Showing papers in "Taxon in 2014"

Holotype specimens and type citations: general issues.

Abstract: As specification of a holotype has only been necessary for valid publication of a name of a species or infraspecific taxon since 1 January 1990, for names published before that date it is often uncertain if a holotype exists, and, if it does, where it is located. The rules governing holotype recognition are outlined and suggestions for best practice are made.

A molecular phylogeny and new subgeneric classification of Sporobolus (Poaceae: Chloridoideae: Sporobolinae)

Abstract: The grass subtribe Sporobolinae contains six genera: Calamovilfa (5 spp. endemic to North America), Crypsis (10 spp. endemic to Asia and Africa), Psilolemma (1 sp. endemic to Africa), Spartina (17 spp. centered in North America), Sporobolus (186 spp. distributed worldwide), and Thellungia (1 sp. endemic to Australia). Most species in this subtribe have spikelets with a single floret, 1-veined (occasionally 3 or more) lemmas, a ciliate membrane or line of hairs for a ligule, and fruits with free pericarps (modified caryopses). Phylogenetic analyses were conducted on 177 species (281 samples), of which 145 species were in the Sporobo - linae, using sequence data from four plastid regions (rpl32-trnL spacer, ndhA intron, rps16-trnK spacer, rps16 intron) and the nuclear ribosomal internal transcribed spacer regions (ITS) to infer evolutionary relationships and provide an evolutionary framework on which to revise the classification. The phylogenetic analysis provides weak to moderate support for a paraphyletic Sporobolus that includes Calamovilfa, Crypsis, Spartina, and Thellungia. In the combined plastid tree, Psilolemma jaegeri is sister to a trichotomy that includes an unsupported Urochondra-Zoysia clade (subtr. Zoysiinae), a strongly supported Sporobolus somalensis lineage, and a weakly supported Sporobolus s.l. lineage. In the ITS tree the Zoysiinae is sister to a highly supported Sporobolinae in which a Psilolemma jaegeri-Sporobolus somalensis clade is sister to the remaining species of Sporobolus s.l. Within Sporobolus s.l. the nuclear and plastid analyses identify the same 16 major clades of which 11 are strongly supported in the ITS tree and 12 are strongly supported in the combined plastid tree. The positions of three of these clades representing proposed sections Crypsis, Fimbriatae, and Triachyrum are discordant in the nuclear and plastid trees, indicating their origins may involve hybridization. Seven species fall outside the major clades in both trees, and the placement of ten species of Sporobolus are discordant in the nuclear and plastid trees. We propose incorporating Calamovilfa, Crypsis, Spartina, Thellungia, and Eragrostis megalosperma within Sporobolus, and make the requisite 35 new combinations or new names. The molecular results support the recognition of 11 sections and 11 subsections

Which name(s) should be used for Araucaria‐like fossil wood?—Results of a poll

Abstract: Araucarioxylon Kraus is a widely known fossil-genus generally applied to woods similar to that of the extant Arau- cariaceae. However, since 1905, several researchers have pointed out that this name is an illegitimate junior nomenclatural synonym. At least four generic names are in current use for fossil wood of this type: Agathoxylon Hartig, Araucarioxylon, Dadoxylon Endl. and Dammaroxylon J.Schultze-Motel. This problem of inconsistent nomenclatural application is compounded by the fact that woods of this type represent a wide range of plants including basal pteridosperms, cordaitaleans, glossopterids, primitive conifers, and araucarian conifers, with a fossil record that extends from the Devonian to Holocene. Conservation of Araucarioxylon has been repeatedly suggested but never officially proposed. Since general use is a strong argument for con- servation, a poll was conducted amongst fossil wood anatomists in order to canvass current and preferred usage. It was found that the community is divided, with about one-fifth recommending retention of the well-known Araucarioxylon, whereas the majority of others advocated use of the legitimate Agathoxylon. The arguments of the various colleagues who answered the poll are synthesized and discussed. There is clearly little support for conservation of Araucarioxylon. A secondary aspect of the poll tackled the issue as to whether Araucaria-like fossil woods should be either gathered into a unique fossil-genus, or whether two fossil-genera should be recognized, based on the respective presence or absence of axial parenchyma. A majority of colleagues favoured having one fossil-genus only. Agathoxylon can be used legitimately and appears to be the most appropriate name for such woods. However, its original diagnosis must be expanded if those woods lacking axial parenchyma are to be included.

