Genetic Diversity in Partially Selfing Populations with the Stepping-Stone Structure
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Evolution of Genetic Systems in Filamentous Ascomycetes
Evolution of Genetic Systems in Filamentous Ascomycetes Evolutie van genetische systemen in hyphenvormende zakjeszwammen 0000 0513 3836 Promotor: dr. R.F. Hoekstra hoogleraar in de populatie- en kwantitatieve genetica fjtfoiißi f ßin Maarten J. Nauta Evolution of Genetic Systems in Filamentous Ascomycetes Proefschrift ter verkrijging van de graad van doctor in de landbouw- en milieuwetenschappen op gezag van de rector magnificus, dr. C.M. Karssen, in het openbaar te verdedigen op woensdag 12januar i 1994 des namiddags te vier uur in de Aula van de Landbouwuniversiteit te Wageningen. 15 0 S(p^ZJ> These investigations were supported by the Netherlands Organization for Scientific Research (N.W.O.). BibUt/FHEEK LAMDbOirWUNIVERSITEJi. WAGE NINGE N CIP-GEGEVENS KONINKLIJKE BIBLIOTHEEK, DEN HAAG Nauta, Maarten J. Evolution of genetic systems in filamentous ascomycetes / Maarten J. Nauta. - [ S.l. : s.n.]. -111 . Thesis Wageningen. - With ref. - With summary in Dutch. ISBN 90-5485-199-6 Subject headings: population genetics / ascomycetes. omslagontwerp: Ernst van Cleef foto omslag: Barrages tussen verschillende stammen van Podospora anserina als gevolg van vegetatieve incompatibiliteit. (met dank aan Inge Haspels) aan mijn ouders Voorwoord Dit proefschrift is het resultaat van vier jaar onderzoek, verricht bij de vakgroep Erfelijkheidsleer van de Landbouwuniversiteit in Wageningen. In zekere zin valt zo'n proefschrift te vergelijken met een levend wezen. Uit de genetica is bekend dat de verschijningsvorm van elk levend wezen tot stand komt door een combinatie van erfelijke aanleg en invloeden uit de omgeving. Voor een proefschrift geldt eigenlijk hetzelfde: Zowel het werk van de auteur, als de bijdragen van zijn omgeving zijn onontbeerlijk om tot een verschijningsvorm te komen. -
Evolutionary Pathways to Self-Fertilization in a Tristylous Plant
Review BlackwellOxford,NPHNew0028-646X1469-8137©293710.1111/j.1469-8137.2009.02937.xJune0546???556???ResearchXX The 2009Phytologist Authors UK Review Publishing (2009). Ltd Journal compilation © New Phytologist (2009) Research reviewXX Evolutionary pathways to self- fertilization in a tristylous plant species Author for correspondence: Spencer C. H. Barrett, Rob W. Ness and Mario Vallejo-Marín Spencer C. H. Barrett Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, Tel: +1 416 978 5603 Email: [email protected] Ontario, Canada, M5S 3B2 Received: 23 April 2009 Accepted: 20 May 2009 Summary New Phytologist (2009) 183: 546–556 Evolutionary transitions from outcrossing to selfing occur commonly in heterostylous doi: 10.1111/j.1469-8137.2009.02937.x genera. The morphological polymorphisms that characterize heterostyly provide opportunities for different pathways for selfing to evolve. Here, we investigate the Key words: developmental instability, origins and pathways by which selfing has evolved in tristylous Eichhornia paniculata Eichhornia, herkogamy, heterostyly, multiple by providing new evidence based on morphology, DNA sequences and genetic analysis. origins, pathways to self-fertilization. The primary pathway from outcrossing to selfing involves the stochastic loss of the short-styled morph (S-morph) from trimorphic populations, followed by the spread of selfing variants of the mid-styled morph (M-morph). However, the discovery of selfing variants of the long-styled morph (L-morph) in Central America indicates a secondary pathway and distinct origin for selfing. Comparisons of multi-locus nucleo- tide sequences from 27 populations sampled from throughout the geographical range suggest multiple transitions to selfing. Genetic analysis of selfing variants of the L- and M-morphs demonstrates recessive control of the loss of herkogamy, although the number of factors appears to differ between the forms. -
Population Structure
