popart: full-feature software for haplotype network construction
Jessica W. Leigh,David Bryant +1 more
Reads0
Chats0
TLDR
Popart is presented, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication‐ready figure production.Abstract:
Summary
Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level.
Here, we present popart, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production.
popart also provides a platform for the implementation and distribution of new network-based methods – we describe one such new method, integer neighbour-joining.
The software is open source and freely available for all major operating systems.read more
Citations
More filters
Journal Article
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
Journal ArticleDOI
On the origin and continuing evolution of SARS-CoV-2
Xiaolu Tang,Changcheng Wu,Xiang Li,Yuhe Song,Yuhe Song,Xinmin Yao,Xinkai Wu,Yuange Duan,Hong Zhang,Yirong Wang,Zhaohui Qian,Jie Cui,Jian Lu +12 more
TL;DR: The results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by natural selection besides recombination.
Journal ArticleDOI
A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution
Massimo Iorizzo,Shelby Ellison,Douglas Senalik,Douglas Senalik,Peng Zeng,Pimchanok Satapoomin,Jiaying Huang,Megan J. Bowman,Marina Iovene,Walter Sanseverino,Pablo Federico Cavagnaro,Pablo Federico Cavagnaro,Mehtap Yildiz,Alicja Macko-Podgórni,Emilia Morańska,Ewa Grzebelus,Dariusz Grzebelus,Hamid Ashrafi,Zhijun Zheng,Shifeng Cheng,David M. Spooner,David M. Spooner,Allen Van Deynze,Philipp W. Simon,Philipp W. Simon +24 more
TL;DR: A high-quality chromosome-scale assembly and analysis of the carrot genome is reported, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade, and a candidate gene, DCAR_032551, is identified that conditions carotenoid accumulation (Y) in carrot taproot and is coexpressed with several isoprenoid biosynthetic genes.
Journal ArticleDOI
From People to Panthera : Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo.
Denise McAloose,Melissa Laverack,Leyi Wang,Mary Lea Killian,Leonardo C. Caserta,Fangfeng Yuan,Patrick K. Mitchell,Krista Queen,Matthew R. Mauldin,Brittany D. Cronk,Susan L. Bartlett,John M. Sykes,Stephanie Zec,Tracy Stokol,Karen Ingerman,Martha A. Delaney,Richard L. Fredrickson,Marina Ivančić,Melinda Jenkins-Moore,Katie Mozingo,Kerrie Franzen,Nichole Hines Bergeson,Laura B. Goodman,Haibin Wang,Ying Fang,Colleen Olmstead,Colleen McCann,Patrick Thomas,Erin L. Goodrich,François Elvinger,David C. Smith,Suxiang Tong,Sally Slavinski,Paul P. Calle,Karen A. Terio,Mia Kim Torchetti,Diego G. Diel +36 more
TL;DR: These were the first confirmed cases of natural SARS-CoV-2 animal infections in the United States and the first in nondomestic species in the world and provide epidemiological and genetic evidence for human-to-animal transmission of the virus.
Journal ArticleDOI
Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events.
Jacob E. Lemieux,Jacob E. Lemieux,Katherine J. Siddle,Katherine J. Siddle,Bennett M. Shaw,Bennett M. Shaw,Christine Loreth,Stephen F. Schaffner,Stephen F. Schaffner,Adrianne Gladden-Young,Gordon Adams,Timelia Fink,Christopher Tomkins-Tinch,Christopher Tomkins-Tinch,Lydia A. Krasilnikova,Lydia A. Krasilnikova,Katherine C. DeRuff,Melissa Rudy,Matthew R. Bauer,Matthew R. Bauer,Kim A. Lagerborg,Kim A. Lagerborg,Erica Normandin,Erica Normandin,Sinéad B. Chapman,Steven K. Reilly,Steven K. Reilly,Melis N. Anahtar,Aaron E. Lin,Aaron E. Lin,Amber Carter,Cameron Myhrvold,Cameron Myhrvold,Molly Kemball,Molly Kemball,Sushma Chaluvadi,Caroline N. Cusick,Katelyn Flowers,Anna Neumann,Felecia Cerrato,Maha R. Farhat,Damien Slater,Jason B. Harris,John A. Branda,David C. Hooper,Jessie M. Gaeta,Travis P. Baggett,James J. O’Connell,Andreas Gnirke,Tami D. Lieberman,Tami D. Lieberman,Anthony A. Philippakis,Meagan Burns,Catherine M. Brown,Jeremy Luban,Jeremy Luban,Edward T. Ryan,Sarah E Turbett,Regina C. LaRocque,William P. Hanage,Glen R. Gallagher,Lawrence C. Madoff,Lawrence C. Madoff,Sandra Smole,Virginia M. Pierce,Eric S. Rosenberg,Pardis C. Sabeti,Daniel J. Park,Bronwyn MacInnis,Bronwyn MacInnis +69 more
TL;DR: Investigating the introduction and spread of severe acute respiratory syndrome coronavirus 2 in the Boston area across the first wave of the pandemic provides powerful evidence of the importance of superspreading events in shaping the course of this pandemic and illustrates how some introductions, when amplified under unfortunate circumstances, can have an outsized effect with devastating consequences that extend far beyond the initial events themselves.
References
More filters
Journal ArticleDOI
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Journal ArticleDOI
Arlequin (version 3.0): An integrated software package for population genetics data analysis
TL;DR: Arlequin ver 3.0 as discussed by the authors is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework.
Journal ArticleDOI
DnaSP v5
Pablo Librado,Julio Rozas +1 more
TL;DR: Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets, including visualizing sliding window results integrated with available genome annotations in the UCSC browser.
Journal ArticleDOI
Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.
TL;DR: In this article, a framework for the study of molecular variation within a single species is presented, where information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes.