bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeny of Chamaecrista Moench (Leguminosae­Caesalpinioideae) based on nuclear and chloroplast DNA regions
Authors: de Souza Conceição Adilva , Paganucci de Queiroz Luciano , Lewis Gwilym Peter , Gomes de Andrade Maria José , Machado de Almeida Paulo Ricardo , Schnadelbach Alessandra Selbach , Berg Cássio van den 
Published: February 2019

AbstractChamaecrista Moench is a genus of caesalpinioid legumes with about 330 species mostly from the New World. The phylogeny of the genus was studied using sequence data from nuclear ITS and plastid trnL­F DNA spacers, representing all six sections of Chamaecrista. Separate and combined analyses recovered the same major clades with high bootstrap and posterior probabilities support, except for the subclades of representatives of sections Caliciopsis, Chamaecrista, and Xerocalyx. The monophyly of Chamaecrista was highly supported in all analyses. Sections Apoucouita and Xerocalyx were supported as monophyletic, sect. Absus was paraphyletic and subsect. Baseophyllum was resolved more closely related to species of sections Chamaecrista, Caliciopsis, and Xerocalyx than to subsect. Absus. The monotypic section Grimaldia was embedded within subsect. Absus. Section Chamaecrista was paraphyletic with respect to sections Caliciopsis and Xerocalyx. Our analyses suggest that the diversification patterns in Chamaecrista occurred through an initial shift from rainforest trees to a more diverse clade of savannah shrubs. Within the latter group, two main subclades were recovered: (1) a planaltine and high­mountain clade characterized by absence of extrafloral nectaries and the appearance of sticky glandular hairs; and (2) a mostly herbaceous clade with axillary fascicled inflorescences and reduced chromosome numbers. This last group is more diverse in open grassland areas and includes many colonizers of waste ground.
Phylogenetic relationships of diploid and polyploid species inLudwigiasect.Isnardia(Onagraceae) based on chloroplast and nuclear DNAs
Authors: Hung Kuo-Hsiang , Schaal Barbara A. , Hsu Tsai-Wen , Chiang Yu-Chung , Peng Ching-I , Chiang Tzen-Yuh 
Published: February 2019

AbstractLudwigia, a genus with rampant interspecific hybridization, is an ideal model for examining the impact of gene introgression and polyploidization on species diversification. We examined the evolution of theLudwigiasect.Isnardia, which is a polyploid complex (x= 8) of five species distributed in North America. The phylogeny ofL. sect.Isnardiawas reconstructed based on sequences of cpDNAatpB­rbcLintergenic spacer and nrITS (internal transcribed spacer). MostL. sect.Isnardiaspecies are polyphyletic at both loci, indicating possible recurrent hybridization, based on maximum likelihood trees rooted atL. sect.Microcarpium. A minimum spanning network was also constructed to examine genealogical relationships among haplotypes. In the cpDNA network, haplotypes of tetraploidL. spathulataare nested at the most interior nodes, suggesting a parental genome origin of an extinct diploid or an unsampled extant diploid with a DD cytotype. AllopolyploidL. arcuata contributed its cpDNA to hexaploid L. repens and L. brevipes. ITS haplotypes of diploid L. palustris were clustered with L. spathulata, suggestingL. palustrisas the paternal genome donor.Ludwigia brevipesmay have arisen via bi3directional hybridization betweenL. palustrisandL. arcuatafollowed by polyploidy. Genetic and phylogenetic analyses using molecular markers with different inheritance modes provided sufficient insights into the reticulate evolution of the species ofL. sect.Isnardia. Interspecific hybridization and polyploidy play a key role in the species evolution inL. sect.Isnardia.
Nuclear and chloroplast DNA variation in Cephalaria squamiflora (Dipsacaceae), a disjunct Mediterranean species
Authors: Rosselló Josep A. , Cosín Raúl , Bacchetta Gianluigi , Brullo Salvatore , Mayol Maria 
Published: February 2019

