Mammalian Evolution May Not Be Strictly Bifurcating Open Access Research Article
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Ecological Causes of Uneven Diversification and Richness in the Mammal Tree of Life
bioRxiv preprint doi: https://doi.org/10.1101/504803; this version posted March 28, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Ecological causes of uneven diversification and richness in the mammal tree of life 2 Short title: Ecological causes of diversification in mammals 3 4 Nathan S. Upham1*, Jacob A. Esselstyn2, and Walter Jetz1* 5 6 Author affiliations: 1Department of Ecology & Evolutionary Biology, Yale University, New 7 Haven, CT 06511 USA. 2Department of Biological Sciences and Museum of Natural Science, 8 Louisiana State University, Baton Rouge, LA 70803 USA. 9 10 *Corresponding authors: 165 Prospect St., OML 122, New Haven, CT 06511 USA; 11 [email protected]; [email protected] 12 bioRxiv preprint doi: https://doi.org/10.1101/504803; this version posted March 28, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 13 Abstract 14 The uneven distribution of species in the tree of life is rooted in unequal speciation and 15 extinction among groups. Yet the causes of differential diversification are little known despite 16 their relevance for sustaining biodiversity into the future. Here we investigate rates of species 17 diversification across extant Mammalia, a compelling system that includes our own closest 18 relatives. -
Treefinder Manual
TREEFINDER MANUAL - Version of October 2008 - Gangolf Jobb Email: [email protected] TREEFINDER computes phylogenetic trees from molecular sequences. The program infers even large trees by maximum likelihood under a variety of models of sequence evolution. It accepts both nucleotide and amino acid data and takes rate heterogeneity into account. Separate models can be assumed for user-defined data partitions, separate rates, separate edge lengths, separate character compositions. All parameters can be estimated from the data. Tree search can be guided by user-supplied topological constraints and start trees. There is a model proposer to propose appropriate models of sequence evolution. Confidence of inferred trees can be assessed by parametric and non-parametric bootstrapping, various paired-sites tests (ELW, BP, KH, SH, WSH, AU), also in combination with information criteria, edge support by LR-ELW. There are tools to manipulate trees and sequence data, visualize base frequencies, compute consensus and distance trees, count topologies. Confidence limits and other statistics can be obtained for all numerical results. The program can estimate divergence times by rate smoothing. A graphical user interface makes the use of TREEFINDER very intuitive. Data files and reconstruction parameters can be chosen interactively, results will be displayed on the screen. TREEFINDER is programmable in the functional and system independent programming language TL, which offers a wide range of functionality and enables the researcher to create problem -
Dissfernando.Pdf
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Mammalian Evolution May Not Be Strictly Bifurcating Open Access
View metadata, citation and similar papers at core.ac.uk brought to you by CORE Mammalian Evolution May not Be Strictly Bifurcating provided by PubMed Central Bjo¨rn M. Hallstro¨m1 and Axel Janke*,2 1Department of Cell and Organism Biology, Division of Evolutionary Molecular Systematics, University of Lund, Lund, Sweden 2LOEWE—Biodiversita¨t und Klima Forschungszentrum BiK-F, Frankfurt, Germany *Corresponding author: E-mail: [email protected]. Associate editor: Arndt von Haeseler Abstract The massive amount of genomic sequence data that is now available for analyzing evolutionary relationships among 31 placental mammals reduces the stochastic error in phylogenetic analyses to virtually zero. One would expect that this would make it possible to finally resolve controversial branches in the placental mammalian tree. We analyzed a 2,863,797 nucleotide- Research article long alignment (3,364 genes) from 31 placental mammals for reconstructing their evolution. Most placental mammalian relationships were resolved, and a consensus of their evolution is emerging. However, certain branches remain difficult or virtually impossible to resolve. These branches are characterized by short divergence times in the order of 1–4 million years. Computer simulations based on parameters from the real data show that as little as about 12,500 amino acid sites could be sufficient to confidently resolve short branches as old as about 90 million years ago (Ma). Thus, the amount of sequence data should no longer be a limiting factor in resolving the relationships among placental mammals. The timing of the early radiation of placental mammals coincides with a period of climate warming some 100–80 Ma and with continental fragmentation. -
