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      Extensive host-switching of avian feather lice following the Cretaceous-Paleogene mass extinction event

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          Abstract

          Nearly all lineages of birds host parasitic feather lice. Based on recent phylogenomic studies, the three major lineages of modern birds diverged from each other before the Cretaceous-Paleogene (K-Pg) mass extinction event. In contrast, studies of the phylogeny of feather lice on birds, indicate that these parasites diversified largely after this event. However, these studies were unable to reconstruct the ancestral avian host lineage for feather lice. Here we use genome sequences of a broad diversity of lice to reconstruct a phylogeny based on 1,075 genes. By comparing this louse evolutionary tree to the avian host tree, we show that feather lice began diversifying on the common ancestor of waterfowl and landfowl, then radiated onto other avian lineages by extensive host-switching. Dating analyses and cophylogenetic comparisons revealed that two of three lineages of birds that diverged before the K-Pg boundary acquired their feather lice after this event via host-switching.

          Abstract

          Robert de Moya et al. use comparative genomics of avian lice to reconstruct the phylogeny of these parasites. They show that feather lice diversified on the common ancestor of waterfowl and landfowl, and then radiated onto other avian lineages through host-switching.

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          SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

          We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/. © The Willi Hennig Society 2010.
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            ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

            Motivation: The estimation of species phylogenies requires multiple loci, since different loci can have different trees due to incomplete lineage sorting, modeled by the multi-species coalescent model. We recently developed a coalescent-based method, ASTRAL, which is statistically consistent under the multi-species coalescent model and which is more accurate than other coalescent-based methods on the datasets we examined. ASTRAL runs in polynomial time, by constraining the search space using a set of allowed ‘bipartitions’. Despite the limitation to allowed bipartitions, ASTRAL is statistically consistent. Results: We present a new version of ASTRAL, which we call ASTRAL-II. We show that ASTRAL-II has substantial advantages over ASTRAL: it is faster, can analyze much larger datasets (up to 1000 species and 1000 genes) and has substantially better accuracy under some conditions. ASTRAL’s running time is O ( n 2 k | X | 2 ) , and ASTRAL-II’s running time is O ( n k | X | 2 ) , where n is the number of species, k is the number of loci and X is the set of allowed bipartitions for the search space. Availability and implementation: ASTRAL-II is available in open source at https://github.com/smirarab/ASTRAL and datasets used are available at http://www.cs.utexas.edu/~phylo/datasets/astral2/. Contact: smirarab@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
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              Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.

              As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is an important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences of the body louse and its primary bacterial endosymbiont Candidatus Riesia pediculicola. The body louse has the smallest known insect genome, spanning 108 Mb. Despite its status as an obligate parasite, it retains a remarkably complete basal insect repertoire of 10,773 protein-coding genes and 57 microRNAs. Representing hemimetabolous insects, the genome of the body louse thus provides a reference for studies of holometabolous insects. Compared with other insect genomes, the body louse genome contains significantly fewer genes associated with environmental sensing and response, including odorant and gustatory receptors and detoxifying enzymes. The unique architecture of the 18 minicircular mitochondrial chromosomes of the body louse may be linked to the loss of the gene encoding the mitochondrial single-stranded DNA binding protein. The genome of the obligatory louse endosymbiont Candidatus Riesia pediculicola encodes less than 600 genes on a short, linear chromosome and a circular plasmid. The plasmid harbors a unique arrangement of genes required for the synthesis of pantothenate, an essential vitamin deficient in the louse diet. The human body louse, its primary endosymbiont, and the bacterial pathogens that it vectors all possess genomes reduced in size compared with their free-living close relatives. Thus, the body louse genome project offers unique information and tools to use in advancing understanding of coevolution among vectors, symbionts, and pathogens.
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                Author and article information

                Contributors
                rdemoya2@illinois.edu
                Journal
                Commun Biol
                Commun Biol
                Communications Biology
                Nature Publishing Group UK (London )
                2399-3642
                29 November 2019
                29 November 2019
                2019
                : 2
                : 445
                Affiliations
                [1 ]Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL USA
                [2 ]ISNI 0000 0004 1936 9991, GRID grid.35403.31, Department of Entomology, , University of Illinois, ; Urbana, IL USA
                [3 ]ISNI 0000 0004 1936 914X, GRID grid.266818.3, Department of Biology, , University of Nevada, ; Reno, NV USA
                [4 ]ISNI 0000 0004 1937 2197, GRID grid.169077.e, Department of Entomology, , Purdue University, ; West Lafayette, IN USA
                [5 ]ISNI 0000 0004 0483 4475, GRID grid.488640.6, Museum of New Zealand Te Papa Tongarewa, ; Wellington, New Zealand
                [6 ]ISNI 0000 0001 2270 9879, GRID grid.35937.3b, Department of Life Sciences, , The Natural History Museum, ; London, UK
                [7 ]GRID grid.441915.c, Biotério da Universidade Iguaçu, ; Nova Iguaçu, RJ Brazil
                [8 ]ISNI 0000 0004 1936 9609, GRID grid.21613.37, Department of Entomology, , University of Manitoba, ; Winnipeg, Manitoba Canada
                [9 ]ISNI 0000 0001 2181 3113, GRID grid.166341.7, Department of Ornithology, , Academy of Natural Sciences of Drexel University, ; Philadelphia, PA USA
                Author information
                http://orcid.org/0000-0001-5297-7452
                http://orcid.org/0000-0002-6694-4130
                http://orcid.org/0000-0002-0124-8601
                http://orcid.org/0000-0001-7941-5724
                http://orcid.org/0000-0002-4151-816X
                Article
                689
                10.1038/s42003-019-0689-7
                6884534
                31815200
                725fcbe9-10c4-496d-8fa0-401866020323
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 11 July 2019
                : 8 November 2019
                Categories
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                Custom metadata
                © The Author(s) 2018

                coevolution,phylogenetics
                coevolution, phylogenetics

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