AbstractCephalaria squamiflora is a chamaephyte restricted to rupicolous habitats in islands of the Western (Balearic Islands, Sardinia) and Eastern Mediterranean (Crete and few Aegean islands). Four narrowly distributed races (subspp. squamiflora, mediterranea, ebusitana, balearica) have been described to encompass the morphological variation within the species. We have used nuclear ribosomal ITS and cpDNA sequences to assess how the patterns of molecular differentiation are related to taxonomic and geographic boundaries. Extensive intragenomic ITS variation was detected in samples from all territories, the average sequence divergence among cloned ribotypes was 1.339%. The parsimony network of cloned ITS sequences suggests a split between Eastern and Western Mediterranean accessions. Chloroplast DNA sequences showed five distinct haplotypes, only one of which was shared between islands (Majorca and Sardinia). Both nuclear and cpDNA markers supported the monophyly of the C. squamiflora complex and identified a highly structured pattern of molecular variation composed by sister monophyletic lineages that mirror major biogeographic units (Western and Eastern Mediterranean). The molecular evidence supports the hypotheses that vicariance events linked to the geological history of the region or dispersal across the Mediterranean may explain the distribution of the complex.
Palaeobotanical systematics for the phylogenetic age: applying organspecies, form­species and phylogenetic species concepts in a framework of reconstructed fossil and extant whole­plants
Authors: Bateman Richard M. , Hilton Jason 
Published: February 2019

AbstractA typical vascular land­plant consists of ten to twelve definable organs. Most plant fossils have been disarticulated into their component organs, which must therefore be correlated if the fossil plant is to be understood holistically and compared with its presumed descendants in the extant flora. The resulting conceptually reconstructed whole­plants are the crown jewels of palaeobotany, as they permit full morphological comparison with extant plants and provide templates that guide through reciprocal illumination further attempts at reconstruction. Each of the three lines of evidence facilitating whole­plant reconstruction (association/dissociation, morphological similarity and organic connection) yields only a probability statement that the organs in question have been successfully correlated. Disarticulation means (1) that phenotypic variation can be studied only at the level of individual organs, and (2) that in order to be distinguished from all other kinds of the same organ, an organ must bear a unique morphological character state (autapomorphy). In our terminology, each definable kind of organ is an organ­species. The few organ­species perceived as possessing autapomorphies (and thus as unique) are termed autapospecies, whereas the remaining organ­species characterise more than one whole­plant species and hence are termed form­species. The distinction between autapospecies and form­species is dependent on the range of taxa sampled and is wholly character­based; the age of the fossils under comparison is irrelevant, and the state of preservation is relevant only through its influence on the range of characters that can realistically be scored. None of the many other species concepts recognised by (palaeo)biologists is applicable to fossil plants. Our ability to apply this phylogenetically­inspired approach and terminology to formal taxonomy has been increasingly compromised by modifications to successive editions of theInternational Code of Botanical Nomenclature, culminating in the 2001 and 2006Codeswhich reduced palaeobotanical provision to the fatally over­generalised 'morphotaxon' concept. A more conceptually rigorous, palaeobotanically informed revision of theCode, placing nomenclature more clearly in the service of taxonomy, would strengthen the crucial roles of reconstructed plants within palaeobotany and of palaeobotany within 21st Century science.
A combined molecular and morphological approach to the taxonomically intricate European mountain plant Papaver alpinum s.l. (Papaveraceae) — taxa or informal phylogeographical groups?
Authors: Schönswetter Peter , Solstad Heidi , Escobar Garcí Pedro , Elven Reidar 
Published: February 2019

AbstractPapaver alpinum s.l. is an extraordinarily polymorphic taxon distributed throughout southern and central European mountain ranges. We tested previous hypotheses about relationships and taxonomical status of the numerous described taxa within this species or species group by applying different molecular approaches. In addition we re­evaluated morphological characters used in previous taxonomic treatments in the light of the molecular results. The ancestral sequence haplotypes were widespread and dominant throughout the Alps, whereas peripheral populations in other mountain ranges were often characterised by haplotypes directly derived from the central haplotypes involving one or two mutational steps. The AFLP data corroborated the pattern of a 'centrifugal radiation' and additionally showed that most populations were genetically distinct, presumably due to the effect of genetic drift in small and isolated populations. The morphological data did not reveal clear patterns of variation; only the Pyrenean and Sierra Nevada populations differed in two non­overlapping and presumably independent characters. Altogether, our study implies that most previous taxonomic concepts of P. alpinum s. l. were highly artificial, and that either nearly all populations have to be raised to some taxonomic rank or that, preferably, no infraspecific taxa should be recognised at all. The only segregate possibly deserving taxonomic rank, based on both morphology and genetics, is the Iberian P. alpinum subsp. lapeyrousianum.
×Chiranthomontodendron: the correct nothogeneric name for the artificial hybrid Chiranthodendron × Fremontodendron (Malvaceae: Malvoideae)
Authors: Dorr Laurence J. 
Published: February 2019

