bluuebunny/crossref_metadata_2025_split huggingface dataset:
Apportionment of institutional votes for the Nomenclature Section: A rebuttal to Smith & al.
Authors: Applequist Wendy L. , Callmander Martin W. , Davidse Gerrit , Sennikov Alexander , Thulin Mats , Vorster Piet , Yatskievych George 
Published: February 2019

AbstractSmith & al. (2010) have suggested that the apportionment of institutional votes for the Nomenclature Section of the International Botanical Congress based upon taxonomic activity represents a “colonial legacy” that disadvantages developing nations, and that institutional votes should instead be distributed based at least in part upon a country's human population and the size of its flora. While we agree that increasing participation by developing‐country taxonomists is an important goal, we believe that Smith & al. fail to support their claim that the current practice of plant nomenclature is harmful to developing nations. No evidence has been offered of regional biases regarding proposals to change the wording of the Code, which represent the vast majority of the votes taken at any Nomenclature Section, nor has the current process of apportionment of institutional votes been shown to be biased. The reform measures proposed by Smith & al. would, as we show, introduce explicit discrimination based on nationality into the International code of botanical nomenclature, undermining the international cooperation among taxonomists that is necessary for the smooth functioning of a universally accepted system of nomenclature. Rather than making hasty and perhaps harmful changes to the current means of voting, we suggest that the international taxonomic community should consider carefully what measures will best facilitate participation without creating new sources of injustice.
Typification of names of American species of vascular plants proposed by Linnaeus and based on Loefling's Iter Hispanicum (1758)
Authors: Dorr Laurence J. , Wiersema John H. 
Published: February 2019

AbstractNeotypes are proposed for the names of ten species of American plants that Linnaeus based in whole or in part on descriptions in Loefling's Iter Hispanicum: Allionia incarnata, Allionia violacea, Ayenia tomentosa, Byttneria scabra, Krameria ixine, Lecythis ollaria, Moniera trifolia, Viola arborea, Viola calceolaria, and Viola oppositifolia. Lectotypes are proposed for the names of six species of American plants that Linnaeus based in whole or in part on descriptions in the same work: Ayenia magna, Cecropia peltata, Ellisia acuta, Jussiaea pubescens, Loranthus occidentalis, and Spermacoce strigosa. A neotype also is proposed for a Jacquin name, Hybanthus havanensis, which Linnaeus renamed as Viola hybanthus. We also argue that Laetia americana is neotypified by the type applied to the illegitimate name Laetia apetala.
Paraphyletic groups as natural units of biological classification
Authors: Hörandl Elvira , Stuessy Tod F. 
Published: February 2019

AbstractDespite the broad acceptance of phylogenetic principles in biological classification, a fundamental question still exists on how to classify paraphyletic groups. Much of the controversy appears due to (1) historical shifts in terminology and definitions, (2) neglect of focusing on evolutionary processes for understanding origins of natural taxa, (3) a narrow perspective on dimensions involved with reconstructing phylogeny, and (4) acceptance of lower levels of information content and practicability as a trade‐off for ease of arriving at formal classifications. Monophyly in evolutionary biology originally had a broader definition, that of describing a group with common ancestry. This definition thus includes both paraphyletic and monophyletic groups in the sense of Hennig. We advocate returning to a broader definition, supporting use of Ashlock's term holophyly as replacement for monophyly s.str. By reviewing processes involved in the production of phylogenetic patterns (budding, merging, and splitting), we demonstrate that paraphyly is a natural transitional stage in the evolution of taxa, and that it occurs regularly along with holophyly. When a new holophyletic group arises, it usually coexists for some time with its paraphyletic stem group. Paraphyly and holophyly, therefore, represent relational and temporal evolutionary stages. Paraphyletic groups exist at all levels of diversification in all kingdoms of eukaryotes, and they have traditionally been recognized because of their descent‐based similarity. We review different methodological approaches for recognition of monophyletic groups s.l. (i.e., both holophyletic and paraphyletic), which are essential for discriminating from polyphyly that is unacceptable in classification. For arriving at taxonomic decisions, natural processes, information content, and practicability are essential criteria. We stress using shared descent as a primary grouping principle, but also emphasize the importance of degrees of divergence plus similarity (cohesiveness of evolutionary features) as additional criteria for classification.
Phylogeny of subtribe Gentianinae (Gentianaceae): Biogeographic inferences despite limitations in temporal calibration points
Authors: Favre Adrien , Yuan Yong-Ming , Küpfer Philippe , Alvarez Nadir 
Published: February 2019