Molecular Evolution and Phylogenetic Importance of a Gamete Recognition Gene Zan Reveals a Unique Contribution to Mammalian Speciation
Molecular evolution and phylogenetic importance of a gamete recognition gene Zan reveals a unique contribution to mammalian speciation. by Emma K. Roberts A Dissertation In Biological Sciences Submitted to the Graduate Faculty of Texas Tech University in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Approved Robert D. Bradley Chair of Committee Daniel M. Hardy Llewellyn D. Densmore Caleb D. Phillips David A. Ray Mark Sheridan Dean of the Graduate School May, 2020 Copyright 2020, Emma K. Roberts Texas Tech University, Emma K. Roberts, May 2020 ACKNOWLEDGMENTS I would like to thank numerous people for support, both personally and professionally, throughout the course of my degree. First, I thank Dr. Robert D. Bradley for his mentorship, knowledge, and guidance throughout my tenure in in PhD program. His ‘open door policy’ helped me flourish and grow as a scientist. In addition, I thank Dr. Daniel M. Hardy for providing continued support, knowledge, and exciting collaborative efforts. I would also like to thank the remaining members of my advisory committee, Drs. Llewellyn D. Densmore III, Caleb D. Phillips, and David A. Ray for their patience, guidance, and support. The above advisors each helped mold me into a biologist and I am incredibly gracious for this gift. Additionally, I would like to thank numerous mentors, friends and colleagues for their advice, discussions, experience, and friendship. For these reasons, among others, I thank Dr. Faisal Ali Anwarali Khan, Dr. Sergio Balaguera-Reina, Dr. Ashish Bashyal, Joanna Bateman, Karishma Bisht, Kayla Bounds, Sarah Candler, Dr. Juan P. Carrera-Estupiñán, Dr. Megan Keith, Christopher Dunn, Moamen Elmassry, Dr. -
A Powerful Graphical Analysis Environment for Molecular Phylogenetics Gangolf Jobb1*, Arndt Von Haeseler2,3 and Korbinian Strimmer1
Jobb et al. BMC Evolutionary Biology (2015) 15:243 DOI 10.1186/s12862-015-0513-z RETRACTION NOTE Open Access Retraction Note: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics Gangolf Jobb1*, Arndt von Haeseler2,3 and Korbinian Strimmer1 Retraction The editors of BMC Evolutionary Biology retract this article [1] due to the decision by the corresponding author, Gangolf Jobb, to change the license to the software described in the article. The software is no longer available to all scientists wishing to use it in certain territories. This breaches the journal’seditorial policy on software availability [2] which has been in effect since the time of publication. The other authors of the article, Arndt von Haeseler and Korbinian Strimmer, have no control over the licensing of the software and support the retraction of this article. Author details 1Department of Statistics, University of Munich, Ludwigstr. 33, D-80539 Munich, Germany. 2Department of Computer Science, University of Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany. 3John von Neumann Institute for Computing, Forschungszentrum Jülich, D-52425 Jülich, Germany. Received: 19 October 2015 Accepted: 20 October 2015 References 1. Jobb G, von Haeseler A, Strimmer K. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol. 2004;4:18. 2. BMC Evolutionary Biology’s Instructions for Authors of Software Articles: http://www.biomedcentral.com/bmcevolbiol/authors/instructions/software. Accessed 15 October 2015. Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance * Correspondence: [email protected] • Inclusion in PubMed, CAS, Scopus and Google Scholar The online version of the original article can be found under • Research which is freely available for redistribution doi:10.1186/1471-2148-4-18. -
Evolution 1 Ecological Causes of Uneven Diversification and Richness