AbstractThe nothogeneric name ×Chiranthomontodendron is proposed to accommodate an artificial hybrid between species of Chiranthodendron and Fremontodendron, and the nothospecies ×Chiranthomontodendron lenzii is described from cultivated material.
Molecular phylogeny of Acacia Mill. (Mimosoideae: Leguminosae): Evidence for major clades and informal classification
Authors: Murphy Daniel J. , Brown Gillian K. , Miller Joseph T. , Ladiges Pauline Y. 
Published: February 2019

AbstractSequences of nuclear ribosomal DNA internal (ITS) and external (ETS) transcribed spacers were used to generate a phylogeny of Acacia Mill. s.str. (synonyms: Acacia subg. Phyllodineae (DC.) Seringe; Racosperma Mart.). This study included 109 exemplar taxa from all seven sections recognised in previous classifications, and represents the largest sampling of diversity for molecular phylogenetics of Acacia s.str. undertaken so far. Four main clades were identified from the combined dataset of ITS and ETS using parsimony and Bayesian analyses. Two of these clades consist mostly of uninerved phyllodinous taxa assigned to sect. Phyllodineae. One clade includes taxa related to A. victoriae and A. pyrifolia, and the second comprises taxa in the A. murrayana species group. These taxa occur predominantly in semi‐arid and arid regions. Relationships also resolve the previously identified Pulchelloidea clade, which includes members of sects. Pulchellae, Alatae, Phyllodineae and Lycopodiifoliae. A large clade with limited phylogenetic resolution was also identified (the "p.u.b. clade"). This is an assemblage of plurinerved and uninerved phyllodinous taxa and also bi‐pinnate taxa from sect. Botrycephalae. Clades are discussed with reference to morphological characters, and while some morphological states are correlated with clades, including seedling ontogeny, inflorescence and phyllode nerves, clear synapomorphies remain to be identified. Traditional classifications of Acacia s.str. are artificial and a preliminary informal classification based on phylogenetic relationships within Acacia s.str. is proposed.
Molecular phylogeny of Salix L. (Salicaceae) inferred from three chloroplast datasets and its systematic implications
Authors: Chen Jia-Hui , Sun Hang , Wen Jun , Yang Yong-Ping 
Published: February 2019

AbstractSalix is a taxonomically difficult genus and its generic limits and infrageneric division are still highly controversial. We employed sequences of the chloroplast rbcL gene, trnD‐T spacer and atpB‐rbcL spacer for phylogenetic analyses of Salix. The results strongly support that Salix, Toisusu and Chosenia form a monophyletic group, confirming the merge of Toisusu and Chosenia with Salix. Within Salix s.l., two major clades are recognizable; one contains species of subgenus Salix (excluding sections Triandrae and Urbanianae), with the New World and the Old World species forming strongly supported clades, respectively; and the other includes sections Triandrae, Urbanianae, Chosenia and all species of subgenera Chamaetia and Vetrix, with the latter two subgenera forming a robustly supported subclade but with low resolution. A new infrageneric classification of Salix is herein proposed. The previously recognized subgenus Salix is split into three subgenera: Salix, Chosenia and Triandrae, and subgenera Chamaetia and Vetrix are combined as subgenus Vetrix.
Phylogeny and taxonomy of the bluebell genus Hyacinthoides, Asparagaceae [Hyacinthaceae]
Authors: Grundmann Michael , Rumsey Fred J. , Ansell Stephen W. , Russell Stephen J. , Darwin Sarah C. , Vogel Johannes C. , Spencer Mark , Squirrell Jane , Hollingsworth Peter M. , Ortiz Santiago , Schneider Harald 
Published: February 2019

