scholarly journals Population genetics of transposable element load: a mechanistic account of observed overdispersion

2020 ◽  
Author(s):  
Ronald D. Smith ◽  
Joshua R. Puzey ◽  
Gregory D. Conradi Smith
Keyword(s):  
Population Genetics ◽  
Transposable Element ◽  
Natural Populations ◽  
Purifying Selection ◽  
Death Process ◽  
Stationary Population ◽  
Population Distributions ◽  
Evolutionary Genetic ◽  
Genetic Mechanisms ◽  
Copy And Paste

AbstractIn an empirical analysis of transposable element (TE) abundance within natural populations of Mimulus guttatus and Drosophila melanogaster, we found a surprisingly high variance of TE count (e.g., variance-to-mean ratio on the order of 10 to 100). To obtain insight regarding those evolutionary genetic mechanisms that are may underlie the overdispersed population distributions of TE abundance, we developed a mathematical model of TE population genetics that includes the dynamics of element proliferation and purifying selection on TE load. The modeling approach begins with a master equation for a birth-death process and it extends the predictions of the classical theory of TE dynamics in several ways. In particular, moment-based analysis of stationary population distributions of TE load reveal that overdispersion is most likely to arise via copy-and-paste (as opposed to cut-and-paste) dynamics. Parameter studies suggest that overdispersed population distributions of TE abundance are probably not a consequence of purifying selection on total element load.

On the evolution and population genetics of hybrid-dysgenesis-causing transposable elements in Drosophila

1986 ◽  
Vol 312 (1154) ◽  
pp. 205-215 ◽  
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Transposable Elements ◽  
Transposable Element ◽  
Natural Populations ◽  
Element Composition ◽  
Hybrid Dysgenesis ◽  
Evolutionary Significance ◽  
Genetic Elements ◽  
Transposable Genetic Elements

Much has been learned about transposable genetic elements in Drosophila , but questions still remain, especially concerning their evolutionary significance. Three such questions are considered here, (i) Has the behaviour of transposable elements been most influenced by natural selection at the level of the organism, the population, or the elements themselves? (ii) How did the elements originate in the genome of the species? (iii) Why are laboratory stocks different from natural populations with respect to their transposable element composition? No final answers to these questions are yet available, but by focusing on the two families of hybrid dysgenesis-causing elements, the P and I factors, we can draw some tentative conclusions.

scholarly journals piRNA Clusters Need a Minimum Size to Control Transposable Element Invasions

2020 ◽  
Vol 12 (5) ◽  
pp. 736-749 ◽  
Author(s):  
Robert Kofler
Keyword(s):  
Population Genetics ◽  
Transposable Element ◽  
Minimum Size ◽  
Total Size ◽  
Evolutionary Forces ◽  
A Genome ◽  
In Trans ◽  
Single Insertion

Abstract piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. Moreover, larger piRNA clusters accounting for up to 3% of the genome may be necessary when populations are small, transposition rates are high, and TE insertions are recessive. If piRNA clusters are too small, the load of deleterious TE insertions that accumulate during a TE invasion may drive populations extinct before an effective piRNA-based defense against the TE can be established. Our findings are solely based on three well-supported assumptions: 1) TEs multiply within genomes, 2) TEs are mostly deleterious, and 3) piRNA clusters act as transposon traps, where a single insertion in a cluster silences all TE copies in trans. Interestingly, the piRNA clusters of some species meet our observed minimum size requirements, whereas the clusters of other species do not. Species with small piRNA clusters, such as humans and mice, may experience severe fitness reductions during invasions of novel TEs, which is possibly even threatening the persistence of some populations. This work also raises the important question of how piRNA clusters evolve. We propose that the size of piRNA clusters may be at an equilibrium between evolutionary forces that act to expand and contract piRNA clusters.

scholarly journals The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens

2015 ◽  
Vol 25 (1) ◽  
pp. 42-66 ◽  
Author(s):  
Benjamin A. Wilson ◽  
Nandita R. Garud ◽  
Alison F. Feder ◽  
Zoe J. Assaf ◽  
Pleuni S. Pennings
Keyword(s):  
Drug Resistance ◽  
Population Genetics ◽  
Natural Populations ◽  
Resistance Evolution

scholarly journals Conserved noncoding elements influence the transposable element landscape in Drosophila

2018 ◽  
Author(s):  
Manee M. Manee ◽  
John Jackson ◽  
Casey M. Bergman
Keyword(s):  
Transposable Element ◽  
Significant Proportion ◽  
Purifying Selection ◽  
Noncoding Dna ◽  
Frequency Spectra ◽  
Noncoding Regions ◽  
Selective Constraints ◽  
Large Numbers ◽  
Random Expectation ◽  
Conserved Noncoding Elements