Population Structure Population Structure Nonrandom Mating HWE assumes that mating is random in the population Most natural populations deviate in some way from random mating There are various ways in which a species might deviate from random mating We will focus on the two most common departures from random mating: inbreeding population subdivision or substructure Population Structure Nonrandom Mating: Inbreeding Inbreeding occurs when individuals are more likely to mate with relatives than with randomly chosen individuals in the population Increases the probability that offspring are homozygous, and as a result the number of homozygous individuals at genetic markers in a population is increased Increase in homozygosity can lead to lower fitness in some species Increase in homozygosity can have a detrimental effect: For some species the decrease in fitness is dramatic with complete infertility or inviability after only a few generations of brother-sister mating Population Structure Nonrandom Mating: Population Subdivision For subdivided populations, individuals will appear to be inbred due to more homozygotes than expected under the assumption of random mating. Wahlund Effect: Reduction in observed heterozygosity (increased homozygosity) because of pooling discrete subpopulations with different allele frequencies that do not interbreed as a single randomly mating unit. Population Structure Wright's F Statistics Sewall Wright invented a set of measures called F statistics for departures from HWE for subdivided populations. F stands for fixation index, where fixation being increased homozygosity FIS is also known as the inbreeding coefficient. The correlation of uniting gametes relative to gametes drawn at random from within a subpopulation (Individual within the Subpopulation) FST is a measure of population substructure and is most useful for examining the overall genetic divergence among subpopulations Is defined as the correlation of gametes within subpopulations relative to gametes drawn at random from the entire population (Subpopulation within the Total population). -
Inbreeding Depression in Two Populations of Arenaria Uni¯Ora (Caryophyllaceae) with Contrasting Mating Systems
Heredity 86 (2001) 184±194 Received 16 November 1999, accepted 17 October 2000 Inbreeding depression in two populations of Arenaria uni¯ora (Caryophyllaceae) with contrasting mating systems LILA FISHMAN Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544 U.S.A. I used parallel family-structured crossing designs to investigate the relative performance of self and outcross progeny in sel®ng and predominantly outcrossing populations of the annual plant Arenaria uni¯ora. The selfer population experienced much lower inbreeding depression (d 0.05 0.02 SE) than the outcrossers (d 0.19 0.02 SE). The negative association between genetic load and sel®ng rate suggests that purgable partially recessive alleles are the primary source of inbreeding depression, as does its late expression in both populations. Inbreeding depression in the selfer population, which naturally consists of highly inbred lines, was used to calculate the mean dominance (h 0.33) and incidence rate (U 0.30) of deleterious mutations. In the outcrosser population, signi®cant variation among individuals in the expression of inbreeding depression may re¯ect lineage-speci®c dierences in inbreeding history or, more probably, random variation in mutational load. The low (0.5) inbreeding depression of outcrossers suggests that the maintenance of a mixed mating system in some A. uni¯ora populations and the evolution of nearly cleistogamous self-pollination in others may re¯ect local pollinator-mediated selection for sel®ng rather than the constant 3:2 genetic advantage invoked by many models. Keywords: Arenaria uni¯ora, genetic load, inbreeding depression, mating system, sel®ng. -
Population Genetics of the Wild Yeast Saccharomyces Paradoxus
Copyright 2004 by the Genetics Society of America Population Genetics of the Wild Yeast Saccharomyces paradoxus Louise J. Johnson,*,1 Vassiliki Koufopanou,* Matthew R. Goddard,† Richard Hetherington,* Stefanie M. Scha¨fer*,2 and Austin Burt* *Department of Biological Sciences and †NERC Centre for Population Biology, Imperial College at Silwood Park, Ascot SL5 7PY, United Kingdom Manuscript received November 4, 2002 Accepted for publication September 22, 2003 ABSTRACT Saccharomyces paradoxus is the closest known relative of the well-known S. cerevisiae and an attractive model organism for population genetic and genomic studies. Here we characterize a set of 28 wild isolates from a 10-km2 sampling area in southern England. All 28 isolates are homothallic (capable of mating-type switching) and wild type with respect to nutrient requirements. Nine wild isolates and two lab strains of S. paradoxus were surveyed for sequence variation at six loci totaling 7 kb, and all 28 wild isolates were then genotyped at seven polymorphic loci. These data were used to calculate nucleotide diversity and number of segregating sites in S. paradoxus and to investigate geographic differentiation, population Extensive incompatibilities .