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Leo W. Beukeboom

Bio: Leo W. Beukeboom is an academic researcher from University of Groningen. The author has contributed to research in topics: Nasonia & Nasonia vitripennis. The author has an hindex of 46, co-authored 195 publications receiving 8301 citations. Previous affiliations of Leo W. Beukeboom include Leiden University & Max Planck Society.


Papers
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Journal ArticleDOI
15 Jan 2010-Science
TL;DR: Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation.
Abstract: We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.

838 citations

Journal ArticleDOI
TL;DR: Because B chromosomes interact with the standard chromosomes, they can play an important role in genome evolution and may be useful for studying molecular evolutionary processes.
Abstract: B chromosomes are extra chromosomes to the standard complement that occur in many organisms They can originate in a number of ways including derivation from autosomes and sex chromosomes in intraa

581 citations

Journal ArticleDOI
TL;DR: A distillation of questions about the mechanisms of speciation, the genetic basis of speciating and the relationship between speciation and diversity are presented.
Abstract: Speciation has been a major focus of evolutionary biology research in recent years, with many important advances. However, some of the traditional organising principles of the subject area no longer provide a satisfactory framework, such as the classification of speciation mechanisms by geographical context into allopatric, parapatric and sympatry classes. Therefore, we have asked where speciation research should be directed in the coming years. Here, we present a distillation of questions about the mechanisms of speciation, the genetic basis of speciation and the relationship between speciation and diversity. Our list of topics is not exhaustive; rather we aim to promote discussion on research priorities and on the common themes that underlie disparate speciation processes.

396 citations

Journal ArticleDOI
Patrick Abbot1, Jun Abe2, John Alcock3, Samuel Alizon, João Alpedrinha4, Malte Andersson5, Jean-Baptiste André6, Minus van Baalen6, Francois Balloux7, Sigal Balshine8, Nicholas H. Barton9, Leo W. Beukeboom10, Jay M. Biernaskie4, Trine Bilde11, Gerald Borgia12, Michael D. Breed13, Sam P. Brown4, Redouan Bshary, Angus Buckling4, Nancy Tyler Burley14, Max N. Burton-Chellew4, Michael A. Cant15, Michel Chapuisat16, Eric L. Charnov17, Tim H. Clutton-Brock18, Andrew Cockburn19, Blaine J. Cole20, Nick Colegrave21, Leda Cosmides22, Iain D. Couzin23, Jerry A. Coyne24, Scott Creel25, Bernard J. Crespi26, Robert L. Curry27, Sasha R. X. Dall15, Troy Day28, Janis L. Dickinson29, Lee Alan Dugatkin30, Claire El Mouden4, Stephen T. Emlen29, Jay D. Evans31, Régis Ferrière32, Jeremy Field33, Susanne Foitzik34, Kevin R. Foster4, William A. Foster18, Charles W. Fox35, Juergen Gadau3, Sylvain Gandon, Andy Gardner4, Michael G. Gardner36, Thomas Getty37, Michael A. D. Goodisman38, Alan Grafen4, Richard K. Grosberg39, Christina M. Grozinger40, Pierre-Henri Gouyon, Darryl T. Gwynne41, Paul H. Harvey4, Ben J. Hatchwell42, Jürgen Heinze43, Heikki Helanterä44, Ken R. Helms45, Kim Hill3, Natalie Jiricny4, Rufus A. Johnstone18, Alex Kacelnik4, E. Toby Kiers46, Hanna Kokko19, Jan Komdeur10, Judith Korb47, Daniel J. C. Kronauer48, Rolf Kümmerli49, Laurent Lehmann, Timothy A. Linksvayer50, Sébastien Lion51, Bruce E. Lyon52, James A. R. Marshall42, Richard McElreath39, Yannis Michalakis, Richard E. Michod53, Douglas W. Mock54, Thibaud Monnin6, Robert Montgomerie28, Allen J. Moore15, Ulrich G. Mueller55, Ronald Noë56, Samir Okasha57, Pekka Pamilo44, Geoff A. Parker58, Jes S. Pedersen50, Ido Pen10, David W. Pfennig59, David C. Queller60, Daniel J. Rankin61, Sarah E. Reece21, Hudson K. Reeve29, Max Reuter62, Gilbert Roberts63, Simon K. A. Robson64, Denis Roze6, François Rousset65, Olav Rueppell66, Joel L. Sachs67, Lorenzo A. Santorelli4, Paul Schmid-Hempel68, Michael P. Schwarz36, Thomas C. Scott-Phillips21, Janet Shellmann-Sherman29, Paul W. Sherman29, David M. Shuker69, jeff smith60, Joseph C. Spagna70, Beverly I. Strassmann71, Andrew V. Suarez72, Liselotte Sundström44, Michael Taborsky73, Peter D. Taylor28, Graham J. Thompson74, John Tooby22, Neil D. Tsutsui75, Kazuki Tsuji76, Stefano Turillazzi77, Francisco Úbeda78, Edward L. Vargo79, Bernard Voelkl80, Tom Wenseleers81, Stuart A. West4, Mary Jane West-Eberhard82, David F. Westneat35, Diane C. Wiernasz20, Geoff Wild74, Richard Wrangham1, Andrew J. Young15, David W. Zeh48, David W. Zeh83, Jeanne A. Zeh83, Andrew G. Zink84 
Vanderbilt University1, Shizuoka University2, Arizona State University3, University of Oxford4, University of Gothenburg5, Pierre-and-Marie-Curie University6, Imperial College London7, McMaster University8, Institute of Science and Technology Austria9, University of Groningen10, Aarhus University11, University of Maryland, College Park12, University of Colorado Boulder13, University of California, Irvine14, University of Exeter15, University of Lausanne16, University of New Mexico17, University of Cambridge18, Australian National University19, University of Houston20, University of Edinburgh21, University of California, Santa Barbara22, Princeton University23, University of Chicago24, Montana State University25, Simon Fraser University26, Villanova University27, Queen's University28, Cornell University29, University of Louisville30, United States Department of Agriculture31, École Normale Supérieure32, University of Sussex33, Ludwig Maximilian University of Munich34, University of Kentucky35, Flinders University36, Michigan State University37, Georgia Institute of Technology38, University of California, Davis39, Pennsylvania State University40, University of Toronto41, University of Sheffield42, University of Regensburg43, University of Helsinki44, University of Vermont45, VU University Amsterdam46, University of Osnabrück47, Harvard University48, Swiss Federal Institute of Aquatic Science and Technology49, University of Copenhagen50, Royal Holloway, University of London51, University of California, Santa Cruz52, University of Arizona53, University of Oklahoma54, University of Texas at Austin55, University of Strasbourg56, University of Bristol57, University of Liverpool58, University of North Carolina at Chapel Hill59, Rice University60, University of Zurich61, University College London62, Newcastle University63, James Cook University64, University of Montpellier65, University of North Carolina at Greensboro66, University of California, Riverside67, ETH Zurich68, University of St Andrews69, William Paterson University70, University of Michigan71, University of Illinois at Urbana–Champaign72, University of Bern73, University of Western Ontario74, University of California, Berkeley75, University of the Ryukyus76, University of Florence77, University of Tennessee78, North Carolina State University79, Humboldt University of Berlin80, Katholieke Universiteit Leuven81, Smithsonian Institution82, University of Nevada, Reno83, San Francisco State University84
24 Mar 2011-Nature
TL;DR: It is argued that inclusive fitness theory has been of little value in explained the natural world, and that it has led to negligible progress in explaining the evolution of eusociality, but these arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature.
Abstract: Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. Nowak et al. argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature. We will focus our comments on three general issues.

