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Upadhaya A, Upadhaya SGC, Brueggeman R. Association mapping with a diverse population of Puccinia graminis f. sp. tritici identified avirulence loci interacting with the barley Rpg1 stem rust resistance gene. BMC Genomics 2024; 25:751. [PMID: 39090588 PMCID: PMC11295639 DOI: 10.1186/s12864-024-10670-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is an important disease of barley and wheat. A diverse sexual Pgt population from the Pacific Northwest (PNW) region of the US contains a high proportion of individuals with virulence on the barley stem rust resistance (R) gene, Rpg1. However, the evolutionary mechanisms of this virulence on Rpg1 are mysterious considering that Rpg1 had not been deployed in the region and the gene had remained remarkably durable in the Midwestern US and prairie provinces of Canada. METHODS AND RESULTS To identify AvrRpg1 effectors, genome wide association studies (GWAS) were performed using 113 Pgt isolates collected from the PNW (n = 89 isolates) and Midwest (n = 24 isolates) regions of the US. Disease phenotype data were generated on two barley lines Morex and the Golden Promise transgenic (H228.2c) that carry the Rpg1 gene. Genotype data was generated by whole genome sequencing (WGS) of 96 isolates (PNW = 89 isolates and Midwest = 7 isolates) and RNA sequencing (RNAseq) data from 17 Midwestern isolates. Utilizing ~1.2 million SNPs generated from WGS and phenotype data (n = 96 isolates) on the transgenic line H228.2c, 53 marker trait associations (MTAs) were identified. Utilizing ~140 K common SNPs generated from combined analysis of WGS and RNAseq data, two significant MTAs were identified using the cv Morex phenotyping data. The 55 MTAs defined two distinct avirulence loci, on supercontig 2.30 and supercontig 2.11 of the Pgt reference genome of Pgt isolate CRL 75-36-700-3. The major avirulence locus designated AvrRpg1A was identified with the GWAS using both barley lines and was delimited to a 35 kb interval on supercontig 2.30 containing four candidate genes (PGTG_10878, PGTG_10884, PGTG_10885, and PGTG_10886). The minor avirulence locus designated AvrRpg1B identified with cv Morex contained a single candidate gene (PGTG_05433). AvrRpg1A haplotype analysis provided strong evidence that a dominant avirulence gene underlies the locus. CONCLUSIONS The association analysis identified strong candidate AvrRpg1 genes. Further analysis to validate the AvrRpg1 genes will fill knowledge gaps in our understanding of rust effector biology and the evolution and mechanism/s of Pgt virulence on Rpg1.
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Affiliation(s)
- Arjun Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Sudha G C Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
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Klimova A, Ruiz Mondragón KY, Aguirre-Planter E, Valiente A, Lira R, Eguiarte LE. Genomic analysis unveils reduced genetic variability but increased proportion of heterozygotic genotypes of the intensively managed mezcal agave, Agave angustifolia. AMERICAN JOURNAL OF BOTANY 2023; 110:e16216. [PMID: 37478873 DOI: 10.1002/ajb2.16216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/23/2023]
Abstract
PREMISE The central Oaxaca Basin has a century-long history of agave cultivation and is hypothesized to be the region of origin of other cultivated crops. Widely cultivated for mezcal production, the perennial crop known as "espadín" is putatively derived from wild Agave angustifolia. Nevertheless, little is known about its genetic relationship to the wild A. angustifolia or how the decades-long clonal propagation has affected its genetics. METHODS Using restriction-site-associated DNA sequencing and over 8000 single-nucleotide polymorphisms, we studied aspects of the population genomics of wild and cultivated A. angustifolia in Puebla and Oaxaca, Mexico. We assessed patterns of genetic diversity, inbreeding, distribution of genetic variation, and differentiation among and within wild populations and plantations. RESULTS Genetic differentiation between wild and cultivated plants was strong, and both gene pools harbored multiple unique alleles. Nevertheless, we found several cultivated individuals with high genetic affinity with wild samples. Higher heterozygosity was observed in the cultivated individuals, while in total, they harbored considerably fewer alleles and presented higher linkage disequilibrium compared to the wild plants. Independently of geographic distance among sampled plantations, the genetic relatedness of the cultivated plants was high, suggesting a common origin and prevalent role of clonal propagation. CONCLUSIONS The considerable heterozygosity found in espadín is contained within a network of highly related individuals, displaying high linkage disequilibrium generated by decades of clonal propagation and possibly by the accumulation of somatic mutations. Wild A. angustifolia, on the other hand, represents a significant genetic diversity reservoir that should be carefully studied and conserved.
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Affiliation(s)
- Anastasia Klimova
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Karen Y Ruiz Mondragón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Erika Aguirre-Planter
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alfonso Valiente
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rafael Lira
- Laboratorio de Recursos Naturales, Unidad de Biotecnología y Prototipos (UBIPRO), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Luis E Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Sun Y, Zhang X, Zhang A, Landis JB, Zhang H, Sun H, Xiang QY(J, Wang H. Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales). Int J Mol Sci 2023; 24:1451. [PMID: 36674965 PMCID: PMC9866071 DOI: 10.3390/ijms24021451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Asexual lineages are perceived to be short-lived on evolutionary timescales. Hence, reports for exceptional cases of putative 'ancient asexuals' usually raise questions about the persistence of such species. So far, there have been few studies to solve the mystery in plants. The monotypic Kingdonia dating to the early Eocene, contains only K. uniflora that has no known definitive evidence for sexual reproduction nor records for having congeneric sexual species, raising the possibility that the species has persisted under strict asexuality for a long period of time. Here, we analyze whole genome polymorphism and divergence in K. uniflora. Our results show that K. uniflora is characterized by high allelic heterozygosity and elevated πN/πS ratio, in line with theoretical expectations under asexual evolution. Allele frequency spectrum analysis reveals the origin of asexuality in K. uniflora occurred prior to lineage differentiation of the species. Although divergence within K. uniflora individuals exceeds that between populations, the topologies of the two haplotype trees, however, fail to match each other, indicating long-term asexuality is unlikely to account for the high allele divergence and K. uniflora may have a recent hybrid origin. Phi-test shows a statistical probability of recombination for the conflicting phylogenetic signals revealed by the split network, suggesting K. uniflora engages in undetected sexual reproduction. Detection of elevated genetic differentiation and premature stop codons (in some populations) in genes regulating seed development indicates mutational degradation of sexuality-specific genes in K. uniflora. This study unfolds the origin and persistence mechanism of a plant lineage that has been known to reproduce asexually and presents the genomic consequences of lack of sexuality.
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Affiliation(s)
- Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aidi Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jacob B. Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Qiu-Yun (Jenny) Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
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da Cunha NL, Xue H, Wright SI, Barrett SCH. Genetic variation and clonal diversity in floating aquatic plants: Comparative genomic analysis of water hyacinth species in their native range. Mol Ecol 2022; 31:5307-5325. [PMID: 35984729 DOI: 10.1111/mec.16664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 07/24/2022] [Accepted: 08/10/2022] [Indexed: 12/15/2022]
Abstract
Many eukaryotic organisms reproduce by sexual and asexual reproduction. Genetic diversity in populations can be strongly dependent on the relative importance of these two reproductive modes. Here, we compare the amounts and patterns of genetic diversity in related water hyacinths that differ in their propensity for clonal propagation - highly clonal Eichhornia crassipes and moderately clonal E. azurea (Pontederiaceae). Our comparisons involved genotype-by-sequencing (GBS) of 137 E. crassipes ramets from 60 locations (193,495 nucleotide sites) and 118 E. azurea ramets from 53 locations (198,343 nucleotide sites) among six hydrological basins in central South America, the native range of both species. We predicted that because of more prolific clonal propagation, E. crassipes would exhibit lower clonal diversity than E. azurea. This prediction was supported by all measures of clonal diversity that we examined. Eichhornia crassipes also had a larger excess of heterozygotes at variant sites, another signature of clonality. However, genome-wide heterozygosity was not significantly different between the species. Eichhornia crassipes had weaker spatial genetic structure and lower levels of differentiation among hydrological basins than E. azurea, probably because of higher clonality and more extensive dispersal of its free-floating life form. Our findings for E. crassipes contrast with earlier studies from the invasive range which have reported very low levels of clonal diversity and extensive geographic areas of genetic uniformity.
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Affiliation(s)
- Nicolay Leme da Cunha
- Grupo de Ecología de la Polinización, INIBIOMA, CONICET-Universidad Nacional del Comahue, San Carlos de Bariloche, Rio Negro, Argentina.,Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Haoran Xue
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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Rau D, Attene G, Rodriguez M, Baghino L, Pisanu AB, Sanna D, Acquadro A, Portis E, Comino C. The Population Structure of a Globe Artichoke Worldwide Collection, as Revealed by Molecular and Phenotypic Analyzes. FRONTIERS IN PLANT SCIENCE 2022; 13:898740. [PMID: 35865281 PMCID: PMC9294547 DOI: 10.3389/fpls.2022.898740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
The knowledge of the organization of the domesticated gene pool of crop species is an essential requirement to understand crop evolution, to rationalize conservation programs, and to support practical decisions in plant breeding. Here, we integrate simple sequence repeat (SSR) analysis and phenotypic characterization to investigate a globe artichoke collection that comprises most of the varieties cultivated worldwide. We show that the cultivated gene pool of globe artichoke includes five distinct genetic groups associated with the major phenotypic typologies: Catanesi (which based on our analysis corresponds to Violetti di Provenza), Spinosi, Violetti di Toscana, Romaneschi, and Macau. We observed that 17 and 11% of the molecular and phenotypic variance, respectively, is between these groups, while within groups, strong linkage disequilibrium and heterozygote excess are evident. The divergence between groups for quantitative traits correlates with the average broad-sense heritability within the groups. The phenotypic divergence between groups for both qualitative and quantitative traits is strongly and positively correlated with SSR divergence (FST) between groups. All this implies a low population size and strong bottleneck effects, and indicates a long history of clonal propagation and selection during the evolution of the domesticated gene pool of globe artichoke. Moreover, the comparison between molecular and phenotypic population structures suggests that harvest time, plant architecture (i.e., plant height, stem length), leaf spininess, head morphology (i.e., head shape, bract shape, spininess) together with the number of heads per plant were the main targets of selection during the evolution of the cultivated germplasm. We emphasize our findings in light of the potential exploitation of this collection for association mapping studies.