AbstractA robust phylogeny for the genus Hyacinthoides (bluebells) was established using cpDNA sequences and evaluated in light of a re‐assessment of morphological diversity, cytology, distribution patterns and field observations. The genus is distributed in the western Mediterranean–Atlantic region and the northern African mountains. Within this area, there is a major divide between an eastern and western clade, each of them with their own radiations, mainly in autumn‐winter flowering taxa in northern Africa and spring flowering taxa in the Iberian Peninsula. We now recognise eleven taxa and one hybrid taxon, which are separated into five clades. Polyploidy is confined to the H. non‐scripta–hispanica clade with diploid and triploid taxa as well as a newly recognized tetraploid taxon. For the eleven taxa, distribution ranges, taxonomy, morphology, descriptions and a new key are presented. The nomenclatural history of the genus has been reviewed. Generitypes have been designated for Hyacinthoides Heist. ex Fabr. and Endymion Dumort. and lectotypes selected for four species, three of which are combined for the first time in Hyacinthoides: H. cedretorum, H. ciliolata and H. flahaultiana. Several important questions worthy of further investigation, such as evolutionary processes and their major drivers, e.g. environmental change in the Mediterranean basin, flower morphology and associated pollinators, or sympatric versus allopatric speciation have come into sharper focus through this phylogenetic investigation.
The systematic position of Meteoriella S. Okamura (Musci) based on molecular and morphological data
Authors: Wang Qinghua , Jia Yu , Liu Yang , Chen Zhiduan 
Published: February 2019

AbstractMeteoriella S. Okamura, an endemic moss genus of eastern Asia, has traditionally been classified in Pterobryaceae or Meteoriaceae. However, recent molecular data has suggested that Meteoriella should be placed in Hylocomiaceae. To elucidate the systematic position of Meteoriella within Hypnales, we analyzed two DNA sequence datasets consisting of two regions mt‐nad5, cp‐rps4) with 64 taxa, and five regions (mt‐nad5, cp‐rps4, cp‐rbcL, cp‐trnL‐F, nr‐ITS2) with 27 taxa, using maximum parsimony and maximum likelihood methods. Analyses of the two datasets strongly supported Meteoriella as sister to Loeskeobryum, which has hitherto been included in the Hylocomiaceae. Although the evolution of Hypnales and the monophyly of Hylocomiaceae remain unresolved, a close relationship between Meteoriella and Hylocomiaceae is clear. Meteoriella shares some morphological characters with Meteoriaceae and Pterobryaceae, apparently owing to convergent evolution related to epiphytic growth. A reappraisal of morphological evidence reveals greater morphological similarity with Hylocomiaceae than previously recognized. The possible systematic position of Meteoriella within Hylocomiaceae is discussed. Loeskeobryum, rather than Orontobryum (suggested by earlier studies), shows the closest phylogenetic relationship with Meteoriella.
The reticulate origin of modern plane trees (Platanus, Platanaceae): A nuclear marker puzzle
Authors: Grimm Guido W. , Denk Thomas 
Published: February 2019

AbstractHybridization plays a major role in speciation. However, hybridization and reticulate evolution in general are poorly understood in tree species because genetic documentation is often missing. Analyses of biparentally inherited gene regions allow detection of reticulate signals. Multicopy and single‐copy nuclear markers may show significant intraindividual variability owing to reticulation processes. Naturally, such processes induce incompatible phylogenetic signal resulting in incongruent genealogies. Data from three nuclear markers, two multicopy nrDNA spacers, and the single‐copy 2nd intron of the LEAFY gene, mirror ancient and recent horizontal gene flow in plane trees (Platanus). In addition to previously assembled data from the internal transcribed spacers (ITS) of the 35S ribosomal DNA, we found atypical 5S rDNA intergenic spacer sequences (5S‐IGS) causing significant intra‐ and interindividual polymorphism, and a conspicuous LEAFY intron dimorphism. A detailed framework of reticulate molecular evolution of Platanus can be erected using splits graphs based on distances between cloned sequences or individuals, and competing topologies. Two hundred and sixty‐one 5S‐IGS sequences and LEAFY genotyping of 71 individuals via sequence analysis and PCR‐RFLP support a previous ITS study (including pseudogenous and non‐pseudogenous variants) suggesting that the modern North American taxa P. rzedowskii and P. occidentalis var. palmeri are the result of ancient hybridization. Platanus occidentalis var. palmeri requires taxonomic revision and is provisionally treated at species rank.
Heldreichia Boiss. (Brassicaceae) revisited: A morphological and molecular study
Authors: Parolly Gerald , Nordt Birgit , Bleeker Walter , Mummenhoff Klaus 
Published: February 2019

