Hybridization As an Invasion of the Genome
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Using Hominin Introgression to Trace Modern Human Dispersals PERSPECTIVE Jo~Ao C
PERSPECTIVE Using hominin introgression to trace modern human dispersals PERSPECTIVE Jo~ao C. Teixeiraa,1 and Alan Coopera,1 Edited by James F. O’Connell, University of Utah, Salt Lake City, UT, and approved June 17, 2019 (received for review March 26, 2019) The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace’s Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic. human evolution | archaic introgression | anthropology | genetics As anatomically modern humans (AMHs) migrated out western Siberia (3, 4). Fig. 1 depicts these events, of Africa and around the rest of the world, they met and infers the migration routes of AMHs by following and interbred with multiple extinct hominin species savannah-like habitats predicted in paleoenvironmental (1). -
Hybrids and Hybrid Zones
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC Hybrids and hybrid zones Arnold’s new book on hybridization1, recently reviewed by Ritchie in TREE 2, has brought attention to an old, controversial but revitalized topic in evolutionary biology. The two reviews2,3 we have read share a sceptical attitude towards studies of hybridization lying outside the hybrid zone theory. They consider Arnold’s book too ‘opinionated’2 and ‘an argument for a greater emphasis on the positive role of hybridization in evolution’ rather than a ‘comprehensive review’3. However, one of the merits of the book is that it devotes a great deal of effort towards reconciling divergent approaches to the topic. Arnold dedicates equal importance to animal and plant studies, as acknowledged by Ritchie2, and also puts much emphasis on the analysis of hybrid zones. In fact, when proposing a model for the birth of new evolutionary hybrid lineages he places his ‘new conceptual framework (the evolutionary novelty model)’ within the hybrid zone framework. Our criticism of this proposal is that it may be too rigid to fit scenarios departing from the specific model of hybrid speciation proposed by Grant4, that is, recombinational speciation. In our opinion, relying exclusively on the hybrid zone framework to assess the role of hybrids in evolution is misleading. Hybrid zones usually imply relatively recent events and species with strong reproductive barriers. The tension zone model assumes that hybrid zones are maintained by a balance between selection against hybrid individuals and dispersal of parental individuals into the hybrid zone5. -
Advances on Research Epigenetic Change of Hybrid and Polyploidy in Plants
African Journal of Biotechnology Vol. 10(51), pp. 10335-10343, 7 September, 2011 Available online at http://www.academicjournals.org/AJB DOI: 10.5897/AJB10.1893 ISSN 1684–5315 © 2011 Academic Journals Review Advances on research epigenetic change of hybrid and polyploidy in plants Zhiming Zhang†, Jian Gao†, Luo Mao, Qin Cheng, Zeng xing Li Liu, Haijian Lin, Yaou Shen, Maojun Zhao and Guangtang Pan* Maize Research Institute, Sichuan Agricultural University, Xinkang road 46, Ya’an, Sichuan 625014, People’s Republic of China. Accepted 15 April, 2011 Hybridization between different species, and subsequently polyploidy, play an important role in plant genome evolution, as well as it is a widely used approach for crop improvement. Recent studies of the last several years have demonstrated that, hybridization and subsequent genome doubling (polyploidy) often induce an array of variations that could not be explained by the conventional genetic paradigms. A large proportion of these variations are epigenetic in nature. Epigenetic can be defined as a change of the study in the regulation of gene activity and expression that are not driven by gene sequence information. However, the ramifications of epigenetic in plant biology are immense, yet unappreciated. In contrast to the ease with which the DNA sequence can be studied, studying the complex patterns inherent in epigenetic poses many problems. In this view, advances on researching epigenetic change of hybrid and polyploidy in plants will be initially set out by summarizing the latest researches and the basic studies on epigenetic variations generated by hybridization. Moreover, polyploidy may shed light on the mechanisms generating these variations. -
Horizontal Gene Transfer