Phylogenetic relationships in Helichrysum (Compositae: Gnaphalieae) and related genera: Incongruence between nuclear and plastid phylogenies, biogeographic and morphological patterns, and implications for generic delimitation

Abstract: 39 p., tablas, mapas, graf. -- Post-print del articulo publicado en Journal of Biogeography. Version revisada y corregida.

Deconstructing the Tricholomataceae (Agaricales) and introduction of the new genera Albomagister, Corneriella, Pogonoloma and Pseudotricholoma

Abstract: The family Tricholomataceae, contained within the Tricholomatoid clade, has traditionally been one of the largest families of the Agaricales. However, in this sense it is highly polyphyletic and requires emendation. Here, we present a phylogeny of the Tricholomatoid clade based on nucleotide sequence data from two nuclear ribosomal RNA genes (large subunit and small subunit) and the second-largest subunit of RNA polymerase II (rpb2). Our aim is to delimit the Tricholomataceae and identify monophyletic groups within the Tricholomatoid clade. We also infer a separate phylogeny, based on the three genes above, in addition to sequences of the nuclear ribosomal internal transcribed spacers (ITS), in order to evaluate generic-level boundaries within the Tricholomataceae s.str. Based on this analysis we recover seven monophyletic genera within the Tricholomataceae s.str. that correspond to Leucopaxillus, Tricholoma, Pseudotricholoma stat. nov., Porpoloma s.str., Dennisiomyces, Corneriella gen. nov., and Albomagister gen. nov. Of the 98 genera that have been traditionally assigned to the Tricholomataceae sensu Singer, only four can be placed within it ( Tricholoma, Porpoloma, Dennisiomyces, Leucopaxillus). The genus Porpoloma is highly polyphyletic and divided into four genera: Porpoloma s.str., Corneriella gen. nov., Pseudotricholoma stat. nov., and Pogonoloma stat. nov. In all, four new genera are proposed. Taxonomic descriptions, and a key to genera of the Tricholomat - aceae as emended here are also presented.

Resolved phylogeny of Cleomaceae based on all three genomes

Abstract: Cleomaceae is a small pantropical family that is emerging as a promising system to investigate C4 photosynthesis, floral evolution, and comparative genomics. However, our understanding of these phenomena is hindered by a lack of a strong phylogenetic hypothesis, despite a number of previous studies. We reconstructed the phylogeny of the family using data from all three genomes, including three cpDNA (ndhF, matK, ycf1), one mtDNA (rps3), and one nrDNA (ITS) regions. Analyses strongly supported 15 clades: (1) Clade 1, which includes two Old World species, Cleome khorassanica and C. turkmena; (2) Cleome s.str., which includes the type C. ornithopodioides and Old World species; (3) Droserifolia, corresponding to three Old World species, C. droserifolia, C. fimbriata, C. quinquenervia; (4) Polanisia, equivalent to this New World genus; (5) Angustifolia, which includes four Old World species; (6) North American cleomoids, which includes four genera, Cleomella, Peritoma, Oxystylis, and Wislizenia; (7) Australian, which includes Old world species and worldwide weed Arivela viscosa; (8) Gynandropsis, equivalent to this monotypic genus; (9) Clade 6, which includes Old World species of Cleome and Dipterygium; (10) Dactylaena, corresponding to this genus and Physostemon; (11) African, which includes species distributed in Old World; (12) Andean, which includes Podandrogyne and tropical New World species of Cleome; (13) Melidiscus, which includes New World tropical species; (14) Cleoserrata, which includes New World tropical species; and (15) Tarenaya, a large New World clade. Major relationships amongst the clades are strongly supported for the first time, including North American cleomoids sister to all remaining Cleom aceae. While five genera are confirmed or newly identified here to be non-monophyletic (Cleome, Cleomella, Hemiscola, Peritoma, Tarenaya), six are supported (Cleoserrata, Dactylaena, Melidiscus, Physostemon, Podandrogyne, Polanisia). Thus, there are many taxonomic and evolutionary implications to our revised phylogenetic hypothesis.

