bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thompsonella and the “Echeveria group” (Crassulaceae): phylogenetic relationships based on molecular and morphological characters
Authors: Carrillo-Reyes Pablo , Sosa Victoria , Mort Mark E. 
Published: February 2019

AbstractBroad phylogenetic analyses of Crassulaceae have retrieved a large clade comprising as much as one‐third of the species diversity present in the family as a whole. This so‐called Acre clade (Sedoideae) includes familiar genera such as Echeveria, Graptopetalum, and Thompsonella, and while it is consistently recovered in studies at the family level, relationships within the clade as well as the monophyly of many of the constituant genera have yet to be established. Results of a phylogenetic study of a genus within the Acre clade, Thompsonella, are here reported. Morphological evidence was gathered and molecular (nuclear ETS and ITS) DNA sequences were generated for forty‐seven taxa from the Acre clade, including all recognized members of Thompsonella. Parsimony analysis of the combined data retrieved Thompsonella as a monophyletic group and retrieved species in Graptopetalum, Thompsonella, Echeveria, Pachyphytum and Sedum sect. Pachysedum in a clade; this group was previously identified as the “Echeveria group”. Results indicate that only a few genera in the Acre clade are monophyletic and that to establish their generic limits further sampling mainly in the large Echeveria and Sedum genera is needed. Results from morphological and molecular analyses disagree in the position of T. mixtecana. However, an additional restricted analysis performed solely with cpDNA (rps16) placed this species within Thompsonella, suggesting a hybrid origin.
Nomenclatural note on the subgenera of Parodia (Cactaceae – Cactoideae)
Authors: Eggli Urs , Machado Marlon , Nyffeler Reto 
Published: February 2019

AbstractThe nomenclatural problems involved with subgeneric names under Parodia are elucidated, and the nomenclature of all existing names is evaluated in detail. Subgeneric names under Notocactus are similarly covered in a second part. A third part consists of a list of published subgeneric names for the group arranged alphabetically by the epithet of the name of the species indicating the type.
Phylogenetic analysis of Cabombaceae and Nymphaeaceae based on vegetative and leaf architectural characters
Authors: Taylor David Winship 
Published: February 2019

AbstractVegetative and leaf architectural characters are used to assess the phylogenetic relationships of species of Cabombaceae and Nymphaeaceae. Twenty‐eight species representing all eight genera and the five subgenera of Nymphaea are analyzed. These morphological analyses give robust support to other molecular and morphological analyses of the relationships of the two families. There is strong support for the two families to be monophyletic, and that Euryale and Victoria are closely related. Strict consensus analyses show that within the Nymphaeaceae, Nuphar is the first sister clade, followed by Barclaya and finally by a polytomy of Ondinea, Euryale‐Victoria and Nymphaea. The relationships of Ondinea are uncertain, in part due to missing characters. Finally, the genera of each family are monophyletic. Each genus has a suite of distinctive vegetative characteristics that are used to make an identification key of the genera. Although the value of vegetative and leaf architectural characters is shown, inclusion of atypical leaves, for example some types of submerged leaves, results in less resolved or robust trees.
Differentiation of perianth organs in Nymphaeales
Authors: Warner Kate A. , Rudall Paula J. , Frohlich Michael W. 
Published: February 2019

