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Lemant J, Le Sueur C, Manojlović V, Noble R. Robust, Universal Tree Balance Indices. Syst Biol 2022; 71:1210-1224. [PMID: 35412638 PMCID: PMC9773123 DOI: 10.1093/sysbio/syac027] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/27/2022] [Accepted: 04/05/2022] [Indexed: 01/04/2023] Open
Abstract
Balance indices that quantify the symmetry of branching events and the compactness of trees are widely used to compare evolutionary processes or tree-generating algorithms. Yet, existing indices are not defined for all rooted trees, are unreliable for comparing trees with different numbers of leaves, and are sensitive to the presence or absence of rare types. The contributions of this article are twofold. First, we define a new class of robust, universal tree balance indices. These indices take a form similar to Colless' index but can account for population sizes, are defined for trees with any degree distribution, and enable meaningful comparison of trees with different numbers of leaves. Second, we show that for bifurcating and all other full m-ary cladograms (in which every internal node has the same out-degree), one such Colless-like index is equivalent to the normalized reciprocal of Sackin's index. Hence, we both unify and generalize the two most popular existing tree balance indices. Our indices are intrinsically normalized and can be computed in linear time. We conclude that these more widely applicable indices have the potential to supersede those in current use. [Cancer; clone tree; Colless index; Sackin index; species tree; tree balance.].
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Affiliation(s)
- Jeanne Lemant
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
| | - Cécile Le Sueur
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Veselin Manojlović
- Department of Mathematics, City, University of London, Northampton Square, London EC1V 0HB, UK
| | - Robert Noble
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- Department of Mathematics, City, University of London, Northampton Square, London EC1V 0HB, UK
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Ozer MS, Yildiz HA, Incir C, Deger MD, Bozkurt O, Ergor G, Tuncok Y, Esen N, Esen AA. Urinary microbiota; Which non-ınvasive urine collection method should we use? Int J Clin Pract 2021; 75:e14193. [PMID: 33797158 DOI: 10.1111/ijcp.14193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 03/27/2021] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE The aim of this study is to establish the optimal non-invasive urine sample collection method for the microbiota studies. METHODOLOGY Twelve men with bladder carcinoma underwent first voided and midstream urine collection. Urine samples were analysed using V3-V4 regions of bacterial 16s ribosomal RNAs. Bacterial groups with relative abundance above 1% were analysed in first voided urine and midstream urine samples at phylum, class, order and family level. At the genus level, all of the identified bacterial groups' relative abundances were analysed. The statistical significance (P < .05) of differences between first voided and midstream urine sample microbiota was evaluated using the Wilcoxon test. RESULTS According to the analysis, 8 phyla, 14 class, 23 orders, 39 families and 29 different genera were identified in the first voided and the midstream urine samples. Statistical differences were not identified between first voided and midstream urine samples of all bacteria groups except the Clostridiales at order level (p:0.04) and Clostridia at class level (P: .04). CONCLUSIONS Either first voided or midstream urine samples can be used in urinary microbiota studies as we determined that there is no statistically significant difference between them regarding the results of 16s ribosomal RNA analysis.
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Affiliation(s)
- Muhammed Selcuk Ozer
- Department of Urology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | | | - Canet Incir
- Department of Medical Pharmacology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Muslim Dogan Deger
- Department of Urology, Edirne Sultan 1. Murat State Hospital, Edirne, Turkey
| | - Ozan Bozkurt
- Department of Urology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Gul Ergor
- Department of Public Health, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Yesim Tuncok
- Department of Medical Pharmacology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Nuran Esen
- Department of Microbiology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Ahmet Adil Esen
- Department of Urology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
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Hu GL, Gao K, Wang JS, Hebert PDN, Hua BZ. Molecular phylogeny and species delimitation of the genus Dicerapanorpa (Mecoptera: Panorpidae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Given that species is the fundamental unit in systematic biology, rigorous species delimitation is crucial for taxonomic studies, yet routine species delimitation remains an ongoing challenge in the taxonomic practice of insects. The two-horned scorpionfly Dicerapanorpa is a small genus in Panorpidae (Mecoptera) endemic to the Qinling-Bashan and Hengduan mountains, a biodiversity hotspot. However, species of Dicerapanorpa are difficult to delineate owing to marked intraspecific variation and interspecific similarity. Here, we investigate the diversity and species boundaries of Dicerapanorpa using an integrative approach based on DNA barcoding, morphological, geometric morphometric and molecular phylogenetic analyses. This integrative analyses confirmed the 13 described species of Dicerapanorpa and revealed three new species: Dicerapanorpa lativalva sp. nov., Dicerapanorpa hualongshana sp. nov. and Dicerapanorpa minshana sp. nov. Most molecular operational taxonomic units are in congruence with morphological clusters. Possible reasons for several discordances in Dicerapanorpa are tentatively discussed.