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Affiliation(s)
- Domenico Rau
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Limbo Baghino
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Anna Barbara Pisanu
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Davide Sanna
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Cinzia Comino
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
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Gutiérrez-Corbo C, Domínguez-Asenjo B, Pérez-Pertejo Y, García-Estrada C, Bello FJ, Balaña-Fouce R, Reguera RM. Axenic interspecies and intraclonal hybrid formation in Leishmania: Successful crossings between visceral and cutaneous strains. PLoS Negl Trop Dis 2022; 16:e0010170. [PMID: 35139072 PMCID: PMC8827483 DOI: 10.1371/journal.pntd.0010170] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/13/2022] [Indexed: 12/29/2022] Open
Abstract
Diseases caused by trypanosomatids are serious public health concerns in low-income endemic countries. Leishmaniasis is presented in two main clinical forms, visceral leishmaniasis-caused by L. infantum and L. donovani-and cutaneous leishmaniasis-caused by many species, including L. major, L. tropica and L. braziliensis. As for certain other trypanosomatids, sexual reproduction has been confirmed in these parasites, and formation of hybrids can contribute to virulence, drug resistance or adaptation to the host immune system. In the present work, the capability of intraclonal and interspecies genetic exchange has been investigated using three parental strains: L. donovani, L. tropica and L. major, which have been engineered to express different fluorescent proteins and antibiotic resistance markers in order to facilitate the phenotypic selection of hybrid parasites after mating events. Stationary and exponential-phase promastigotes of each species were used, in in vitro experiments, some of them containing LULO cells (an embryonic cell line derived from Lutzomyia longipalpis). Several intraclonal hybrids were obtained with L. tropica as crossing progenitor, but not with L. donovani or L. major. In interspecies crossings, three L. donovani x L. major hybrids and two L. donovani x L. tropica hybrids were isolated, thereby demonstrating the feasibility to obtain in vitro hybrids of parental lines causing different tropism of leishmaniasis. Ploidy analysis revealed an increase in DNA content in all hybrids compared to the parental strains, and nuclear analysis showed that interspecies hybrids are complete hybrids, i.e. each of them showing at least one chromosomal set from each parental. Regarding kDNA inheritance, discrepancies were observed between maxi and minicircle heritage. Finally, phenotypic studies showed either intermediate phenotypes in terms of growth profiles, or a decreased in vitro infection capacity compared to the parental cells. To the best of our knowledge, this is the first time that in vitro interspecies outcrossing has been demonstrated between Leishmania species with different tropism, thus contributing to shed light on the mechanisms underlying sexual reproduction in these parasites.
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Affiliation(s)
- Camino Gutiérrez-Corbo
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, León, Spain
| | | | - Yolanda Pérez-Pertejo
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Carlos García-Estrada
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Felio J Bello
- Facultad de Ciencias Agropecuarias, Programa de Medicina Veterinaria, Universidad de la Salle, Bogotá, Colombia
| | - Rafael Balaña-Fouce
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, León, Spain
- * E-mail: (RB-F); (RMR)
| | - Rosa M. Reguera
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, León, Spain
- * E-mail: (RB-F); (RMR)
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Reproduction in Trypanosomatids: Past and Present. BIOLOGY 2021; 10:biology10060471. [PMID: 34071741 PMCID: PMC8230138 DOI: 10.3390/biology10060471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 01/07/2023]
Abstract
Simple Summary The reproduction of trypanosomatids is a fundamental issue for host–parasite interaction, and its biological importance lies in knowing how these species acquire new defense mechanisms against the countermeasures imposed by the host, which is consistent with the theory of the endless race or the Red Queen hypothesis for the existence of meiotic sex. Moreover, the way these species re-produce may also be at the origin of novel and more virulent clades and is relevant from a thera-peutic or vaccination point of view, as sex may contribute to increased tolerance and even to the rapid acquisition of drug resistance mechanisms. Kinetoplastids are single-celled organisms, many of them being responsible for important parasitic diseases, globally termed neglected diseases, which are endemic in low-income countries. Leishmaniasis, African (sleeping sickness) and American trypanosomiasis (Chagas disease) caused by trypanosomatids are among the most ne-glected tropical scourges related to poverty and poor health systems. The reproduction of these microorganisms has long been considered to be clonal due to population genetic observations. However, there is increasing evidence of true sex and genetic exchange events under laboratory conditions. We would like to highlight the importance of this topic in the field of host/parasite in-terplay, virulence, and drug resistance. Abstract Diseases caused by trypanosomatids (Sleeping sickness, Chagas disease, and leishmaniasis) are a serious public health concern in low-income endemic countries. These diseases are produced by single-celled parasites with a diploid genome (although aneuploidy is frequent) organized in pairs of non-condensable chromosomes. To explain the way they reproduce through the analysis of natural populations, the theory of strict clonal propagation of these microorganisms was taken as a rule at the beginning of the studies, since it partially justified their genomic stability. However, numerous experimental works provide evidence of sexual reproduction, thus explaining certain naturally occurring events that link the number of meiosis per mitosis and the frequency of mating. Recent techniques have demonstrated genetic exchange between individuals of the same species under laboratory conditions, as well as the expression of meiosis specific genes. The current debate focuses on the frequency of genomic recombination events and its impact on the natural parasite population structure. This paper reviews the results and techniques used to demonstrate the existence of sex in trypanosomatids, the inheritance of kinetoplast DNA (maxi- and minicircles), the impact of genetic exchange in these parasites, and how it can contribute to the phenotypic diversity of natural populations.
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López-Márquez V, Lozano-Martín C, Hadjioannou L, Acevedo I, Templado J, Jimenez C, Taviani M, Machordom A. Asexual reproduction in bad times? The case of Cladocora caespitosa in the eastern Mediterranean Sea. CORAL REEFS (ONLINE) 2021; 40:663-677. [PMID: 33437112 PMCID: PMC7791332 DOI: 10.1007/s00338-020-02040-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
UNLABELLED We analysed the patterns of genetic variability of eastern Mediterranean populations of the scleractinian coral Cladocora caespitosa, from the Aegean and Levantine seas, using 19 polymorphic microsatellite loci, 11 of which were newly characterized. The observed genetic pattern reflects a scenario of isolation by environment: F ST comparisons showed a higher degree of genetic differentiation between the two Cypriot populations that are separated by only 11 km than between these two Levantine populations and the Aegean population in Greece, which are separated by 1300 km. We hypothesize that local-scale oceanographic factors influenced the dispersal of planulae between the geographically close populations, playing a crucial role in the genetic structure of this coastal coral. Yet, despite being characterized as a species with limited dispersal and high self-recruitment, large-scale migration does eventually occur as first-generation migrants were identified between the most distant populations. In line with previous findings of reproductive plasticity in C. caespitosa, we also found localized differences in reproduction mode (sexual vs. asexual) within a geographically limited context. Several individuals were identified as clones, indicating the predominance of asexual reproduction in one of the Cypriot populations. We interpret this predominance either as a direct response to or as an indirect consequence of perturbations suffered by this C. caespitosa population. These perturbations are caused by unfavourable environmental conditions that threatened local survival, in particular water temperature changes and windstorm swells. Asexual reproduction may be a mechanism used by C. caespitosa to counteract mortality events and recolonize devastated areas, and likely accounts for the occasional high levels of clonality and low levels of genetic diversity. Local adaptations such as these should therefore be considered in conservation and management strategies to maintain and preserve the gene pool of this endangered species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at (10.1007/s00338-020-02040-3).
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Affiliation(s)
- Violeta López-Márquez
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - Carlos Lozano-Martín
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - Louis Hadjioannou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- Enalia Physis Environmental Research Centre, Nicosia, Cyprus
| | - Iván Acevedo
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - José Templado
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - Carlos Jimenez
- Enalia Physis Environmental Research Centre, Nicosia, Cyprus
- Energy, Environment and Water Research Centre, The Cyprus Institute, Nicosia, Cyprus
| | - Marco Taviani
- ISMAR-CNR, Istituto di Scienze Marine, Consiglio Nazionale delle Ricerche, Via Gobetti 101, 40129 Bologna, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
- Department of Biology, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA 02543 USA
| | - Annie Machordom
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006 Madrid, Spain
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Edwards TP, Trigiano RN, Ownley BH, Windham AS, Wyman CR, Wadl PA, Hadziabdic D. Genetic Diversity and Conservation Status of Helianthus verticillatus, an Endangered Sunflower of the Southern United States. Front Genet 2020; 11:410. [PMID: 32499812 PMCID: PMC7243268 DOI: 10.3389/fgene.2020.00410] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Evaluating species diversity and patterns of population genetic variation is an essential aspect of conservation biology to determine appropriate management strategies and preserve the biodiversity of native plants. Habitat fragmentation and potential habitat loss are often an outcome of a reduction in naturally occurring wildfires and controlled prescribed burning, as seen in Helianthus verticillatus (whorled sunflower). This endangered, wild relative of the common sunflower, Helianthus annuus, is endemic to four locations in Alabama, Georgia, and Tennessee, United States. Despite its endangered status, there is no recovery plan for H. verticillatus, and knowledge related to its basic plant biology and importance in ecosystem services is mostly unknown. In this study, we utilized 14 microsatellite loci to investigate fine-scale population structure and genetic diversity of H. verticillatus individuals found on two sampling sites within the Georgia population. Our results indicated moderate genetic diversity and the presence of two distinct genetic clusters. Analyses of molecular variance indicated that the majority of variance was individually based, thus confirming high genetic differentiation and limited gene flow between H. verticillatus collection sites. The evidence of a population bottleneck in these sites suggests a recent reduction in population size that could be explained by habitat loss and population fragmentation. Also, high levels of linkage disequilibrium were detected, putatively suggesting clonal reproduction among these individuals. Our study provides a better understanding of fine-scale genetic diversity and spatial distribution of H. verticillatus populations in Georgia. Our results can underpin an original recovery plan for H. verticillatus that could be utilized for the conservation of this endangered species and to promote its persistence in the wild.
