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Emma C. Teeling

Bio: Emma C. Teeling is an academic researcher from University College Dublin. The author has contributed to research in topics: Human echolocation & Genome. The author has an hindex of 44, co-authored 125 publications receiving 9939 citations. Previous affiliations of Emma C. Teeling include University of California & University of Porto.


Papers
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Journal ArticleDOI
28 Oct 2011-Science
TL;DR: Molecular phylogenetic analysis, calibrated with fossils, resolves the time frame of the mammalian radiation and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and KPg mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively.
Abstract: Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.

1,284 citations

Journal ArticleDOI
14 Dec 2001-Science
TL;DR: Crown-group Eutheria may have their most recent common ancestry in the Southern Hemisphere (Gondwana), and placental phylogeny is investigated using Bayesian and maximum-likelihood methods and a 16.4-kilobase molecular data set.
Abstract: Molecular phylogenetic studies have resolved placental mammals into four major groups, but have not established the full hierarchy of interordinal relationships, including the position of the root. The latter is critical for understanding the early biogeographic history of placentals. We investigated placental phylogeny using Bayesian and maximum-likelihood methods and a 16.4-kilobase molecular data set. Interordinal relationships are almost entirely resolved. The basal split is between Afrotheria and other placentals, at about 103 million years, and may be accounted for by the separation of South America and Africa in the Cretaceous. Crown-group Eutheria may have their most recent common ancestry in the Southern Hemisphere (Gondwana).

1,239 citations

Journal ArticleDOI
28 Jan 2005-Science
TL;DR: The results support the hypothesis that megabats are nested among four major microbat lineages, which originated in the early Eocene, coincident with a significant global rise in temperature, increase in plant diversity and abundance, and the zenith of Tertiary insect diversity.
Abstract: Bats make up more than 20% of extant mammals, yet their evolutionary history is largely unknown because of a limited fossil record and conflicting or incomplete phylogenies. Here, we present a highly resolved molecular phylogeny for all extant bat families. Our results support the hypothesis that megabats are nested among four major microbat lineages, which originated in the early Eocene [52 to 50 million years ago (Mya)], coincident with a significant global rise in temperature, increase in plant diversity and abundance, and the zenith of Tertiary insect diversity. Our data suggest that bats originated in Laurasia, possibly in North America, and that three of the major microbat lineages are Laurasian in origin, whereas the fourth is Gondwanan. Combining principles of ghost lineage analysis with molecular divergence dates, we estimate that the bat fossil record underestimates (unrepresented basal branch length, UBBL) first occurrences by, on average, 73% and that the sum of missing fossil history is 61%.

979 citations

Journal ArticleDOI
06 Jan 2006-Science
TL;DR: The phylogenetic performance of distinct gene classes showed that Y-chromosome segments are appreciably more informative than mitochondrial DNA, X-linked, or autosomal genes in resolving the rapid Felidae species radiation.
Abstract: Modern felid species descend from relatively recent (<11 million years ago) divergence and speciation events that produced successful predatory carnivores worldwide but that have confounded taxonomic classifications. A highly resolved molecular phylogeny with divergence dates for all living cat species, derived from autosomal, X-linked, Y-linked, and mitochondrial gene segments (22,789 base pairs) and 16 fossil calibrations define eight principal lineages produced through at least 10 intercontinental migrations facilitated by sea-level fluctuations. A ghost lineage analysis indicates that available felid fossils underestimate (i.e., unrepresented basal branch length) first occurrence by an average of 76%, revealing a low representation of felid lineages in paleontological remains. The phylogenetic performance of distinct gene classes showed that Y-chromosome segments are appreciably more informative than mitochondrial DNA, X-linked, or autosomal genes in resolving the rapid Felidae species radiation.