AbstractPerianth differentiation into distinct morphological whorls (sepals and petals) can be difficult to assess, particularly in early‐divergent angiosperms. The perianth of members of Nymphaeales (Cabomba,Brasenia,Barclaya,Euryale,Nuphar,Nymphaea,Victoria,Ondinea) has been described as differentiated into sepals and petals, undifferentiated or presenting examples of both states. In this paper, we review perianth structure in Nymphaeales using morphology and ontogeny in order to determine whether their perianths are dimorphic. The results indicate that although there are differences between the outer and inner perianth series, the organs display few “typical” sepal‐petal characteristics. Our observations of the perianth ofNupharandNymphaea, and reports onEuryale, show that sepaloid (green) and petaloid (yellow) areas can both occur on individual perianth organs, and that sepaloid areas occur mostly in the regions of the perianth organ that were exposed when the flower was in bud. SEM study revealed further morphological differences between the sepaloid and petaloid areas ofNupharandNymphaeaand also between the exposed and covered regions of the perianth ofCabomba,BraseniaandBarclaya. We discuss the implications of these results with respect to current concepts of perianth differentiation.
Utility of Amborellatrichopoda and Nupharadvena expressed sequence tags for comparative sequence analysis
Authors: Duarte Jill M. , Wall Kerr P. , Zahn Laura M. , Soltis Pamela S. , Soltis Douglas E. , Leebens-Mack Jim , Carlson John E. , Ma Hong W. , dePamphilis Claude W. 
Published: February 2019

AbstractExpressed sequence tags (ESTs) for the basal angiosperms Amborella trichopoda (Amborellaceae) and the water lily Nuphar advena (Nymphaeaceae) have proven valuable in identification of gene pairs to study the timing of duplication events relative to the most recent common ancestor (MRCA) of all extant angiosperms. Here we discuss how ESTs for these taxa are also useful for deducing gene families that were present in the MRCA of all flowering plants. For example, 4,572 gene clusters identified in an analysis of the rice and Arabidopsis proteomes contained putative orthologs of Amborella or Nuphar. Homologs of many developmentally important genes were identified from Amborella or Nuphar in these gene clusters. This number of ancestral genes is expected to increase as the number of Amborella and water lily ESTs increases. Genes found unduplicated in the rice and Arabidopsis genomes may be especially useful for phylogenetic analyses including diverse angiosperm lineages. We identify 595 of these single copy genes with putative orthologs in Amborella or Nuphar. Phylogenetic analysis of one of these nuclear single‐copy genes encoding the enzyme carboxymethylenebutenolidase yields a topology that places Amborella and Nuphar as the sisters to all other extant lineages of angiosperms and is generally consistent with current angiosperm phylogenies based mainly on chloroplast, mitochondrial, and nuclear ribosomal sequences.
A molecular phylogeny of the Solanaceae
Authors: Olmstead Richard G. , Bohs Lynn , Migid Hala Abdel , Santiago-Valentin Eugenio , Garcia Vicente F. , Collier Sarah M. 
Published: February 2019

AbstractA phylogeny of Solanaceae is presented based on the chloroplast DNA regions ndhF and trnLF. With 89 genera and 190 species included, this represents a nearly comprehensive genus‐level sampling and provides a framework phylogeny for the entire family that helps integrate many previously‐published phylogenetic studies within Solanaceae. The four genera comprising the family Goetzeaceae and the monotypic families Duckeodendraceae, Nolanaceae, and Sclerophylaceae, often recognized in traditional classifications, are shown to be included in Solanaceae. The current results corroborate previous studies that identify a monophyletic subfamily Solanoideae and the more inclusive “x = 12” clade, which includes Nicotiana and the Australian tribe Anthocercideae. These results also provide greater resolution among lineages within Solanoideae, confirming Jaltomata as sister to Solanum and identifying a clade comprised primarily of tribes Capsiceae (Capsicum and Lycianthes) and Physaleae. Stronger evidence also is provided for the inclusion of Capsicum within a paraphyletic Lycianthes. Solanaceae are a predominantly New World group, with several lineages represented on other continents. Apart from events within Solanum (for which sampling in this study is inadequate for biogeographic interpretations) the Old World representatives of Solanaceae can be accounted for by eight or nine dispersal events.
A new phylogeny‐based sectional classification for the large African orchid genus Disa
Authors: Bytebier Benny , Bellstedt Dirk U. , Linder Peter H. 
Published: February 2019

