REVIEW Selectionism and Neutralism in Molecular Evolution
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Chromosomal Evolution in Raphicerus Antelope Suggests Divergent X
www.nature.com/scientificreports OPEN Chromosomal evolution in Raphicerus antelope suggests divergent X chromosomes may drive speciation through females, rather than males, contrary to Haldane’s rule Terence J. Robinson1*, Halina Cernohorska2, Svatava Kubickova2, Miluse Vozdova2, Petra Musilova2 & Aurora Ruiz‑Herrera3,4 Chromosome structural change has long been considered important in the evolution of post‑zygotic reproductive isolation. The premise that karyotypic variation can serve as a possible barrier to gene fow is founded on the expectation that heterozygotes for structurally distinct chromosomal forms would be partially sterile (negatively heterotic) or show reduced recombination. We report the outcome of a detailed comparative molecular cytogenetic study of three antelope species, genus Raphicerus, that have undergone a rapid radiation. The species are largely conserved with respect to their euchromatic regions but the X chromosomes, in marked contrast, show distinct patterns of heterochromatic amplifcation and localization of repeats that have occurred independently in each lineage. We argue a novel hypothesis that postulates that the expansion of heterochromatic blocks in the homogametic sex can, with certain conditions, contribute to post‑ zygotic isolation. i.e., female hybrid incompatibility, the converse of Haldane’s rule. This is based on the expectation that hybrids incur a selective disadvantage due to impaired meiosis resulting from the meiotic checkpoint network’s surveillance of the asymmetric expansions of heterochromatic blocks in the homogametic sex. Asynapsis of these heterochromatic regions would result in meiotic silencing of unsynapsed chromatin and, if this persists, germline apoptosis and female infertility. Te chromosomal speciation theory 1,2 also referred to as the “Hybrid dysfunction model”3, has been one of the most intriguing questions in biology for decades. -
Gabriel Dover)
Dear Mr Darwin (Gabriel Dover) Home | Intro | About | Feedback | Prev | Next | Search Steele: Lamarck's Was Signature Darwin Wrong? Molecular Drive: the Third Force in evolution Geneticist Gabriel Dover claims that there is a third force in evolution: 'Molecular Drive' beside natural selection and neutral drift. Molecular drive is operationally distinct from natural selection and neutral drift. According to Dover it explains biological phenomena, such as the 700 copies of a ribosomal RNA gene and the origin of the 173 legs of the centipede, which natural selection and neutral drift alone cannot explain. by Gert Korthof version 1.3 24 Mar 2001 Were Darwin and Mendel both wrong? Molecular Drive is, according to Dover, an important factor in evolution, because it shapes the genomes and forms of organisms. Therefore Neo-Darwinism is incomplete without Molecular Drive. It is no wonder that the spread of novel genes was ascribed to natural selection, because it was the only known process that could promote the spread of novel genes. Dover doesn't reject the existence of natural selection but points out cases where natural selection clearly fails as a mechanism. Molecular drive is a non-Darwinian mechanism because it is independent of selection. We certainly need forces in evolution, since natural selection itself is not a force. It is the passive outcome of other processes. It is not an active process, notwithstanding its name. Natural selection as an explanation is too powerful for its own good. Molecular drive is non-Mendelian because some DNA segments are multiplied disproportional. In Mendelian genetics genes are present in just two copies (one on the maternal and one on the paternal chromosome). -
Phylogenetic Systematics and the Evolutionary History of Some Intestinal Flatworm Parasites (Trematoda: Digenea: Plagiorchi01dea) of Anurans
PHYLOGENETIC SYSTEMATICS AND THE EVOLUTIONARY HISTORY OF SOME INTESTINAL FLATWORM PARASITES (TREMATODA: DIGENEA: PLAGIORCHI01DEA) OF ANURANS by RICHARD TERENCE 0'GRADY B.Sc, University Of British Columbia, 1978 M.Sc, McGill University, 1981 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES Department Of Zoology We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA March 1987 © Richard Terence O'Grady, 1987 In presenting this thesis in partial fulfilment of the requirements for an advanced degree at the University of British Columbia, I agree that the Library shall make it freely available for reference and study. I further agree that permission for extensive copying of this thesis for scholarly purposes may be granted by the Head of my Department or by his or her representatives. It is understood that copying or publication of this thesis for financial gain shall not be allowed without my written permission. Department of Zoology The University of British Columbia 2075 Wesbrook Place Vancouver, Canada V6T 1W5 Date: March 24, 1987 i i Abstract Historical structuralism is presented as a research program in evolutionary biology. It uses patterns of common ancestry as initial hypotheses in explaining evolutionary history. Such patterns, represented by phylogenetic trees, or cladograms, are postulates of persistent ancestral traits. These traits are evidence of historical constraints on evolutionary change. Patterns and processes consistent with a cladogram are considered to be consistent with an initial hypothesis of historical constraint. As an application of historical structuralism, a phylogenetic analysis is presented for members of the digenean plagiorchioid genera Glypthelmins Stafford, 1905 and Haplometrana Lucker, 1931. -
