simuPOP: a forward-time population genetics simulation environment

Peng, Bo; Kimmel, Marek

doi:10.1093/bioinformatics/bti584

Cited by 306 publications

(300 citation statements)

References 6 publications

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“…S. mutans sequences were derived by Sanger sequencing following PCR amplification of a region of the spaP gene directly from DNA insulated from human mouthwash samples. Population simulations were conducted using simuPOP (53). Correlation of population subsistence with mean population copy number was performed as previously described (31,33).…”

Section: Methodsmentioning

confidence: 99%

Evolution of the rapidly mutating human salivary agglutinin gene ( DMBT1 ) and population subsistence strategy

Polley

Louzada

Forni

et al. 2015

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

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The dietary change resulting from the domestication of plant and animal species and development of agriculture at different locations across the world was one of the most significant changes in human evolution. An increase in dietary carbohydrates caused an increase in dental caries following the development of agriculture, mediated by the cariogenic oral bacterium Streptococcus mutans. Salivary agglutinin [SAG, encoded by the deleted in malignant brain tumors 1 (DMBT1) gene] is an innate immune receptor glycoprotein that binds a variety of bacteria and viruses, and mediates attachment of S. mutans to hydroxyapatite on the surface of the tooth. In this study we show that multiallelic copy number variation (CNV) within DMBT1 is extensive across all populations and is predicted to result in between 7-20 scavenger-receptor cysteinerich (SRCR) domains within each SAG molecule. Direct observation of de novo mutation in multigeneration families suggests these CNVs have a very high mutation rate for a protein-coding locus, with a mutation rate of up to 5% per gamete. Given that the SRCR domains bind S. mutans and hydroxyapatite in the tooth, we investigated the association of sequence diversity at the SAG-binding gene of S. mutans, and DMBT1 CNV. Furthermore, we show that DMBT1 CNV is also associated with a history of agriculture across global populations, suggesting that dietary change as a result of agriculture has shaped the pattern of CNV at DMBT1, and that the DMBT1-S. mutans interaction is a promising model of host-pathogenculture coevolution in humans.copy number variation | agriculture | DMBT1 | mutation | structural variation

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Section: Methodsmentioning

confidence: 99%

Evolution of the rapidly mutating human salivary agglutinin gene ( DMBT1 ) and population subsistence strategy

Polley

Louzada

Forni

et al. 2015

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

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“…The evolutionary relationships between the diverged alleles encoding for the ferrichrome ABC transporter and the large ribosomal protein L10 was visualized in splits graphs using SplitsTree4 (ref. 79), and branch lengths and number of splits in the observed phylogenetic networks were compared with those from simulated populations using simuPOP 80 . Population genetic simulations assuming a base mutation rate μ = 10 −9 were performed across a range of values for the population mutation parameter theta (θ = 4N e μ) and the recombination rate (R) to estimate effective population size (N e ) and recombination rates relative to the mutation rate (R/μ).…”

Section: Letter Researchmentioning

confidence: 99%

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Möck

Otillar

Strauss

et al. 2017

Nature

328

303

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The Southern Ocean houses a diverse and productive community of organisms 1,2 . Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice 3-7 . How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus 8,9 , based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation.

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“…First, a coalescent simulation program, SIMCOAL2 (Laval and Excoffier, 2004) was used to produce populations in approximate mutation-drift equilibrium. These populations were then used to initialize the forward-time simulation program SimuPop (Peng and Kimmel, 2005). In the forward simulation, populations were held to a 1:1 sex ratio with random mating.…”

Section: Simulation Proceduresmentioning

confidence: 99%

Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

2016

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Contemporary effective population size (N e ) can be estimated using linkage disequilibrium (LD) observed across pairs of loci presumed to be selectively neutral and unlinked. This method has been commonly applied to data sets containing 10-100 loci to inform conservation and study population demography. Performance of these N e estimates could be improved by incorporating data from thousands of loci. However, these thousands of loci exist on a limited number of chromosomes, ensuring that some fraction will be physically linked. Linked loci have elevated LD due to limited recombination, which if not accounted for can cause N e estimates to be downwardly biased. Here, we present results from coalescent and forward simulations designed to evaluate the bias of LD-based N e estimates (N e ). Contrary to common perceptions, increasing the number of loci does not increase the magnitude of linkage. Although we show it is possible to identify some pairs of loci that produce unusually large r 2 values, simply removing large r 2 values is not a reliable way to eliminate bias. Fortunately, the magnitude of bias inN e is strongly and negatively correlated with the process of recombination, including the number of chromosomes and their length, and this relationship provides a general way to adjust for bias. Additionally, we show that with thousands of loci, precision ofN e is much lower than expected based on the assumption that each pair of loci provides completely independent information. Heredity (Wright, 1931), which determines the rate of evolutionary change due to genetic drift and informs the equilibrium level of genetic variation and the effectiveness of selection. N e is often much lower than census size (Frankham, 1995), demonstrating that simply counting individuals is insufficient to predict rates of evolutionary change. In addition to the number of mating individuals, N e is affected by sex ratio, variation in reproductive success, age structure, migration and other demographic factors. It is an extremely relevant metric in conservation biology, with low N e leading to inbreeding and reduced genetic diversity (Ellstrand and Elam, 1993). See Charlesworth (2009) for a primer on N e , and Wang (2005) for a review of estimation methods.Populations with smaller N e undergo more genetic drift than larger populations. This genetic drift randomly generates associations between alleles at different loci, known as linkage (or gametic) disequilibrium (LD) at a rate inversely proportional to N e . As a result, measures of LD between independently-segregating loci can be used to provide an estimate of N e (Sved, 1971;Hill, 1981;Waples, 1991). Over the past decades, many studies have leveraged data sets consisting of a few dozen loci for genetic estimates of N e (Luikart et al., 2010). While these studies continue to be useful, especially for long-running

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simuPOP: a forward-time population genetics simulation environment

Abstract: simuPOP is freely available at http://simupop.sourceforge.net, distributed under GPL license.

Cited by 306 publications

References 6 publications

Evolution of the rapidly mutating human salivary agglutinin gene ( DMBT1 ) and population subsistence strategy

Evolution of the rapidly mutating human salivary agglutinin gene ( DMBT1 ) and population subsistence strategy

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

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