Population Genomics of Transitions to Selfing in Brassicaceae Model Systems
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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. -
The Selfing Syndrome Overshadows Other Differences When Comparing
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.26.398016; this version posted November 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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 The selfing syndrome overshadows other differences when 2 comparing fitness across Capsella species 3 4 5 Marion Orsucci1, Theofilos Vanikiotis2, Maria Guerrina1, Tianlin Duan1, Sylvain Glémin3, Martin 6 Lascoux1 7 8 1 Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life 9 Laboratory, Uppsala University, 75236 Uppsala, Sweden 10 2 Department of Biological Applications & Technology, University of Ioannina, Leof. S. 11 Niarchou GR-451 10, Ioannina, Greece 12 3 UMR CNRS 6553 ECOBIO, Campus Beaulieu, bât 14a, p.118, CS 74205, 35042 Rennes, 13 France 14 15 16 Corresponding authors: Martin Lascoux ([email protected]), Marion Orsucci 17 ([email protected]) 18 19 20 Running title: Influence of mating system on life history traits in Capsella spp. 21 22 23 Key words: mating system, ploidy, life history traits, environmental disturbance 24 25 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.26.398016; this version posted November 27, 2020. 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. 26 SUMMARY 27 Self-fertilization has recurrently evolved from outcrossing. Self-fertilization provides an advantage 28 in the short-term as individuals do not require a mate to reproduce, but self-fertilization is also 29 associated with both decreased genetic diversity and accumulation of weakly deleterious mutations, 30 which could, however, be alleviated in polyploid selfers. -
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. -
Genetic Diversity in Partially Selfing Populations with the Stepping-Stone Structure
Heredity 77 (1996) 469—475 Received 20 October 1995 Genetic diversity in partially selfing populations with the stepping-stone structure HIDENORI TACHIDA*t & HIROSHI YOSHIMARU tDepartment of Biology, Faculty of Science, Kyushu University 33, Fukuoka 812, Japan and tPopulation Genetics Laboratory, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305, Japan Amethod to compute identity coefficients of two genes in the stepping-stone model with partial selfing is developed. The identity coefficients in partially selfing populations are computed from those in populations without selfing as functions of s (selfing rate), m (migra- tion rate), N (subpopulation size), n (number of subpopulations) and u (mutation rate). For small m, 1/N and u, it is shown that approximate formulae for the identity coefficients of two genes from different individuals are the same as those in random mating populations if we replace N in the latter with N(1 —s12).Thus,the effects of selfing on genetic variability are summarized as reducing variation within subpopulations and increasing differentiation among subpopulations by reducing the subpopulation size. The extent of biparental inbreeding as measured by the genotypic correlation between truly outcrossed mates was computed in the one-dimensional stepping-stone model. The correlation was shown to be independent of the selfing rate and starts to fall off as the migration rate increases when mN is larger than 0.1. Keywords:biparentalinbreeding, fixation index, genetic variability, geographical differentia- tion, selfing, stepping-stone model. Introduction Model analysis Manyplant species are partially self-fertilizing Genesare defined to be identical by descent if they (Brown, 1990; Murawski & Hamrick, 1991, 1992; have a common ancestor gene and there is no muta- Kitamura et a!., 1994). -
Functional Role of Polymerase IV During Pollen Development in Capsella
