Combining Data in Phylogenetic Systematics: An Empirical Approach Using Three Molecular Data Sets in the Solanaceae

1994 ◽  
Vol 43 (4) ◽  
pp. 467-481 ◽  
Author(s):  
R. G. Olmstead ◽  
J. A. Sweere
Keyword(s):  
Molecular Data ◽  
Empirical Approach ◽  
Phylogenetic Systematics ◽  
Data Sets ◽  
Combining Data

scholarly journals TRIBES AND CLADES WITHIN APIACEAE SUBFAMILY APIOIDEAE: THE CONTRIBUTION OF MOLECULAR DATA

2001 ◽  
Vol 58 (2) ◽  
pp. 301-330 ◽  
Author(s):  
S. R. DOWNIE ◽  
G. M. PLUNKETT ◽  
M. F. WATSON ◽  
K. SPALIK ◽  
D. S. KATZ-DOWNIE ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Data Sets ◽  
Combining Data ◽  
Restriction Sites ◽  
Dna Restriction ◽  
Cladistic Analyses

Phylogenetic analyses of chloroplast gene (rbcL, matK), intron (rpl16, rps16, rpoC1) and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences and chloroplast DNA restriction sites, with supplementary data from variation in size of the chloroplast genome inverted repeat, have been used to elucidate major clades within Apiaceae (Umbelliferae) subfamily Apioideae Drude. This paper summarizes the results of previously published molecular cladistic analyses and presents a provisional classification of the subfamily based on taxonomic congruence among the data sets. Ten tribes (Aciphylleae M. F. Watson & S. R. Downie, Bupleureae Spreng., Careae Baill., Echinophoreae Benth., Heteromorpheae M. F. Watson & S. R. Downie, Oenantheae Dumort., Pleurospermeae M. F. Watson & S. R. Downie, Pyramidoptereae Boiss., Scandiceae Spreng. and Smyrnieae Spreng.) are erected or confirmed as monophyletic, with Scandiceae comprising subtribes Daucinae Dumort., Scandicinae Tausch and Torilidinae Dumort. Seven additional clades are also recognized but have yet to be treated formally, and at least 23 genera examined to date are of dubious tribal or clade placement. The utility of these different molecular markers for phylogenetic inference in Apioideae is compared based on maximum parsimony analyses of subsets of previously published molecular data sets. Of the six loci sequenced, the ITS region is seen to be evolving most rapidly and rbcL is the most conservative. Intermediate in rate of evolution are matK and the three chloroplast introns; with rpl16 and rps16 evolving slightly faster than matK or rpoC1. The analysis of restriction sites, however, provided 2–4 times more parsimony informative characters than any single DNA locus sequenced, with estimates of divergence just slightly lower than that of the ITS region. The trees obtained from separate analyses of these reduced data sets are consistent with regard to the major clades inferred and the relationships among them. Similar phylogenies are obtained by combining data or combining trees, representing the supermatrix and supertree approaches to phylogenetic analysis, respectively. The inferred relationship among the tribes and informally recognized major clades within Apioideae is presented.

scholarly journals Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life

2017 ◽  
Author(s):  
Ross Mounce
Keyword(s):  
Large Scale ◽  
Phylogenetic Signal ◽  
Scientific Progress ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Phylogenetic Groups ◽  
Use Of Data ◽  
Wide Range ◽  
Cladistic Analyses