bioRxiv preprint doi: https://doi.org/10.1101/504803; this version posted January 4, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 BIOLOGICAL SCIENCES: Evolution 2 Ecological causes of uneven diversification and richness in the mammal tree of life 3 Short title: Ecological causes of diversification in mammals 4 5 Nathan S. Upham1*, Jacob A. Esselstyn2, and Walter Jetz1* 6 7 Author affiliations: 1Department of Ecology & Evolutionary Biology, Yale University, New 8 Haven, CT 06511 USA. 2Department of Biological Sciences and Museum of Natural Science, 9 Louisiana State University, Baton Rouge, LA 70803 USA. 10 11 *Corresponding author: Nathan S. Upham; address: 165 Prospect St., OML 122, New Haven, CT 12 06511 USA; phone: 773-263-1533; email: [email protected]. bioRxiv preprint doi: https://doi.org/10.1101/504803; this version posted January 4, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 13 Abstract 14 The uneven distribution of species in the tree of life is rooted in unequal speciation and 15 extinction among groups. Yet the causes of differential diversification are little known despite 16 their relevance for sustaining biodiversity into the future. Here we investigate rates of species 17 diversification across extant Mammalia, a compelling system that includes our own closest 18 relatives. -
Discovery of Prosimian and Afrotherian Foamy Viruses And
Katzourakis et al. Retrovirology 2014, 11:61 http://www.retrovirology.com/content/11/1/61 RESEARCH Open Access Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution Aris Katzourakis1*†, Pakorn Aiewsakun1†, Hongwei Jia2, Nathan D Wolfe3,4,5, Matthew LeBreton6, Anne D Yoder7 and William M Switzer2* Abstract Background: Foamy viruses (FVs) are a unique subfamily of retroviruses that are widely distributed in mammals. Owing to the availability of sequences from diverse mammals coupled with their pattern of codivergence with their hosts, FVs have one of the best-understood viral evolutionary histories ever documented, estimated to have an ancient origin. Nonetheless, our knowledge of some parts of FV evolution, notably that of prosimian and afrotherian FVs, is far from complete due to the lack of sequence data. Results: Here, we report the complete genome of the first extant prosimian FV (PSFV) isolated from a lorisiforme galago (PSFVgal), and a novel partial endogenous viral element with high sequence similarity to FVs, present in the afrotherian Cape golden mole genome (ChrEFV). We also further characterize a previously discovered endogenous PSFV present in the aye-aye genome (PSFVaye). Using phylogenetic methods and available FV sequence data, we show a deep divergence and stable co-evolution of FVs in eutherian mammals over 100 million years. Nonetheless, we found that the evolutionary histories of bat, aye-aye, and New World monkey FVs conflict with the evolutionary histories of their hosts. By combining sequence analysis and biogeographical knowledge, we propose explanations for these mismatches in FV-host evolutionary history. -
Life-History Traits Drive the Evolutionary Rates of Mammalian Coding and Noncoding Genomic Elements
Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements Sergey I. Nikolaev*†, Juan I. Montoya-Burgos‡, Konstantin Popadin§, Leila Parand*, Elliott H. Margulies¶, National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program¶ʈ**, and Stylianos E. Antonarakis* *Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva, Switzerland; ‡Department of Animal Biology, University of Geneva, 30 Quai Ansermet, 1211 Geneva, Switzerland; §Institute for Information Transmission Problems RAS, Bolshoi Karetny Pereulok 19, Moscow 127994, Russia; and ¶Genome Technology Branch and ʈIntramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 Edited by Morris Goodman, Wayne State University School of Medicine, Detroit, MI, and approved October 23, 2007 (received for review June 19, 2007) A comprehensive phylogenetic framework is indispensable for spread throughout the population because of random genetic investigating the evolution of genomic features in mammals as a drift (17). Because the effect of positive selection is negligible whole, and particularly in humans. Using the ENCODE sequence (i.e., most new mutations have s Ͻ 0), the nearly neutral theory data, we estimated mammalian neutral evolutionary rates and deals mainly with slightly deleterious mutations. Given that the selective pressures acting on conserved coding and noncoding probability of fixation of slightly deleterious mutations depends elements. We show that neutral evolutionary rates can be ex- on the effective population size, there is a class of these plained by the generation time (GT) hypothesis. Accordingly, mutations that can be fixed in small populations because of primates (especially humans), having longer GTs than other mam- random drift but are counter-selected, through purifying selec- mals, display slower rates of neutral evolution. -
A Radiation of Arboreal Basal Eutherian Mammals Beginning in the Late Cretaceous of India