AbstractTwenty‐five years after the last major revision, the results of a molecular phylogenetic analysis have necessitated a re‐classification of the Disinae (Orchidoideae, Orchidaceae). The small genus Schizodium, endemic to the Cape Floristic Region, is deeply embedded in the genus Disa and its generic status can thus no longer be maintained. We propose a monogeneric subtribe Disinae and a subdivision of Disa into eighteen sections and one nothosection. Excluding the latter, the sections are monophyletic, well‐supported, morphologically distinguishable and are delimited to maximize the congruence with the previous classification. All 180 described and one undescribed species, as well as four named, natural hybrids are enumerated and assigned to sections and the nothosection.
Establishing an Agenda for Calcareous Dinoflagellate Research (Thoracosphaeraceae, Dinophyceae) including a nomenclatural synopsis of generic names
Authors: Elbrächter Malte , Gottschling Marc , Hildebrand-Habel Tania , Keupp Helmut , Kohring Rolf , Lewis Jane , Meier Sebastian K.J. , Montresor Marina , Streng Michael , Versteegh Gerard J.M. , Willems Helmut , Zonneveld Karin 
Published: February 2019

AbstractCalcareous dinoflagellates are considered to be a monophyletic group of peridinoid taxa that have the potential to produce calcified exoskeletal structures during the life cycle, or that derive from such forms. Frequently, these calcareous bodies are excellently preserved in the fossil record and have received increased attention during the past three decades with regard to their use in biostratigraphy, climate and environmental reconstruction. Fossil and extant taxa have been classified in various, partly concurring, systematic concepts, using character complexes of the theca, cyst wall ultrastructure and archaeopyle/operculum morphology. The significance of such character complexes is briefly discussed in the light of molecular data that have been accumulated during the past decade. Over the years, the number of published taxonomic names has increased, partly due to nomenclatural changes. We propose that the entirety of calcareous dinoflagellates, and non‐calcareous relatives derived from them, is accommodated in a single family of the order Peridiniales, the Thoracosphaeraceae, combining the former segregated taxonomic units Calciodinelloideae, a subfamily within Peridiniaceae, and Thoracosphaerales, a separate dinoflagellate order. As a result of a meeting of calcareous dinoflagellate specialists, we outline major subjects that are in need of re‐investigation and ‐evaluation (an Agenda for Calcareous Dinoflagellate Research). In order to contribute to a consistent and stable nomenclature and taxonomy of calcareous dinoflagellates, we list 97 published generic names assigned to known calcareous dinoflagellates in a nomenclatural synopsis, with species names indicating their types and information on type locality and stratigraphy. We evaluate the status of these names—whether validly published and, if so, whether legitimate—, a crucial first step for any revisionary work in the future.
DNA barcoding of a large genus, Aspalathus L. (Fabaceae)
Authors: Edwards Dawn , Horn Anne , Taylor Diane , Savolainen Vincent , Hawkins Julie A. 
Published: February 2019

AbstractThe DNA barcode potential of three regions (the nuclear ribosomal ITS and the plastid psbA‐trnH and trnT‐trnL intergenic spacers) was investigated for the plant genus Aspalathus L. (Fabaceae: Crotalarieae). Aspalathus is a large genus (278 species) that revealed low levels of DNA sequence variation in phylogenetic studies. In a 51‐species dataset for the psbA‐trnH and ITS regions, 45% and 16% of sequences respectively were identical to the sequence of at least one other species, with two species undiscriminated even when the two regions were combined. In contrast, trnT‐trnL discriminated between all species in this dataset. In a larger ITS and trnT‐trnL dataset, including a further 82 species, 7 species in five pairwise comparisons remained undiscriminated when the two regions were combined. Four of the five pairs of species not discriminated by sequence data were readily distinguished using a combination of qualitative and quantitative morphological data. The difficulty of barcoding in this group is increased by the presence of intraspecific variation in all three regions studied. In the case of psbA‐trnH, three intraspecific samples had a sequence identical to at least one other species. Overall, psbA‐trnH, currently a candidate for plant barcoding, was the least discriminatory region in our study.
Characters, taxonomic groups, and relationships in botany 1770–1850 as exemplified by the work of Henri Cassini
Authors: Stevens Peter F. 
Published: February 2019

