Inferred Clades of Transposable Elements in Drosophila Suggest Co-evolution with piRNAs

AbstractTransposable elements (TEs) are self-replicating “genetic parasites” ubiquitous to eukaryotic genomes. In addition to conflict between TEs and their host genomes, TEs of the same family are in competition with each other. They compete for the same genomic niches while experiencing the same regime of copy-number selection. This suggests that competition among TEs may favor the emergence of new variants that can outcompete their brethren. To investigate the sequence evolution of TEs, we developed a method to infer clades: collections of TEs that share SNP variants and represent distinct TE family lineages. We applied this method to a panel of 85 Drosophila melanogaster genomes and found that the genetic variation of several TE families shows significant population structure that arises from the population-specific expansions of single clades. We used population genetic theory to classify these clades into younger versus older clades and found that younger clades are associated with a greater abundance of sense and antisense piRNAs per copy than older ones. Further, we find that the abundance of younger, but not older clades, is positively correlated with antisense piRNA production, suggesting a general pattern where hosts preferentially produce antisense piRNAs from recently active TE variants. Together these findings suggest a co-evolution of TEs and hosts, where new TE variants arise by mutation, then increase in copy number, and the host then responds by producing antisense piRNAs which may be used to silence these emerging variants.

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A spectral theory for Wright’s inbreeding coefficients and related quantities

PLoS Genetics ◽

10.1371/journal.pgen.1009665 ◽

2021 ◽

Vol 17 (7) ◽

pp. e1009665

Author(s):

Olivier François ◽

Clément Gain

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Population Genetic ◽

Principal Component ◽

Large Data ◽

Population Subdivision ◽

Adaptive Genetic Variation ◽

Genomic Locus ◽

Inbreeding Coefficients ◽

Definition Of

Wright’s inbreeding coefficient, FST, is a fundamental measure in population genetics. Assuming a predefined population subdivision, this statistic is classically used to evaluate population structure at a given genomic locus. With large numbers of loci, unsupervised approaches such as principal component analysis (PCA) have, however, become prominent in recent analyses of population structure. In this study, we describe the relationships between Wright’s inbreeding coefficients and PCA for a model of K discrete populations. Our theory provides an equivalent definition of FST based on the decomposition of the genotype matrix into between and within-population matrices. The average value of Wright’s FST over all loci included in the genotype matrix can be obtained from the PCA of the between-population matrix. Assuming that a separation condition is fulfilled and for reasonably large data sets, this value of FST approximates the proportion of genetic variation explained by the first (K − 1) principal components accurately. The new definition of FST is useful for computing inbreeding coefficients from surrogate genotypes, for example, obtained after correction of experimental artifacts or after removing adaptive genetic variation associated with environmental variables. The relationships between inbreeding coefficients and the spectrum of the genotype matrix not only allow interpretations of PCA results in terms of population genetic concepts but extend those concepts to population genetic analyses accounting for temporal, geographical and environmental contexts.

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Genetic variation and population structure of clonal Zingiber zerumbet at a fine geographic scale: a comparison with two closely related selfing and outcrossing Zingiber species

BMC Ecology and Evolution ◽

10.1186/s12862-021-01853-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Rong Huang ◽