652 citations

Journal ArticleDOI
Arang Rhie1, Shane A. McCarthy2, Shane A. McCarthy3, Olivier Fedrigo4, Joana Damas5, Giulio Formenti4, Sergey Koren1, Marcela Uliano-Silva6, William Chow3, Arkarachai Fungtammasan, J. H. Kim7, Chul Hee Lee7, Byung June Ko7, Mark Chaisson8, Gregory Gedman4, Lindsey J. Cantin4, Françoise Thibaud-Nissen1, Leanne Haggerty9, Iliana Bista2, Iliana Bista3, Michelle Smith3, Bettina Haase4, Jacquelyn Mountcastle4, Sylke Winkler10, Sylke Winkler11, Sadye Paez4, Jason T. Howard, Sonja C. Vernes11, Sonja C. Vernes12, Sonja C. Vernes13, Tanya M. Lama14, Frank Grützner15, Wesley C. Warren16, Christopher N. Balakrishnan17, Dave W Burt18, Jimin George19, Matthew T. Biegler4, David Iorns, Andrew Digby, Daryl Eason, Bruce C. Robertson20, Taylor Edwards21, Mark Wilkinson22, George F. Turner23, Axel Meyer24, Andreas F. Kautt24, Andreas F. Kautt25, Paolo Franchini24, H. William Detrich26, Hannes Svardal27, Hannes Svardal28, Maximilian Wagner29, Gavin J. P. Naylor30, Martin Pippel11, Milan Malinsky31, Milan Malinsky3, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout32, Marlys L. Houck33, Ann C Misuraca33, Sarah B. Kingan34, Richard Hall34, Zev N. Kronenberg34, Ivan Sović34, Christopher Dunn34, Zemin Ning3, Alex Hastie, Joyce V. Lee, Siddarth Selvaraj, Richard E. Green32, Nicholas H. Putnam, Ivo Gut35, Jay Ghurye36, Erik Garrison32, Ying Sims3, Joanna Collins3, Sarah Pelan3, James Torrance3, Alan Tracey3, Jonathan Wood3, Robel E. Dagnew8, Dengfeng Guan2, Dengfeng Guan37, Sarah E. London38, David F. Clayton19, Claudio V. Mello39, Samantha R. Friedrich39, Peter V. Lovell39, Ekaterina Osipova11, Farooq O. Al-Ajli40, Farooq O. Al-Ajli41, Simona Secomandi42, Heebal Kim7, Constantina Theofanopoulou4, Michael Hiller43, Yang Zhou, Robert S. Harris44, Kateryna D. Makova44, Paul Medvedev44, Jinna Hoffman1, Patrick Masterson1, Karen Clark1, Fergal J. Martin9, Kevin L. Howe9, Paul Flicek9, Brian P. Walenz1, Woori Kwak, Hiram Clawson32, Mark Diekhans32, Luis R Nassar32, Benedict Paten32, Robert H. S. Kraus24, Robert H. S. Kraus11, Andrew J. Crawford45, M. Thomas P. Gilbert46, M. Thomas P. Gilbert47, Guojie Zhang, Byrappa Venkatesh48, Robert W. Murphy49, Klaus-Peter Koepfli50, Beth Shapiro32, Beth Shapiro51, Warren E. Johnson50, Warren E. Johnson52, Federica Di Palma53, Tomas Marques-Bonet, Emma C. Teeling54, Tandy Warnow55, Jennifer A. Marshall Graves56, Oliver A. Ryder33, Oliver A. Ryder57, David Haussler32, Stephen J. O'Brien58, Jonas Korlach34, Harris A. Lewin5, Kerstin Howe3, Eugene W. Myers11, Eugene W. Myers10, Richard Durbin3, Richard Durbin2, Adam M. Phillippy1, Erich D. Jarvis51, Erich D. Jarvis4 
National Institutes of Health1, University of Cambridge2, Wellcome Trust Sanger Institute3, Rockefeller University4, University of California, Davis5, Leibniz Association6, Seoul National University7, University of Southern California8, European Bioinformatics Institute9, Dresden University of Technology10, Max Planck Society11, Radboud University Nijmegen12, University of St Andrews13, University of Massachusetts Amherst14, University of Adelaide15, University of Missouri16, East Carolina University17, University of Queensland18, Clemson University19, University of Otago20, University of Arizona21, Natural History Museum22, Bangor University23, University of Konstanz24, Harvard University25, Northeastern University26, University of Antwerp27, National Museum of Natural History28, University of Graz29, University of Florida30, University of Basel31, University of California, Santa Cruz32, Zoological Society of San Diego33, Pacific Biosciences34, Pompeu Fabra University35, University of Maryland, College Park36, Harbin Institute of Technology37, University of Chicago38, Oregon Health & Science University39, Qatar Airways40, Monash University Malaysia Campus41, University of Milan42, Goethe University Frankfurt43, Pennsylvania State University44, University of Los Andes45, Norwegian University of Science and Technology46, University of Copenhagen47, Agency for Science, Technology and Research48, Royal Ontario Museum49, Smithsonian Institution50, Howard Hughes Medical Institute51, Walter Reed Army Institute of Research52, University of East Anglia53, University College Dublin54, University of Illinois at Urbana–Champaign55, La Trobe University56, University of California, San Diego57, Nova Southeastern University58
28 Apr 2021-Nature
TL;DR: The Vertebrate Genomes Project (VGP) as mentioned in this paper is an international effort to generate high quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
Abstract: High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

647 citations


Cited by
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Journal ArticleDOI
TL;DR: An advanced version of the Molecular Evolutionary Genetics Analysis software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis, is released, which enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny.
Abstract: We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.

37,956 citations

28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

14,171 citations

Journal ArticleDOI
TL;DR: Primer3’s current capabilities are described, including more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers.
Abstract: Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3’s functionality. In this article, we describe Primer3’s current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. Additional enhancements include more precise control of primer placement—a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.

7,286 citations

01 Aug 2000
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

4,833 citations