Showing papers in "Taxon in 2012"

A revised family–level classification for eupolypod II ferns (Polypodiidae: Polypodiales)

Abstract: We present a family-level classification for the eupolypod II clade of leptosporangiate ferns, one of the two major lineages within the Eupolypods, and one of the few parts of the fern tree of life where family-level relationships were not well understood at the time of publication of the 2006 fern classification by Smith & al. Comprising over 2500 species, the composition and particularly the relationships among the major clades of this group have historically been contentious and defied phylogenetic resolution until very recently. Our classification reflects the most current available data, largely derived from published molecular phylogenetic studies. In comparison with the five-family (Aspleniaceae, Blechnaceae, Onocleaceae, Thelypteridaceae, Woodsiaceae) treatment of Smith & al., we recognize 10 families within the eupolypod II clade. Of these, Aspleniaceae, Thelypteridaceae, Blechnaceae, and Onocleaceae have the same composition as treated by Smith & al. Woodsia- ceae, which Smith & al. acknowledged as possibly non-monophyletic in their treatment, is circumscribed here to include only Woodsia and its segregates; the other "woodsioid" taxa are divided among Athyriaceae, Cystopteridaceae, Diplaziopsidaceae, Rhachidosoraceae, and Hemidictyaceae. We provide circumscriptions for each family, which summarize their morphological, geographical, and ecological characters, as well as a dichotomous key to the eupolypod II families. Three of these families— Diplaziopsidaceae, Hemidictyaceae, and Rhachidosoraceae—were described in the past year based on molecular phylogenetic analyses; we provide here their first morphological treatment.

Molecular phylogenetics and classification of Euphorbia subgenus Chamaesyce (Euphorbiaceae)

Abstract: Euphorbia subg. Chamaesyce contains around 600 species and includes the largest New World radiation within the Old World-centered genus Euphorbia. It is one of the few plant lineages to include members with C3, C4 and CAM photosynthesis, showing multiple adaptations to warm and dry habitats. The subgenus includes North American-centered groups that were previously treated at various taxonomic ranks under the names of “Agaloma ”, “Poinsettia ”, and “Chamaesyce ”. Here we provide a well-resolved phylogeny of Euphorbia subg. Chamaesyce using nuclear ribosomal ITS and chloroplast ndhF sequences, with substantially increased taxon sampling compared to previous studies. Based on the phylogeny, we discuss the Old World origin of the subgenus, the evolution of cyathial morphology and growth forms, and then provide a formal sectional classification, with descriptions and species lists for each section or subsection we recognize.

Systematics and evolution of the needle grasses (Poaceae: Pooideae: Stipeae) based on analysis of multiple chloroplast loci, ITS, and lemma micromorphology

Abstract: We conducted a molecular phylogenetic study of the tribe Stipeae using nine plastid DNA sequences (trnK-matK, matK, trnH-psbA, trnL-F, rps3, ndhF, rpl32-trnL, rps16-trnK, rps16 intron), the nuclear ITS DNA regions, and micromorphological characters from the lemma surface Our large original dataset includes 156 accessions representing 139 species of Stipeae representing all genera currently placed in the tribe The maximum likelihood and Bayesian analyses of DNA sequences provide strong support for the monophyly of Stipeae; including, in phylogenetic order, Macrochloa as remote sister lineage to all other Stipeae, then a primary stepwise divergence of three deep lineages with a saw-like (SL) lemma epidermal pattern (a plesiomorphic state) The next split is between a lineage (SL1) which bifurcates into separate Eurasian and American clades, and a lineage of three parts; a small Patis (SL2) clade, as sister to Piptatherum sstr (SL3), and the achnatheroid clade (AC) The AC exhibits a maize-like lemma epidermal pattern throughout AC consists of a core clade of Austral-Eurasian distribution and a “major American clade” of North and South American distribution The base chromosome number for Stipeae is somewhat ambiguous but based on our survey it seems most likely to be x = 11 or 12 Our phylogenetic hypothesis supports the recognition of the following genera and groups (listed by region): Eurasia—Achnatherum, “Miliacea group”, “Neotrinia” (monotypic), Orthoraphium (monotypic), Patis (also 1 from North America), Piptatherum sstr, Psammochloa (monotypic), Ptilagrostis, Stipa, “Timouria group”, and Trikeraia; Mediterranean—Ampelodesmos (monotypic), Celtica (monotypic), Macrochloa (monotypic), and “Stipella-Inaequiglumes group”; Australasia —Anemanthele (monotypic), and Austrostipa; North America (NA)—“Eriocoma group”, Hesperostipa, Oryzopsis (monotypic), Piptatheropsis, “Pseudoeriocoma group”, and “Stillmania” (monotypic); South America—Aciachne, Amelichloa (also NA), Anatherostipa (sstr), Jarava (polyphyletic), Lorenzochloa, Nassella (also NA), Ortachne, Pappostipa (also NA), and Piptochaetium (also NA) Monophyly of Phaenospermateae including Duthieinae is demonstrated, and its inclusion within or treatment as sister to Stipeae is rejected