%0.3ف structure, and linkage disequilibrium. Synonymous site diversity is between gene genealogies indicate frequent recombination between unlinked loci, but there is no evidence of recombination within genes. Some localized clonal growth is apparent. The frequency of outcrossing relative to inbreeding is estimated at 1.1% on the basis of heterozygosity. Thus, all three modes of reproduction known in the lab (clonal replication, inbreeding, and outcrossing) have been important in molding genetic variation in this species. -
A Southern California Freeway Is a Physical and Social Barrier to Gene Flow in Carnivores
Molecular Ecology (2006) 15, 1733–1741 doi: 10.1111/j.1365-294X.2006.02907.x FAST-TRACKBlackwell Publishing Ltd A southern California freeway is a physical and social barrier to gene flow in carnivores SETH P. D. RILEY,*† JOHN P. POLLINGER,* RAYMOND M. SAUVAJOT,*† ERIC C. YORK,† CASSITY BROMLEY,† TODD K. FULLER‡ and ROBERT K. WAYNE* *Department of Ecology and Evolutionary Biology, 621 Charles Young Dr. South, University of California, Los Angeles, CA 90095, USA, †Santa Monica Mountains National Recreation Area, National Park Service, 401 W. Hillcrest Dr., Thousand Oaks, CA 91360, USA, ‡Department of Natural Resources Conservation, Holdsworth Natural Resources Center, 160 Holdsworth Way, Amherst, MA 01003-9285, USA Abstract Roads present formidable barriers to dispersal. We examine movements of two highly mobile carnivores across the Ventura Freeway near Los Angeles, one of the busiest highways in the United States. The two species, bobcats and coyotes, can disappear from habitats isolated and fragmented by roads, and their ability to disperse across the Ventura Freeway tests the limits of vertebrates to overcome anthropogenic obstacles. We combine radio- telemetry data and genetically based assignments to identify individuals that have crossed the freeway. Although the freeway is a significant barrier to dispersal, we find that carnivores can cross the freeway and that 5–32% of sampled carnivores crossed over a 7-year period. However, despite moderate levels of migration, populations on either side of the freeway are genetically differentiated, and coalescent modelling shows their genetic isolation is consistent with a migration fraction less than 0.5% per generation. These results imply that individuals that cross the freeway rarely reproduce. -
Population Structure, Genetic Diversity, and Gene Introgression of Two Closely Related Walnuts (Juglans Regia and J
Article Population Structure, Genetic Diversity, and Gene Introgression of Two Closely Related Walnuts (Juglans regia and J. sigillata) in Southwestern China Revealed by EST-SSR Markers Xiao-Ying Yuan, Yi-Wei Sun, Xu-Rong Bai, Meng Dang, Xiao-Jia Feng, Saman Zulfiqar and Peng Zhao * Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; [email protected] (X.-Y.Y.); [email protected] (Y.-W.S.); [email protected] (X.-R.B.); [email protected] (M.D.); [email protected] (X.-J.F.); [email protected] (S.Z.) * Correspondence: [email protected]; Tel./Fax: +86-29-88302411 Received: 20 September 2018; Accepted: 12 October 2018; Published: 16 October 2018 Abstract: The common walnut (Juglans regia L.) and iron walnut (J. sigillata Dode) are well-known economically important species cultivated for their edible nuts, high-quality wood, and medicinal properties and display a sympatric distribution in southwestern China. However, detailed research on the genetic diversity and introgression of these two closely related walnut species, especially in southwestern China, are lacking. In this study, we analyzed a total of 506 individuals from 28 populations of J. regia and J. sigillata using 25 EST-SSR markers to determine if their gene introgression was related to sympatric distribution. In addition, we compared the genetic diversity estimates between them. Our results indicated that all J. regia populations possess slightly higher genetic diversity than J. sigillata populations. The Geostatistical IDW technique (HO, PPL, NA and PrA) revealed that northern Yunnan and Guizhou provinces had high genetic diversity for J. -
The Comparison Between Wright's Fixation Index (FST) and The
