4 results on '"Manpreet K. Kohli"'
Search Results
2. Assessing support for Blaberoidea phylogeny suggests optimal locus quality
- Author
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Megan M. Wilson, Frédéric Legendre, Jessica L. Ware, Philippe Grandcolas, Benjamin Wipfler, Dominic A. Evangelista, Sabrina Simon, Olivier Béthoux, Manpreet K. Kohli, Akito Y. Kawahara, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), The University of Tennessee [Knoxville], Adelphi University, Wageningen University and Research [Wageningen] (WUR), Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers), University of Florida [Gainesville] (UF), American Museum of Natural History (AMNH), Zoologisches Forschungsmuseum Alexander Koenig, Centre de Recherche en Paléontologie - Paris (CR2P), and Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0106 biological sciences ,0301 basic medicine ,Long branch attraction ,Phylogenetic tree ,[SDV]Life Sciences [q-bio] ,Locus (genetics) ,Biology ,PE&RC ,010603 evolutionary biology ,01 natural sciences ,Biosystematiek ,03 medical and health sciences ,030104 developmental biology ,Taxon ,Evolutionary biology ,Phylogenetics ,Insect Science ,Phylogenomics ,Life Science ,Biosystematics ,Stabilizing selection ,EPS ,Clade ,Ecology, Evolution, Behavior and Systematics - Abstract
International audience; Phylogenomics seeks to use next‐generation data to robustly infer an organism's evolutionary history. Yet, the practical caveats of phylogenomics motivate investigation of improved efficiency, particularly when quality of phylogenies are questionable. To achieve improvements, one goal is to maintain or enhance the quality of phylogenetic inference while severely reducing dataset size. We approach this by assessing which kinds of loci in phylogenomic alignments provide the majority of support for a phylogenetic inference of cockroaches in Blaberoidea. We examine locus substitution rate, saturation, evolutionary divergence, rate heterogeneity, stabilizing selection, and a priori information content as traits that may determine optimality. Our controlled experimental design is based on 265 loci for 102 blaberoidean taxa and 22 outgroup species. Loci with high substitution rate, low saturation, low sequence distance, low rate heterogeneity, and strong stabilizing selection derive more support for phylogenetic relationships. We found that some phylogenetic information content estimators may not be meaningful for assessing information content a priori. We use these findings to design concatenated datasets with an optimized subsample of 100 loci. The tree inferred from the optimized subsample alignment was largely identical to that inferred from all 265 loci but with less evidence of long branch attraction, improved statistical support, and potential 4‐6x improvements to computation time. Supported by phylogenetic and morphological evidence, we erect three newly named clades (Anallactinae Evangelista & Wipfler subfam. nov., Orkrasomeria tax. nov. Evangelista, Wipfler, & Béthoux and Hemithyrsocerini Evangelista tribe nov.) and propose other taxonomic modifications. The diagnosis of Pseudophyllodromiidae Grandcolas, 1996 is modified to accommodate Anallactinae and Pseudophyllodromiinae Vickery & Kevan, 1983. The diagnosis of Ectobiidae Brunner von Wattenwyl, 1865 is modified to add novel morphological characters.
- Published
- 2021
3. Counting the spots: a molecular and morphological phylogeny of the spotted darnerBoyeria(Odonata: Anisoptera: Aeshnidae) with an emphasis on European taxa
- Author
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Ole Müller, Thomas Schneider, Manpreet K. Kohli, and Jessica L. Ware
- Subjects
Taxon ,Phylogenetic tree ,biology ,Insect Science ,Boyeria ,Zoology ,Aeshnidae ,Anisoptera ,biology.organism_classification ,Clade ,Odonata ,Boyeria cretensis ,Ecology, Evolution, Behavior and Systematics - Abstract
Boyeria irene and Boyeria cretensis are species of spotted dragonflies belonging to the ‘darner’ family, Aeshnidae. In 1991, Peters classified Boyeria from Crete as B. cretensis, based on adult morphological characters. In this study, we used molecular evidence to determine if indeed B. irene and B. cretensis are different species. DNA was sequenced from samples of B. irene (from France, Switzerland, Tunisia, Spain and Italy) and B. cretensis (from Crete). These species were recovered as two different clades with strong support. We conclude that B. irene and B. cretensis are different species, with evidence based on molecular and morphological differences. In addition, we present the first phylogenetic hypothesis for Boyeria for which we have sequenced all but three species. Lastly, we discuss different scenarios that may have led to the present-day distribution and speciation patterns of Mediterranean Boyeria.
- Published
- 2013
4. The Fossil Calibration Database, A New Resource for Divergence Dating
- Author
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Michael J. Benton, Philip C. J. Donoghue, N. Adam Smith, Kristin S. Lamm, Marcel van Tuinen, Jessica L. Ware, P. David Polly, José S. L. Patané, Matthew T. Carrano, Matthew J. Phillips, Nathan D. Smith, Manpreet K. Kohli, Dan Leehr, Walter G. Joyce, Randall B. Irmis, Jason J. Head, Elizabeth J. Hermsen, James F. Parham, Rachel C. M. Warnock, Daniel T. Ksepka, James F. Allman, and Karen Cranston
- Subjects
Databases, Factual ,IMPACT ,UNCERTAINTY ,divergence dating ,Biology ,computer.software_genre ,Time ,Access to Information ,CLOCKS ,Paleontology ,AGE ,Resource (project management) ,Time estimation ,Genetics ,Calibration ,Stratigraphy (archaeology) ,Divergence (statistics) ,TREE ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Internet ,Series (stratigraphy) ,fossil ,Fossil Record ,Database ,Fossils ,Geological evidence ,LIFE ,TIME-ESTIMATION ,Data Interpretation, Statistical ,computer - Abstract
Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important, and often least appreciated, step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for non- specialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open- access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as one key pipeline for peer-reviewed calibrations to enter the database.
- Published
- 2015
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