Molecular Evolution
SYSTEMATICS & EVOLUTION Molecular Evolution GINCY C GEORGE (Assistant Professor On Contract) Molecular Evolution Molecular Evolution • Molecular evolution is the area of evolutionary biology that studies evolutionary change at the level of the DNA sequence. Molecular Evolution • It includes the study of rates of sequence change, relative importance of adaptive and neutral changes, and changes in genome structure. Molecular evolution examines DNA and proteins, addressing two types of questions: How do DNA and proteins evolve? How are genes and organisms evolutionarily related? Study of how genes and proteins evolve and how are organisms related based on their DNA sequence • Molecular evolution therefore is the determination and comparative study of DNA and deduced amino acid sequences. • Sequences from different organisms or populations are matched or aligned • Evolution at molecular level is observable at the base (nucleotide) level changes in the DNA and amino acid changes in proteins • Both can be studied by examining the differences between species • Both polymorphism and evolutionary changes between species can be explained by two processes ie; • Natural selection and Neutral drift • The main factors that influence Natural selection and Neutral drift are population size and the selection coefficient of the different genotypes • If the population is small and the selection coefficient low; genetic drift dominates, • Whereas natural selection dominates if the population and selection coefficients are large • Evolution of Modern species -
Concerted Evolution at the Population Level: Pupfish Hindill Satellite DNA Sequences JOHN F
Proc. Nati. Acad. Sci. USA Vol. 91, pp. 994-998, February 1994 Evolution Concerted evolution at the population level: Pupfish HindIll satellite DNA sequences JOHN F. ELDER, JR.* AND BRUCE J. TURNER Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 Communicated by Bruce Wallace, October 18, 1993 ABSTRACT The canonical monomers (170 bp) of an organisms. There are very little data on their variation within abundant (1.9 x 10' copies per diploid genome) satellite DNA or divergence among conspecific natural populations. sequence family In the genome of Cyprinodon wriegau, a We report here sequence comparisons ofthe predominant "pph" that ranges along the Atlantic coast fom Cape Cod or "canonical" monomers of a satellite DNA array in sam- to central Mexico, are divergent in base sequence in 10 of 12 ples of 12 natural populations of Cyprinodon variegatus smle collected from natural populations. The divergence (Cyprinodontidae), a coastal killifish species. Ten of these Involves sbsitions, deletis, and insertions, is marked in samples have distinctive and characteristic canonical mono- scoe (mean pairwise sequence slarit = 61.6%; range = mers with high levels of intraindividual and intrapopulation 35-95.9%), Is largely ed to the 3' half of the monomer, homogeneity.t In other words, this satellite DNA has appar- and Is not correlated with the disace among cllg sites. ently undergone concerted evolution at or near the level of Repetitive loning and direct genomic sequencing expriments the local population. failed to detect intrapopulation and intraindividual variation, A preliminary account of some of our early findings has hig levels of sequence homogeneity within popu- appeared in a symposium volume (6). -
Molecular Facts and Evolutionary Theory
Journal and Proceedings of The Royal Society of New South Wales Volume 120 Parts 1 and 2 [Issued September, 1987] pp.39-48 Return to CONTENTS Molecular Facts and Evolutionary Theory George L. Gabor Miklos Evolutionary biology has had a fascinating recent history. It was realized more than a century ago that the way of approaching many evolutionary problems lay in studies of morphology. However, as pointed out by Bateson in 1922, “discussions of evolution came to an end primarily because no progress was being made. Morphology having been explored in the minutest corners, we turned elsewhere. We became geneticists in the conviction that there at least must evolutionary wisdom be found.” At the same time, while it was clear that morphology must have its bases in embryology, it was instead the mathematically oriented theory of neo-Darwinism that rose to prominence over the next half century. This theory is essentially an amalgam of Mendelian genetics and classical Darwinian selection, firmly based on changes in gene frequencies at particular loci. In the late 1960s, it began to be evaluated at a crude molecular level using gel electrophoresis techniques that allowed the examination of polymorphisms at many enzyme coding loci. In the mid 1970s the technological advances of genetic engineering ushered in an entirely new era of molecular biology. The molecular biologist became the successor to the pure geneticist, and the focus switched back to the molecular analysis of development. The molecular biology of recombinant DNA revolutionized the previous concepts of genome organization and function and led to a reappraisal of the importance of neo-Darwinism. -