Yu Wang ◽

Kuan Li ◽

Ying-Qiang Wang

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Plant Species ◽

Population Genetic ◽

Clonal Plants ◽

Zingiber Zerumbet ◽

Population Genetic Diversity ◽

Local Populations ◽

High Level

Abstract Background There has always been controversy over whether clonal plants have lower genetic diversity than plants that reproduce sexually. These conflicts could be attributed to the fact that few studies have taken into account the mating system of sexually reproducing plants and their phylogenetic distance. Moreover, most clonal plants in these previous studies regularly produce sexual progeny. Here, we describe a study examining the levels of genetic diversity and differentiation within and between local populations of fully clonal Zingiber zerumbet at a microgeographical scale and compare the results with data for the closely related selfing Z. corallinum and outcrossing Z. nudicarpum. Such studies could disentangle the phylogenetic and sexually reproducing effect on genetic variation of clonal plants, and thus contribute to an improved understanding in the clonally reproducing effects on genetic diversity and population structure. Results The results revealed that the level of local population genetic diversity of clonal Z. zerumbet was comparable to that of outcrossing Z. nudicarpum and significantly higher than that of selfing Z. corallinum. However, the level of microgeographic genetic diversity of clonal Z. zerumbet is comparable to that of selfing Z. corallinum and even slightly higher than that of outcrossing Z. nudicarpum. The genetic differentiation among local populations of clonal Z. zerumbet was significantly lower than that of selfing Z. corallinum, but higher than that of outcrossing Z. nudicarpum. A stronger spatial genetic structure appeared within local populations of Z. zerumbet compared with selfing Z. corallinum and outcrossing Z. nudicarpum. Conclusions Our study shows that fully clonal plants are able not only to maintain a high level of within-population genetic diversity like outcrossing plants, but can also maintain a high level of microgeographic genetic diversity like selfing plant species, probably due to the accumulation of somatic mutations and absence of a capacity for sexual reproduction. We suggest that conservation strategies for the genetic diversity of clonal and selfing plant species should be focused on the protection of all habitat types, especially fragments within ecosystems, while maintenance of large populations is a key to enhance the genetic diversity of outcrossing species.

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Posterior predictive checks to quantify lack-of-fit in admixture models of latent population structure

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1412301112 ◽

2015 ◽

Vol 112 (26) ◽

pp. E3441-E3450 ◽

Cited By ~ 6

Author(s):

David Mimno ◽

David M. Blei ◽

Barbara E. Engelhardt

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Population Genetic ◽

Association Studies ◽

Model Fit ◽

Widespread Application ◽

Posterior Predictive Checks ◽

Genomic Studies ◽

Population Genetic Variation

Admixture models are a ubiquitous approach to capture latent population structure in genetic samples. Despite the widespread application of admixture models, little thought has been devoted to the quality of the model fit or the accuracy of the estimates of parameters of interest for a particular study. Here we develop methods for validating admixture models based on posterior predictive checks (PPCs), a Bayesian method for assessing the quality of fit of a statistical model to a specific dataset. We develop PPCs for five population-level statistics of interest: within-population genetic variation, background linkage disequilibrium, number of ancestral populations, between-population genetic variation, and the downstream use of admixture parameters to correct for population structure in association studies. Using PPCs, we evaluate the quality of the admixture model fit to four qualitatively different population genetic datasets: the population reference sample (POPRES) European individuals, the HapMap phase 3 individuals, continental Indians, and African American individuals. We found that the same model fitted to different genomic studies resulted in highly study-specific results when evaluated using PPCs, illustrating the utility of PPCs for model-based analyses in large genomic studies.

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Reproductive system and population structure in two Hedysarum subspecies. I. Genetic variation within and between populations

Genome ◽

10.1139/g91-061 ◽

1991 ◽

Vol 34 (3) ◽

pp. 396-406 ◽

Cited By ~ 9

Author(s):