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Affiliation(s)
- Tyler P Edwards
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Bonnie H Ownley
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Alan S Windham
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Christopher R Wyman
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Phillip A Wadl
- United States Department of Agriculture, Agriculture Research Service, U.S. Vegetable Laboratory, Charleston, SC, United States
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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10
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Sharma Poudel R, Richards J, Shrestha S, Solanki S, Brueggeman R. Transcriptome-wide association study identifies putative elicitors/suppressor of Puccinia graminis f. sp. tritici that modulate barley rpg4-mediated stem rust resistance. BMC Genomics 2019; 20:985. [PMID: 31842749 PMCID: PMC6915985 DOI: 10.1186/s12864-019-6369-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 12/04/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stem rust is an economically important disease of wheat and barley. However, studies to gain insight into the molecular basis of these host-pathogen interactions have primarily focused on wheat because of its importance in human sustenance. This is the first extensive study utilizing a transcriptome-wide association mapping approach to identify candidate Puccinia graminis f. sp. tritici (Pgt) effectors/suppressors that elicit or suppress barley stem rust resistance genes. Here we focus on identifying Pgt elicitors that interact with the rpg4-mediated resistance locus (RMRL), the only effective source of Pgt race TTKSK resistance in barley. RESULTS Thirty-seven Pgt isolates showing differential responses on RMRL were genotyped using Restriction Site Associated DNA-Genotyping by Sequencing (RAD-GBS), identifying 24 diverse isolates that were used for transcript analysis during the infection process. In planta RNAseq was conducted with the 24 diverse isolates on the susceptible barley variety Harrington, 5 days post inoculation. The transcripts were mapped to the Pgt race SCCL reference genome identifying 114 K variants in predicted genes that would result in nonsynonymous amino acid substitutions. Transcriptome wide association analysis identified 33 variants across 28 genes that were associated with dominant RMRL virulence, thus, representing candidate suppressors of resistance. Comparative transcriptomics between the 9 RMRL virulent -vs- the 15 RMRL avirulent Pgt isolates identified 44 differentially expressed genes encoding candidate secreted effector proteins (CSEPs), among which 38 were expressed at lower levels in virulent isolates suggesting that they may represent RMRL avirulence genes. Barley transcript analysis after colonization with 9 RMRL virulent and 15 RMRL avirulent isolates inoculated on the susceptible line Harrington showed significantly lower expression of host biotic stress responses specific to RMRL virulent isolates suggesting virulent isolates harbor effectors that suppress resistance responses. CONCLUSIONS This transcriptomic study provided novel findings that help fill knowledge gaps in the understanding of stem rust virulence/avirulence and host resistance in barley. The pathogen transcriptome analysis suggested RMRL virulence might depend on the lack of avirulence genes, but evidence from pathogen association mapping analysis and host transcriptional analysis also suggested the alternate hypothesis that RMRL virulence may be due to the presence of suppressors of defense responses.
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Affiliation(s)
| | - Jonathan Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University, Baton Rouge, LA, USA
| | - Subidhya Shrestha
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
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11
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Lelwala RV, Scott JB, Ades PK, Taylor PWJ. Population Structure of Colletotrichum tanaceti in Australian Pyrethrum Reveals High Evolutionary Potential. PHYTOPATHOLOGY 2019; 109:1779-1792. [PMID: 31179858 DOI: 10.1094/phyto-03-19-0091-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Colletotrichum tanaceti, the causal agent of anthracnose, is an emerging pathogen of commercially grown pyrethrum (Tanacetum cinerariifolium) in Australia. A microsatellite marker library was developed to understand the spatio-genetic structure over three sampled years and across two regions where pyrethrum is cultivated in Australia. Results indicated that C. tanaceti was highly diverse with a mixed reproductive mode; comprising both sexual and clonal reproduction. Sexual reproduction of C. tanaceti was more prevalent in Tasmania than in Victoria. Little differentiation was observed among field populations likely due to isolation by colonization but most of the genetic variation was occurring within populations. C. tanaceti was likely to have had a long-distance gene and genotype flow among distant populations within a state and between states. Anthropogenic transmission of propagules and wind dispersal of ascospores are the most probable mechanisms of long-distance dispersal of C. tanaceti. Evaluation of putative population histories suggested that C. tanaceti most likely originated in Tasmania and expanded from an unidentified host onto pyrethrum. Victoria was later invaded by the Tasmanian population. With the mixed mode of reproduction and possible long-distance gene flow, C. tanaceti is likely to have a high evolutionary potential and thereby has ability to adapt to management practices in the future.
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Affiliation(s)
- Ruvini V Lelwala
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia 3010
| | - Jason B Scott
- Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania, Australia 7320
| | - Peter K Ades
- School of Ecosystem and Forest Sciences, University of Melbourne, Victoria, Australia 3010
| | - Paul W J Taylor
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia 3010
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12
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Manangwa O, De Meeûs T, Grébaut P, Ségard A, Byamungu M, Ravel S. Detecting Wahlund effects together with amplification problems: Cryptic species, null alleles and short allele dominance in Glossina pallidipes populations from Tanzania. Mol Ecol Resour 2019; 19:757-772. [PMID: 30615304 DOI: 10.1111/1755-0998.12989] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/27/2018] [Accepted: 12/19/2018] [Indexed: 12/20/2022]
Abstract
Population genetics is a convenient tool to study the population biology of non-model and hard to sample species. This is particularly true for parasites and vectors. Heterozygote deficits and/or linkage disequilibrium often occur in such studies and detecting the origin of those (Wahlund effect, reproductive system or amplification problems) is uneasy. We used new tools (correlation between the number of times a locus is found in significant linkage disequilibrium and its genetic diversity, correlations between Wright's FIS and FST , FIS and number of missing data, FIT and allele size and standard errors comparisons) for the first time on a real data set of tsetse flies, a vector of dangerous diseases to humans and domestic animals in sub-Saharan Africa. With these new tools, and cleaning data from null allele, temporal heterogeneity and short allele dominance effects, we unveiled the coexistence of two highly divergent cryptic clades in the same sites. These results are in line with other studies suggesting that the biodiversity of many taxa still largely remain undescribed, in particular pathogenic agents and their vectors. Our results also advocate that including individuals from different cohorts tends to bias subdivision measures and that keeping loci with short allele dominance and/or too frequent missing data seriously jeopardize parameter's estimations. Finally, separated analyses of the two clades suggest very small tsetse densities and relatively large dispersal.
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Affiliation(s)
- Oliver Manangwa
- Vector and Vector Borne Disease Research Institute, Tanga, Tanzania
| | | | - Pascal Grébaut
- Intertryp, IRD, CIRAD, Univ Montpellier, Montpellier, France
| | - Adeline Ségard
- Intertryp, IRD, CIRAD, Univ Montpellier, Montpellier, France
| | | | - Sophie Ravel
- Intertryp, IRD, CIRAD, Univ Montpellier, Montpellier, France
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13
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Sefbom J, Kremp A, Rengefors K, Jonsson PR, Sjöqvist C, Godhe A. A planktonic diatom displays genetic structure over small spatial scales. Environ Microbiol 2018; 20:2783-2795. [PMID: 29614214 DOI: 10.1111/1462-2920.14117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 03/22/2018] [Indexed: 11/30/2022]
Abstract
Marine planktonic microalgae have potentially global dispersal, yet reduced gene flow has been confirmed repeatedly for several species. Over larger distances (>200 km) geographic isolation and restricted oceanographic connectivity have been recognized as instrumental in driving population divergence. Here we investigated whether similar patterns, that is, structured populations governed by geographic isolation and/or oceanographic connectivity, can be observed at smaller (6-152 km) geographic scales. To test this we established 425 clonal cultures of the planktonic diatom Skeletonema marinoi collected from 11 locations in the Archipelago Sea (northern Baltic Sea). The region is characterized by a complex topography, entailing several mixing regions of which four were included in the sampling area. Using eight microsatellite markers and conventional F-statistics, significant genetic differentiation was observed between several sites. Moreover, Bayesian cluster analysis revealed the co-occurrence of two genetic groups spread throughout the area. However, geographic isolation and oceanographic connectivity could not explain the genetic patterns observed. Our data reveal hierarchical genetic structuring whereby despite high dispersal potential, significantly diverged populations have developed over small spatial scales. Our results suggest that biological characteristics and historical events may be more important in generating barriers to gene flow than physical barriers at small spatial scales.
