Tackling the population genetics of clonal and partially clonal organisms

Halkett, Fabien; Simon, Jean‐Christophe; Balloux, François

doi:10.1016/j.tree.2005.01.001

Cited by 415 publications

(454 citation statements)

References 77 publications

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“…Further, new methods to analyze data are being developed at a rapid pace, using for instance the Bayesian or the coalescence frameworks, or coupling geography and genetics to unravel migration and speciation histories, which should allow even more power-ful inferences on the evolutionary processes. However, further theoretical development is badly needed to apply the extant molecular methods to the variety and specificities of the fungal life cycles, such as pervasive clonality and alternation between haplo-and di-ploid phases (Balloux & Lugon-Moulin, 2002;Halkett et al, 2005). Fungi are of prime interest not only because they are major parasites of plants and animals, but they also constitute tractable and highly useful models for understanding evolutionary processes.…”

Section: Resultsmentioning

confidence: 99%

“…tritici, studies measuring linkage disequilibrium in European populations similarly indicated a strongly clonal structure (Hovmoller et al, 2002). Moreover, the high degrees of heterozygosity observed at microsatellite markers (Enjalbert et al, 2002) and in IGS sequences (RooseAmsaleg et al, 2002) provided evidence for a Meselson Effect, where ancient asexual lineages exhibit high divergence between their homologous chromosomes due to the accumulation of independent mutations on different alleles (Halkett et al, 2005). The evolution of selfing from outcrossing has received much attention for hermaphroditic plants, but relatively little work is available on sexual fungi that are capable of both selfing and outcrossing fertilisation.…”

Section: Mating Systemsmentioning

confidence: 99%

“…Deciphering the relative importance of clonal vs selfing vs outcrossing vs parasexual events in fungal populations is thus an intricate task, where molecular markers are indispensable tools, in particular microsatellites. As proposed by Halkett et al (2005), a sequential analysis is necessary to infer the mating behaviour of a population, first identifying clones, then partitioning polymorphism within and between clones to test for Hardy-Weinberg equilibrium, linkage disequilibrium between loci and recombination signal. Analysis of genetic information for a given species will also depend heavily on its ploidy and on its life cycle: tests based on intra-individual heterozygosity of loci will be only available in diploids/dikaryons species, while haploids will allow more accurate studies of linkage disequilibrium, with access to the gametic phase.…”

Section: Mating Systemsmentioning

confidence: 99%

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Population genetics of fungal diseases of plants

et al. 2008

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Summary :Although parasitism is one of the most common lifestyles among eukaryotes, population genetics on parasites lag far behind those on free-living organisms. Yet, the advent of molecular markers offers great tools for studying important processes, such as dispersal, mating systems, adaptation to host and speciation. Here we highlight some studies that used molecular markers to address questions about the population genetics of fungal (including oomycetes) plant pathogens. We conclude that population genetics approaches have provided tremendous insights into the biology of a few fungal parasites and warrant more wide use in phytopathology. However, theoretical advances are badly needed to best apply the existing methods. Fungi are of prime interest not only because they are major parasites of plants and animals, but they also constitute tractable and highly useful models for understanding evolutionary processes. We hope that the emerging field of fungal evolution will attract more evolutionary biologists in the near future. (0)1 69 15 73 53. E-mail: Tatiana.Giraud@u-psud.fr genetics studies have also valuable practical applications, for instance for studying the evolution of drug resistance or new virulence. Another reason to study parasites is that they display a huge diversity of life cycles and lifestyles, thus providing great opportunity for comparative studies to test pathogen-specific questions or general issues about evolution. Nevertheless, the field of parasitology has yet to attract more evolutionary biologists. This is even truer for the field of phytopathology, despite the importance of crop diseases for human activities. Furthermore, there are few connections so far between scientists in the fields of parasitology and phytopathology despite their obvious common interests. Here we highlight some studies that used molecular markers to address questions about the population genetics of fungal plant pathogens, fungi being taken sensus lato, i.e. including oomycetes. We do not aim providing an exhaustive review, but instead we use selected examples, mainly from our own works, to illustrate peculiarities of the phytopathogenic lifestyle. We focus on the study of mating systems (i.e. selfing, outcrossing, clonality), between and within population dispersal and population structure due to host adaptation.