Genetic Variation: The genetic substrate for natural selection Horizontal Gene Transfer Dr. Carol E. Lee, University of Wisconsin Copyright ©2020; Do not upload without permission What about organisms that do not have sexual reproduction? In prokaryotes: Horizontal gene transfer (HGT): Also termed Lateral Gene Transfer - the lateral transmission of genes between individual cells, either directly or indirectly. Could include transformation, transduction, and conjugation. This transfer of genes between organisms occurs in a manner distinct from the vertical transmission of genes from parent to offspring via sexual reproduction. These mechanisms not only generate new gene assortments, they also help move genes throughout populations and from species to species. HGT has been shown to be an important factor in the evolution of many organisms. From some basic background on prokaryotic genome architecture Smaller Population Size • Differences in genome architecture (noncoding, nonfunctional) (regulatory sequence) (transcribed sequence) General Principles • Most conserved feature of Prokaryotes is the operon • Gene Order: Prokaryotic gene order is not conserved (aside from order within the operon), whereas in Eukaryotes gene order tends to be conserved across taxa • Intron-exon genomic organization: The distinctive feature of eukaryotic genomes that sharply separates them from prokaryotic genomes is the presence of spliceosomal introns that interrupt protein-coding genes Small vs. Large Genomes 1. Compact, relatively small genomes of viruses, archaea, bacteria (typically, <10Mb), and many unicellular eukaryotes (typically, <20 Mb). In these genomes, protein-coding and RNA-coding sequences occupy most of the genomic sequence. 2. Expansive, large genomes of multicellular and some unicellular eukaryotes (typically, >100 Mb). In these genomes, the majority of the nucleotide sequence is non-coding. -
Korunes Duke 0066D 14983.Pdf
How Linkage Disequilibrium and Recombination Shape Genetic Variation Within and Between Species by Katharine L Korunes University Program in Genetics and Genomics Duke University Date:_______________________ Approved: ___________________________ Mohamed Noor, Supervisor ___________________________ Mark Rausher, Chair ___________________________ Paul Magwene ___________________________ John Willis ___________________________ Jeff Sekelsky Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the University Program in Genetics and Genomics in the Graduate School of Duke University 2019 ABSTRACT How Linkage Disequilibrium and Recombination Shape Genetic Variation Within and Between Species by Katharine L Korunes University Program in Genetics and Genomics Duke University Date:_______________________ Approved: ___________________________ Mohamed Noor, Supervisor ___________________________ Mark Rausher, Chair ___________________________ Paul Magwene ___________________________ John Willis ___________________________ Jeff Sekelsky An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the University Program in Genetics and Genomics in the Graduate School of Duke University 2019 Copyright by Katharine L Korunes 2019 Abstract Meiotic recombination creates genetic diversity by shuffling combinations of alleles across loci, yet alleles at neighboring loci often remain non-randomly associated. This non-random association is -
Maize Nested Introgression Library Provides Evidence for the Involvement of 2 Liguleless1 in Resistance to Northern Leaf Blight 3
bioRxiv preprint doi: https://doi.org/10.1101/818518; this version posted October 24, 2019. 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. 1 Maize nested introgression library provides evidence for the involvement of 2 liguleless1 in resistance to northern leaf blight 3 4 Judith M. Kolkmana, Josh Strableb, Kate Harlineb, Dallas E. Kroonc,1, Tyr Wiesner-Hanksd,2, 5 Peter J. Bradburyc, and Rebecca J. Nelsona,d 6 a School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, 7 NY 14853, USA. 8 b School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY 14853, USA. 9 c US Department of Agriculture, Agricultural Research Service, Ithaca, NY 14853, USA 10 d School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY 14853, 11 USA. 12 1 Present address: DuPont de Nemours, Inc., Experimental Station, 200 Powder Mill Road, Wilmington, DE 19083, 13 USA 14 2 Present address: PepsiCo, 4295 Tenderfoot Rd., Rhinelander WI, 54501, USA 15 3 To whom correspondence should be addressed. Email: [email protected] 16 Keywords 17 Zea mays, Setosphaeria turcica, near-isogenic lines, liguleless1 18 Author contributions: 19 J.M.K., R.J.N., and J.S. designed research 20 J.M.K. performed research 21 J.M.K., P.B., J.S., D.K., K.H., and T.W-H. contributed new reagents/analytic tools 22 J.M.K., K.H., D.K. analyzed data 23 JMK, RJN wrote the paper 24 1 bioRxiv preprint doi: https://doi.org/10.1101/818518; this version posted October 24, 2019. -
Microevolution and the Genetics of Populations Microevolution Refers to Varieties Within a Given Type