AbstractThe subtribe Gentianinae comprises ca. 425 species, most of them within the well‐studied genus Gentiana and mainly distributed over the Eurasian continent. Phylogenetic relationships between Gentiana and its closest relatives, the climbing gentians (Crawfurdia, Tripterospermum) and the new genus Metagentiana, remain unclear. All three genera were recently found to be polyphyletic, possibly because of poor sampling of Tripterospermum and Crawfurdia. Highest diversity of Gentianinae occurs in the western Himalaya, but the absence of uncontroversial fossil evidence limits our understanding of its biogeography. In the present study, we generated ITS and atpB‐rbcL sequences for 19 species of Tripterospermum, 9 of Crawfurdia and 11 of Metagentiana, together representing about 60 percent of the species diversity of these genera. Our results show that only Metagentiana is polyphyletic and divided into three monophyletic entities. No unambiguous synapomorphies were associated with the three Metagentiana entities. Different combinations of three approximate calibration points were used to generate three divergence time estimation scenarios. Although dating hypotheses were mostly inconsistent, they concurred in associating radiation of Gentiana to an orogenic phase of the Himalaya between 15 and 10 million years ago. Our study illustrates the conceptual difficulties in addressing the time frame of diversification in a group lacking sufficient fossil number and quality.
Generic delimitation and historical biogeography in the early‐divergent 'ambavioid' lineage of Annonaceae: Cananga, Cyathocalyx and Drepananthus
Authors: Surveswaran Siddharthan , Wang Rui Jiang , Su Yvonne C.F. , Saunders Richard M.K. 
Published: February 2019

AbstractGeneric delimitation of Cyathocalyx and Drepananthus has been controversial, with some authors recognizing them as distinct genera, and others recognizing a more broadly defined Cyathocalyx, inclusive of Drepananthus. Some doubt also exists regarding the relationships between these taxa and Cananga. Molecular phylogenetic analyses are presented based on combined psbA‐trnH spacer, trnL‐F, matK and rbcL sequences. Results indicate that Cananga, Cyathocalyx s.str. and Drepananthus form three generally well‐supported clades, although with inadequate resolution of relationships among the three clades. Morphological variation is re‐evaluated, and the narrower delimitation of Cyathocalyx proposed, necessitating 21 new nomenclatural combinations following the recognition of Drepananthus as a distinct genus. Divergence times are estimated using an uncorrelated lognormal distributed (UCLD) relaxed molecular clock. Historical biogeographical analysis suggests that the ambavioid lineage originated in Africa, with subsequent dispersal into Asia. Alternative hypotheses for this dispersal, involving rafting on the Indian tectonic plate versus migration via the extensive boreotropical forests associated with the Eocene thermal maximum, are evaluated, and the latter route identified as the most consistent with the divergence age estimates and the geological and palaeoclimatic data.
Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence
Authors: Crespo Ana , Kauff Frank , Divakar Pradeep K. , del Prado Ruth , Pérez-Ortega Sergio , de Paz Guillermo Amo , Ferencova Zuzana , Blanco Oscar , Roca-Valiente Beatriz , Núñez-Zapata Jano , Cubas Paloma , Argüello Arturo , Elix John A. , Esslinger Theodore L. , Hawksworth David L. , Millanes Ana , Molina M. Carmen , Wedin Mats , Ahti Teuvo , Aptroot Andre , Barreno Eva , Bungartz Frank , Calvelo Susana , Candan Mehmet , Cole Mariette , Ertz Damien , Goffinet Bernard , Lindblom Louise , Lücking Robert , Lutzoni Francois , Mattsson Jan-Eric , Messuti María Inés , Miadlikowska Jolanta , Piercey-Normore Michele , Rico Víctor J. , Sipman Harrie J.M. , Schmitt Imke , Spribille Toby , Thell Arne , Thor Göran , Upreti Dalip K. , Lumbsch H. Thorsten 
Published: February 2019