In this thesis I attempt to gather together a wide range of cladistic analyses of fossil and extant taxa representing a diverse array of phylogenetic groups. I use this data to quantitatively compare the effect of fossil taxa relative to extant taxa in terms of support for relationships, number of most parsimonious trees (MPTs) and leaf stability. In line with previous studies I find that the effects of fossil taxa are seldom different to extant taxa – although I highlight some interesting exceptions. I also use this data to compare the phylogenetic signal within vertebrate morphological data sets, by choosing to compare cranial data to postcranial data. Comparisons between molecular data and morphological data have been previously well explored, as have signals between different molecular loci. But comparative signal within morphological data sets is much less commonly characterized and certainly not across a wide array of clades. With this analysis I show that there are many studies in which the evidence provided by cranial data appears to be be significantly incongruent with the postcranial data – more than one would expect to see just by the effect of chance and noise alone. I devise and implement a modification to a rarely used measure of homoplasy that will hopefully encourage its wider usage. Previously it had some undesirable bias associated with the distribution of missing data in a dataset, but my modification controls for this. I also take an in-depth and extensive review of the ILD test, noting it is often misused or reported poorly, even in recent studies. Finally, in attempting to collect data and metadata on a large scale, I uncovered inefficiencies in the research publication system that obstruct re-use of data and scientific progress. I highlight the importance of replication and reproducibility – even simple reanalysis of high profile papers can turn up some very different results. Data is highly valuable and thus it must be retained and made available for further re-use to maximize the overall return on research investment.

scholarly journals Phylogenetic analysis of large molecular data sets

2017 ◽  
pp. 99
Author(s):  
Pamela S. Soltis ◽  
Douglas E. Soltis
Keyword(s):  
Large Data ◽  
Molecular Data ◽  
Global Optimum ◽  
Large Data Sets ◽  
Phylogeny Reconstruction ◽  
Local Optimum ◽  
Data Sets ◽  
Additional Consideration ◽  
Technological Advances ◽  
The Difference

Technological advances in molecular biology have greatly increased the speed and efficiency of DNA sequencing, making it possible to construct large molecular data sets for phylogeny reconstruction relatively quickly. Despite their potential for improving our understanding of phylogeny, these large data sets also provide many challenges. In this paper, we discuss several of these challenges, including 1) the failure of a search to find the most parsimonious trees (the local optimum) in a reasonable amount of time, 2) the difference between a local optimum and the global optimum, and 3) the existence of multiple classes (islands) of most parsimonious trees. We also discuss possible strategies to improve the' likelihood of finding the most parsimonious tree(s) and present two examples from our work on angiosperm phylogeny. We conclude with a discussion of two alternatives to analyses of entire large data sets, the exemplar approach and compartmentalization, and suggest that additional consideration must be given to issues of data analysis for large data sets, whether morphological or molecular.

Generic Delimitations and Relationships of the Cape Genera Capnophyllum, Dasispermum, and Sonderina, the North African Genera Krubera and Stoibrax, and a New Monotypic Genus of the Subfamily Apioideae (Apiaceae)

2009 ◽  
Vol 34 (3) ◽  
pp. 580-594 ◽  
Author(s):  
Anthony R. Magee ◽  
Ben-Erik van Wyk ◽  
Patricia M. Tilney ◽  
Stephen R. Downie
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Monotypic Genus ◽  
North African ◽  
African Species ◽  
Dna Sequence Data ◽  
The North ◽  
Relationship Of

Generic circumscriptions and phylogenetic relationships of the Cape genera Capnophyllum, Dasispermum, and Sonderina are explored through parsimony and Bayesian inference analyses of nrDNA ITS and cpDNA rps16 intron sequences, morphology, and combined molecular and morphological data. The relationship of these genera with the North African genera Krubera and Stoibrax is also assessed. Analyses of both molecular data sets place Capnophyllum, Dasispermum, Sonderina, and the only southern African species of Stoibrax (S. capense) within the newly recognized Lefebvrea clade of tribe Tordylieae. Capnophyllum is strongly supported as monophyletic and is distantly related to Krubera. The monotypic genus Dasispermum and Stoibrax capense are embedded within a paraphyletic Sonderina. This complex is distantly related to the North African species of Stoibrax in tribe Apieae, in which the type species, Stoibrax dichotomum, occurs. Consequently, Dasispermum is expanded to include both Sonderina and Stoibrax capense. New combinations are formalized for Dasispermum capense, D. hispidum, D. humile, and D. tenue. An undescribed species from the Tanqua Karoo in South Africa is also closely related to Capnophyllum and the Dasispermum–Sonderina complex. The genus Scaraboides is described herein to accommodate the new species, S. manningii. This monotypic genus shares the dorsally compressed fruit and involute marginal wings with Capnophyllum, but is easily distinguished by its erect branching habit, green leaves, scabrous umbels, and fruit with indistinct median and lateral ribs, additional solitary vittae in each marginal wing, and parallel, closely spaced commissural vittae. Despite the marked fruit similarities with Capnophyllum, analyses of DNA sequence data place Scaraboides closer to the Dasispermum–Sonderina complex, with which it shares the erect habit, green (nonglaucous) leaves, and scabrous umbels.