Chapter 8: Evolution Lesson 8.3: Microevolution and the Genetics of Populations Microevolution refers to varieties within a given type. Change happens within a group, but the descendant is clearly of the same type as the ancestor. This might better be called variation, or adaptation, but the changes are "horizontal" in effect, not "vertical." Such changes might be accomplished by "natural selection," in which a trait within the present variety is selected as the best for a given set of conditions, or accomplished by "artificial selection," such as when dog breeders produce a new breed of dog. Lesson Objectives ● Distinguish what is microevolution and how it affects changes in populations. ● Define gene pool, and explain how to calculate allele frequencies. ● State the Hardy-Weinberg theorem ● Identify the five forces of evolution. Vocabulary ● adaptive radiation ● gene pool ● migration ● allele frequency ● genetic drift ● mutation ● artificial selection ● Hardy-Weinberg theorem ● natural selection ● directional selection ● macroevolution ● population genetics ● disruptive selection ● microevolution ● stabilizing selection ● gene flow Introduction Darwin knew that heritable variations are needed for evolution to occur. However, he knew nothing about Mendel’s laws of genetics. Mendel’s laws were rediscovered in the early 1900s. Only then could scientists fully understand the process of evolution. Microevolution is how individual traits within a population change over time. In order for a population to change, some things must be assumed to be true. In other words, there must be some sort of process happening that causes microevolution. The five ways alleles within a population change over time are natural selection, migration (gene flow), mating, mutations, or genetic drift. -
Horizontal Gene Transfer Elements: Plasmids in Antarctic Microorganisms
Chapter 5 Horizontal Gene Transfer Elements: Plasmids in Antarctic Microorganisms Matías Giménez, Gastón Azziz, Paul R. Gill, and Silvia Batista Abstract Plasmids play an important role in the evolution of microbial communi- ties. These mobile genetic elements can improve host survival and may also be involved in horizontal gene transfer (HGT) events between individuals. Diverse culture-dependent and culture-independent approaches have been used to character- ize these mobile elements. Culture-dependent methods are usually associated with classical microbiological techniques. In the second approach, development of spe- cific protocols for analysis of metagenomes involves many challenges, including assembly of sequences and availability of a reliable database, which are crucial. In addition, alternative strategies have been developed for the characterization of plas- mid DNA in a sample, generically referred to as plasmidome. The Antarctic continent has environments with diverse characteristics, including some with very low temperatures, humidity levels, and nutrients. The presence of microorganisms and genetic elements capable of being transferred horizontally has been confirmed in these environments, and it is generally accepted that some of these elements, such as plasmids, actively participate in adaptation mechanisms of host microorganisms. Information related to structure and function of HGT elements in Antarctic bac- teria is very limited compared to what is known about HGT in bacteria from temper- ate/tropical environments. Some studies are done with biotechnological objectives. The search for mobile elements, such as plasmids, may be related to improve the expression of heterologous genes in host organisms growing at very low tempera- tures. More recently, however, additional studies have been done to detect plasmids in isolates, associated or not with specific phenotypes such as drug resistance. -
An Anomalous Hybrid Zone in Drosophila
Evolution, 59(12), 2005, pp. 2602±2607 AN ANOMALOUS HYBRID ZONE IN DROSOPHILA ANA LLOPART,1,2 DANIEL LACHAISE,3,4 AND JERRY A. COYNE5,6 1Department of Biological Sciences, University of Iowa, 215 Biology Building (BB), Iowa City, Iowa 52242 2E-mail: [email protected] 3Centre National de la Recherche Scienti®que, Laboratoire Populations, GeÂneÂtique, et Evolution, 91198 Gif sur Yvette Cedex, France 4E-mail: [email protected] 5Department of Ecology and Evolution, University of Chicago, 1101 East 57 Street, Chicago, Illinois 60637 6E-mail: [email protected] Abstract. Despite the genetic tractability of many of Drosophila species, the genus has few examples of the ``classic'' type of hybrid zone, in which the ranges of two species overlap with a gradual transition from one species to another through an area where hybrids are produced. Here we describe a classic hybrid zone in Drosophila that involves two sister species, Drosophila yakuba and D. santomea, on the island of SaÄo TomeÂ. Our transect of this zone has yielded several surprising and anomalous ®ndings. First, we detected the presence of an additional hybrid zone largely outside the range of both parental species. This phenomenon is, to our knowledge, unique among animals. Second, the genetic analysis using diagnostic molecular markers of the ¯ies collected in this anomalous hybrid zone indicates that nearly all hybrid males are F1s that carry the D. santomea X chromosome. This F1 genotype is much more dif®cult to produce in the laboratory compared to the genotype from the reciprocal cross, showing that sexual isolation as seen in the laboratory is insuf®cient to explain the genotypes of hybrids found in the wild. -
Comprehensive Analysis of Mobile Genetic Elements in the Gut Microbiome Reveals Phylum-Level Niche-Adaptive Gene Pools