AbstractParmelioid lichens are a diverse and ubiquitous group of foliose lichens. Generic delimitation in parmelioid lichens has been in a state of flux since the late 1960s with the segregation of the large, heterogeneous genus Parmelia into numerous smaller genera. Recent molecular phylogenetic studies have demonstrated that some of these new genera were monophyletic, some were not, and others, previously believed to be unrelated, fell within single monophyletic groups, indicating the need for a revision of the generic delimitations. This study aims to give an overview of current knowledge of the major clades of all parmelioid lichens. For this, we assembled a dataset of 762 specimens, including 31 of 33 currently accepted parmelioid genera (and 63 of 84 accepted genera of Parmeliaceae). We performed maximum likelihood and Bayesian analyses of combined datasets including two, three and four loci. Based on these phylogenies and the correlation of morphological and chemical characters that characterize monophyletic groups, we accept 27 genera within nine main clades. We re‐circumscribe several genera and reduce Parmelaria to synonymy with Parmotrema. Emodomelanelia Divakar & A. Crespo is described as a new genus (type: E. masonii). Nipponoparmelia (Kurok.) K.H. Moon, Y. Ohmura & Kashiw. ex A. Crespo & al. is elevated to generic rank and 15 new combinations are proposed (in the genera Flavoparmelia, Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A short discussion of the accepted genera is provided and remaining challenges and areas requiring additional taxon sampling are identified.
Evolutionary history and taxonomy of the Cuscuta umbellata complex (Convolvulaceae): Evidence of extensive hybridization from discordant nuclear and plastid phylogenies
Authors: Costea Mihai , Stefanović Saša 
Published: February 2019

AbstractThe Cuscuta umbellata complex is one of the 15 major clades recently circumscribed in C. subg.Grammica. Most of its members occur in North America and the Caribbean (C. desmouliniana, C. lacerata, C. leptantha, C. liliputana, C. odontolepis, C. polyanthemos, C. tuberculata, C. umbellata), but three species (C. acuta, C. membranacea, C. umbellata) grow in South America, and one (C. hyalina) is found as a native species in India, Pakistan and Eastern to South Africa. Basic morphology, scanning electron microscopy and sequence data from the nuclear internal transcribed spacer (ITS) and the plastid trnL‐F region were used to reconstruct the phylogeny, gain a better understanding of the evolutionary history, and determine species boundaries. Our results show that in its currently accepted delimitation C. umbellata is polyphyletic. Discordances between phylogenies derived from plastid and nuclear data strongly suggest that at least four independent hybridization events have occurred in the evolution of this species group, rendering relationships among its members more complex than previously thought. One of these reticulation events involves C. umbellata var. reflexa, a taxon that has been considered synonymous to C. umbellata var. umbellata in the last decades. This hybrid is morphologically intermediate but distinct from its putative parents, C. odontolepis or C. acuta on the maternal side, and C. umbellata (var. umbellata) on the paternal side, which supports its treatment as a new species, C. legitima. Cuscuta umbellata is further redefined to exclude C. umbellata var. dubia, which is merged into C. desmouliniana. A new classification is provided, together with an identification key, descriptions, illustrations, and geographical distributions for the twelve species of the clade.
Lecto‐ and epitypification of Ficus racemosa L. (Moraceae)
Authors: Upadhyay Gautam Kumar , Srivastava Sunil Kumar 
Published: February 2019

AbstractA lectotype and an epitype for Ficus racemosa L., the name for the species commonly known as "Clustered Fig", are proposed. The name was apparently based primarily on a plate in Rheede's Hortus Malabaricus labelled "Atty‐Alu", a Malayalam dialect name for the plant figured. However, as the plate shows ambiguity by portraying a branch having figs in simple or true racemes, whereas the accompanying text describes the infructescences as panicled, an epitype is designated here to fix the application of this name in accordance with its current usage.
Neckera and Thamnobryum (Neckeraceae, Bryopsida): Paraphyletic assemblages
Authors: Olsson Sanna , Enroth Johannes , Buchbender Volker , Hedenäs Lars , Huttunen Sanna , Quandt Dietmar 
Published: February 2019