Plant diversification in the Espinhaço Range: Insights from the biogeography of Minaria (Apocynaceae)

Abstract: The Espinhaco Range, eastern Brazil, is a region with remarkable floristic diversity and endemism, which are mainly concentrated in the campo rupestre. Minaria (Apocynaceae) is a genus with 21 species, most of which are endemic to the Espinhaco Range. In the present study, we investigated the biogeography of Minaria as the basis for understanding the origin and maintenance of plant diversity and endemism in the campo rupestre of the Espinhaco Range. We assessed the ecological divergence between clades, reconstructed the historical biogeography and dated the phylogeny of Minaria based on plastid and nuclear DNA. According to our estimates, Minaria arose in the Espinhaco Range during the Neogene. Its distribution is postulated to have been driven by a trend toward long-term retraction, interrupted by a few episodes of expansion. Ecologically, Minaria species do not present any obvious innovations that could explain their diversification by adaptive radiation. Appar- ently, the higher-altitude rocky savannas in the Espinhaco Range have offered stable environments in which dry seasons and fire regimes are less intense than in savannas at lower altitudes. Isolated on rocky outcrops, lineages would be more likely to differentiate by non-adaptive radiation, which may result in high plant diversity and endemism.

Molecular phylogenetics and generic taxonomy of Blechnaceae ferns

Abstract: The fern family Blechnaceae is cosmopolitan; however, the vast majority of species are placed in Blechnum, which occurs predominantly in the Southern Hemisphere. There are two areas that are particularly species–rich: the south–west Pacific (including Australasia), and Central and South America. Using chloroplast DNA sequences, we report the first comprehensive phylogenetic analysis of the Blechnaceae, including all genera widely recognised in recent treatments, and over half of the species. There is strong support for several major clades, which we characterise morphologically and geographically, and some of their interrelationships. Blechnum is confirmed as polyphyletic. Blechnum indicum and B. serrulatum are more closely related to Salpichlaena and Stenochlaena, and are segregated as a new genus, Telmatoblechnum. Alternative generic circumscriptions are discussed for the remainder of Blechnum. In the absence of morphological characters to diagnose the clades within core Blechnum, and for the sake of taxonomic stability, we advocate a broad circumscription for Blechnum. Brainea and Sadleria are retained as their relationships are not well resolved, but Doodia and Pteridoblechnum are clearly nested within the core of Blechnum and we provide four new names in Blechnum. Additionally, given the focus of our sampling, we discuss the biogeography of the south–west Pacific, where immigration has been more important in community assembly than what might be superficially inferred from patterns of endemism (with ca. 60% of species endemic to individual land areas).

A multi-step comparison of short-read full plastome sequence assembly methods in grasses