Revision of Autolytinae (Syllidae: Polychaeta)

Zootaxa ◽  
2004 ◽  
Vol 680 (1) ◽  
pp. 1 ◽  
Author(s):  
ARNE NYGREN
Keyword(s):  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Nominal Species ◽  
Strict Consensus Tree ◽  
Incertae Sedis ◽  
Nomina Dubia ◽  
Morphological And Molecular Data ◽  
Combined Data

Autolytinae is revised based on available types, and newly collected specimens. Out of 170 nominal species, 18 are considered as incertae sedis, 43 are regarded as junior synonyms, and 25 are referred to as nomina dubia. The relationships of Autolytinae is assessed from 51 morphological characters and 211 states for 76 ingroup-taxa, and 460 molecular characters from mitochondrial 16S rDNA and nuclear 18S rDNA for 31 ingroup-taxa; outgroups include 12 non-autolytine syllid polychaetes. Two analyses are provided, one including morphological data only, and one with combined morphological and molecular data sets. The resulting strict consensus tree from the combined data is chosen for a reclassification. Three main clades are identified: Procerini trib. n., Autolytini Grube, 1850, and Epigamia gen. n. Proceraea Ehlers, 1864 and Myrianida Milne Edwards, 1845 are referred to as nomen protectum, while Scolopendra Slabber, 1781, Podonereis Blainville, 1818, Amytis Savigny, 1822, Polynice Savigny, 1822, and Nereisyllis Blainville, 1828 are considered

scholarly journals Gene Expression Does Not Support the Developmental Hourglass Model in Three Animals with Spiralian Development

2019 ◽  
Vol 36 (7) ◽  
pp. 1373-1383 ◽  
Author(s):  
Longjun Wu ◽  
Kailey E Ferger ◽  
J David Lambert
Keyword(s):  
Gene Expression ◽  
Large Fraction ◽  
Molecular Data ◽  
Development Stage ◽  
Data Sets ◽  
Rna Seq ◽  
Developmental Evolution ◽  
Phylotypic Stage ◽  
Hourglass Model ◽  
Almost All

Abstract It has been proposed that animals have a pattern of developmental evolution resembling an hourglass because the most conserved development stage—often called the phylotypic stage—is always in midembryonic development. Although the topic has been debated for decades, recent studies using molecular data such as RNA-seq gene expression data sets have largely supported the existence of periods of relative evolutionary conservation in middevelopment, consistent with the phylotypic stage and the hourglass concepts. However, so far this approach has only been applied to a limited number of taxa across the tree of life. Here, using established phylotranscriptomic approaches, we found a surprising reverse hourglass pattern in two molluscs and a polychaete annelid, representatives of the Spiralia, an understudied group that contains a large fraction of metazoan body plan diversity. These results suggest that spiralians have a divergent midembryonic stage, with more conserved early and late development, which is the inverse of the pattern seen in almost all other organisms where these phylotranscriptomic approaches have been reported. We discuss our findings in light of proposed reasons for the phylotypic stage and hourglass model in other systems.

scholarly journals Phylogenetic position and taxonomy of Cycloseris explanulata and C. wellsi (Scleractinia: Fungiidae): lost mushroom corals find their way home

2012 ◽  
Vol 81 (3) ◽  
pp. 125-146 ◽  
Author(s):  
Francesca Benzoni ◽  
Roberto Arrigoni ◽  
Fabrizio Stefani ◽  
Bastian T. Reijnen ◽  
Simone Montano ◽  
...  
Keyword(s):  
Molecular Study ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Distribution Data ◽  
Data Sets ◽  
Free Living ◽  
New Findings ◽  
The Family ◽  
Ecological Implications ◽  
History Of