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Affiliation(s)
- Josefin Sefbom
- Department of Marine Sciences, University of Gothenburg, Gothenberg, Sweden
| | - Anke Kremp
- Marine Research Centre, Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Karin Rengefors
- Aquatic Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Per R Jonsson
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Gothenberg, Sweden
| | - Conny Sjöqvist
- Marine Research Centre, Finnish Environment Institute (SYKE), Helsinki, Finland.,Environmental and Marine Biology, Åbo Akademi University, Åbo, Finland
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Gothenberg, Sweden
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14
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Bentley KE, Mauricio R. High degree of clonal reproduction and lack of large-scale geographic patterning mark the introduced range of the invasive vine, kudzu (Pueraria montana var. lobata), in North America. AMERICAN JOURNAL OF BOTANY 2016; 103:1499-1507. [PMID: 27555435 DOI: 10.3732/ajb.1500434] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 06/20/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Pueraria montana var. lobata, or kudzu, is an invasive species whose invasion in North America is not genetically well characterized. The clonality of kudzu introduces challenges to population genetic analyses that can bias the assessment of spatial patterns of genotypes. Assessing patterns of genetic diversity while considering clonality is necessary to understand the invasion and spread of kudzu in its invasive range. METHODS We screened 1747 individuals from 87 populations across the invasive range with 15 microsatellite markers and a 789 bp chloroplast region. We performed detailed clonal analyses and tested levels of genetic diversity, population structure, and phylogeographic relationships. KEY RESULTS Kudzu exhibited a clonal rate of 80%, and was more heterozygous than other long-lived perennials. We detected only 353 distinct clonal lineages, with over 60% sharing a maternal haplotype. Populations were established with few genotypes, many consisting of only a single clone. We found no isolation by distance. Despite high genetic diversity, we found little geographic patterning. CONCLUSIONS Kudzu is highly clonal with few genetically distinct lineages and haplotypes existing in the introduced range. Our data are consistent with a large single introduction, or a few at most. Introduced lineages are geographically randomly distributed but isolated, suggesting that genotypes rarely expand into already established populations. No route of expansion was detectable from an original introduction. The invasion of kudzu does not seem to have been dominated by a single genotype, thus standing genetic variation and phenotypic plasticity are more likely mechanisms explaining kudzu's invasion success.
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Affiliation(s)
- Kerin E Bentley
- Department of Genetics, Davison Life Sciences Building, University of Georgia, Athens, Georgia 30602 USA
| | - Rodney Mauricio
- Department of Genetics, Davison Life Sciences Building, University of Georgia, Athens, Georgia 30602 USA
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15
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Effects of complex life cycles on genetic diversity: cyclical parthenogenesis. Heredity (Edinb) 2016; 117:336-347. [PMID: 27436524 DOI: 10.1038/hdy.2016.52] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 06/02/2016] [Accepted: 06/08/2016] [Indexed: 11/08/2022] Open
Abstract
Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks).
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16
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Hartfield M. Evolutionary genetic consequences of facultative sex and outcrossing. J Evol Biol 2015; 29:5-22. [DOI: 10.1111/jeb.12770] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 01/16/2023]
Affiliation(s)
- M. Hartfield
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto ON Canada
- Bioinformatics Research Centre; University of Aarhus; Aarhus Denmark
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17
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Roulin AC, Mariadassou M, Hall MD, Walser JC, Haag C, Ebert D. High genetic variation in resting-stage production in a metapopulation: Is there evidence for local adaptation? Evolution 2015; 69:2747-56. [DOI: 10.1111/evo.12770] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 07/20/2015] [Accepted: 08/20/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Anne C. Roulin
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
- Institute of Plant Biology; University of Zurich; Zollikerstrasse 107 8008 Zurich Switzerland
| | | | - Matthew D. Hall
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
- School of Biological Sciences; Monash University; Melbourne 3800 Australia
| | - Jean-Claude Walser
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
- Genetic Diversity Centre; Universitätstrasse 16, CHN E 55 8092 Zürich Switzerland
| | - Christoph Haag
- CNRS-UMR5175 CEFE; 1919, Route de Mende 34293 Montpellier France
| | - Dieter Ebert
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
- Tvärminne Zoological Station; Helsinki University; Hanko Finland
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18
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Rougeron V, De Meeûs T, Bañuls AL. Response to Tibayrenc et al.: can recombination in Leishmania parasites be so rare? Trends Parasitol 2015; 31:280-1. [PMID: 26142922 DOI: 10.1016/j.pt.2015.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/11/2015] [Accepted: 05/13/2015] [Indexed: 11/20/2022]
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19
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Pelin A, Selman M, Aris-Brosou S, Farinelli L, Corradi N. Genome analyses suggest the presence of polyploidy and recent human-driven expansions in eight global populations of the honeybee pathogen Nosema ceranae. Environ Microbiol 2015; 17:4443-58. [PMID: 25914091 DOI: 10.1111/1462-2920.12883] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/13/2015] [Accepted: 04/15/2015] [Indexed: 12/23/2022]
Abstract
Nosema ceranae is a microsporidian pathogen whose infections have been associated with recent global declines in the populations of western honeybees (Apis mellifera). Despite the outstanding economic and ecological threat that N. ceranae may represent for honeybees worldwide, many aspects of its biology, including its mode of reproduction, propagation and ploidy, are either very unclear or unknown. In the present study, we set to gain knowledge in these biological aspects by re-sequencing the genome of eight isolates (i.e. a population of spores isolated from one single beehive) of this species harvested from eight geographically distant beehives, and by investigating their level of polymorphism. Consistent with previous analyses performed using single gene sequences, our analyses uncovered the presence of very high genetic diversity within each isolate, but also very little hive-specific polymorphism. Surprisingly, the nature, location and distribution of this genetic variation suggest that beehives around the globe are infected by a population of N. ceranae cells that may be polyploid (4n or more), and possibly clonal. Lastly, phylogenetic analyses based on genome-wide single-nucleotide polymorphism data extracted from these parasites and mitochondrial sequences from their hosts all failed to support the current geographical structure of our isolates.
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Affiliation(s)
- Adrian Pelin
- Canadian Institute for Advanced Research, Department of Biology; University of Ottawa, Ottawa, ON, Canada
| | - Mohammed Selman
- Canadian Institute for Advanced Research, Department of Biology; University of Ottawa, Ottawa, ON, Canada
| | - Stéphane Aris-Brosou
- Departments of Biology and of Mathematics & Statistics, University of Ottawa, Ottawa, ON, Canada
| | - Laurent Farinelli
- FASTERIS S.A., Ch. du Pont-du-Centenaire 109, P.O. Box 28, Plan-les-Ouates, CH-1228, Geneva, Switzerland
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology; University of Ottawa, Ottawa, ON, Canada
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20
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Genetic identities and local inbreeding in pure diploid clones with homoplasic markers: SNPs may be misleading. INFECTION GENETICS AND EVOLUTION 2015; 33:227-32. [PMID: 25960105 DOI: 10.1016/j.meegid.2015.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/06/2015] [Accepted: 05/07/2015] [Indexed: 11/21/2022]
Abstract
Expected values for observed heterozygosity, genetic diversity, and inbreeding of individuals relative to inbreeding of the population (F(IS)) are derived in the case of one locus displaying homoplasy with K possible allelic states (KAM model) in a clonal diploid population. Heterozygosity (H(O)) and genetic diversity (H(S)) are substantially affected by homoplasy as long as the number of alleles K ⩽ 10, while F(IS) remains weakly affected in any case. Simulations suggest that in big populations, or in case of maximum homoplasy (K = 2), expected values can appear far from the observed ones because equilibrium takes too many generations to be reached at homoplasic markers in clonally propagating populations. This raises some concern on the use of SNPs, at least in clonal populations.
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21
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Burrell AM, Pepper AE, Hodnett G, Goolsby JA, Overholt WA, Racelis AE, Diaz R, Klein PE. Exploring origins, invasion history and genetic diversity ofImperata cylindrica(L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing. Mol Ecol 2015; 24:2177-93. [DOI: 10.1111/mec.13167] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 12/31/2022]
Affiliation(s)
- A. Millie Burrell
- Institute for Plant Genomics and Biotechnology; Department of Horticultural Sciences; Texas A&M University; College Station TX 77843-2123 USA
| | - Alan E. Pepper
- Department of Biology; Texas A&M University; College Station TX 77843-3258 USA
| | - George Hodnett
- Department of Soil and Crop Sciences; Texas A&M University; College Station TX 77843-2474 USA
| | - John A. Goolsby
- Cattle Fever Tick Research Laboratory; USDA-ARS; Moore Air Base Building 6419 Edinburg TX 78541 USA
| | - William A. Overholt
- Biological Control and Containment Laboratory; University of Florida; 2199 South Rock Road Fort Pierce FL 34945-3138 USA
| | - Alexis E. Racelis
- Department of Biology; University of Texas Pan American; 1201 West University Drive Edinburg TX 78539 USA
| | - Rodrigo Diaz
- Biological Control and Containment Laboratory; University of Florida; 2199 South Rock Road Fort Pierce FL 34945-3138 USA
| | - Patricia E. Klein
- Institute for Plant Genomics and Biotechnology; Department of Horticultural Sciences; Texas A&M University; College Station TX 77843-2123 USA
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Ramírez JD, Llewellyn MS. Reproductive clonality in protozoan pathogens--truth or artefact? Mol Ecol 2014; 23:4195-202. [PMID: 25060834 DOI: 10.1111/mec.12872] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/13/2014] [Accepted: 07/17/2014] [Indexed: 02/06/2023]
Abstract
The debate around the frequency and importance of genetic exchange in parasitic protozoa is now several decades old. Recently, fresh assertions have been made that predominant clonal evolution explains the population structures of several key protozoan pathogens. Here, we present an alternative perspective. On the assumption that much apparent clonality may be an artefact of inadequate sampling and study design, we review current research to define why sex might be so difficult to detect in protozoan parasite populations. In doing so, we contrast laboratory models of genetic exchange in parasitic protozoa with natural patterns of genetic diversity and consider the fitness advantage of sex at different evolutionary scales. We discuss approaches to improve the accuracy of efforts to characterize genetic exchange in the field. We also examine the implications of the first population genomic studies for the debate around sex and clonality in parasitic protozoa and discuss caveats for the future.