383 citations

Journal ArticleDOI
TL;DR: A conceptual model is proposed to contrast various scenarios for changes in genomic networks, which may serve as a framework to explain the different evolutionary dynamics of polyploidy in animals and plants.
Abstract: Polyploidy is rarer in animals than in plants. Why? Since Muller's observation in 1925, many hypotheses have been proposed and tested, but none were able to completely explain this intriguing fact. New genomic technologies enable the study of whole genomes to explain the constraints on or consequences of polyploidization, rather than focusing on specific genes or life history characteristics. Here, we review a selection of old and recent literature on polyploidy in animals, with emphasis on the consequences of polyploidization for gene expression patterns and genomic network interactions. We propose a conceptual model to contrast various scenarios for changes in genomic networks, which may serve as a framework to explain the different evolutionary dynamics of polyploidy in animals and plants. We also present new insights of genetic sex determination in animals and our emerging understanding of how animal sex determination systems may hamper or enable polyploidization, including some recent data on haplodiploids. We discuss the role of polyploidy in evolution and ecology, using a gene regulation perspective, and conclude with a synopsis regarding the effects of whole genome duplications on the balance of genomic networks. See also the sister articles focusing on plants by Ashman et al. and Madlung and Wendel in this themed issue.

336 citations


Cited by
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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 Article
Fumio Tajima1
30 Oct 1989-Genomics
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.

11,521 citations

Journal Article
TL;DR: For the next few weeks the course is going to be exploring a field that’s actually older than classical population genetics, although the approach it’ll be taking to it involves the use of population genetic machinery.
Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

9,847 citations

Journal Article
TL;DR: FastTree as mentioned in this paper uses sequence profiles of internal nodes in the tree to implement neighbor-joining and uses heuristics to quickly identify candidate joins, then uses nearest-neighbor interchanges to reduce the length of the tree.
Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

2,436 citations