Hedi Baatout ◽

Daniel Combes ◽

Mohamed Marrakchi

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Genetic Variability ◽

Population Genetic ◽

Allozyme Variation ◽

Wild Populations ◽

Population Means ◽

Quantitative Characters ◽

Different Populations ◽

Population Genetic Variation

Several samples of wild populations of two subspecies of the genus Hedysarum (H. spinosissimum subspecies capitatum, an outcrosser, and H. spinosissimum subspecies euspinosissimum, a selfer) were examined with respect to variability of 25 quantitative characters and allozyme variation at 13 loci. The amount of phenotypic and genetic variation within and among populations was documented. For most of the 25 quantitative characters, the differences between population means and between the total variances of the populations were higher in the selfer than in the outbreeder. Significant among-population genetic variation was found for nearly all characters in the two subspecies, but the outbreeder had higher within-population variability than the selfer with heterogeneity among characters. However, allozyme variation at 13 loci in about the same number of populations showed higher levels of genetic variability in the outcrossing subspecies capitatum compared with the selfing subspecies euspinosissimum, based on measures of mean number of alleles per locus, mean proportion of polymorphic loci, and mean heterozygosity. Therefore, H. spinosissimum subsp. capitatum appeared to be highly polymorphic in contrast to the greater monomorphism within populations of H. spinosissimum subsp. euspinosissimum. The genetic affinities of different populations of a subspecies are uniformly high, with Nei's genetic identity ranging from 0.983 to 0.997 in the selfing subspecies euspinosissimum and from 0.922 to 1.000 in the outcrossing subspecies capitatum.Key words: Hedysarum, genetic variation, populations, electrophoresis.

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A Spectral Theory for Wright’s Inbreeding Coefficients and Related Quantities

10.1101/2020.10.07.329755 ◽

2020 ◽

Author(s):

Olivier François ◽

Clément Gain

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Population Genetic ◽

Principal Component ◽

Population Subdivision ◽

Genomic Locus ◽

Equivalent Definition ◽

Average Value ◽

Inbreeding Coefficients ◽

Definition Of

AbstractWright’s inbreeding coefficient, FST, is a fundamental measure in population genetics. Assuming a predefined population subdivision, this statistic is classically used to evaluate population structure at a given genomic locus. With large numbers of loci, unsupervised approaches such as principal component analysis (PCA) have, however, become prominent in recent analyses of population structure. In this study, we describe the relationships between Wright’s inbreeding coefficients and PCA for a model of K discrete populations. Our theory provides an equivalent definition of FST based on the decomposition of the genotype matrix into between and within-population matrices. Assuming that a separation condition is fulfilled, our main result states that the proportion of genetic variation explained by the first (K − 1) principal components can be accurately approximated by the average value of FST over all loci included in the genotype matrix. This equivalent definition of FST can be used to evaluate the fit of discrete population models to the data. It is also useful for computing inbreeding coefficients from surrogate genotypes, for example, obtained after correction of experimental artifacts or after removing genetic variation associated with environmental variables. The relationships between inbreeding coefficients and the spectrum of the genotype matrix not only allow interpretations of PCA results in terms of population genetic concepts but extend those concepts to population genetic analyses accounting for temporal, geographical and environmental contexts.

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Miniature inverted-repeat transposable elements: discovery, distribution, and activity

Genome ◽

10.1139/gen-2012-0174 ◽

2013 ◽

Vol 56 (9) ◽

pp. 475-486 ◽

Cited By ~ 40

Author(s):

Isam Fattash ◽

Rebecca Rooke ◽

Amy Wong ◽

Caleb Hui ◽

Tina Luu ◽

...

Keyword(s):

Transposable Elements ◽

Inverted Repeat ◽

Copy Number ◽

Copy Numbers ◽

Number Increase ◽

Eukaryotic Organisms ◽

Eukaryotic Genomes ◽

Copy Number Increase

Eukaryotic organisms have dynamic genomes, with transposable elements (TEs) as a major contributing factor. Although the large autonomous TEs can significantly shape genomic structures during evolution, genomes often harbor more miniature nonautonomous TEs that can infest genomic niches where large TEs are rare. In spite of their cut-and-paste transposition mechanisms that do not inherently favor copy number increase, miniature inverted-repeat transposable elements (MITEs) are abundant in eukaryotic genomes and exist in high copy numbers. Based on the large number of MITE families revealed in previous studies, accurate annotation of MITEs, particularly in newly sequenced genomes, will identify more genomes highly rich in these elements. Novel families identified from these analyses, together with the currently known families, will further deepen our understanding of the origins, transposase sources, and dramatic amplification of these elements.