bioRxiv preprint doi: https://doi.org/10.1101/863522; this version posted December 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Functional role of Polymerase IV during pollen development in Capsella 2 Zhenxing Wang1*, Nicolas Butel1*, Juan Santos-González1, Filipe Borges2,3, Jun Yi1, 3 Robert A. Martienssen2, German Martinez1, Claudia Köhler1 4 1 Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean 5 Center for Plant Biology, Uppsala 75007, Sweden 6 2 Howard Hughes Medical Institute and Cold Spring Harbor Laboratory, 1 Bungtown 7 Road, Cold Spring Harbor, New York 11724, USA. 8 3 Present address: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, Université Paris- 9 Saclay, 78000, Versailles, France 10 *both authors contributed equally to this work 11 Corresponding Author: [email protected] 12 13 Short title: Requirement of Polymerase IV in Capsella pollen. 14 One-sentence summary: Loss of Polymerase IV function in Capsella rubella causes 15 microspore arrest, revealing an important functional role of Polymerase IV during pollen 16 development. 17 The author responsible for distribution of materials integral to the findings presented in 18 this article in accordance with the policy described in the Instructions for Authors 19 (www.plantcell.org) is: Claudia Köhler ([email protected]) 20 21 22 23 1 bioRxiv preprint doi: https://doi.org/10.1101/863522; this version posted December 3, 2019. -
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. -
Evolution and Diversification of the Plant Gibberellin Receptor GID1
Evolution and diversification of the plant gibberellin receptor GID1 Hideki Yoshidaa,b, Eiichi Tanimotoc, Takaaki Hiraia, Yohei Miyanoirid,e, Rie Mitania, Mayuko Kawamuraa, Mitsuhiro Takedad,f, Sayaka Takeharaa, Ko Hiranoa, Masatsune Kainoshod,g, Takashi Akagih, Makoto Matsuokaa,1, and Miyako Ueguchi-Tanakaa,1 aBioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Aichi, Japan; bKihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813 Kanagawa, Japan; cGraduate School of Natural Sciences, Nagoya City University, Nagoya, 467-8501 Aichi, Japan; dStructural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, 464-8601 Aichi, Japan; eResearch Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, Suita, 565-0871 Osaka, Japan; fDepartment of Structural BioImaging, Faculty of Life Sciences, Kumamoto University, 862-0973 Kumamoto, Japan; gGraduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, 192-0397 Tokyo, Japan; and hGraduate School of Agriculture, Kyoto University, 606-8502 Kyoto, Japan Edited by Mark Estelle, University of California, San Diego, La Jolla, CA, and approved July 10, 2018 (received for review April 9, 2018) The plant gibberellin (GA) receptor GID1 shows sequence similarity erwort Marchantia polymorpha (5–7). Furthermore, Hirano et al. to carboxylesterase (CXE). Here, we report the molecular evolution (5) reported that GID1s in the lycophyte Selaginella moellen- of GID1 from establishment to functionally diverse forms in dorffii (SmGID1s) have unique properties in comparison with eudicots. By introducing 18 mutagenized rice GID1s into a rice angiosperm GID1s: namely, lower affinity to bioactive GAs and gid1 null mutant, we identified the amino acids crucial for higher affinity to inactive GAs (lower specificity). -
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. -
Evolution of Flowering Time in the Tetraploid Capsella Bursa-Pastoris (Brassicaceae)
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 367 Evolution of Flowering Time in the Tetraploid Capsella bursa-pastoris (Brassicaceae) TANJA SLOTTE ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 UPPSALA ISBN 978-91-554-7024-1 2007 urn:nbn:se:uu:diva-8311 ! " #$$" $%$$ & & & ' ( ) * ( + )( #$$"( & ! * ) ) ,-( . ( /0"( 1$ ( ( 2+ 3" 4345514"$#14( . 6 & &* & * ( 2 2 & & * * & * & ( ! * & ( . 7 & * . * & & & & & * ( & & * & * 8 & ( ) & & * * ( . 4 4& * && * * && & * ( + * 9) ,9 ) - & & * : ( ) !"!#$% ,%- & 9) &!'$()* &! ,&- * & * ( && & * & * & ; ( ) % & * & && & * ( 2 8 & & * +, - & * 8 9) . / $ / * / $ * / ) %0/ / $ 12345 / , < ) 6 + #$$" 2++ 0540#1 2+ 3" 4345514"$#14 % %%% 4 / , %== (:(= > ? % %%% 4 /- looking carefully, a shepherd’s purse is blooming under the fence Bash List of papers This thesis is based on the following papers, which are referred to by their Roman numerals: I Slotte, T., Ceplitis, A., Neuffer, B., Hurka, H., and M. Lascoux. 2006. Intrageneric phylogeny of Capsella (Brassicaceae) and the -
IEG News June Edition