AbstractRecent phylogenetic analyses indicated that the backbone phylogeny of the pleurocarpous moss family Neckeraceae falls into three distinct clades. Here the detailed composition and phylogenetic relationships of the two major clades (the Neckera clade and the Thamnobryum clade) are analysed. The phylogenetic analyses, based on sequence data from the plastid rpl16 intron and the rps4-trnT-trnL-trnF cluster as well as the nuclear ITS1 and 2, retained this tripartition and revealed a strong biogeographic pattern, especially inside the Neckera clade. In addition, several morphological characters that have been held as unique and characteristic to a certain group of mosses and therefore valuable in taxonomic classification, were shown to be highly homoplastic and subjected to convergent evolution. Consequently, the circumscriptions of Leptodon and Thamnobryum are amended, the new genera Exsertotheca, Echinodiopsis and Thamnomalia (each with two species), and Alleniella (with ten species) are formally described and several implied nomenclatural changes are proposed, including synonymisation of Alsia with Neckera and Cryptoleptodon with Leptodon.
Molecular phylogeny of Camphorosmeae (Camphorosmoideae, Chenopodiaceae): Implications for biogeography, evolution of C4‐photosynthesis and taxonomy
Authors: Kadereit Gudrun , Freitag Helmut 
Published: February 2019

AbstractCamphorosmeae constitute a species‐rich tribe of Chenopodiaceae‐Camphorosmoideae that consists mostly of subshrubs and annuals, distributed in steppes and semi‐deserts of Australia, Eurasia, North Africa, southern Africa and North America. We study (1) the relationships of Camphorosmeae to major lineages of the closely related Salsoloideae and (2) the diversification of the tribe with focus on the non‐Australian members using sequence variation of five different markers (rbcLgene,ndhFgene,atpB‐rbcLspacer,psbB‐psbHspacer, ITS) and morphological characters. The cpDNA analyses revealed six early‐branching lineages in Camphorosmoideae/Salsoloideae (Camphorosmeae, Salsoleae s.str., Caroxyloneae,Salsola kaliclade,Nanophytonclade,Salsola genistoidesclade) and supported partly (ndhFandatpB‐rbcLspacer) the sister‐group relationship of Camphorosmeae and all Salsolean clades. The distinctness of Camphorosmeae and Salsoleae s.l. is further supported by seed, stigma and pollen morphology. Molecular clock estimates point to an earlier radiation in Salsoleae s.l. (Early to Middle Oligocene) than in Camphorosmeae (Early Miocene). In Salsoleae s.l. early radiation might have been enhanced by multiple evolution of C4‐photosynthesis which facilitated the spread into drier habitats of Eurasia. In Camphorosmeae, C4‐photosynthesis likely evolved two times, probably in the Middle Miocene. During the Miocene Camphorosmeae spread from Eurasia to Australia, North America and at least two times to South Africa. Only the Australian lineage diversified, the others remained species‐poor. The molecular trees congruently resolve three major clades of unclear relationship within Camphorosmeae, Chenolea clade (five widely disjunct and morphologically divergent C3‐species, possibly remnants of old lineages), Sclerolaena clade (ca. 150 C3‐species from Central Asia [3 spp.] and Australia [147 spp.], probably the results of a rapid radiation during the Pliocene) andBassia/Camphorosmaclade (ca. 23 C4‐species and one C3/C4‐intermediate which are widely distributed in Eurasia and southern Africa). The phylogenies show the artificial state of the current generic and subtribal classifications of Eurasian, North American and South African Camphorosmeae. All non‐monotypic genera exceptCamphorosmaandNeokochiawere found to be polyphyletic. A revised classification of the tribe is proposed including reinstatement of the newly defined subfamily Camphorosmoideae, description of the new generaSpirobassia(1 sp.),Eokochia(1 sp.),Grubovia(3 spp.) andSedobassia(1 sp.), and several new combinations and synonymizations.
Molecular phylogenetics of the Mesoamerican bamboo Olmeca (Poaceae, Bambuseae): Implications for taxonomy
Authors: Ruiz-Sanchez Eduardo , Sosa Victoria , Mejía-Saules M. Teresa 
Published: February 2019

AbstractPhylogenetic analyses based on five DNA plastid sequences from representative taxa of the Neotropical woody bamboo subtribe Guaduinae were performed to determine the generic limits of Olmeca and the relationships among its species. The phylogenetic position of a putative new taxon from Mexico was also determined. It appeared that, additional to the two species recognized in Olmeca, two Mesoamerican species of Aulonemia—A. clarkiae and A. fulgor—should be transferred to Olmeca. This transfer is supported by morphology. Individuals of an undescribed taxon from the Isthmus of Tehuantepec, Mexico, were also retrieved embedded in the Olmeca group and are newly described as O. zapotecorum. The distribution range of the redefined genus Olmeca, currently composed of five species, now extends from southern Mexico to Honduras.
Phylogenetic relationships in the order Cucurbitales and a new classification of the gourd family (Cucurbitaceae)
Authors: Schaefer Hanno , Renner Susanne S. 
Published: February 2019

