Large Global Effective Population Sizes in Paramecium

Snoke, Margaret S.; Berendonk, Thomas U.; Barth, Dana; Lynch, Michael

doi:10.1093/molbev/msl128

Cited by 41 publications

(33 citation statements)

References 27 publications

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“…It has been argued that effective population size is inversely proportional to body size: as body size decreases, the effective population size increases (40). Effective population size estimates of ciliates are extremely limited and are restricted to members of the genera Paramecium and Tetrahymena (32,55). These analyses have indicated that the effective population of T. thermophila is small but that of Paramecium is large.…”

Section: Discussionmentioning

confidence: 99%

High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous CiliateCarchesium polypinumin the Grand River Basin (North America)

Gentekaki

Lynn

2009

Appl Environ Microbiol

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Studies that assess intraspecific genetic variation in ciliates are few and quite recent. Consequently, knowledge of the subject and understanding of the processes that underlie it are limited. We sought to assess the degree of intraspecific genetic variation in Carchesium polypinum (Ciliophora: Peritrichia), a cosmopolitan, freshwater ciliate. We isolated colonies of C. polypinum from locations in the Grand River basin in Southwestern Ontario, Canada. We then used the nuclear markers-ITS1, ITS2, and the hypervariable regions of the large subunit rRNA-and an 819-bp fragment of the mitochondrial cytochrome c oxidase I gene (cox-1) to investigate the intraspecific genetic variation of C. polypinum and the degree of resolution of the above-mentioned markers at the population level. We also sought to determine whether the organism demonstrated any population structure that mapped onto the geography of the region. Our study shows that there is a high degree of genetic diversity at the isolate level, revealed by the mitochondrial markers but not the nuclear markers. Furthermore, our results indicate that C. polypinum is likely not a single morphospecies as previously thought.Studies of intraspecific genetic variation in macroorganisms have provided insights into microevolutionary processes and speciation in these organisms. However, our understanding of the intraspecific genetic diversity of microbial eukaryotes and its temporal and spatial distribution is neither deep nor broad due to the limited number of studies that deal with these topics (2,5,7,31).Many of the studies assessing within-species genetic variation and its distribution have used random amplified polymorphic DNA (RAPD) fingerprinting. Typically, the amount of genetic variation is very low within a species (35,36,56), with some exceptions (20, 57). However, there are several problems arising from the use of RAPDs as the sole source of data, including reproducibility and scoring concerns (54).Sequences of the internal transcribed spacers (ITS), namely, ITS1 and ITS2, of the rRNA region have also been used to study the genetic diversity and population structure of protists (2, 6, 44). In several instances, the ITS sequences of populations of ciliates from across the globe have been nearly identical, indicating very low genetic variation (4, 13, 59, 62). On the other hand, the hypervariable regions of the large subunit (LSU) rRNA have revealed moderate genetic diversity in ciliates at the population level (15, 51).Mitochondrial DNA (mtDNA) has been employed only sparingly in population studies of protists, even though it is routinely used in similar studies of metazoans (3,7,8). Of the mitochondrial genes, the apocytochrome b gene (cob) and the cytochrome c oxidase I (cox-1) gene (cox-1) have been used for population-level analyses of ciliates. Estimation of intraspecific nucleotide diversity of the cob gene from three species of the prostome ciliate Coleps showed only minor differences (5). On the other hand, the cox-1 gene revealed genetic diversity that...

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Section: Discussionmentioning

confidence: 99%

High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous CiliateCarchesium polypinumin the Grand River Basin (North America)

Gentekaki

Lynn

2009

Appl Environ Microbiol

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“…One commonly used index is based on the level of polymorphism within a species (Tajima 1983). Although widely applied to animals and plants, this measure is difficult to apply to microbes due to uncertainties regarding species boundaries and other factors (Daubin and Moran 2004;Katz et al 2006;Snoke et al 2006). An alternative index of the degree of genetic drift can be based on the efficacy of purifying selection in protein-coding sequences (Yang and Bielawski 2000;Daubin and Moran 2004;Novichkov et al 2009).…”

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confidence: 99%

The consequences of genetic drift for bacterial genome complexity

2009

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Genetic drift, which is particularly effective within small populations, can shape the size and complexity of genomes by affecting the fixation of deleterious mutations. In Bacteria, assessing the contribution of genetic drift to genome evolution is problematic because the usual methods, based on intraspecific polymorphisms, can be thwarted by difficulties in delineating species' boundaries. The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria.

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“…The effective population size is an important variable that can determine different evolutionary dynamics; still, very few studies have calculated this value for microbes. In one of the few studies available, a large effective population size (7.5x10 7 ) was estimated for Paramecium [7]. These estimates were an order of magnitude larger than other calculations for macroorganisms.…”

Section: The Emergence Of Microbial Population Geneticsmentioning

confidence: 80%

“…For instance, small multicellular populations are more prone to evolve randomly by genetic drift than large populations, as well as to experience accidental extinctions [5]. Opposite to most multicellular organisms, microbes normally have huge population sizes, high reproductive rates and the potential ability for long-distance dispersal [6][7][8]. These characteristics could have a considerable influence on the diversification patterns of microbes, which could then differ from the patterns observed in multicellular organisms.…”

Section: Microbial Vs Macrobialmentioning

confidence: 99%

Population genetics: the next stop for microbial ecologists?

Logares

2011

Open Life Sciences

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Microbes play key roles in the functioning of the biosphere. Still, our knowledge about their total diversity is very limited. In particular, we lack a clear understanding of the evolutionary dynamics occurring within their populations (i.e. among members of the same biological species). Unlike animals and plants, microbes normally have huge population sizes, high reproductive rates and the potential for unrestricted dispersal. As a consequence, the knowledge of population genetics acquired from studying animals and plants cannot be applied without extensive testing to microbes. Next generation molecular tools, like High Throughput Sequencing (e.g. 454 and Illumina) coupled to Single Cell Genomics, now allow investigating microbial populations at a very fine scale. Such techniques have the potential to shed light on several ecological and evolutionary processes occurring within microbial populations that so far have remained hidden. Furthermore, they may facilitate the identification of microbial species. Eventually, we may find an answer to the question of whether microbes and multicellular organisms follow the same or different rules in their population diversification patterns.

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Large Global Effective Population Sizes in Paramecium

Cited by 41 publications

References 27 publications

High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous CiliateCarchesium polypinumin the Grand River Basin (North America)

High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous CiliateCarchesium polypinumin the Grand River Basin (North America)

The consequences of genetic drift for bacterial genome complexity

Population genetics: the next stop for microbial ecologists?

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