Genetics: Published Articles Ahead of Print, published on March 4, 2007 as 10.1534/genetics.106.062901 The effect of dominance on the use of the QST-FST contrast to detect natural selection on quantitative traits Carlos López-Fanjul 1, Almudena Fernández 2 and Miguel A. Toro 2 1Departamento de Genética, Facultad de Ciencias Biológicas, Universidad Complutense, 28040 Madrid, Spain. 2Departamento de Mejora Genética Animal, SGIT-INIA, 28040 Madrid, Spain. Corresponding author: Carlos López-Fanjul Departamento de Genética, Facultad de Ciencias Biológicas, Universidad Complutense, 28040 Madrid, Spain. Phone No.: 34-1-394-4852 Fax No.: 34-1-394-4844 e-mail: [email protected] 1 The comparison between Wright’s among-population fixation index FST (a descriptor of the effect of the breeding structure on population diversity for neutral genes) and Spitze’s quantitative index of population divergence QST (defined as Vb/(Vb+2Vw), where Vb and Vw are, respectively, the between- and the additive within- population components of variance for the trait considered) is widely used to assess the relative importance of selection and drift as determinants of the genetic differentiation for quantitative traits. For neutral genes with additive gene action between and within loci, QST is the quantitative analogue of FST. Otherwise, divergent or convergent selection is invoked, respectively, as a cause of the observed increase (QST > FST) or decrease (QST < FST) of QST from its neutral expectation (QST = FST). However, the validity of the QST-FST contrast has been questioned, as neutral non-additive gene action (dominance and/or epistasis) can mimic the additive expectations under selection (LÓPEZ-FANJUL et al. -
Definition and Estimation of Higher-Order Gene Fixation Indices
Copyright 0 1987 by the Genetics Society of America Definition and Estimation of Higher-Order Gene Fixation Indices Kermit Ritland Department of Botany, University of Toronto, Toronto, M5S IAl Canada Manuscript received March 26, 1987 Revised copy accepted August 15, 1987 ABSTRACT Fixation indices summarize the associations between genes that arise from the joint effects of inbreeding and selection. In this paper, fixation indices are derived for pairs, triplets and quadruplets of genes at a single multiallelic locus. The fixation indices are obtained by dividing cumulants by constants; the cumulants describe the statistical distribution of alleles and the constants are functions of gene frequency. The use of cumulants instead of moments is necessary only for four-gene indices, when the fourth cumulant is used. A second type of four-gene index is also required, and this index is based upon the covariation of second-order cumulants. At multiallelic loci, a large number of indices is possible. If alleles are selectively neutral, the number of indices is reduced and the relationship between gene identity and gene cumulants is shown.-Two-gene indices can always be estimated from genotypic frequency data at a single polymorphic locus. Three-gene indices are also estimable except when allele frequency equals one-half. Four-gene indices are not estimable unless selection is assumed to have an equal effect upon each allele (such as under selective neutrality) and the locus contains at least three alleles of unequal frequency. For diallelic or selected loci, an alternative four- gene fixation index is proposed. This index incorporates both types of four-gene associations but cannot be related to gene identity. -
Clonal Reproduction in Fungi COLLOQUIUM
PAPER Clonal reproduction in fungi COLLOQUIUM John W. Taylora,1, Christopher Hann-Sodena, Sara Brancoa, Iman Sylvaina, and Christopher E. Ellisonb Departments of aPlant and Microbial Biology and bIntegrative Biology, University of California, Berkeley, CA 94720 Edited by John C. Avise, University of California, Irvine, CA, and approved April 2, 2015 (received for review February 17, 2015) Research over the past two decades shows that both recombina- Clearly, mycologists have more work to do with these extremely tion and clonality are likely to contribute to the reproduction of all important fungi. fungi. This view of fungi is different from the historical and still commonly held view that a large fraction of fungi are exclusively Population Genetic Evidence for Recombination clonal and that some fungi have been exclusively clonal for Evidence that clonality was not limited to Glomales but instead hundreds of millions of years. Here, we first will consider how was widespread in fungi came from the oft-cited statistic that these two historical views have changed. Then we will examine 20% of fungi are asexual (12). This fraction represented the the impact on fungal research of the concept of restrained re- number of fungi for which sexual reproduction had not been combination [Tibayrenc M, Ayala FJ (2012) Proc Natl Acad Sci USA observed or was rarely observed. At a time when observation of 109 (48):E3305–E3313]. Using animal and human pathogenic fungi, the sexual morphology of a fungus was required for its classifi- we examine extrinsic restraints on recombination associated with cation, these fungi were classified in the Deuteromycota, apart bottlenecks in genetic variation caused by geographic dispersal from sexual fungi. -