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Affiliation(s)
- Juan David Ramírez
- Unidad Clinico-Molecular de Enfermedades Infecciosas (UCMEI), Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Carrera 24 No. 63C-69, Bogotá, Colombia
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Stoeckel S, Masson JP. The exact distributions of F(IS) under partial asexuality in small finite populations with mutation. PLoS One 2014; 9:e85228. [PMID: 24465510 PMCID: PMC3897417 DOI: 10.1371/journal.pone.0085228] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/18/2013] [Indexed: 11/18/2022] Open
Abstract
Reproductive systems like partial asexuality participate to shape the evolution of genetic diversity within populations, which is often quantified by the inbreeding coefficient FIS. Understanding how those mating systems impact the possible distributions of FIS values in theoretical populations helps to unravel forces shaping the evolution of real populations. We proposed a population genetics model based on genotypic states in a finite population with mutation. For populations with less than 400 individuals, we assessed the impact of the rates of asexuality on the full exact distributions of FIS, the probabilities of positive and negative FIS, the probabilities of fixation and the probabilities to observe changes in the sign of FIS over one generation. After an infinite number of generations, we distinguished three main patterns of effects of the rates of asexuality on genetic diversity that also varied according to the interactions of mutation and genetic drift. Even rare asexual events in mainly sexual populations impacted the balance between negative and positive FIS and the occurrence of extreme values. It also drastically modified the probability to change the sign of FIS value at one locus over one generation. When mutation prevailed over genetic drift, increasing rates of asexuality continuously increased the variance of FIS that reached its highest value in fully asexual populations. In consequence, even ancient asexual populations showed the entire FIS spectrum, including strong positive FIS. The prevalence of heterozygous loci only occurred in full asexual populations when genetic drift dominated.
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Affiliation(s)
- Solenn Stoeckel
- INRA, UMR1349 Institute for Genetics, Environment and Plant Protection, Le Rheu, France
| | - Jean-Pierre Masson
- INRA, UMR1349 Institute for Genetics, Environment and Plant Protection, Le Rheu, France
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24
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Islam MS, Roush TL, Walker MA, Granett J, Lin H. Reproductive mode and fine-scale population genetic structure of grape phylloxera (Daktulosphaira vitifoliae) in a viticultural area in California. BMC Genet 2013; 14:123. [PMID: 24367928 PMCID: PMC3890642 DOI: 10.1186/1471-2156-14-123] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 12/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Grape phylloxera (Daktulosphaira vitifoliae) is one of the world's most important viticultural pests. However, the reproductive mode, genetic structure and host adaptation of phylloxera in various viticultural environments remains unclear. We examined reproductive mode and genetic structure of phylloxera by analyzing microsatellite makers across the samples from four vineyard-sites in California. RESULT The phylloxera populations in California are believed to have predominantly parthenogenetic reproduction. Therefore, genetic diversity of phylloxera is expected to be limited. However, this study showed relatively high levels of diversity in Napa and Yolo county populations with a large number of unique genotypes, average number of alleles (2.1 to 2.9) and observed heterozygosities (0.330 to 0.388) per vineyard-sites. Reproduction diversity index (G: N-unique genotypes versus number of samples) ranged from 0.500 to 0.656 among vineyard-sites. Both significant and non-significant Psex (probability of sexual reproduction) were observed among different repeated genotypes within each vineyard. Moreover, high variation of FIS was observed among different loci in each vineyard-site. Genetic structure analysis (UPGMA) and various measures of population differentiations (FST, PCA, and gene flow estimates) consistently separated AXR#1 (Vitis vinifera x V. rupestris-widely planted in California during the 1960s and 1970s) associated populations from the populations associated with other different rootstocks. CONCLUSION Genetic diversity, G: N ratio, Psex and FIS consistently suggested the occurrence of both parthenogenetic and sexual reproduction in California populations. This study clearly identified two major groups of phylloxera obtained from various rootstocks, with one group exclusively associated with only AXR#1 rootstock, defined as "biotype B", and another group associated with vinifera-based rootstocks, known as "biotype A".
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Affiliation(s)
| | | | | | | | - Hong Lin
- USDA, Agricultural Resarch Service, USDA-ARS, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757, USA.
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25
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Barnabe C, Buitrago R, Bremond P, Aliaga C, Salas R, Vidaurre P, Herrera C, Cerqueira F, Bosseno MF, Waleckx E, Breniere SF. Putative panmixia in restricted populations of Trypanosoma cruzi isolated from wild Triatoma infestans in Bolivia. PLoS One 2013; 8:e82269. [PMID: 24312410 PMCID: PMC3843716 DOI: 10.1371/journal.pone.0082269] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 10/29/2013] [Indexed: 01/26/2023] Open
Abstract
Trypanosoma cruzi, the causative agent of Chagas disease, is subdivided into six discrete typing units (DTUs; TcI-TcVI) of which TcI is ubiquitous and genetically highly variable. While clonality is the dominant mode of propagation, recombinant events play a significant evolutive role. Recently, foci of wild Triatoma infestans have been described in Bolivia, mainly infected by TcI. Hence, for the first time, we evaluated the level of genetic exchange within TcI natural potentially panmictic populations (single DTU, host, area and sampling time). Seventy-nine TcI stocks from wild T. infestans, belonging to six populations were characterized at eight microsatellite loci. For each population, Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), and presence of repeated multilocus genotypes (MLG) were analyzed by using a total of seven statistics, to test the null hypothesis of panmixia (H0). For three populations, none of the seven statistics allowed to rejecting H0; for another one the low size did not allow us to conclude, and for the two others the tests have given contradictory results. Interestingly, apparent panmixia was only observed in very restricted areas, and was not observed when grouping populations distant of only two kilometers or more. Nevertheless it is worth stressing that for the statistic tests of "HWE", in order to minimize the type I error (i. e. incorrect rejection of a true H0), we used the Bonferroni correction (BC) known to considerably increase the type II error ( i. e. failure to reject a false H0). For the other tests (LD and MLG), we did not use BC and the risk of type II error in these cases was acceptable. Thus, these results should be considered as a good indicator of the existence of panmixia in wild environment but this must be confirmed on larger samples to reduce the risk of type II error.
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Affiliation(s)
- Christian Barnabe
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
| | - Rosio Buitrago
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
| | - Philippe Bremond
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
| | - Claudia Aliaga
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
| | - Renata Salas
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
| | - Pablo Vidaurre
- Servicio Departamental de Salud (SEDES) of La Paz, La Paz, Bolivia
| | - Claudia Herrera
- Department of Tropical Medicine, Tulane University, School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
| | - Frédérique Cerqueira
- Plateforme Génomique Environnementale du Labex Centre "Méditerranéen Environnement Biodiversité", Séquençage – Génotypage, Université Montpellier 2, Montpellier, France
| | - Marie-France Bosseno
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
| | - Etienne Waleckx
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
| | - Simone Frédérique Breniere
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
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Prospero S, Lutz A, Tavadze B, Supatashvili A, Rigling D. Discovery of a new gene pool and a high genetic diversity of the chestnut blight fungus Cryphonectria parasitica in Caucasian Georgia. INFECTION GENETICS AND EVOLUTION 2013; 20:131-9. [PMID: 23994123 DOI: 10.1016/j.meegid.2013.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 11/24/2022]
Abstract
In this study, we investigated the population genetic structure and possible origins of the plant pathogen Cryphonectria parasitica in Caucasian Georgia, a region within the centre of origin of the host species Castanea sativa. A total of 427 C. parasitica isolates from nine populations were genotyped at 10 microsatellite loci. A high genetic diversity was detected, but the overall Georgian population was dominated by three haplotypes which were present in most individual populations. Two of them have not been previously found in Europe. Bayesian clustering analysis and principal component analysis could not identify their source population, neither in Asia nor in North America. On the other hand, one haplotype is frequent in Central Europe and probably naturally invaded Caucasian Georgia from neighbouring Turkey. Seventy-three haplotypes were unique to specific populations, and 66 of them were represented by a single isolate. Allele patterns suggest that most of these haplotypes emerged locally through sexual recombination between haplotypes of the Georgian and the central European gene pool. Due to the high incidence of haplotypes not otherwise present in Europe, Caucasian Georgia represents an additional source of diversity for the European C. parasitica population.
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Affiliation(s)
- S Prospero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH-8903 Birmensdorf, Switzerland.
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Piffaretti J, Clamens AL, Vanlerberghe-Masutti F, Gupta RK, Call E, Halbert S, Jousselin E. Regular or covert sex defines two lineages and worldwide superclones within the leaf-curl plum aphid (Brachycaudus helichrysi, Kaltenbach). Mol Ecol 2013; 22:3916-32. [PMID: 23786407 DOI: 10.1111/mec.12371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 04/25/2013] [Accepted: 04/25/2013] [Indexed: 10/26/2022]
Abstract
Asexual reproduction occurs widely in plants and animals, particularly in insects. Aphid species usually reproduce by cyclic parthenogenesis, but many species include obligate asexual lineages. We recently showed that the leaf-curl plum aphid, Brachycaudus helichrysi, actually encompasses two lineages, B. helichrysi H1 and H2. Ecological data suggest that these lineages have different life cycles. We conducted a large population genetics study, based on 14 microsatellite loci, to infer their respective life cycles and investigate their population structure and geographical distribution. Brachycaudus helichrysi H1 displayed the genetic signature of cyclical parthenogenesis, using plum trees as primary hosts for sexual reproduction, as classically described for B. helichrysi. This global survey showed that the Central Asian population of H1 was clearly differentiated from American-European populations. By contrast, B. helichrysi H2 displayed the typical signature of obligate asexual reproduction. H2 encompassed at least eight highly successful genotypes or superclones. This lack of ability to undergo sexual reproduction was confirmed for one of the superclones by sex induction experiments. We found only one B. helichrysi H2 population that underwent sexual reproduction, which was collected from peach trees, in Northern India. Our results confirm that H1 and H2 have different life cycles. Brachycaudus helichrysi H1 is clearly heteroecious using plum trees as primary hosts, while B. helichrysi H2 encompasses several anholocyclic lineages, and some heteroecious populations that until now have only been found associated with peach trees as primary hosts. We discuss implications of these findings for the pest status of B. helichrysi lineages.