Abstract: Technological advances have allowed phylogenomic studies of plants, such as full chloroplast genome (plastome) analysis, to become increasingly popular and economically feasible. Although next-generation short-read sequencing allows for full plastomes to be sequenced relatively rapidly, it requires additional attention using software to assemble these reads into comprehensive sequences. Here we compare the use of three de novo assemblers combined with three contig assembly methods. Seven plastome sequences were analyzed. Three of these were Sanger-sequenced. The other four were assembled from short, single-end read files generated from next-generation libraries. These plastomes represented a total of six grass species (Poaceae), one of which was sequenced in duplicate by the two methods to allow direct comparisons for accuracy. Enumeration of missing sequence and ambiguities allowed for assessments of completeness and efficiency. All methods that used de Bruijn-based de novo assemblers were shown to produce assemblies comparable to the Sanger-sequenced plastomes but were not equally efficient. Contig assembly methods that utilized automatable and repeatable processes were generally more efficient and advantageous when applied to larger scale projects with many full plastomes. However, contig assembly methods that were less automatable and required more manual attention did show utility in determining plastomes with lower read depth that were not able to be assembled when automatable procedures were implemented. Although the methods here were used exclusively to generate grass plastomes, these could be applied to other taxonomic groups if previously sequenced plastomes were available. In addition to comparing sequencing methods, a supplemental guide for short-read plastome assembly and applicable scripts were generated for this study.

High-performance digitization of natural history collections: Automated imaging lines for herbarium and insect specimens

Abstract: The digitization of natural history collections calls for new, efficient solutions. Digitization of millions of specimens, with reasonable digitization costs and high statistical repeatability requires increased automation and industrial-scale work- flows. However, the variation in specimen form, size and coloring creates challenges for digitization methodology, pushing development towards optional actions. In this paper, we report the results of the digitization of herbarium and beetle collections using automated imaging lines. The technology of the imaging lines was based on a common innovation, but the versions used were applied to either 2-D sheets or small 3-D objects. The aim was to develop processes for enhancing the digitization of natural history specimens, but at the same time, to produce end products with high quality. Results showed that the herbarium and beetle collections could be digitized by using automation at the rate of hundreds or thousands of individual specimens per day. This is 5-10 times faster than the more manual methods of digitization which were previously used. The produced data, images and specimen label data were uniform in quality and could be viewed within minutes after being produced. Results indicate that the efficiency of digitization can be raised for different types of natural history specimens by use of automation and well-defined processes, and the increase in production rate does not reduce the quality of the end-results.

Phylogenetic structure and clade circumscriptions in the Gardenieae complex (Rubiaceae)

Abstract: In this study we investigate the large and diverse Rubiaceae-Gardenieae and closely related tribes Bertiereae, Coffeeae, Cremasporeae, Octotropideae, and Pavetteae. Some of the tribes or groups have been shown to be monophyletic and strongly supported, but the phylogeny of this large complex is still far from being satisfactorily elucidated particularly for Gardenieae, both in terms of intertribal relationships as well as tribal delimitations. We reconstruct the phylogeny of the complex using an extensive sampling of 108 genera and five plastid DNA regions. Phylogenetic relationships demonstrate that Gardenieae sensu Andreasen & Bremer is polyphyletic, as Burchellia, Didymosalpinx, Monosalpinx, and Mantalania are closer to Octotropideae-Cremasporeae. In addition, Pavetteae and the investigated members of Aulacocalyceae are nested in a supported but partially unresolved Gardenieae-Pavetteae clade. Within this clade, several strongly supported groups are resolved: an Aidia group, an Alibertia group, a Gardenia group, Pavetteae including Pelagodendron, a Porterandia group, a Randia group, a Rothmannia group (including Aulacocalyx and Heinsenia), a Sherbournia group, and the two isolated genera Massularia and Schumanniophyton. The latter genus presented a high rate of genetic substitutions, which resulted in perturbations of the phylogenetic reconstruction. A revised tribal circumscription is given for Gardenieae, the Alibertia group is recognized at tribal level as an emended Cordiereae, and a new tribe, Sherbournieae, is described to accommodate the members of the Sherbournia group.