bioRxiv preprint doi: https://doi.org/10.1101/214213; this version posted December 22, 2017. 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. 1 Comprehensive analysis of mobile genetic elements in the gut microbiome 2 reveals phylum-level niche-adaptive gene pools 3 Xiaofang Jiang1,2,†, Andrew Brantley Hall2,3,†, Ramnik J. Xavier1,2,3,4, and Eric Alm1,2,5,* 4 1 Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, 5 Cambridge, MA 02139, USA 6 2 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 7 3 Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard 8 Medical School, Boston, MA 02114, USA 9 4 Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General 10 Hospital and Harvard Medical School, Boston, MA 02114, USA 11 5 MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 12 02142, USA 13 † Co-first Authors 14 * Corresponding Author bioRxiv preprint doi: https://doi.org/10.1101/214213; this version posted December 22, 2017. 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. 15 Abstract 16 Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer 17 could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could 18 threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological 19 importance and medical relevance, MGEs from the gut microbiome have not been systematically 20 characterized. -
Gene Flow by Pollen Into Small Populations
Proc. Natl. Acad. Sci. USA Vol. 86, pp. 9044-9047, November 1989 Population Biology Gene flow by pollen into small populations: Data from experimental and natural stands of wild radish (Raphanus sativus/spatial isolation/interpopulation mating) NORMAN C. ELLSTRANDt, B. DEVLINt, AND DIANE L. MARSHALL§ Department of Botany and Plant Sciences and Program in Genetics, University of California, Riverside, CA 92521-0124 Communicated by R. W. Allard, August 14, 1989 (received for review August 18, 1988) ABSTRACT Gene flow can have an especially strong im- much from population to population, whether it varies within pact on the evolution of small populations. However, empirical a population over a season, and whether it varies with spatial studies on the actual rates and patterns of gene flow into small isolation from the nearest conspecific. More data are needed populations are few. Thus, we sought to measure gene flow into that focus more closely on a number ofpopulations ofa single small populations of wild radish, Raphanus sativus. We found species. significant differences in gene flow receipt among experimental Therefore, we selected wild radish, Raphanus sativus L. populations and within those populations over a season. A (Brassicaceae), to measure patterns of gene flow by pollen maximum-likelihood estimate revealed that almost all of the into small populations. This species is especially suitable for gene flow into these synthetic populations had its origin in both experimental and descriptive gene flow studies because relatively distant (>650 m), large natural populations rather it is a common outcrossing weed in southern California (8), than the proximal (255400 m), small synthetic populations. -
The Speciation History of Heliconius: Inferences from Multilocus DNA Sequence Data
The speciation history of Heliconius: inferences from multilocus DNA sequence data by Margarita Sofia Beltrán A thesis submitted for the degree of Doctor of Philosophy of the University of London September 2004 Department of Biology University College London 1 Abstract Heliconius butterflies, which contain many intermediate stages between local varieties, geographic races, and sympatric species, provide an excellent biological model to study evolution at the species boundary. Heliconius butterflies are warningly coloured and mimetic, and it has been shown that these traits can act as a form of reproductive isolation. I present a species-level phylogeny for this group based on 3834bp of mtDNA (COI, COII, 16S) and nuclear loci (Ef1α, dpp, ap, wg). Using these data I test the geographic mode of speciation in Heliconius and whether mimicry could drive speciation. I found little evidence for allopatric speciation. There are frequent shifts in colour pattern within and between sister species which have a positive and significant correlation with species diversity; this suggests that speciation is facilitated by the evolution of novel mimetic patterns. My data is also consistent with the idea that two major innovations in Heliconius, adult pollen feeding and pupal-mating, each evolved only once. By comparing gene genealogies from mtDNA and introns from nuclear Tpi and Mpi genes, I investigate recent speciation in two sister species pairs, H. erato/H. himera and H. melpomene/H. cydno. There is highly significant discordance between genealogies of the three loci, which suggests recent speciation with ongoing gene flow. Finally, I explore the phylogenetic relationships between races of H. melpomene using an AFLP band tightly linked to the Yb colour pattern locus (which determines the yellow bar in the hindwing).