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Affiliation(s)
- J Piffaretti
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), Centre de Biologie pour la Gestion des Populations, Campus International de Baillarguet CS 30 016, Montferrier-sur-Lez, F-34 988, France.
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Haag KL, Traunecker E, Ebert D. Single-nucleotide polymorphisms of two closely related microsporidian parasites suggest a clonal population expansion after the last glaciation. Mol Ecol 2012; 22:314-26. [PMID: 23163569 DOI: 10.1111/mec.12126] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 10/03/2012] [Accepted: 10/07/2012] [Indexed: 11/27/2022]
Abstract
The mode of reproduction of microsporidian parasites has remained puzzling since many decades. It is generally accepted that microsporidia are capable of sexual reproduction, and that some species have switched to obligate asexuality, but such process had never been supported with population genetic evidence. We examine the mode of reproduction of Hamiltosporidium tvaerminnensis and Hamiltosporidium magnivora, two closely related microsporidian parasites of the widespread freshwater crustacean Daphnia magna, based on a set of 129 single-nucleotide polymorphisms distributed across 16 genes. We analyse 20 H. tvaerminnensis isolates from localities representative of the entire species' geographic distribution along the Skerry Island belt of the Baltic Sea. Five isolates of the sister species H. magnivora were used for comparison. We estimate the recombination rates in H. tvaerminnensis to be at least eight orders of magnitude lower than in H. magnivora and not significantly different from zero. This is corroborated by the higher divergence between H. tvaerminnensis alleles (including fixed heterozygosity), as compared to H. magnivora. Our study confirms that sexual recombination is present in microsporidia, that it can be lost, and that asexuals may become epidemic.
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Affiliation(s)
- Karen L Haag
- Zoological Institute, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.
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Barrès B, Dutech C, Andrieux A, Halkett F, Frey P. Exploring the role of asexual multiplication in poplar rust epidemics: impact on diversity and genetic structure. Mol Ecol 2012; 21:4996-5008. [DOI: 10.1111/mec.12008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 07/06/2012] [Accepted: 07/15/2012] [Indexed: 11/28/2022]
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Ivens ABF, Kronauer DJC, Pen I, Weissing FJ, Boomsma JJ. Reproduction and dispersal in an ant-associated root aphid community. Mol Ecol 2012; 21:4257-69. [PMID: 22804757 DOI: 10.1111/j.1365-294x.2012.05701.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Clonal organisms with occasional sex are important for our general understanding of the costs and benefits that maintain sexual reproduction. Cyclically parthenogenetic aphids are highly variable in their frequency of sexual reproduction. However, studies have mostly focused on free-living aphids above ground, whereas dispersal constraints and dependence on ant-tending may differentially affect the costs and benefits of sex in subterranean aphids. Here, we studied reproductive mode and dispersal in a community of root aphids that are obligately associated with the ant Lasius flavus. We assessed the genetic population structure of four species (Geoica utricularia, Tetraneura ulmi, Forda marginata and Forda formicaria) in a Dutch population and found that all species reproduce predominantly if not exclusively asexually, so that populations consist of multiple clonal lineages. We show that population viscosity is high and winged aphids rare, consistent with infrequent horizontal transmission between ant host colonies. The absence of the primary host shrub (Pistacia) may explain the absence of sex in three of the studied species, but elm trees (Ulmus) that are primary hosts of the fourth species (T. ulmi) occurred within a few km of the study population. We discuss the extent to which obligate ant-tending and absence of primary hosts may have affected selection for permanent parthenogenesis, and we highlight the need for further study of these aphids in Southern Europe where primary hosts may occur close to L. flavus populations, so that all four root aphid species would have realistic opportunities for completing their sexual life cycle.
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Affiliation(s)
- A B F Ivens
- Theoretical Biology, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
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Allen DE, Lynch M. The effect of variable frequency of sexual reproduction on the genetic structure of natural populations of a cyclical parthenogen. Evolution 2012; 66:919-926. [PMID: 22380451 PMCID: PMC4521562 DOI: 10.1111/j.1558-5646.2011.01488.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclical parthenogens are a valuable system in which to empirically test theoretical predictions as to the genetic consequences of sexual reproduction in natural populations, particularly if the frequency of sexual relative to asexual reproduction can be quantified. In this study, we used a series of lake populations of the cyclical parthenogen, Daphnia pulicaria, that vary consistently in their investment in sexual reproduction, to address the questions of whether the ecological variation in investment in sex is detectable at the genetic level, and if so, whether the genetic patterns seen are consistent with theoretical predictions. We show that there is variation in the genetic structure of these populations in a manner consistent with their investment in sexual reproduction. Populations engaging in a high frequency of sex were in Hardy-Weinberg and gametic phase equilibrium, and showed little genotypic differentiation across sampled years. In contrast, populations with a lower frequency of sex deviated widely from equilibrium, had reduced multilocus clonal diversity, and showed significant temporal genotypic deviation.
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Affiliation(s)
- Desiree E Allen
- Department of Biology, Indiana University, Bloomington, Indiana 47405 E-mail:
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47405 E-mail:
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Saleh D, Xu P, Shen Y, Li C, Adreit H, Milazzo J, Ravigné V, Bazin E, Nottéghem JL, Fournier E, Tharreau D. Sex at the origin: an Asian population of the rice blast fungus Magnaporthe oryzae reproduces sexually. Mol Ecol 2012; 21:1330-44. [PMID: 22313491 DOI: 10.1111/j.1365-294x.2012.05469.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Sexual reproduction may be cryptic or facultative in fungi and therefore difficult to detect. Magnaporthe oryzae, which causes blast, the most damaging fungal disease of rice, is thought to originate from southeast Asia. It reproduces asexually in all rice-growing regions. Sexual reproduction has been suspected in limited areas of southeast Asia, but has never been demonstrated in contemporary populations. We characterized several M. oryzae populations worldwide both biologically and genetically, to identify candidate populations for sexual reproduction. The sexual cycle of M. oryzae requires two strains of opposite mating types, at least one of which is female-fertile, to come into contact. In one Chinese population, the two mating types were found to be present at similar frequencies and almost all strains were female-fertile. Compatible strains from this population completed the sexual cycle in vitro and produced viable progenies. Genotypic richness and linkage disequilibrium data also supported the existence of sexual reproduction in this population. We resampled this population the following year, and the data obtained confirmed the presence of all the biological and genetic characteristics of sexual reproduction. In particular, a considerable genetic reshuffling of alleles was observed between the 2 years. Computer simulations confirmed that the observed genetic characteristics were unlikely to have arisen in the absence of recombination. We therefore concluded that a contemporary population of M. oryzae, pathogenic on rice, reproduces sexually in natura in southeast Asia. Our findings provide evidence for the loss of sexual reproduction by a fungal plant pathogen outside its centre of origin.
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Affiliation(s)
- Dounia Saleh
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR BGPI, Montpellier, France
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Rougeron V, Bañuls AL, Carme B, Simon S, Couppié P, Nacher M, Hide M, De Meeûs T. Reproductive strategies and population structure in Leishmania: substantial amount of sex in Leishmania Viannia guyanensis. Mol Ecol 2011; 20:3116-27. [PMID: 21722225 DOI: 10.1111/j.1365-294x.2011.05162.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Leishmania species of the subgenus Viannia and especially Leishmania Viannia guyanensis are responsible for a large proportion of New World leishmaniasis cases. Since a recent publication on Leishmania Viannia braziliensis, the debate on the mode of reproduction of Leishmania parasites has been reopened. A predominant endogamic reproductive mode (mating with relatives), together with strong Wahlund effects (sampling of strains from heterogeneous subpopulations), was indeed evidenced. To determine whether this hypothesis can be generalized to other Leishmania Viannia species, we performed a population genetic study on 153 human strains of L. (V.) guyanensis from French Guiana based on 12 microsatellite loci. The results revealed important homozygosity and very modest linkage disequilibrium, which is in agreement with a high level of sexual recombination and substantial endogamy. These results also revealed a significant isolation by distance with relatively small neighbourhoods and hence substantial viscosity of Leishmania populations in French Guiana. These results are of epidemiological relevance and suggest a major role for natural hosts and/or vectors in parasite strain diffusion across the country as compared to human hosts.
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Affiliation(s)
- Virginie Rougeron
- Laboratoire MIVEGEC (UMR IRD 224-CNRS 5290-Université Montpellier 1) Montpellier, France.
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Very low microsatellite polymorphism and large heterozygote deficits suggest founder effects and cryptic structure in the parasite Perkinsus olseni. INFECTION GENETICS AND EVOLUTION 2011; 11:904-11. [DOI: 10.1016/j.meegid.2011.02.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 02/07/2011] [Accepted: 02/22/2011] [Indexed: 11/18/2022]
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Dobata S, Sasaki T, Mori H, Hasegawa E, Shimada M, Tsuji K. Persistence of the single lineage of transmissible 'social cancer' in an asexual ant. Mol Ecol 2010; 20:441-55. [PMID: 21155912 DOI: 10.1111/j.1365-294x.2010.04954.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
How cooperation can arise and persist, given the threat of cheating phenotypes, is a central problem in evolutionary biology, but the actual significance of cheating in natural populations is still poorly understood. Theories of social evolution predict that cheater lineages are evolutionarily short-lived. However, an exception comes from obligate socially parasitic species, some of which thought to have arisen as cheaters within cooperator colonies and then diverged through sympatric speciation. This process requires the cheater lineage to persist by avoiding rapid extinction that would result from the fact that the cheaters inflict fitness cost on their host. We examined whether this prerequisite is fulfilled, by estimating the persistence time of cheaters in a field population of the parthenogenetic ant Pristomyrmex punctatus. Population genetic analysis found that the cheaters belong to one monophyletic lineage which we infer has persisted for 200-9200 generations. We show that the cheaters migrate and are thus horizontally transmitted between colonies, a trait allowing the lineage to avoid rapid extinction with its host colony. Although horizontal transmission of disruptive cheaters has the potential to induce extinction of the entire population, such collapse is likely averted when there is spatially restricted migration in a structured population, a scenario that matches the observed isolation by distance pattern that we found. We compare our result with other examples of disruptive and horizontally transmissible cheater lineages in nature.