Phylogeny of Curcuma (Zingiberaceae) based on plastid and nuclear sequences: Proposal of the new subgenus Ecomata

Abstract: Curcuma L. (Zingiberaceae), with at least 120 species, is the third-largest genus in the primarily tropical Zingiberaceae (ca. 50 genera, > 1500 spp.). It is a diverse polyploid complex containing many taxa of economic, medicinal, ornamental and cultural importance, the type species of the genus, C. longa L. (turmeric) being the best-known example. Curcuma is distributed throughout South and Southeast Asia, with a few species extending to China, Australia and the South Pacific. The highest diversity is concentrated in monsoonal Asia from India to Indochina (Škorničková, 2007). Despite the considerable economic potential of this genus, its phylogeny and taxonomy remain poorly understood, mainly due to extensive polyploidization (2x–15x) and hybridization (Leong-Škorničková & al., 2007; Záveská & al., 2011) resulting in different levels of genetic and morphological variation among species and in blurred species boundaries (Škorničková, 2007). The nomenclatural complexity of the group, together with the cultivation and spread by humans of numerous species across the tropics, has further contributed to the misapplication of names (LeongŠkorničková & al., 2008a, b, 2010). Recent explorations of the Phylogeny of Curcuma (Zingiberaceae) based on plastid and nuclear sequences: Proposal of the new subgenus Ecomata

Morphology, ploidy and molecular phylogenetics reveal a new diploid species from Africa in the baobab genus Adansonia (Malvaceae: Bombacoideae)

Abstract: The genus Adansonia has a disjunct geographical distribution: six species are endemic in Madagascar, one in Africa, and one in Australia. The well-known African baobab (Adansonia digitata) is an iconic tree with considerable ethnobotanical significance. In contrast to the other seven species, which are diploid, A. digitata is tetraploid. A common ancestor of A. digitata and the other diploid baobab species would be diploid; however, there are no diploid species recorded on the African mainland. Examining variation in floral and pollen characters and chromosome number in specimens from Africa identified a new diploid baobab species, Adansonia kilima sp. nov., which co-exists with A. digitata in Africa. Adansonia kilima is restricted to moderate elevations (650-1500 m), in contrast to A. digitata, which is widespread throughout Africa but prefers elevations below 800 m. Adansonia kilima is superficially similar to A. digitata, but can be differentiated on the basis of floral morphology, pollen, and chromosome number. We used two chloroplast DNA markers and the nuclear ITS to examine phylogenetic relationships within Adansonia. Three lineages were observed: one containing the Malagasy species, one containing the Australian species, and one containing the African species. The relationships between these clades were difficult to resolve, but a link between the African and Australian clades emerged when the analysis used fewer replicate samples of individual Malagasy taxa, included indel characters and included fewer outgroup taxa. The ITS phylogeny demonstrated that A. digitata and A. kilima are geneti- cally similar, suggesting that tetraploidy evolved relatively recently.

