheat is presented, along with a method to determine the level of DNA preservation with a set of PCR primers based on the nuclear high-molecular-weight glutenin gene.
Abstract: In this paper we present a simple and reliable method for the extraction of nuclear DNA from grains of herbarium specimens ofemmer wheat, along with a method to determine the level of DNA preservation with a set ofPCR primers based on the nuclear high-molecular-weight glutenin gene. The method gave PCR products of between 80 and 1,030 bp. PCR products from each set of amplification reactions were cloned and sequenced in order to confirm their identity. We have found excellent levels of DNA preservation in grain between 49 and 107 years old, consistently amplifying products of at least 350 bp.
Journal Article•
TL;DR: In this paper, the authors used maximum parsimony and Bayesian analyses using molecular data and combined anatomical-molecular data to show that Icacinaceae s.str. are not monophyletic and their closest relatives remain unclear.
Abstract: Wood samples from 53 species belonging to 41 genera of the Icacinaceae s.l. are investigated using light and scanning electron microscopy. The traditionally circumscribed Icacinaceae fall apart into four segregate families that are clearly nested within asterids, i.e., Icacinaceae s.str. (near or in Garryales), Cardiopteridaceae and Stemonuraceae (both Aquifoliales), and Pennantiaceae (Apiales). From a wood anatomical point of view, these families cannot easily be distinguished from each other. However, some features such as vessel distribution, perforation plate morphology, size and arrangement of vessel pits, fibre wall thickness, and the occurrence of cambial variants can be used to assign various species to one of the four families. The wood structure of the four segregate families is in general agreement with their suggested putative relatives, but the occurrence of lianas versus erect trees and shrubs is a confusing factor in getting clear phylogenetic signal from the wood structure. Maximum parsimony and Bayesian analyses using molecular data and combined anatomical-molecular data show that Icacinaceae s.str. are not monophyletic, and their closest relatives remain unclear. The combined analyses provide moderate support for a clade including Cassinopsis, the Apodytes-group, the Emmotum-group (all Icacinaceae s.str.), and the genus Oncotheca. This clade is situated at the base of lamiids and may be closely related to Garryales. The remaining lineage of Icacinaceae s.str., the Icacina-group represented by many climbing taxa exhibiting cambial variants, is strongly supported and might be sister to the rest of lamiids.
TL;DR: The presented results support trnH-psbA as appropriate for completing the plant section of the Moorea Biocode, although the use of additional markers will be necessary.
Abstract: The Moorea Biocode seeks to compile an integrative taxonomy based on morphological, ecological, and molecular data for the entire macrobiota of the island of Moorea, French Polynesia. As a case study exploring the utility of selected molecular data for species identification within this integrative taxonomic framework, chloroplast DNA from three regions (rbcL, trnSGG, trnH-psbA) were sequenced for all species of filmy ferns (Hymenophyllaceae) known from Moorea. The relative utility of each of these regions for the purposes of phylogenetic analysis and DNA-based identification was inferred by estimating support for phylogenetic trees reconstructed from each region and by calculating intraspecific and interspecific distance values (uncorrected p) between taxa for each region. All three of these regions were found to be potentially useful for phylogenetic studies at the appropriate taxonomic level. trnH-psbA was determined to have the greatest utility as a potential marker for DNA-based identification because of its high interspecific variability and high degree of amplification success. rbcL and trnH-psbA were successfully used in combination with morphological characters to identify a previously unidentified Moorean filmy fern species, Polyphlebium borbonlcum. The presented results support trnH-psbA as appropriate for completing the plant section of the Moorea Biocode, although the use of additional markers will be necessary.
TL;DR: A taxonomic revision of marattioid ferns is presented here, and species-level detail is given for Marattia s.l.str.
Abstract: Recent phylogenetic investigations of marattioid ferns (Marattiaceae) have generated a refined understanding of genus- and species-level relationships within the family. A taxonomic revision of marattioid ferns is presented here. This new taxonomy is congruent with the current understanding of the phylogeny ofmarattioid ferns based on both molecular and morphological data. Marattiaceae is recognized here in the broad and most commonly used sense, encompassing all extant genera. Marattia as traditionally defined is paraphyletic, and is split here into three morphologically distinct and monophyletic genera: Marattia s.str. is restricted to the Neotropics and Hawaii; Eupodium, a distinctive Neotropical genus that has not been recognized by recent authors, is resurrected; and a newly described genus Ptisana comprises the Paleotropical species. Angiopteris is circumscribed broadly to include Archangiopteris, Macroglossum, Protomarattia, and Protangiopteris. Neither Danaea nor Christensenia require changes to their circumscriptions. As Marattia s.l. is undergoing the most drastic change in this taxonomy, species-level detail is given for Marattia s.str. and the segregated genera Eupodium and Ptisana. New combinations are made in Eupodium and Ptisana. Considerable monographic work still remains to be done, and is of particular importance given the threatened status of many presently poorly understood species in this family.
TL;DR: The taxonomic status of Taxus in Pakistan was confused and uncertain due to opposing views about specimen identities and character combinations allowed the reliable identification of specimens of T. fuana, T. baccata and T. wallichiana.
Abstract: The taxonomic status of Taxus in Pakistan was confused and uncertain due to opposing views about specimen identities. We used 27 morphological characters of 62 selected herbarium specimens of T. baccata, T. wallichiona and tentatively identified T. fuana to investigate the taxonomic status of Taxus in Pakistan by principal component analysis (PCA). Three discrete clusters representing the three species were identified in the PCA scatter plot. Character combinations allowed the reliable identification of specimens of T. fuana, T. baccata and T. wallichiana. Sequence data of nuclear ribosomal DNA ITS and the chloroplast trnL-F region were used to further delimitate T. baccata, T. wallichiana and T. fuana. Using maximum parsimony analysis three distinct clades were obtained representing the three species with strong bootstrap support. Based on both morphological and molecular sequence data, the Taxus species occurring in the western Himalaya including Pakistan was shown to be T. fuana and not T. wallichiana or T. baccata. The distinct species status of T. fuana, T. baccata and T. wallichiana was also well supported and found to be well correlated with their geographic distributions. The geographic ranges of the three species were updated based on the present study.