AbstractThe small Southwest Asian scree plant genus Heldreichia Boiss. (Brassicaceae) with its diversity centre in Anatolia, is revised in a morphological and molecular (ITS sequence) monograph. Heldreichia taxa under study appear to be monophyletic in the Bayesian tree; the tribal position remains unclear. A re‐evaluation of morphological characters resulted in a new taxonomic concept of Heldreichia. We suggest only one single polymorphic species, H. bupleurifolia, with four largely geovicarious subspecies, including a new subspecies, H. bupleurifolia subsp. polymorpha, for the westernmost populations of the Taurus range. Geographical areas with higher morphological and molecular diversity correspond to the generally accepted speciation and diversity centres of the Taurus range. Inter‐pluvial migration events between isolated mountain ranges may have contributed to the morphological and genetic diversity within Heldreichia. Populations with non‐entire leaf margins, traditionally named H. rotundifolia, should have evolved polytopically. Keys, a distribution map and illustrations are provided for all accepted subspecific taxa. Heldreichia bupleurifolia var. subtriloba and H. kotschyi are lectotypified.
Disintegrating Portulacaceae: A new familial classification of the suborder Portulacineae (Caryophyllales) based on molecular and morphological data
Authors: Nyffeler Reto , Eggli Urs 
Published: February 2019

AbstractTraditional classifications of the suborder Portulacineae recognize six families: Basellaceae, Cactaceae, Didiereaceae, Halophytaceae, Hectorellaceae, and Portulacaceae. However, phylogenetic analyses based on molecular sequence data indicate that the traditional family Portulacaceae is paraphyletic and consists of three distinct lineages that also include Cactaceae, Didiereaceae, and Hectorellaceae. We use sequence data from the chloroplast genes matK and ndhF representing 64 species of Portulacineae and outgroups to reconstruct their phylogenetic relationships with Bayesian and maximum parsimony inference methods. Evidence from these molecular phylogenetic analyses as well as from comparative morphological investigations allow us to propose a revised familial classification of the suborder Portulacineae. We recognize eight monophyletic families: Anacampserotaceae (Anacampseros, Grahamia, Talinopsis), Basellaceae, Cactaceae, Didiereaceae (incl. Calyptrotheca, Ceraria, Portulacaria), Halophytaceae, Montiaceae (incl. Hectorellaceae, Calandrinia, Cistanthe, Claytonia, Lewisia, Montia, Phemeranthus), Portulacaceae (Portulaca only), and Talinaceae (Amphipetalum, Talinella, Talinum). We provide a synopsis for this revised family classification with an identification key mainly based on habit and fruit characters, and family diagnoses with information on distribution, taxonomic diversity, and a brief discussion on phylogenetics and classification.
Molecular systematics of Echinops L. (Asteraceae, Cynareae): A phylogeny based on ITS and trnL-trnF sequences with emphasis on sectional delimitation
Authors: Sánchez-Jiménez Ismael , Lazkov Georgy A. , Hidalgo Oriane , Garnatje Teresa 
Published: February 2019

AbstractThe monogeneric subtribe Echinopsinae of Cynareae (Asteraceae) was analysed using nrDNA ITS and plastid trnL-trnF for 81 of the ca. 120 species, representing all Echinops sections except Cenchrolepis and Pterolepis. Maximum parsimony and Bayesian analyses were used for each dataset and for the combined data. The resulting molecular phylogenetic framework resolves Echinops as monophyletic and confirms the inclusion of E. acantholepis (= Acantholepis orientalis) within the genus. Echinops is divided into two lineages, one consisting of E. sect. Chamaechinops and sect. Acantholepis (almost exclusively annual or biennial), and the other the remaining sections (almost all perennial). Our results support an infrageneric classification of Echinops into nine previously recognized sections: Acantholepis (= Nanechinops), Chamaechinops, Echinops (= Terma), Hamolepis, Hololeuce, Oligolepis, Phaeochaete, Psectra and Ritropsis, all resolved as strongly monophyletic after some species relocations. The status of E. sect. Phaeochaete and the sectional assignment of E. onopordum, E. pungens and E. transcaucasicus remain to be clarified. The evolution of involucral bracts is congruent with the phylogenetic framework and supports the sectional classification. Annual pollen type does not constitute an autapomorphy of the clade grouping the annuals but may represent the ancestral character state for the entire genus.