A fully resolved chloroplast phylogeny of the brassica crops and wild relatives (Brassicaceae: Brassiceae): Novel clades and potential taxonomic implications

Abstract: Brassicas boast an enormous diversity of economically important products. Strikingly, relationships among main lineages are still unknown. The phylogeny of the tribe Brassiceae (Brassicaceae) was reconstructed for 89 species using four plastid regions (rpl32-trnL, atpI-atpH, psbD-trnT, ycf6-psbM ). Representatives of almost all genera were sampled, covering the entire natural range of the tribe from Central Asia to the western Mediterranean, including four previously unsampled genera (Ammosperma, Eremophyton, Fezia, Pseudofortuynia). Phylogenetic analysis recovered eight well-supported clades in the tribe including a new African clade (Henophyton) comprised of genera that have not been previously sampled. Relationships within and between the eight major clades are strongly supported for the first time. The earliest-divergent lineages in the tribe are the clades Vella and Zilla. Henophyton is sister to the clade that includes the lineages Nigra, Crambe, Cakile, Savignya, and Oleracea. Core Brassiceae—a new clade defined here—is comprised of two subclades: (1) Nigra, Crambe, and Cakile and (2) Savignya and Oleracea. Within the Oleracea lineage, a new Core Oleracea clade is defined. Several genera were confirmed to be polyphyletic or paraphyletic, including Brassica, Erucastrum, Sinapis, Diplotaxis and Cakile. Economically important spe- cies belonging to the genera Brassica were primarily distributed across the two most species-rich lineages, Nigra or Oleracea. Collectively, the finding of these novel clades has numerous taxonomic implications.

Automatic Extraction of Leaf Characters from Herbarium Specimens

Abstract: Herbarium specimens are a vital resource in botanical taxonomy. Many herbaria are undertaking large-scale digitization projects to improve access and to preserve delicate specimens, and in doing so are creating large sets of images. Leaf characters are important for describing taxa and distinguishing between them and they can be measured from herbarium specimens. Here, we demonstrate that herbarium images can be analysed using suitable software and that leaf characters can be extracted automatically. We describe a low-cost digitization process that we use to create a set of 1,895 images of Tilia L. specimens, and novel botanical image processing software. The output of the software is a set of leaf characters. As a demonstration of this approach, we extract the length and width of a large number of leaves automatically from images of whole herbarium specimens. We show that the lengths and widths that we extract are very strongly correlated with values in a published account of cultivated species, but are also consistently smaller. We discuss some particular features of herbarium specimens that may affect the results of this form of analysis, and consider further applications to extract characters such as leaf shape and margin characters.

Cryptic taxa should have names: Reflections in the glasswort genus Salicornia (Amaranthaceae)

Abstract: Incongruence between morphology and molecules, i.e., genetic differentiation of lineages that are morphologically identical, or morphological variation among accessions sharing identical genotypes, has been increasingly reported and is most problematic in taxa with reduced morphologies. We here review and discuss these issues for plant taxonomy, taking Salicornia, one of the taxonomically most challenging genera of angiosperms, as a model. We argue in favour of a taxonomic system that remains as much 'workable' as possible for traditional morphology-based taxonomy, but avoids merging genetically widely divergent lineages despite their morphological similarity. Our revised classification of Eurasian taxa includes four species, ten subspecies and one nothosubspecies. The molecular and morphological characteristics as well as the geographical distribu- tion of each taxon are described. A key to the Eurasian taxa based on morphology and geographical distribution is presented.

Revised systematics of Mediterranean Arundo (Poaceae) based on AFLP fingerprints and morphology

Abstract: The systematics of the genus Arundo (Poaceae) remains poorly resolved because of the overlap of morphologi- cal characters classically used in the taxonomy of the genus and insufficient variation of DNA sequences. The main aim of this study is to delimit genetic clusters with AFLP fingerprints and to compare them with morphological data. On the basis of extensive sampling in the Mediterranean area, AFLP markers clearly showed five clusters. Despite overlapping values, morphometric analyses strongly confirm these clusters, and new qualitative features allow the recognition of five taxa: the Taiwanese A. formosana, the cosmopolitan A. donax, the circum-Mediterranean A. micrantha, the Italo-Balkan A. plinii and the Franco-Ligurian A. donaciformis (Loisel.) Hardion & al. comb. nov. Additionally, this study shows a correlation between genetic diversity, caryopsis production and ploidy level. However, the lack of genetic diversity for A. micrantha and A. donax in the Mediterranean area remains enigmatic.