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Section: Resultsmentioning

confidence: 99%

Section: Mating Systemsmentioning

confidence: 99%

Section: Mating Systemsmentioning

confidence: 99%

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Population genetics of fungal diseases of plants

et al. 2008

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“…Patterns of heterozygosity are an important indicator of both outcrossing and clonality (9,10), and hence a genomic characterization of heterozygosity should prove useful for disentangling these issues. However, all population genomic studies of S. cerevisiae to date have been based on the analysis of haploid genomes or diploid strains derived from single spores (8,11), therefore obscuring heterozygosity.…”

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confidence: 99%

Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae

Magwene

Kayıkçı

Granek

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

160

179

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We carried out a population genomic survey of Saccharomyces cerevisiae diploid isolates and find that many budding yeast strains have high levels of genomic heterozygosity, much of which is likely due to outcrossing. We demonstrate that variation in heterozygosity among strains is correlated with a life-history tradeoff that involves how readily yeast switch from asexual to sexual reproduction under nutrient stress. This trade-off is reflected in a negative relationship between sporulation efficiency and pseudohyphal development and correlates with variation in the expression of RME1, a transcription factor with pleiotropic effects on meiosis and filamentous growth. Selection for alternate lifehistory strategies in natural versus human-associated environments likely contributes to differential maintenance of genomic heterozygosity through its effect on the frequency that yeast lineages experience sexual cycles and hence the opportunity for inbreeding. In addition to elevated levels of heterozygosity, many strains exhibit large genomic regions of loss-of-heterozygosity (LOH), suggesting that mitotic recombination has a significant impact on genetic variation in this species. This study provides new insights into the roles that both outcrossing and mitotic recombination play in shaping the genome architecture of Saccharomyces cerevisiae. This study also provides a unique case where stark differences in the genomic distribution of genetic variation among individuals of the same species can be largely explained by a lifehistory trade-off.T he frequency of sex and the nature of breeding systems have a profound effect on genome variation and evolution. For example, inbred populations have an increased frequency of homozygous genotypes (1), lower effective rates of recombination (2), and smaller effective population sizes relative to outcrossed populations with the same number of individuals (3). Likewise, clonal populations are expected to exhibit high levels of heterozygosity coupled with increased allelic diversity but decreased genotypic diversity relative to sexual populations (4).The budding yeast Saccharomyces cerevisiae is one of the best studied model organisms, but relatively little is known about the importance of sexual versus asexual reproduction and inbreeding versus outcrossing in shaping genome evolution in this species. One recent study estimated that outcrossing occurs approximately once every 50,000 generations in S. cerevisiae (5), but low rates of outcrossing do not preclude the possibility that outcrossing has an important impact on genetic variation. Studies of the closely related yeast Saccharomyces paradoxus suggest that sexual cycles are rare relative to asexual cycles and that when sex does occur it primarily involves inbreeding (6, 7). However, S. paradoxus exhibits distinctly different intra-and interpopulation patterns of variation than does S. cerevisiae (8), and hence these findings may not be generalizable across the Saccharomyces genus.Patterns of heterozygosity are an important indica...

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“…At the single locus level, clonality will lead to an excess of heterozygotes in diploid organisms, while at the multilocus level, clonality will produce widespread, identical genotypes, non-random associations between alleles at different loci (linkage disequilibrium) and congruence in different intraspecific gene phylogenies [53,54,55]. A clonal population structure does not imply that genetic exchange is absent in the species, only that it is too rare to erode the basic genetic patterns of clonality.…”

Section: Mode Of Reproductionmentioning

confidence: 99%

The molecular epidemiology of parasite infections: Tools and applications

Lymbery

Thompson

2012

Molecular and Biochemical Parasitology

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Molecular epidemiology, broadly defined, is the application of molecular genetic techniques to the dynamics of disease in a population. In this review, we briefly describe molecular and analytical tools available for molecular epidemiological studies and then provide an overview of how they can be applied to better understand parasitic disease. A range of new molecular tools have been developed in recent years, allowing for the direct examination of parasites from clinical or environmental samples, and providing access to relatively cheap, rapid, high throughput molecular assays. At the same time, new analytical approaches, in particular those derived from coalescent theory, have been developed to provide more robust estimates of evolutionary processes and demographic parameters from multilocus, genotypic data. To date, the primary application of molecular epidemiology has been to provide specific and sensitive identification of parasites and to resolve taxonomic issues, particularly at the species level and below. Population genetic studies have also been used to determine the extent of genetic diversity among populations of parasites and the degree to which this diversity is associated with different host cycles or epidemiologically important phenotypes. Many of these studies have also shed new light on transmission cycles of parasites, particularly the extent to which zoonotic transmission occurs, and on the prevalence and importance of mixed infections with different parasite species or intraspecific variants (polyparasitism). A major challenge, and one which is now being addressed by an increasing number of studies, is to find and utilise genetic markers for complex traits of epidemiological significance, such as drug resistance, zoonotic potential and virulence.

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Tackling the population genetics of clonal and partially clonal organisms

Cited by 415 publications

References 77 publications

Population genetics of fungal diseases of plants

Population genetics of fungal diseases of plants

Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae

The molecular epidemiology of parasite infections: Tools and applications

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