Taxonomy and evolutionary history of Alyssum montanum (Brassicaceae) and related taxa in southwestern Europe and Morocco: Diversification driven by polyploidy, geographic and ecological isolation

Abstract: The Alyssum montanum-A. repens polyploid complex is a group of related perennial taxa with a diversity centre in the European (Sub)Mediterranean, controversial taxonomic treatments, and a poorly known evolutionary history. In the present study, morphological, ploidy level and genetic (AFLPs and chloroplast DNA sequences) data were collected to address the taxonomy and evolution of a sublineage of this complex distributed in southwestern Europe and Morocco. As a result, a new taxonomic treatment, differing substantially from recent concepts, is presented, including an identification key, synonymy and typifications. The recognition of several previously described but recently not accepted endemics is favoured (A. flexi- caule, A. orophilum, A. rhodanense), whereas the existence of southern Iberian endemics is not supported. Most of the Iberian Peninsula is occupied by a single species for which the name A. fastigiatum is applicable. Populations from the summit areas of the Pyrenees represent a separate species, which is described here as A. cacuminum. Populations from coastal sand dunes in the Basque country (Bay of Biscay) and Galicia, recently recognised as two subspecies of A. loiseleurii, are elevated to species rank according to their genetic and morphological divergence. Alyssum atlanticum is resolved as a species confined to northern Africa and not reaching southern Spain. The distribution of A. montanum in a strict sense is much more restricted than previously reported, being delimited by the Pyrenees in the south, and the Alps in the northeast. The species complex studied here is composed of several polyploid stenoendemics confined to different mountain ranges or specific lowland habitats, and a few relatively widely distributed species. We infer that hybridisation and polyploidisation events, along with ecological and geographic isolation, have stimulated speciation in this complex. Hypotheses about the origin and evolutionary history of the species are discussed.

Bridging the Alps and the Middle East: Evolution, phylogeny and systematics of the genus Wulfenia (Plantaginaceae)

Abstract: The genus Wulfenia (Plantaginaceae) demonstrates a striking disjunction between the southeastern Alps (Carnic Alps), the southeastern Dinaric Alps (Prokletije Mountains, Balkan Peninsula) and the Amanos mountains of southern Turkey. This puzzling biogeographic pattern has interested botanists for more than 100 years and Wulfenia has been widely regarded as a Tertiary relict of at least Miocene age in southeastern Europe. Specifically, the identity of populations in the Prokletije Mountains either referred to as disjunct populations of W. carinthiaca or a separate species, “W. blecicii ”, has been much debated. Here we analyze AFLP, plastid and nuclear ribosomal sequence data in conjunction with a morphometrical analysis to clarify the taxonomy of the genus and the relationships of the populations to one another. Furthermore, we employ a molecular dating strategy to put these results in a time frame to assess the Miocene relict–hypothesis. Our results provide evidence for a new classification of the genus with four species, W. orientalis, W. glanduligera comb. & stat. nov., W. baldaccii and W. carinthiaca. The split of the last species into populations disjunctly distributed in the southeastern Alps (W. carinthiaca s.str.) and southeastern Dinaric Alps (“W. blecicii ”), is not supported either by molecular or morphological data, while we find enough evidence in DNA sequence data, growth site specifics and morphology for W. orientalis var. glanduligera to be treated at the species rank. Our dating analysis suggests that the extant genus is rather young with a crown node age of only about 1.24 Ma and 0.61 Ma for the European populations despite a stem node age of about 10.69 Ma. Thus, Wulfenia as a genus is likely a Miocene relict but its uninterrupted presence on the Balkan Peninsula cannot be demonstrated.