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Affiliation(s)
- S Dobata
- Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, Meguro, Tokyo, Japan.
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Inference of population structure of Leishmania donovani strains isolated from different Ethiopian visceral leishmaniasis endemic areas. PLoS Negl Trop Dis 2010; 4:e889. [PMID: 21103373 PMCID: PMC2982834 DOI: 10.1371/journal.pntd.0000889] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 10/21/2010] [Indexed: 11/28/2022] Open
Abstract
Background Parasites' evolution in response to parasite-targeted control strategies, such as vaccines and drugs, is known to be influenced by their population genetic structure. The aim of this study was to describe the population structure of Ethiopian strains of Leishmania donovani derived from different areas endemic for visceral leishmaniasis (VL) as a prerequisite for the design of effective control strategies against the disease. Methodology/Principal Findings Sixty-three strains of L. donovani newly isolated from VL cases in the two main Ethiopian foci, in the north Ethiopia (NE) and south Ethiopia (SE) of the country were investigated by using 14 highly polymorphic microsatellite markers. The microsatellite profiles of 60 previously analysed L. donovani strains from Sudan, Kenya and India were included for comparison. Multilocus microsatellite typing placed strains from SE and Kenya (n = 30) in one population and strains from NE and Sudan (n = 65) in another. These two East African populations corresponded to the areas of distribution of two different sand fly vectors. In NE and Sudan Phlebotomus orientalis has been implicated to transmit the parasites and in SE and Kenya P. martini. The genetic differences between parasites from NE and SE are also congruent with some phenotypic differences. Each of these populations was further divided into two subpopulations. Interestingly, in one of the subpopulations of the population NE we observed predominance of strains isolated from HIV-VL co-infected patients and of strains with putative hybrid genotypes. Furthermore, high inbreeding irreconcilable from strict clonal reproduction was found for strains from SE and Kenya indicating a mixed-mating system. Conclusions/Significance This study identified a hierarchical population structure of L. donovani in East Africa. The existence of two main, genetically and geographically separated, populations could reflect different parasite-vector associations, different ecologies and varying host backgrounds and should be further investigated. In the Horn of Africa, visceral leishmaniasis, caused by protozoan parasites of the Leishmania donovani complex, continues to pose a major health problem affecting the poorest of the poor. Population genetic studies are crucial for the development of drugs and vaccines against microorganisms. However, our knowledge about the population structure of L. donovani parasites in this region is still very limited. Using a highly discriminatory multilocus microsatellite typing approach, we found a remarkably high genetic diversity among the East African strains of L. donovani studied which grouped into two genetically and geographically distinct populations comprising parasites from SE and Kenya, and those from NE and Sudan. Despite Leishmania being widely regarded as a clonal organism, our results suggest a possible co-existence of clonal and sexually reproducing strains of L. donovani from SE. The information obtained by the present study is helpful for future design of parasite-targeted control measures in East Africa.
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"Everything you always wanted to know about sex (but were afraid to ask)" in Leishmania after two decades of laboratory and field analyses. PLoS Pathog 2010; 6:e1001004. [PMID: 20808896 PMCID: PMC2924324 DOI: 10.1371/journal.ppat.1001004] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Leishmaniases remain a major public health problem today (350 million people at risk, 12 million infected, and 2 million new infections per year). Despite the considerable progress in cellular and molecular biology and in evolutionary genetics since 1990, the debate on the population structure and reproductive mode of Leishmania is far from being settled and therefore deserves further investigation. Two major hypotheses coexist: clonality versus sexuality. However, because of the lack of clear evidence (experimental or biological confirmation) of sexuality in Leishmania parasites, until today it has been suggested and even accepted that Leishmania species were mainly clonal with infrequent genetic recombination (see [1] for review). Two recent publications, one on Leishmania major (an in vitro experimental study) and one on Leishmania braziliensis (a population genetics analysis), once again have challenged the hypothesis of clonal reproduction. Indeed, the first study experimentally evidenced genetic recombination and proposed that Leishmania parasites are capable of having a sexual cycle consistent with meiotic processes inside the insect vector. The second investigation, based on population genetics studies, showed strong homozygosities, an observation that is incompatible with a predominantly clonal mode of reproduction at an ecological time scale (∼20–500 generations). These studies highlight the need to advance the knowledge of Leishmania biology. In this paper, we first review the reasons stimulating the continued debate and then detail the next essential steps to be taken to clarify the Leishmania reproduction model. Finally, we widen the discussion to other Trypanosomatidae and show that the progress in Leishmania biology can improve our knowledge of the evolutionary genetics of American and African trypanosomes.
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Baumgartner K, Travadon R, Bruhn J, Bergemann SE. Contrasting patterns of genetic diversity and population structure of Armillaria mellea sensu stricto in the eastern and western United States. PHYTOPATHOLOGY 2010; 100:708-718. [PMID: 20528189 DOI: 10.1094/phyto-100-7-0708] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
ABSTRACT Armillaria mellea infects hundreds of plant species in natural and managed ecosystems throughout the Northern hemisphere. Previously reported nuclear genetic divergence between eastern and western U.S. isolates is consistent with the disjunct range of A. mellea in North America, which is restricted mainly to both coasts of the United States. We investigated patterns of population structure and genetic diversity of the eastern (northern and southern Appalachians, Ozarks, and western Great Lakes) and western (Berkeley, Los Angeles, St. Helena, and San Jose, CA) regions of the United States. In total, 156 diploid isolates were genotyped using 12 microsatellite loci. Absence of genetic differentiation within either eastern subpopulations (theta(ST) = -0.002, P = 0.5 ) or western subpopulations (theta(ST) = 0.004, P = 0.3 ) suggests that spore dispersal within each region is sufficient to prevent geographic differentiation. In contrast to the western United States, our finding of more than one genetic cluster of isolates within the eastern United States (K = 3), revealed by Bayesian assignment of multilocus genotypes in STRUCTURE and confirmed by genetic multivariate analyses, suggests that eastern subpopulations are derived from multiple founder sources. The existence of amplifiable and nonamplifiable loci and contrasting patterns of genetic diversity between the two regions demonstrate that there are two geographically isolated, divergent genetic pools of A. mellea in the United States.
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Affiliation(s)
- Kendra Baumgartner
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Department of Plant Pathology, University of California, One Shields Avenue, Davis 95616, USA
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Riester M, Stadler PF, Klemm K. Reconstruction of pedigrees in clonal plant populations. Theor Popul Biol 2010; 78:109-17. [PMID: 20566407 DOI: 10.1016/j.tpb.2010.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 05/13/2010] [Accepted: 05/14/2010] [Indexed: 11/25/2022]
Abstract
We present a Bayesian method for the reconstruction of pedigrees in clonal populations using co-dominant genomic markers such as microsatellites and single nucleotide polymorphisms (SNPs). The accuracy of the algorithm is demonstrated for simulated data. We show that the joint estimation of parameters of interest such as the rate of self-fertilization is possible with high accuracy even with marker panels of moderate power. Classical methods can only assign a very limited number of statistically significant parentages in this case and would therefore fail. Statistical confidence is estimated by Markov Chain Monte Carlo (MCMC) sampling. The method is implemented in a fast and easy to use open source software that scales to large datasets with many thousand individuals.
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Affiliation(s)
- Markus Riester
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
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Vandepitte K, Roldán-Ruiz I, Jacquemyn H, Honnay O. Extremely low genotypic diversity and sexual reproduction in isolated populations of the self-incompatible lily-of-the-valley (Convallaria majalis) and the role of the local forest environment. ANNALS OF BOTANY 2010; 105:769-776. [PMID: 20228091 PMCID: PMC2859916 DOI: 10.1093/aob/mcq042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 01/19/2010] [Accepted: 02/03/2010] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Clonal growth is a common phenomenon in plants and allows them to persist when sexual life-cycle completion is impeded. Very low levels of recruitment from seed will ultimately result in low levels of genotypic diversity. The situation can be expected to be exacerbated in spatially isolated populations of obligated allogamous species, as low genotypic diversities will result in low availability of compatible genotypes and low reproductive success. Populations of the self-incompatible forest herb lily-of-the-valley (Convallaria majalis) were studied with the aim of inferring the relative importance of sexual and asexual recruitment. Then the aim was to establish a relationship between genotypic diversity, sexual reproduction and the local forest environment. METHODS Highly polymorphic microsatellite markers were used to investigate clonal diversities and population genetic structure of 20 populations of C. majalis in central Belgium. KEY RESULTS Most of the populations studied consisted of a single genotype and linkage disequilibrium within populations was high, manifesting clonal growth as the main mode of reproduction. A population consisting of multiple genotypes mainly occurred in locations with a thin litter layer and high soil phosphorus levels, suggesting environment-mediated sporadic recruitment from seed. Highly significant genetic differentiation indicated that populations are reproductively isolated. In agreement with the self-incompatibility of C. majalis, monoclonal populations showed very low or even absent fruit set. CONCLUSIONS Lack of sexual recruitment in spatially isolated C. majalis populations has resulted in almost monoclonal populations with reduced or absent sexual reproduction, potentially constraining their long-term persistence. The local forest environment may play an important role in mediating sexual recruitment in clonal forest plant species.