Statement About Pnas Paper “The New Mutation Theory of Phenotypic Evolution”
July 30, 2007 (revised) Brief Historical Perspectives of the Paper “THE NEW MUTATION THEORY OF PHENOTYPIC EVOLUTION” Proceedings of the National Academy of Sciences, USA, 104:12235-12242, Published July 17, 2007 online. Masatoshi Nei The following is the author’s account of the history of development of the mutation theory of phenotypic evolution and related matters. Darwinism (1) Charles Darwin proposed that evolution occurs by natural selection in the presence of fluctuating variation. (2) At his time, the mechanism of generation of new variation was not known, and he assumed that new variation is generated by climatic changes, inheritance of acquired characters, spontaneous variations, etc. However, he believed that new variation occurs in random direction and evolutionary change is caused by natural selection. (3) He assumed that enormous phenotypic diversity among different phyla and classes is the result of accumulation of gradual evolution by natural selection. Saltationism Several biologists such as Thomas Huxley, William Bateson, and Hugo de Vries argued that the extent of variation between species is much greater than that within 1 species and therefore saltational or macromutational change is necessary to form new species rather than gradual evolution as proposed by Darwin. In this view a new species can be produced by a single macromutation, and therefore natural selection is unimportant. This view was strengthened when de Vries discovered several new forms of evening primroses which were very different from the parental species (Oenothera lamarckiana) and appeared to be new species. This discovery suggested that new species can arise by a single step of macromutation. However, it was later shown that O. -
Evolution by the Birth-And-Death Process in Multigene Families of the Vertebrate Immune System
Proc. Natl. Acad. Sci. USA Vol. 94, pp. 7799–7806, July 1997 Colloquium Paper This paper was presented at a colloquium entitled ‘‘Genetics and the Origin of Species,’’ organized by Francisco J. Ayala (Co-chair) and Walter M. Fitch (Co-chair), held January 30–February 1, 1997, at the National Academy of Sciences Beckman Center in Irvine, CA. Evolution by the birth-and-death process in multigene families of the vertebrate immune system MASATOSHI NEI*, XUN GU, AND TATYANA SITNIKOVA Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802 ABSTRACT Concerted evolution is often invoked to explain the diversity and evolution of the multigene families of major histocompatibility complex (MHC) genes and immunoglobulin (Ig) genes. However, this hypothesis has been controversial because the member genes of these families from the same species are not necessarily more closely related to one another than to the genes from different species. To resolve this controversy, we conducted phylogenetic analyses of several multigene families of the MHC and Ig systems. The results show that the evolutionary pattern of these families is quite different from that of concerted evolution but is in agreement with the birth-and-death model of evolution in which new genes are created by repeated gene duplication and some duplicate genes are maintained in the genome for a long time but others are deleted or become nonfunctional by deleterious mutations. We found little evidence that interlocus gene conversion plays an important role in the evolution of MHC and Ig multigene families. -
Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis Nicolas Galtier
Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis Nicolas Galtier To cite this version: Nicolas Galtier. Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis. PLoS Genetics, Public Library of Science, 2016, 12 (1), 10.1371/journal.pgen.1005774. hal-01900669 HAL Id: hal-01900669 https://hal.archives-ouvertes.fr/hal-01900669 Submitted on 22 Oct 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. RESEARCH ARTICLE Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis Nicolas Galtier* Institut des Sciences de l'Evolution UMR5554, Université Montpellier–CNRS–IRD–EPHE, Montpellier, France * [email protected] Abstract The rate at which genomes adapt to environmental changes and the prevalence of adaptive processes in molecular evolution are two controversial issues in current evolutionary genet- ics. Previous attempts to quantify the genome-wide rate of adaptation through amino-acid substitution have revealed a surprising diversity of patterns, with some species (e.g. Dro- sophila) experiencing a very high adaptive rate, while other (e.g. humans) are dominated by nearly-neutral processes. It has been suggested that this discrepancy reflects between- OPEN ACCESS species differences in effective population size. -
Generating and Filtering Major Phenotypic Novelties: Neogoldschmidtian Saltation Revisited