A molecular phylogeny and classification of the Cteniinae, Farragininae, Gouiniinae, Gymnopogoninae, Perotidinae, and Trichoneurinae (Poaceae: Chloridoideae: Cynodonteae)

Abstract: The classification of twenty Cynodonteae genera (Bewsia, Craspedorhachis, Ctenium, Dignathia, Farrago, Gouinia, Gymnopogon, Latipes, Leptocarydion, Leptothrium, Lophacme, Lopholepis, Mosdenia, Perotis, Schenckochloa, Toliara, Trichoneura, Trigonochloa, Triplasis, Vaseyochloa) has been poorly understood. The goals of this study were to reconstruct the evolutionary history of the tribe Cynodonteae, emphasizing these twenty genera using molecular data with increased species sampling. A phylogenetic analysis was conducted on 159 samples, of which 94 species (140 individuals) were in the Cynodonteae, using four plastid (rpl32-trnL spacer, ndhA intron, rps16-trnK spacer, rps16 intron) and nuclear ITS 1&2 (ribo­ somal internal transcribed spacer regions) sequences to infer evolutionary relationships and revise the classification. Strong support was found for six lineages. Craspedorhachis, Ctenium, Dignathia, Gymnopogon, Trichoneura, and Triplasis appear monophyletic; Leptothrium is paraphyletic with Latipes inermis embedded within; Perotis is paraphyletic with Lopholepis and Toliara embedded within; and Gouinia is monophyletic with the resurrection of Schenckochloa. The molecular results sup­ port the recognition of six subtribes; five (Cteniinae, Farragininae, Gymnopogoninae, Perotidinae, Trichoneurinae) are newly described. A new genus, Tridentopsis, is described; five new combinations, Leptothrium inerme, Perotis arenacea, Perotis ornithocephala, Tridentopsis eragrostoides, and Tridentopsis mutica are made; and Holboellia ornithocephala is lectotypified.

Low-copy nuclear data confirm rampant allopolyploidy in the Cystopteridaceae (Polypodiales)

Abstract: Here we present the first nuclear phylogeny for Cystopteridaceae (Polypodiales), using the single-copy locus gapCp "short". This phylogeny corroborates broad results from plastid data in demonstrating strong support for the monophyly of the family's three genera—Cystopteris, Acystopteris, and Gymnocarpium—and of the major groups within Cystopteris (C. montana, the sudetica and bulbifera clades, and the C. fragilis complex). In addition, it confirms the rampant hybridization (allopoly- ploidy) that has long been suspected within both Cystopteris and Gymnocarpium. In some cases, these data provide the first DNA-sequence-based evidence for previous hypotheses of polyploid species origins (such as the cosmopolitan G. dryopteris being an allotetraploid derivative of the diploids G. appalachianum and G. disjunctum). Most of the allopolyploids, however, have no formal taxonomic names. This pattern is particularly strong within the C. fragilis complex, where our results imply that the eight included accessions of "C. fragilis" represent at least six distinct allopolyploid taxa.

Molecular phylogeny and biogeography of the arctic‐alpine genus Lagotis (Plantaginaceae)

Abstract: It has been suggested that many plants now found in the arctic originated from ancestors that occurred at high altitudes in the southern mountains of the Northern Hemisphere during the Tertiary. However, this hypothesis has rarely been tested using a molecular phylogenetic approach. Here, we present a fossil-calibrated molecular phylogeny of Lagotis, an arctic-alpine genus with the greatest diversity in the Qinghai-Tibetan Plateau (QTP) and Central Asian mountains, based on five chloroplast (matK, psbA-trnH, rps16, trnG-S, trnL-F) and nuclear ribosomal ITS DNA markers. Within this framework, we infer the ancestral area and biogeographic history of the genus. Four major clades (A D) within Lagotis were recovered with strong support, which largely correspond to the previous classification of the genus. Within clade A, Lagotis species from QTP were distributed among several subclades, and L. integrifolia from Central Asia was sister to L. glauca and L. minor from the arctic and subarctic region. The Bayesian molecular dating and the ancestral area reconstruction analyses suggested that Lagotis could have originated in the QTP in the Miocene (Tertiary), and that the genus radiated from the Miocene to Pleistocene. The diversification of Lagotis probably took place predominantly in the QTP and it subsequently spread to the Central Asian highlands, followed by northward migration into the arctic. Our results support the hypothesis that the "Central Asiatic Highland Corridor" as an important route for the migration of the flora between the arctic and QTP.