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Affiliation(s)
- Katrien Vandepitte
- Laboratory of Plant Ecology, University of Leuven, Arenbergpark 31, 3001 Heverlee, Belgium.
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VILLATE LAURE, ESMENJAUD DANIEL, VAN HELDEN MAARTEN, STOECKEL SOLENN, PLANTARD OLIVIER. Genetic signature of amphimixis allows for the detection and fine scale localization of sexual reproduction events in a mainly parthenogenetic nematode. Mol Ecol 2010; 19:856-73. [DOI: 10.1111/j.1365-294x.2009.04511.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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De Meeûs T, Guégan JF, Teriokhin AT. MultiTest V.1.2, a program to binomially combine independent tests and performance comparison with other related methods on proportional data. BMC Bioinformatics 2009; 10:443. [PMID: 20030807 PMCID: PMC2811122 DOI: 10.1186/1471-2105-10-443] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 12/23/2009] [Indexed: 11/10/2022] Open
Abstract
Background Combining multiple independent tests, when all test the same hypothesis and in the same direction, has been the subject of several approaches. Besides the inappropriate (in this case) Bonferroni procedure, the Fisher's method has been widely used, in particular in population genetics. This last method has nevertheless been challenged by the SGM (symmetry around the geometric mean) and Stouffer's Z-transformed methods that are less sensitive to asymmetry and deviations from uniformity of the distribution of the partial P-values. Performances of these different procedures were never compared on proportional data such as those currently used in population genetics. Results We present new software that implements a more recent method, the generalised binomial procedure, which tests for the deviation of the observed proportion of P-values lying under a chosen threshold from the expected proportion of such P-values under the null hypothesis. The respective performances of all available procedures were evaluated using simulated data under the null hypothesis with standard P-values distribution (differentiation tests). All procedures more or less behaved consistently with ~5% significant tests at α = 0.05. Then, linkage disequilibrium tests with increasing signal strength (rate of clonal reproduction), known to generate highly non-standard P-value distributions are undertaken and finally real population genetics data are analysed. In these cases, all procedures appear, more or less equally, very conservative, though SGM seems slightly more conservative. Conclusion Based on our results and those discussed in the literature we conclude that the generalised binomial and Stouffer's Z procedures should be preferred and Z when the number of tests is very small. The more conservative SGM might still be appropriate for meta-analyses when a strong publication bias in favour of significant results is expected to inflate type 2 error.
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Affiliation(s)
- Thierry De Meeûs
- IRD, UMR 177 IRD-CIRAD Trypanosomoses, Centre International de Recherche-Développement sur l'Elevage en zone Subhumide, 01 BP 454 Bobo-Dioulasso 01, Burkina-Faso.
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Genetic diversity and fitness in small populations of partially asexual, self-incompatible plants. Heredity (Edinb) 2009; 104:482-92. [PMID: 19920857 DOI: 10.1038/hdy.2009.159] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
How self-incompatibility systems are maintained in plant populations is still a debated issue. Theoretical models predict that self-incompatibility systems break down according to the intensity of inbreeding depression and number of S-alleles. Other studies have explored the function of asexual reproduction in the maintenance of self-incompatibility. However, the population genetics of partially asexual, self-incompatible populations are poorly understood and previous studies have failed to consider all possible effects of asexual reproduction or could only speculate on those effects. In this study, we investigated how partial asexuality may affect genetic diversity at the S-locus and fitness in small self-incompatible populations. A genetic model including an S-locus and a viability locus was developed to perform forward simulations of the evolution of populations of various sizes. Drift combined with partial asexuality produced a decrease in the number of alleles at the S-locus. In addition, an excess of heterozygotes was present in the population, causing an increase in mutation load. This heterozygote excess was enhanced by the self-incompatibility system in small populations. In addition, in highly asexual populations, individuals produced asexually had some fitness advantages over individuals produced sexually, because sexual reproduction produces homozygotes of the deleterious allele, contrary to asexual reproduction. Our results suggest that future research on the function of asexuality for the maintenance of self-incompatibility will need to (1) account for whole-genome fitness (mutation load generated by asexuality, self-incompatibility and drift) and (2) acknowledge that the maintenance of self-incompatibility may not be independent of the maintenance of sex itself.
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Isolation and characterization of polymorphic microsatellite loci for Imperata cylindrica, an invasive perennial grass. CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9031-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
Leishmania species of the subgenus Viannia and especially Leishmania braziliensis are responsible for a large proportion of New World leishmaniasis cases. The reproductive mode of Leishmania species has often been assumed to be predominantly clonal, but remains unsettled. We have investigated the genetic polymorphism at 12 microsatellite loci on 124 human strains of Leishmania braziliensis from 2 countries, Peru and Bolivia. There is substantial genetic diversity, with an average of 12.4 +/- 4.4 alleles per locus. There is linkage disequilibrium at a genome-wide scale, as well as a substantial heterozygote deficit (more than 50% the expected value from Hardy-Weinberg equilibrium), which indicates high levels of inbreeding. These observations are inconsistent with a strictly clonal model of reproduction, which implies excess heterozygosity. Moreover, there is large genetic heterogeneity between populations within countries (Wahlund effect), which evinces a strong population structure at a microgeographic scale. Our findings are compatible with the existence of population foci at a microgeographic scale, where clonality alternates with sexuality of an endogamic nature, with possible occasional recombination events between individuals of different genotypes. These findings provide key clues on the ecology and transmission patterns of Leishmania parasites.
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ANDREAKIS NIKOS, KOOISTRA WIEBEHCF, PROCACCINI GABRIELE. High genetic diversity and connectivity in the polyploid invasive seaweedAsparagopsis taxiformis(Bonnemaisoniales) in the Mediterranean, explored with microsatellite alleles and multilocus genotypes. Mol Ecol 2009; 18:212-26. [DOI: 10.1111/j.1365-294x.2008.04022.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ramsden C. Population Genetics of Ambystoma jeffersonianum and Sympatric Unisexuals Reveal Signatures of Both Gynogenetic and Sexual Reproduction. COPEIA 2008. [DOI: 10.1643/ce-06-280] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Guillemin ML, Faugeron S, Destombe C, Viard F, Correa JA, Valero M. GENETIC VARIATION IN WILD AND CULTIVATED POPULATIONS OF THE HAPLOID– DIPLOID RED ALGA GRACILARIA CHILENSIS: HOW FARMING PRACTICES FAVOR ASEXUAL REPRODUCTION AND HETEROZYGOSITY. Evolution 2008; 62:1500-19. [DOI: 10.1111/j.1558-5646.2008.00373.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bañuls AL, Hide M, Prugnolle F. Leishmania and the leishmaniases: a parasite genetic update and advances in taxonomy, epidemiology and pathogenicity in humans. ADVANCES IN PARASITOLOGY 2007; 64:1-109. [PMID: 17499100 DOI: 10.1016/s0065-308x(06)64001-3] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Leishmaniases remain a major public health problem today despite the vast amount of research conducted on Leishmania pathogens. The biological model is genetically and ecologically complex. This paper explores the advances in Leishmania genetics and reviews population structure, taxonomy, epidemiology and pathogenicity. Current knowledge of Leishmania genetics is placed in the context of natural populations. Various studies have described a clonal structure for Leishmania but recombination, pseudo-recombination and other genetic processes have also been reported. The impact of these different models on epidemiology and the medical aspects of leishmaniases is considered from an evolutionary point of view. The role of these parasites in the expression of pathogenicity in humans is also explored. It is important to ascertain whether genetic variability of the parasites is related to the different clinical expressions of leishmaniasis. The review aims to put current knowledge of Leishmania and the leishmaniases in perspective and to underline priority questions which 'leishmaniacs' must answer in various domains: epidemiology, population genetics, taxonomy and pathogenicity. It concludes by presenting a number of feasible ways of responding to these questions.
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Affiliation(s)
- Anne-Laure Bañuls
- Institut de Recherche pour le Développement, UMR CNRS/IRD 2724, Génétique et Evolution des Maladies Infectieuses, IRD Montpellier, 911 avenue Agropolis, 34394 Montpellier cedex 5, France
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Vorwerk S, Forneck A. Reproductive mode of grape phylloxera (Daktulosphaira vitifoliae, Homoptera: Phylloxeridae) in Europe: molecular evidence for predominantly asexual populations and a lack of gene flow between them. Genome 2006; 49:678-87. [PMID: 16936847 DOI: 10.1139/g06-028] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genetic structure of European grape phylloxera populations, Daktulosphaira vitifoliae (Homoptera: Phylloxeridae), was analyzed using 6 polymorphic microsatellite markers. Genetic diversity data of 6 populations originating from northern and southern European viticultural regions was assessed for geographic differences, and the structure of 2 additional populations was examined in more detail, focusing on specific host plant and habitat characteristics. To test for "signatures" of clonal reproduction, different population genetic measures were applied to the data obtained from these populations. A total of 195 multilocus genotypes were detected in 360 individuals tested. Significant deviations from Hardy-Weinberg equilibrium, negative FIS values (from -0.148 to -0.658 per population), and the presence of multicopy genotypes revealed that the current major reproductive mode at each of the locations tested was asexual. The high genotypic diversity detected within and among populations, however, together with the occurrence of unique D. vitifoliae genotypes, indicates sexual recombination events took place, probably prior to the multiple introductions into Europe. The absence of overlapping genotypes between the sampling sites suggests low migration rates among the populations studied and implies that the main mode of insect dispersal is through infested plant material carried by human agency. The specific features of European D. vitifoliae habitats are illustrated to discuss the role of habitat and life cycle in the genetic structure of this globally important pest aphid species.
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Affiliation(s)
- Sonja Vorwerk
- Department of Special Crop Cultivation and Crop Physiology, Section of Viticulture, 370a, University of Hohenheim, D-70593 Stuttgart, Germany
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