Chapter 7 Generating and filtering major phenotypic novelties: neoGoldschmidtian saltation revisited Richard N\. Bateman and William A. D/M/che/e ABSTRACT Further developing a controversial neoGoldschmidtian paradigm that we first pub- lished in 1994, we here narrowly define saltational evolution as a genetic modifica- tion that is expressed as a profound phenotypic change across a single generation and results in a potentially independent evolutionary lineage termed a prospecies (the 'hopeful monster' of Richard Goldschmidt). Of several saltational and parasaltational mechanisms previously discussed by us, the most directly relevant to evolutionary-developmental genetics is dichotomous saltation, which is driven by mutation within a single ancestral Uneage. It can result not only in instantaneous speciation but also in the simultaneous origin of a profound phenotypic novelty more likely to be treated as a new supraspecific taxon. Saltational events form unusually long branches on morphological phylogenies, which follow a punctuated equilibrium pattern, but at the time of origin they typically form zero length branches on the contrastingly gradualistic molecular phylogenies. Our chosen case- studies of heterotopy (including homeosis) and heterochrony in fossil seed-ferns and extant orchids indicate that vast numbers of prospecies are continuously generated by mutation of key developmental genes that control morphogenesis. First principles suggest that, although higher plant mutants are more likely to become established than higher animals, the fitness of even plant prospecies is in at least most cases too low to survive competition-mediated selection. The establishment of prospecies is most Hkely under temporary release from selection in environments of low biotic competition for resources, followed by honing to competitive fitness by gradual rein- troduction to neoDarwinian selection. -
Acquired Characters. See Inheritance of Acquired Characters Adoption
Index Notes are indexed only when they significantly amplify the main text. They are identified by N preceding the page number to which they refer, and can be found between pages 385 and 416. Acquired characters. See Inheritance of in macaques, 178–180, 183, 188, 207, acquired characters 220 Adoption, 187–188. See also Foster origins of, 333–336 parents prevalence of, 177 Agency, 208–209, 224, 231. See also stability of, 179, 182–185 Reproducer in tarbutniks, 158–159 Aging, 130 in tits, 169–170 Agriculture, 237, 296–297, 363, Antirrhinum, 141 366–367, N237 Aphids, 83–84 Aisner, R., 170 Arabidopsis, 268–269, 270 Alarm calls, 34–35, 54, 159, 194, 196 Ascaris, 68–69, 83, N68 Alleles 24–25. See also Gene Asexual reproduction metastable, N332 and epigenetic inheritance, 114–118, Alternative splicing, 65–67 138, 148, 250, 275, 277–278, 346 Altruism, 34–5, 187 and sexual reproduction, compared, Amplification of DNA, 69–70 82–84, 103, 346 Animal traditions. See also Behavioral Asimov, Isaac, 78 inheritance; Cultural evolution; Assimilate-stretch principle, 290–292, Lifestyle evolution 308–309, 309–310 in birds and whales, 172–173 Avital, E., 156, 291 in black rats, 170–171 in chimpanzees, 177, 183, 313, 368 Bacillus, 138 complexity of, 178, 180 Bacteria, 237, 328–329 and conservation practices, 190, 370 epigenetic inheritance in, 119, 138, 332 and cumulative evolution, 176–180, genetic systems of, 30, 85, 233 220, 335 mutation in, 79–80, 88, 93–98, 105, in insects, 189–190 106, 322–323, 345–347, 364 448 Index Baldwin, J. -
Book Reviews
Heredity 86 (2001) 385±386 Book reviews Molecular Evolution and Phylogenetics. Masatoshi Nei and will ®nd Molecular Evolution and Phylogenetics as useful as its Sudhir Kumar. Oxford University Press, Oxford. 2000. previous incarnation and all readers will come away with the Pp. 333. Price £65.00, hardback. ISBN 0 19 513584 9. fully justi®ed feeling that there is a lot more to this tree building business than ®rst meets the eye. We live in interesting times. The curse is that it is near impossible to keep up with a ®eld moving as rapidly as molecular evolution. The blessing is that we have clear- References writing proponents, such as the authors of this book, to help FELSENSTEIN, J. 2001. Inferring Phylogenies. Sinauer Associates, Inc., us with comprehensive and comprehensible reviews. Molecu- Sunderland, Massachusetts. lar Evolution and Phylogenetics is essentially a major update LI, W.-H. 1997. Molecular Evolution. Sinauer Associates, Inc., Sunder- of Nei's 1987 book, Molecular Evolutionary Genetics. The land, Massachusetts. title of the newer volume from the doyen of distance methods NEI, M. 1987. Molecular Evolutionary Genetics. Columbia University accurately re¯ects its much greater emphasis on phylogenetic Press, New York. issues. The book begins with chapters on the molecular basis PAGE, R. D. M.AND HOLMES , E. C. 1998 Molecular Evolution: A of evolution, evolutionary change in amino acid and DNA Phylogenetic Approach. Blackwell Science Ltd., Oxford. sequences, and models of nucleotide substitutions. Inferring SWOFFORD, D. L., OLSEN, G. J. , WADDELLP. J.AND HILLIS , D. M. 1996. phylogenies from molecular sequence data is a fast moving Phylogenetic inference.