A radiation of arboreal basal eutherian mammals beginning in the Late Cretaceous of India Anjali Goswamia,b,1, Guntupalli V. R. Prasadc, Paul Upchurchb, Doug M. Boyerd, Erik R. Seifferte, Omkar Vermaf, Emmanuel Gheerbrantg, and John J. Flynnh aDepartment of Genetics, Evolution, and Environment, bDepartment of Earth Sciences, University College London, London WC1E 6BT, United Kingdom; cDepartment of Geology, Centre for Advanced Studies, University of Delhi, Delhi 110 007, India; dDepartment of Anthropology and Archaeology, Brooklyn College, City University of New York, Brooklyn, NY 11210; eDepartment of Anatomical Sciences, Stony Brook University, Stony Brook, NY 11794-8081; fSchool of Sciences, Indira Gandhi National Open University, New Delhi 110 068, India; gUnité Mixte de Recherche 7207 du Centre National de la Recherche Scientifique (CR2P), Département Histoire de la Terre, Muséum National d’Histoire Naturelle, 75005 Paris, France; and hDivision of Paleontology and Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024 Edited* by Elwyn L. Simons, Duke University, Durham, NC, and approved August 15, 2011 (received for review June 6, 2011) India’s Late Cretaceous fossil mammals include the only undis- cluding placentals and their stem relatives) are known from the puted pre-Tertiary Gondwanan eutherians, such as Deccanolestes. Late Cretaceous of Laurasia (North America, Europe, and Asia) Recent studies have suggested a relationship between Deccano- (9), and although a few have been suggested as possible pla- lestes and African and European Paleocene adapisoriculids, which centals [e.g., Protungulatum (10)], none are unequivocally sup- have been variably identified as stem euarchontans, stem pri- ported as a Cretaceous placental mammal (2). -
Massive Loss of Transcription Factors and the Initial Diversification of Placental Mammals
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.26.436744; this version posted March 26, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Massive loss of transcription factors and the initial diversification of placental mammals Xin-Wei Zhao1*†, Jiaqi Wu2†, Hirohisa Kishino1 1Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan. 2School of Life Science and Technology, Tokyo Institute of Technology, Meguro Ward, Tokyo 152- 8550, Japan. *Correspondence to: [email protected] (X.-W.Z.) †These authors contributed equally to this work. ABSTRACT As one of the most successful categories of organisms, mammals occupy a variety of niches on earth as a result of macroevolution. Transcription factors (TFs), the basic regulators of gene expression, may also evolve during mammalian phenotypic diversification and macroevolution. To examine the relationship between TFs and mammalian macroevolution, we analyzed 140,821 de novo-identified TFs and their birth and death histories from 96 mammalian species. Gene tree vs. species tree reconciliation revealed that mammals experienced an upsurge in TF losses around 100 million years ago and also near the K–Pg boundary, thus implying a relationship with the divergence of placental animals. From approximately 100 million years ago to the present, losses dominated TF events without a significant change in TF gains. To quantify the effects of this TF pruning on mammalian macroevolution, we analyzed rates of molecular evolution and expression profiles of regulated target genes. -
Confirming the Phylogeny of Mammals by Use of Large
RESEARCH ARTICLES Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets Arjun B. Prasad,*à Marc W. Allard,§ NISC Comparative Sequencing Program* and Eric D. Green* *Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD; NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD; àIntegrated Biosciences Program, George Washington University; and §Department of Biological Sciences, George Washington University The ongoing generation of prodigious amounts of genomic sequence data from myriad vertebrates is providing unparalleled opportunities for establishing definitive phylogenetic relationships among species. The size and complexities of such comparative sequence data sets not only allow smaller and more difficult branches to be resolved but also present unique challenges, including large computational requirements and the negative consequences of systematic biases. To explore these issues and to clarify the phylogenetic relationships among mammals, we have analyzed a large data set of over 60 megabase pairs (Mb) of high-quality genomic sequence, which we generated from 41 mammals and 3 other vertebrates. All sequences are orthologous to a 1.9-Mb region of the human genome that encompasses the cystic fibrosis transmembrane conductance regulator gene (CFTR). To understand the characteristics and challenges associated with phylogenetic analyses of such a large data set, we partitioned the sequence