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Affiliation(s)
- Gui-Lin Hu
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Kai Gao
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Ji-Shen Wang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Bao-Zhen Hua
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
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Dickinson TA. A növények evolúciója és osztályozása (Evolution and Systematics of Plants). — By J. Podani. Syst Biol 2018. [DOI: 10.1093/sysbio/syy025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Timothy A Dickinson
- Green Plant Herbarium, Royal Ontario Museum, and Department of Ecology & Evolutionary Biology, University of Toronto, Canada
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Podani J. Different from Trees, more than Metaphors: Branching Silhouettes-Corals, Cacti, and the Oaks. Syst Biol 2018; 66:737-753. [PMID: 28334310 DOI: 10.1093/sysbio/syx039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 02/26/2017] [Indexed: 11/12/2022] Open
Abstract
There has long been ambiguity in the use of the term tree in phylogenetic systematics, which is a continuous source of misinterpretation of evolutionary relationships. The basic problem is that while many trees with phylogenetic or evolutionary relevance, such as cladograms, are consistent with graph theory, tree-like visualization of phylogeny may also be done via other types of graphics, especially botanical (or literal) tree drawings. As a consequence, the meaning of such diagrams is not always clear: a given picture may have multiple interpretations in its different parts and two figures that look similar may actually carry quite different information. I show that these are not merely metaphors of phylogeny and may be defined mathematically as geometric shapes called branching silhouette diagrams, the name referring to their most apparent features. They have four basic forms depending on whether the time factor is considered in their construction and the relationships portrayed are of the ancestor-descendant or sister group type. By revitalizing Darwin's early suggestions on the illustration of change in the living world, I propose the term coral for the most common forms of branching silhouette which consider time and show ancestry. The others appear rarely in present-day practice and are mostly of historical value-these are cacti (named after one of Bessey's diagrams) and two types of oaks (with reference to several of Haeckel's motifs used in depicting phylogeny in the nineteenth century). The use of these terms in phylogenetic systematics facilitates better understanding of how organization of biodiversity has been visualized in science [Bessey; cladograms; coral-thinking; Darwin; graph theory; Haeckel; phylogeny; tree thinking.].
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Affiliation(s)
- János Podani
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, L. Eötvös University, and MTA-ELTE-MTM Ecology Research Group, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
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A simple parsimony-based approach to assess ancestor-descendant relationships. UKRAINIAN BOTANICAL JOURNAL 2017. [DOI: 10.15407/ukrbotj74.02.103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Carr TD, Varricchio DJ, Sedlmayr JC, Roberts EM, Moore JR. A new tyrannosaur with evidence for anagenesis and crocodile-like facial sensory system. Sci Rep 2017; 7:44942. [PMID: 28358353 PMCID: PMC5372470 DOI: 10.1038/srep44942] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/14/2017] [Indexed: 11/13/2022] Open
Abstract
A new species of tyrannosaurid from the upper Two Medicine Formation of Montana supports the presence of a Laramidian anagenetic (ancestor-descendant) lineage of Late Cretaceous tyrannosaurids. In concert with other anagenetic lineages of dinosaurs from the same time and place, this suggests that anagenesis could have been a widespread mechanism generating species diversity amongst dinosaurs, and perhaps beyond. We studied the excellent fossil record of the tyrannosaurid to test that hypothesis. Phylogenetic analysis places this new taxon as the sister species to Daspletosaurus torosus. However, given their close phylogenetic relationship, geographic proximity, and temporal succession, where D. torosus (~76.7-75.2 Ma) precedes the younger new species (~75.1-74.4 Ma), we argue that the two forms most likely represent a single anagenetic lineage. Daspletosaurus was an important apex predator in the late Campanian dinosaur faunas of Laramidia; its absence from later units indicates it was extinct before Tyrannosaurus rex dispersed into Laramidia from Asia. In addition to its evolutionary implications, the texture of the facial bones of the new taxon, and other derived tyrannosauroids, indicates a scaly integument with high tactile sensitivity. Most significantly, the lower jaw shows evidence for neurovasculature that is also seen in birds.