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A Field Guide to Eukaryotic Transposable Elements

Annual Review of Genetics ◽

10.1146/annurev-genet-040620-022145 ◽

2020 ◽

Vol 54 (1) ◽

pp. 539-561 ◽

Cited By ~ 1

Author(s):

Jonathan N. Wells ◽

Cédric Feschotte

Keyword(s):

Genetic Variation ◽

Transposable Elements ◽

Dna Sequences ◽

Genetic Factors ◽

Mobile Dna ◽

Substantial Fraction ◽

Evolutionary Origins ◽

Unique Biology ◽

Dramatic Variation ◽

Eukaryotic Genomes

Transposable elements (TEs) are mobile DNA sequences that propagate within genomes. Through diverse invasion strategies, TEs have come to occupy a substantial fraction of nearly all eukaryotic genomes, and they represent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic behavior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species.

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Inferring continuous and discrete population genetic structure across space

10.1101/189688 ◽

2017 ◽

Cited By ~ 7

Author(s):

Gideon S. Bradburd ◽

Graham M. Coop ◽

Peter L. Ralph

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Population Genetic ◽

Natural Variation ◽

Genetic Relatedness ◽

Isolation By Distance ◽

Genetic Data ◽

Secondary Contact ◽

Discrete Population ◽

Geographically Distributed

AbstractA classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations. Here, we present a statistical framework for the simultaneous inference of continuous and discrete patterns of population structure. The method estimates ancestry proportions for each sample from a set of two-dimensional population layers, and, within each layer, estimates a rate at which relatedness decays with distance. This thereby explicitly addresses the “clines versus clusters” problem in modeling population genetic variation. The method produces useful descriptions of structure in genetic relatedness in situations where separated, geographically distributed populations interact, as after a range expansion or secondary contact. We demonstrate the utility of this approach using simulations and by applying it to empirical datasets of poplars and black bears in North America.Author summaryOne of the first steps in the analysis of genetic data, and a principal mission of biology, is to describe and categorize natural variation. A continuous pattern of differentiation (isolation by distance), where individuals found closer together in space are, on average, more genetically similar than individuals sampled farther apart, can confound attempts to categorize natural variation into groups. This is because current statistical methods for assigning individuals to discrete clusters cannot accommodate spatial patterns, and so are forced to use clusters to describe what is in fact continuous variation. As isolation by distance is common in nature, this is a substantial shortcoming of existing methods. In this study, we introduce a new statistical method for categorizing natural genetic variation - one that describes variation as a combination of continuous and discrete patterns. We demonstrate that this method works well and can capture patterns in population genomic data without resorting to splitting populations where they can be described by continuous patterns of variation.

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The population dynamics of transposable elements

Genetics Research ◽

10.1017/s0016672300021455 ◽

1983 ◽

Vol 42 (1) ◽

pp. 1-27 ◽

Cited By ~ 253

Author(s):

Brian Charlesworth ◽

Deborah Charlesworth

Keyword(s):

Population Dynamics ◽

Transposable Elements ◽

Copy Number ◽

Probability Distributions ◽

General Pattern ◽

Simulation Models ◽

Theoretical Models ◽

Infinite Population ◽

Individual Fitness ◽

Set Up

SUMMARYThis paper describes analytical and simulation models of the population dynamics of transposable elements in randomly mating populations. The models assume a finite number of chromosomal sites that are occupable by members of a given family of elements. Element frequencies can change as a result of replicative transposition, loss of elements from occupied sites, selection on copy number per individual, and genetic drift. It is shown that, in an infinite population, an equilibrium can be set up such that not all sites in all individuals are occupied, allowing variation between individuals in both copy number and identity of occupied sites, as has been observed for several element families in Drosophila melanogaster. Such an equilibrium requires either regulation of transposition rate in response to copy number per genome, a sufficiently strongly downwardly curved dependence of individual fitness on copy number, or both. The probability distributions of element frequencies, generated by the effects of finite population size, are derived on the assumption of independence between different loci, and compared with simulation results. Despite some discrepancies due to violation of the independence assumption, the general pattern seen in the simulations agrees quite well with theory.Data from Drosophila population studies are compared with the theoretical models, and methods of estimating the relevant parameters are discussed.

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