Integrating different tools to disentangle species complexes: A case study in Epidendrum (Orchidaceae)

Abstract: Species delimitation remains a central problem in systematic, taxonomic and evolutionary studies. However, the precise delimitation of species depends on the criteria used to identify lineages and the specific species concept that is applied. Recently, multidisciplinary studies using different data sources have significantly improved the delimitation of species within complex taxonomic groups, leading to an integrative taxonomy. To investigate the species delimitation within the Atlantic clade of Epidendrum (subg. Amphyglottium), four different species criteria were examined (phenetic differentiation, monophyly, diagnosability, absence of genetic intermediates). Morphometrics, plastid DNA sequences and nuclear microsatellite markers were used to explore the agreement between patterns recovered and species criteria tested. The conflicts among species criteria are discussed in light of pollination ecology, patterns of gene flow, reproductive isolation mechanisms and selective pressures currently acting in deceptive orchid species. Four currently recognized species from the Atlantic clade could be delimitated, including one newly described species, Epidendrum flammeus. Three out of five species satisfied the monophyly criterion, and few diagnostic flower characters were found among species. In contrast, nuclear microsatellite data correctly assigned individuals to their respective species, even in the presence of weak reproductive isolation and extensive hybridization events reported in the literature. One important implication of this finding is that phylogenetic studies in Epidendrum spp. should make use of singleor low-copy nuclear loci instead of plastid markers, which may be true for other plant groups. The results also indicate that the generalized pollination syndrome found among species of the Atlantic clade, the different levels of gene flow observed between nuclear and plastid markers, and hybridization events are commonly observed as the main evolutionary forces within this orchid group. Finally, we discuss evolutionary processes and taxonomic limits among these species, and we highlight the need to increase the inter-disciplinary approach to investigate species limits in complex plant groups.

Model uncertainty in ancestral area reconstruction: A parsimonious solution?

Abstract: Increasingly complex likelihood-based methods are being developed to infer biogeographic history The results of these methods are highly dependent on the underlying model which should be appropriate for the scenario under investigation Our example concerns the dispersal among the southern continents of the grass subfamily Danthonioideae (Poaceae) We infer ancestral areas and dispersals using likelihood-based Bayesian methods and show the results to be indecisive (reversible-jump Markov chain Monte Carlo; RJ-MCMC) or contradictory (continuous-time Markov chain with Bayesian stochastic search variable selection; BSSVS) compared to those obtained under Fitch parsimony (FP), in which the number of dispersals is minimised The RJ-MCMC and BSSVS results differed because of the differing (and not equally appropriate) treatments of model uncertainty under these methods Such uncertainty may be unavoidable when attempting to infer a complex likelihood model with limited data, but we show with simulated data that it is not necessarily a meaningful reflection of the credibility of a result At higher overall rates of dispersal FP does become increasingly inaccurate However, at and below the rate observed in Danthonioideae multiple dispersals along branches are not observed and the correct root state can be inferred reliably Under these conditions parsimony is a more appropriate model

A case study of intragenomic ITS variation in bryophytes: Assessment of gene flow and role of polyploidy in the origin of European taxa of the Tortula muralis (Musci: Pottiaceae) complex

Abstract: For the first time in bryophyte studies, we performed comprehensive cloning of the ITS region to reveal intraindividual variation of ITS sequences. We assessed relationships among morphologically defined taxa of the polyploid complex of the moss Tortula muralis. Our results detected a monophyletic T. muralis complex comprising T. muralis subsp. mura­ lis, T. muralis subsp. obtusifolia, T. lingulata, T. israelis, and T. edentula. The single accession of T. edentula was found nested within T. obtusifolia, and biphyletic T. israelis was found to be nested within T. muralis. With the exception of T. lingulata, intragenomic ITS sequence variation was high in the T. muralis complex. Most intraindividual sequences were nevertheless only weakly divergent, suggesting their origin via mutations exceeding the rates of concerted evolution. Markedly divergent sequences found within a single individual most probably resulted from gene flow among distant lineages of the complex. Such pattern of ITS variation challenges the traditional morphology-based taxonomy. No phylogenetic signal was associated with ploidy-level variation, suggesting a polytopic origin of the diploids. Interestingly, the pattern of ITS variation together with morphological evidence indicate the autopolyploid origin of some lineages, which renders the T. muralis complex the first group of mosses in which autopolyploidy is implied by molecular markers.