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Affiliation(s)
- Thomas D. Carr
- Carthage College, 2001 Alford Park Drive, Kenosha, WI 53140, USA
| | - David J. Varricchio
- Department of Earth Sciences, Montana State University, P.O. Box 173480, Bozeman, MT 59717-3480, USA
| | - Jayc C. Sedlmayr
- Louisiana State University Health Sciences Centre - School of Medicine, 1901 Perdido Street, New Orleans, LA 70112, USA
| | - Eric M. Roberts
- Geosciences, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Jason R. Moore
- Honors College, University of New Mexico, Albuquerque, NM 87131, USA
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Vaux F, Trewick SA, Morgan-Richards M. Speciation through the looking-glass. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Felix Vaux
- Ecology Group; Institute of Agriculture and Environment; Massey University; Palmerston North New Zealand
| | - Steven A. Trewick
- Ecology Group; Institute of Agriculture and Environment; Massey University; Palmerston North New Zealand
| | - Mary Morgan-Richards
- Ecology Group; Institute of Agriculture and Environment; Massey University; Palmerston North New Zealand
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Kaya S, Çiplak B. Budding speciation via peripheral isolation: thePsorodonotus venosus(Orthoptera, Tettigoniidae) species group example. ZOOL SCR 2016. [DOI: 10.1111/zsc.12174] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sarp Kaya
- Department of Biology; Faculty of Science; Akdeniz University Antalya; Antalya Turkey
| | - Battal Çiplak
- Department of Biology; Faculty of Science; Akdeniz University Antalya; Antalya Turkey
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Vaux F, Trewick SA, Morgan-Richards M. Lineages, splits and divergence challenge whether the terms anagenesis and cladogenesis are necessary. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12665] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Felix Vaux
- Ecology Group; Institute of Agriculture and Environment; Massey University; Palmerston North New Zealand
| | - Steven A. Trewick
- Ecology Group; Institute of Agriculture and Environment; Massey University; Palmerston North New Zealand
| | - Mary Morgan-Richards
- Ecology Group; Institute of Agriculture and Environment; Massey University; Palmerston North New Zealand
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An alternative construction of internodons: the emergence of a multi-level tree of life. Bull Math Biol 2014; 77:23-45. [PMID: 25515028 DOI: 10.1007/s11538-014-0048-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 11/18/2014] [Indexed: 10/24/2022]
Abstract
Internodons are a formalization of Hennig's concept of species. We present an alternative construction of internodons imposing a tree structure on the genealogical network. We prove that the segments (trivial unary trees) from this tree structure are precisely the internodons. We obtain the following spin-offs. First, the generated tree turns out to be an organismal tree of life. Second, this organismal tree is homeomorphic to the phylogenetic Hennigian species tree of life, implying the discovery of a multi-level tree of life: this phylogenetic tree can be obtained by zooming out from the organismal tree, or conversely, the organismal tree of life can be generated by expanding the phylogenetic nodes into unary trees. Finally, the definition of the organismal tree allows an efficient algorithmic transformation of a given genealogical network into its corresponding phylogenetic species tree of life. The latter will be presented in a separate paper.
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