Evolution of Mating Systems: Outcrossing Versus Selfing Spencer C
In The Princeton Guide to Evolution ed. J. Losos. Princeton University Press, Princeton, New Jersey, pp. 356-362. IV.8 Evolution of Mating Systems: Outcrossing versus Selfing Spencer C. H. Barrett OUTLINE that transitions to predominant selfing have occurred on numerous occasions, although selfing lineages are often 1. Definitions and measurement short-lived because of the negative effects of selfing on 2. Variation in mating patterns the genome. 3. Evolution of self-fertilization 4. Mechanisms of selection 5. The problem of mixed mating 6. Evolutionary history GLOSSARY Floral Design and Display. The morphological features of Mating systems vary enormously among groups of or- flowers and inflorescences that influence pollen dis- ganisms. This has led to diverse definitions and ap- persal and mating patterns in flowering plants; floral proaches for investigating their evolution and main- design involves characteristics of individual flowers, tenance. Animal mating systems are characterized by including their size, structure, color, and the spatial different patterns of parental investment in offspring and temporal presentation of female (pistil) and male and variation in the extent to which sexual selection (stamens) sex organs, and floral display concerns shapes male and female traits (see chapter VII.4). A the number of open flowers on a plant and their ar- primary focus of most studies is determining the causes rangement within and among inflorescences. and consequences of variation in mate number for fe- Inbreeding Depression. The reduction in viability and/ males and males. In contrast, in hermaphrodite organ- or fertility of inbred offspring in comparison with isms, particularly plants, the emphasis is largely on de- outbred offspring. -
Allardts Argument Versus Bakerts Contention for the Adaptive
Allard’s argument versus Baker’s contention for the adaptive significance of selfing in a hermaphroditic fish John C. Avise1 and Andrey Tatarenkov Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 Contributed by John C. Avise, October 2, 2012 (sent for review June 29, 2012) Fertilization assurance (Baker’s contention) and multilocus coadap- heterogeneity” and thus “natural selection was the predominant tation (Allard’s argument) are two distinct hypotheses for the integrating force in shaping the specific genetic structure of dif- adaptive significance of self-fertilization in hermaphroditic taxa, ferent local populations as well as the adaptive landscape.” With and both scenarios have been invoked to rationalize isogenicity regard to purported evolutionary benefits of self-fertilization as via incest in various plants and invertebrate animals with predom- a tactical component of a mixed-mating strategy, for shorthand we inant selfing. Here we contrast Allard’s argument and Baker’s con- will refer to this genomic-coadaptation scenario as Allard’s ar- tention as applied to the world’s only known vertebrate that gument for the adaptive significance of selfing. routinely self-fertilizes. We pay special attention to frequencies Soon thereafter, Robert Selander and colleagues published an of locally most common multilocus genotypes in Floridian popula- analogous series of studies documenting multilocus coadaptation tions of the Mangrove Rivulus (Kryptolebias marmoratus). Isoge- in local populations of terrestrial hermaphroditic snails with high nicity patterns in this fish appear inconsistent with Allard’s selfing rates (13–16). Again, specific multilocus suites of alleles argument, thus leaving Baker’s contention as the more plausible appeared to be coadapted to particular ecological conditions and scenario (a result also supported by natural history information for thereby often were driven to moderate or high frequencies in this species).