June 2019 IEG News June edition News from the Head of the Department I wish everyone at the department a nice summer - relaxing vacations, and successful work in the field or elsewhere. Thank you all for contributions during the past academic year! For the upcoming fall, don’t forget the following important events: - The dean of biology has invited all senior scientists (“PIs”) to strategic discussions about biology at Uppsala University on August 28 - see mail sent by Staffan Svärd on June 5 for details and reg- istration. - The annual biology teacher days, August 22-23 - see mail from Henning Blom on June 3 for de- tails and registration. - The annual IEG Day will take place 8th of November - a full day of information, interactions, and discussion on topics of importance to the success of IEG as an excellent academic environment. There will also be research presentations, and a party. Old colleague moves on to new challenges Stefan Bertilsson leaves us for a professor position at the Department of Aquatic Sciences and As- sessment at SLU. Good luck to Stefan in his new job, and we look forward to coming inter-univer- sity cooperation! At the farewell celebration, we equipped him with some relevant tools for his fu- ture at the agricultural university. Stefan will still be around to some extent to finalize supervision. Photos courtesy of Lars Tranvik News from the administration Travelling on a business trip? Business trips must be booked through Lingmerth’s travel agency, which is the university’s pro- cured supplier, read more on the Employee Portal (Medarbetarportalen). -
Genetic Control of Plastidic L-Glutamate Dehydrogenase Isozymes in the Genus Apsella (Brassicaceae)
Heredityl2 (1994) 126—131 Received 1 June 1993 Genetical Society of Great Britain Genetic control of plastidic L-glutamate dehydrogenase isozymes in the genus apsella (Brassicaceae) HERBERT HURKA* & SABINE DURING University of Osnabruck, Faculty of Biology/Chemistry, Botany, Barbarastr. 11, D-49069 Osnabrück, Germany Leafextracts of three Capsella species (Brassicaceae), two diploids and one tetraploid, have been analysed for isozymes of L-glutamate dehydrogenase on polyacrylamide gels. A plastidic GDH (EC 1.4.1.4.) consisted of at least seven bands. Progeny analyses and crossing experiments revealed that within the two diploid species two genetic loci code for this pattern. One of the loci, Gdhl, appeared to be monomorphic. The other locus Gdh2, is polymorphic and segregates for three alleles determining allozymes in accordance with Mendelian inheritance. Estimates of out- crossing rates based on segregation at the Gdh2 locus support the view that one of the diploid species is highly inbred whereas the other is an obligate outbreeder. In the tetraploid species, both loci are apparently duplicated so that four instead of two genes determine the polypeptide structure of plastidic GDH. These loci share the same alleles with the diploid species and no additional allozymes have been detected. Keywords:Capsella,GDH, gene duplication, isozyme loci, polymorphism, subcellular location. Introduction reveals a seven or even more banded pattern (Srivastava & Singh, 1987 for reference). Its subcellular Glutamatedehydrogenase, GDH, EC 1.4.1.2-4, has location and the underlying genetics have not been been found in almost all types of organisms. In higher clearly resolved. Two genes are thought to be respon- plants, organ and tissue specificity as well as subcellular sible for the polypeptide structure of GDH. -
Parental Legacy, Demography, and Admixture Influenced the Evolution
Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae) Dmytro Kryvokhyzha, Adriana Salcedo, Mimmi C. Eriksson, Tianlin Duan, Nilesh Tawari, Jun Chen, Maria Guerrina, Julia Kreiner, Tyler V. Kent, Ulf Lagercrantz, et al. To cite this version: Dmytro Kryvokhyzha, Adriana Salcedo, Mimmi C. Eriksson, Tianlin Duan, Nilesh Tawari, et al.. Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae). PLoS Genetics, Public Library of Science, 2019, 15 (2), pp.e1007949. 10.1371/journal.pgen.1007949. hal-02369510 HAL Id: hal-02369510 https://hal.archives-ouvertes.fr/hal-02369510 Submitted on 19 Nov 2019 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 Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa- pastoris (Brassicaceae) 1☯ 2☯ 1,3 1 Dmytro KryvokhyzhaID , Adriana Salcedo , Mimmi C. ErikssonID , Tianlin DuanID , 4 1 1 2 2 Nilesh Tawari , Jun ChenID , Maria Guerrina , Julia M. Kreiner , Tyler V. KentID , 1 2 1,5 2 Ulf Lagercrantz , John R. StinchcombeID , Sylvain GleÂmin *, Stephen I.