AbstractWe analysed phylogenetic relationships in the order Cucurbitales using 14 DNA regions from the three plant genomes: the mitochondrial nad1 b/c intron and matR gene, the nuclear ribosomal 18S, ITS1‐5.8S‐ITS2, and 28S genes, and the plastid rbcL, matK, ndhF, atpB, trnL, trnL‐trnF, rpl20‐rps12, trnS‐trnG and trnH‐psbA genes, spacers, and introns. The dataset includes 664 ingroup species, representating all but two genera and over 25% of the ca. 2600 species in the order. Maximum likelihood analyses yielded mostly congruent topologies for the datasets from the three genomes. Relationships among the eight families of Cucurbitales were: (Apodanthaceae, Anisophylleaceae, (Cucurbitaceae, ((Coriariaceae, Corynocarpaceae), (Tetramelaceae, (Datiscaceae, Begoniaceae))))). Based on these molecular data and morphological data from the literature, we recircumscribe tribes and genera within Cucurbitaceae and present a more natural classification for this family. Our new system comprises 95 genera in 15 tribes, five of them new: Actinostemmateae, Indofevilleeae, Thladiantheae, Momordiceae, and Siraitieae. Formal naming requires 44 new combinations and two new names in Cucurbitaceae.
Taxonomy of Polygonoideae (Polygonaceae): A new tribal classification
Authors: Sanchez Adriana , Schuster Tanja M. , Burke Janelle M. , Kron Kathleen A. 
Published: February 2019

AbstractThe subfamily Polygonoideae has a world‐wide distribution and is an important component of many countries’ floras. In this study we present the most comprehensive sampling available to date, including data from three chloroplast genes (matK, ndhF, rbcL) for 82 species in Polygonaceae (54 from Polygonoideae). Based on our results, we propose a new taxonomic classification for Polygonoideae that includes five well‐supported tribes: Calligoneae, Fagopyreae, Persicarieae, Polygoneae, and Rumiceae. Overall, the results from molecular data represent significant progress in understanding the evolutionary relationships of major groups within the family. This classification also provides an assessment of diagnostic morphological characters for the tribes. The present work will promote reevaluation of morphological characters within this diverse group, especially synapomorphies for Polygonoideae, and for tribes with a particularly complex history such as Fagopyreae, Persicarieae, and Polygoneae. A new combination, Fagopyrum tibeticum, is proposed.
A case study of DNA barcoding in Chinese Grimmiaceae and a moss recorded in China for the first time
Authors: Liu Yan , Ge Tong Cao , Ge Xue-Jin 
Published: February 2019

AbstractMosses are among the basal lineages of embryophytes and one of the three bryophyte lineages. In the present study, four regions of chloroplast DNA (rbcL‐a, rps4, trnH‐psbA, trnL intron) were used to investigate the applicability of DNA barcoding to four moss genera of Grimmiaceae (Racomitrium, Coscinodon, Grimmia, Schistidium) in China. The species resolution of the four loci examined was 65% (trnH‐psbA), 59% (rps4), 53% (rbcL‐a) and 29% (trnL intron). However, rps4 (59%) provided a higher value of monophyletic species with bootstrap support >50% than trnH‐psbA (47%), rbcL‐a (35%), and trnL intron (18%). No multi‐locus combinations could significantly increase the species resolution but they increased the percentages of monophyletic species with bootstrap support >50% compared to the best single locus. Species of the genus Racomitrium could be resolved completely by rps4 and mostly (>80%) by rbcL‐a or trnH‐psbA. The species of Coscinodon (i.e., C. cribrosus) showed distinct plastid region sequences in rbcL‐a, rps4, trnH‐psbA, and trnL intron. Inter‐specific sequence sharing or high intra‐specific variability led to large amounts of barcoding failure in Grimmia and Schistidium. Furthermore, using a combination of morphological characteristics and DNA barcoding for identification, a moss species, Racomitrium elongatum, was recorded for the first time in China. The results suggest that trnH‐psbA is potentially the best barcode in mosses and rps4 a good supplementary locus for future use, as standard plant barcodes (rbcL + matK) do not perform well in this taxonomic group.