AbstractUsing the French botanist Henri Cassini's work as an example, the complex relationship between characters, groups and relationships in the period 1770–1850 is explored. Cassini thought that classifications should be natural and that groups were to be based on numerous characters, although they would be difficult to recognize and characterize. For the most part he saw relationships between organisms as two dimensional, with one group directly joining two or more other groups. At the same time he asserted that the best way to think about affinities was as if they were linear, largely because this was most compatible with how he thought that the human mind worked. When he discussed relationships between individual plant parts he used words like type, analogy, and hypothesis that were rarely used when he discussed relationships between groups. In Cassini's writings it is difficult to connect his work on the analogies between plant parts with his ideas of affinities between groups. In the early nineteenth century zoologists in particular were developing various ways of thinking about organisms as being related indirectly, whether using abstract types or the taxonomic hierarchy to structure relationships. Similarly, Darwin's discussion of affinities between groups was separate from that on homologies between particular structures, but he saw relationships as being like a tree, with extant taxa being related indirectly by their ancestors.
Phenetics: revolution, reform or natural consequence?
Authors: Jensen Richard J. 
Published: February 2019

AbstractLinnaeus had it right—essentially, a classification should allow ease of identification. However, his classification had a significant shortcoming: it could not be used to determine relationships in any meaningful way. As the desire for a natural system developed and, more especially, as the implications of Darwinian evolution were realized, biologists recognized that a system of classification should serve more than a single, artificial purpose. What that purpose is, or should be, continues to be a point of contention. Application of mathematical tools to taxonomic problems led to a logical conclusion: natural classifications, employing a large suite of characters, could be attained by multivariate analyses. The concept of overall similarity was, perhaps too blithely, likened to both naturalness and information content. Pheneticists were not concerned with approximating phylogeny, but acknowledged that their classifications could form the basis for phylogenetic deductions under certain restricted conditions. Despite the promise of phenetics, the concurrent development of cladistic methodology (both under the rubric of numerical taxonomy, s.l.) shifted focus from classifications with high information‐content, predictivity, and stability, to classifications reflecting hypothesized phylogenetic relationships. While a number of critics raised valid questions about the utility of phenetics and the underlying principles of proposed phenetic taxonomy, many criticisms consisted of over‐simplified or unwarranted objections. Nevertheless, today phenetic analyses are de riguer for identifying fundamental units (populations, species) that form the bases for phylogenetic studies. After all, it is only natural that members of a species show greater overall similarity to each other than to members of different species, a view that can often be applied to higher ranks as well.
Three centuries of paradigm changes in biological classification: Is the end in sight?
Authors: Mishler Brent D. 
Published: February 2019

AbstractClassification has been a centerpiece of biology ever since Linnaeus, providing a framework on which existing knowledge can be organized and predictions about unknown traits can be made. But the basis of biological classification has gone through a series of upheavals over the last three centuries, from being considered a plan in the mind of the creator, to a neutral assessment of overall similarity, to a reflection of evolutionary niches, and finally to a phylogenetic mapping of the tree of life. This paper will consider this historical process, with emphasis on phylogenetic systematics (cladistics), and also consider where we might be heading in the future. It is necessary first, however, to consider the purposes of classification itself, which have not changed much over time.
Generic classification of the Verrucariaceae (Ascomycota) based on molecular and morphological evidence: recent progress and remaining challenges
Authors: Gueidan Cécile , Savić Sanja , Thüs Holger , Roux Claude , Keller Christine , Tibell Leif , Prieto Maria , Heiðmarsson Starri , Breuss Othmar , Orange Alan , Fröberg Lars , Wynns Anja Amtoft , Navarro-Rosinés Pere , Krzewicka Beata , Pykälä Juha , Grube Martin , Lutzoni François 
Published: February 2019