The scleractinian species Psammocora explanulata and Coscinaraea wellsi were originally classified in the family Siderastreidae, but in a recent morpho-molecular study it appeared that they are more closely related to each other and to the Fungiidae than to any siderastreid taxon. A subsequent morpho-molecular study of the Fungiidae provided new insights regarding the phylogenetic relationships within that family. In the present study existing molecular data sets of both families were analyzed jointly with those of new specimens and sequences of P. explanulata and C. wellsi. The results indicate that both species actually belong to the Cycloseris clade within the family Fungiidae. A reappraisal of their morphologic characters based on museum specimens and recently collected material substantiate the molecular results. Consequently, they are renamed Cycloseris explanulata and C. wellsi. They are polystomatous and encrusting like C. mokai, another species recently added to the genus, whereas all Cycloseris species were initially thought to be monostomatous and free-living. In the light of the new findings, the taxonomy and distribution data of C. explanulata and C. wellsi have been updated and revised. Finally, the ecological implications of the evolutionary history of the three encrusting polystomatous Cycloseris species and their free-living monostomatous congeners are discussed.

scholarly journals VikNGS: A C ++ Variant Integration Kit for Next Generation Sequencing Association Analysis

2019 ◽  
Author(s):  
Zeynep Baskurt ◽  
Scott Mastromatteo ◽  
Jiafen Gong ◽  
Richard F Wintle ◽  
Stephen W Scherer ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Association ◽  
Association Analysis ◽  
Supplementary Information ◽  
Next Generation Sequencing Data ◽  
Data Sets ◽  
Next Generation ◽  
Sequencing Data ◽  
Combining Data ◽  
Generation Sequencing

Abstract Integration of next generation sequencing data (NGS) across different research studies can improve the power of genetic association testing by increasing sample size and can obviate the need for sequencing controls. If differential genotype uncertainty across studies is not accounted for, combining data sets can produce spurious association results. We developed the Variant Integration Kit for NGS (VikNGS), a fast cross-platform software package, to enable aggregation of several data sets for rare and common variant genetic association analysis of quantitative and binary traits with covariate adjustment. VikNGS also includes a graphical user interface, power simulation functionality and data visualization tools. Availability The VikNGS package can be downloaded at http://www.tcag.ca/tools/index.html. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4349 ◽  
Author(s):  
Aristóteles Góes-Neto ◽  
Marcelo V.C. Diniz ◽  
Daniel S. Carvalho ◽  
Gilberto C. Bomfim ◽  
Angelo A. Duarte ◽  
...  
Keyword(s):  
Biological Sciences ◽  
Phylogenetic Analysis ◽  
Complex Networks ◽  
Complex Network ◽  
Bootstrap Method ◽  
Molecular Data ◽  
Data Sets ◽  
Fungal Cell ◽  
Taxonomic Groups ◽  
Inference Methods

Complex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular data sets and taxonomic groups, and, also, by comparing complex networks approach to current methods in phylogenetic analysis. In this work, we compare all the four main methods of phylogenetic analysis (distance, maximum parsimony, maximum likelihood, and Bayesian) with a complex networks method that has been used to provide a phylogenetic classification based on a large number of protein sequences as those related to the chitin metabolic pathway and ATP-synthase subunits. In order to perform a close comparison to these methods, we selected Basidiomycota fungi as the taxonomic group and used a high-quality, manually curated and characterized database of chitin synthase sequences. This enzymatic protein plays a key role in the synthesis of one of the exclusive features of the fungal cell wall: the presence of chitin. The communities (modules) detected by the complex network method corresponded exactly to the groups retrieved by the phylogenetic inference methods. Additionally, we propose a bootstrap method for the complex network approach. The statistical results we have obtained with this method were also close to those obtained using traditional bootstrap methods.

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