Phylogeny of the Turneraceae clade (Passifloraceae s.l.): Trans-Atlantic disjunctions and two new genera in Africa

Abstract: Turneraceae, with just over 200 species in 10 genera, is today often included in a widely circumscribed Passifloraceae. The vast majority of the species are found in the New World, whereas generic diversity is largest in the Old World. According to current circumscriptions, three of the genera show trans-Atlantic disjunctions: Turnera with over 135 species in America and two species in Africa (one in the south-western and one in the north-eastern part), Piriqueta with 44 species in America and one in southern Africa, and Erblichia with one species in Central America and four in Madagascar. The phylogeny of Turneraceae is reconstructed based on DNA sequences from plastid trnL-F and nuclear ITS and sampling for all genera, including both New and Old World species for the trans-Atlantic groups to test their monophyly. The genera of Turneraceae form a strongly supported monophyletic group, the Turneraceae clade, within Passifloraceae s.l. The phylogeny is geographically structured, with one clade comprising American species only, except for the two African species of Turnera, and another clade with all other African species plus the Central American Erblichia odorata. Turnera is retrieved as monophyletic with the two African species appearing as close relatives of T. ulmifolia, the type of Turnera. The existence of a trans-Atlantic disjunction in Turnera is therefore supported. It is most likely caused by long-distance dispersal and estimated to be not older than late Miocene. In Piriqueta only the American species are supported as a monophyletic group, whereas the single African species is resolved as a member of the African clade. The trans-Atlantic disjunction in Piriqueta is therefore not supported and the African species is proposed to be placed in a genus of its own, Afroqueta gen. nov., as Afroqueta capensis comb. nov. Erblichia on Madagascar is supported as sister to Mathurina, a genus endemic to Rodrigues Island in the Mascarenes, and does not group with E. odorata in Central America, the type of Erblichia. The trans-Atlantic disjunction in Erblichia is therefore not supported either and the genus Arboa gen. nov. is proposed to accommodate the four Malagasy species, Arboa integrifolia comb. nov., Arboa berneriana comb. nov., Arboa madagascariensis comb. nov., and Arboa antsingyae comb. nov.

Whole-genome triplication and species radiation in the southern African tribe Heliophileae (Brassicaceae)

Abstract: The unigeneric tribe Heliophileae includes ca. 90 Heliophila species, all endemic to southern Africa. The tribe is morphologically the most diverse Brassicaceae lineage in every aspect of habit, foliage, flower and fruit morphology. Despite this diversity, virtually nothing is known about its origin and genome evolution. Here we present the first in-depth information on chromosome numbers, rDNA in situ localization, genome structure, and phylogenetic relationship within Heliophileae. Chromosome numbers determined in 27 Heliophila species range from 2n = 16 to 2n = ca. 88, but 2n = 20 and 22 prevail in 77% of the examined species. Chromosome-number variation largely follows three major lineages (A, B, and C) resolved in the ITS phylogeny. Clade A species mostly have a chromosome number of 2n = 20, whereas 2n = 22 is the dominant number in clade C (2n = 16 and 22 were counted in two diploid species of clade B). The number and position of 5S and 45S rDNA loci cannot be employed as phylogenetically informative characters. Seven species with different chromosome number and from the three ITS clades were analyzed by comparative chromosome painting. In all species analyzed, 90% of painting probes unveiled three homeologous chromosome regions in Heliophila haploid chromosome complements. These results suggest that all Heliophila species, and probably the entire tribe Heliophileae, experienced a whole-genome triplication (WGT) event. We hypothesize that the mesohexaploid ancestor arose through hybridization between genomes resembling the Ancestral Crucifer Karyotype with n = 8. The WGT has been followed by species-specific chromosome rearrangements (diploidization) resulting in descending dysploidy towards extant quasi-diploid genomes. The WGT might have contributed to diversification and species radiation in Heliophileae. To our knowledge, this is the first study to document polyploidy as a potential major mechanism for the radiation of a Cape plant lineage.

Phylogenetic placement, delimitation, and relationships among genera of the enigmatic Nelsonioideae (Lamiales: Acanthaceae).

Abstract: We took a two-tiered approach to test monophyly of Nelsonioideae and place the group within Lamiales, and to determine relationships among taxa within the group. Phylogenetic analysis of a molecula ...