AbstractRecent molecular phylogenetic analyses and morphological studies have shown that it is necessary to revise the present morphology‐based generic delineation of the lichen family Verrucariaceae in order to account for evolutionary relatedness between species. Consequently, several genera were recently described or resurrected, and others were re‐circumscribed. As an additional step toward this generic revision, three new genera (Hydropunctaria, Parabagliettoa, Wahlenbergiella) and eleven new combinations are proposed here. A summary of the current taxonomic and morphological circumscription of all genera investigated so far is also presented. Several monophyletic groups are identified for which further taxonomical changes will be required, but for which taxon and gene sampling is presently viewed as insufficient. Clear morphological synapomorphies were found to be rare for newly delimited genera. In some cases (reduced morphology or plesiomorphism), even the combinations of slightly homoplasious phenotypic characters do not allow a clear morphological generic circumscription. Molecular features are envisioned as characters for delimiting these taxa.
The use of digital image‐based morphometrics to study the phenotypic mosaic in taxa with porous genomes
Authors: Lexer Christian , Joseph Jeffrey , van Loo Marcela , Prenner Gerhard , Heinze Berthold , Chase Mark W. , Kirkup Don 
Published: February 2019

ABSTRACTRapid recent developments in DNA sequencing and genetic marker technologies call for the establishment of cost‐effective, automated phenotyping assays for evolutionary biology and systematics, so that the effects of DNA polymorphisms and epigenetic changes on the phenotype can be evaluated. We discuss the use of digital image‐based morphometrics in evolutionary biology and systematics with special emphasis on studies of taxa with porous genomes, i.e., taxa that do not conform to the traditional view of whole‐genome isolation between species. We outline the phenomenon of the 'phenotypic mosaic' in taxa with porous genomes using well‐documented examples from the literature and describe three important challenges arising for taxonomists: (1) character conflict in phylogenetic studies, (2) biased sampling of traits in morphological studies, and (3) cryptic ecological speciation. We demonstrate the use of geometric morphometrics using a combined molecular and morphometric dataset from an interspecific hybrid zone between two divergent Eurasian species of Populus, P. alba (white poplar) and P. tremula (European aspen). Elliptic Fourier analysis (EFA)‐based morphometric data were collected for 527 leaf specimens from 84 trees with known genomic composition as determined by a set of 30 nuclear DNA microsatellites. In addition, to demonstrate the ease of scoring functionally relevant phenotypes via digital image analysis, quantitative differences in leaf reflectance were examined and their structural basis determined using scanning electron microscopy (SEM). The EFA results indicate a heritable inter‐individual component for symmetric aspects and an important intra‐individual component for asymmetric aspects of variation in leaf outlines. Symmetric traits displayed a striking variety of phenotypes in hybrids compared to their parental species, consistent with the notion of the phenotypic mosaic. Linear discriminant analysis of these morphometric traits revealed (1) clear differentiation between parental species and (2) divergence between recombinant hybrids and their sympatric backcross parent P. alba, mediated primarily by two P. tremula–like and two transgressive traits. Our results demonstrate the usefulness of geometric morphometrics to interrogate multiple independent phenotypic characters and detect individual traits affected by introgression and divergence in taxa with porous genomes. Digital image‐based morphometrics holds great promise for large‐scale studies of relationships between DNA polymorphism and phenotypes in evolutionary biology.
The effect of incongruence on molecular dates
Authors: Pfeil Bernard E. 
Published: February 2019

ABSTRACTDespite what is known about processes that can cause topological incongruence among datasets, combined analysis of concatenated datasets (simultaneous analysis) without examination of congruence is still advocated and practiced. Although the danger in such cases of inferring the incorrect topology is known (and sometimes ignored), here I examine an under‐appreciated effect of the combined analysis of incongruent datasets on molecular date inferences. Using simulated character matrices, a bias towards either increased or decreased dates is demonstrated that increases in its effect with greater proportion of incongruent characters. A general prediction is made regarding the behaviour of molecular date estimates based on the phylogenetic position of taxa that are incongruent. This prediction is borne out in a case study using real data from incongruent nuclear genes in Medicago (Fabaceae).