AbstractHighly conserved noncoding elements (CNEs) comprise a significant proportion of the genomes of multicellular eukaryotes. The function of most CNEs remains elusive, but growing evidence indicates they are under some form of purifying selection. Noncoding regions in many species also harbor large numbers of transposable element (TE) insertions, which are typically lineage specific and depleted in exons because of their deleterious effects on gene function or expression. However, it is currently unknown whether the landscape of TE insertions in noncoding regions is random or influenced by purifying selection on CNEs. Here we combine comparative and population genomic data in Drosophila melanogaster to show that abundance of TE insertions in intronic and intergenic CNEs is reduced relative to random expectation, supporting the idea that selective constraints on CNEs eliminate a proportion of TE insertions in noncoding regions. However, we find no difference in the allele frequency spectra for polymorphic TE insertions in CNEs versus those in unconstrained spacer regions, suggesting that the distribution of fitness effects acting on observable TE insertions is similar across different functional compartments in noncoding DNA. Our results provide evidence that selective constraints on CNEs contribute to shaping the landscape of TE insertion in eukaryotic genomes, and provide further evidence supporting the conclusion that CNEs are indeed functionally constrained and not simply mutational cold spots.

scholarly journals THE EVOLUTION OF SELECTIVELY SIMILAR ELECTRO-PHORETICALLY DETECTABLE ALLELES IN FINITE NATURAL POPULATIONS

Genetics ◽  
1975 ◽  
Vol 80 (2) ◽  
pp. 375-394
Author(s):  
C F Wehrhahn
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Generating Functions ◽  
Natural Populations ◽  
Net Charge ◽  
Electrophoretic Variants ◽  
Allelic State ◽  
Competing Hypotheses ◽  
State Difference ◽  
General Method

Abstract Most of the models of population genetics are not realistic when applied to data on electrophoretic variants of proteins because the same net charge may result from any of several amino acid combinations. In the absence of realistic models they have, however, been widely used to test competing hypotheses about the origin and maintenance of genetic variation in populations. In this paper I present a general method for determining probability generating functions for electrophoretic state differences. Then I use the method to find allelic state difference distributions for selectively similar electrophoretically detectable alleles in finite natural populations. Predicted patterns of genetic variation, both within and among species, are in reasonable accord with those found in the Drosophila willistoni group by Ayala et al. (1972) and by Ayala and Tracey (1974).

scholarly journals Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura

2002 ◽  
Vol 80 (3) ◽  
pp. 163-175 ◽  
Author(s):  
STEPHEN W. SCHAEFFER
Keyword(s):  
Negative Selection ◽  
Genome Rearrangement ◽  
Rare Variants ◽  
Natural Populations ◽  
Population Expansion ◽  
Purifying Selection ◽  
Sequence Length ◽  
Nucleotide Sequence Analysis ◽  
Drosophila Pseudoobscura ◽  
Indel Variation

Positive and negative selection on indel variation may explain the correlation between intron length and recombination levels in natural populations of Drosophila. A nucleotide sequence analysis of the 3·5 kilobase sequence of the alcohol dehydrogenase (Adh) region from 139 Drosophila pseudoobscura strains and one D. miranda strain was used to determine whether positive or negative selection acts on indel variation in a gene that experiences high levels of recombination. A total of 30 deletion and 36 insertion polymorphisms were segregating within D. pseudoobscura populations and no indels were fixed between D. pseudoobscura and its two sibling species D. miranda and D. persimilis. The ratio of Tajima's D to its theoretical minimum value (Dmin) was proposed as a metric to assess the heterogeneity in D among D. pseudoobscura loci when the number of segregating sites differs among loci. The magnitude of the D/Dmin ratio was found to increase as the rate of population expansion increases, allowing one to assess which loci have an excess of rare variants due to population expansion versus purifying selection. D. pseudoobscura populations appear to have had modest increases in size accounting for some of the observed excess of rare variants. The D/Dmin ratio rejected a neutral model for deletion polymorphisms. Linkage disequilibrium among pairs of indels was greater than between pairs of segregating nucleotides. These results suggest that purifying selection removes deletion variation from intron sequences, but not insertion polymorphisms. Genome rearrangement and size-dependent intron evolution are proposed as mechanisms that limit runaway intron expansion.

scholarly journals Applicability of the Mutation–Selection Balance Model to Population Genetics of Heterozygous Protein-Truncating Variants in Humans

2019 ◽  
Vol 36 (8) ◽  
pp. 1701-1710 ◽  
Author(s):  
Donate Weghorn ◽  
Daniel J Balick ◽  
Christopher Cassa ◽  
Jack A Kosmicki ◽  
Mark J Daly ◽  
...  
Keyword(s):  
Population Genetics ◽  
De Novo ◽  
Demographic History ◽  
Purifying Selection ◽  
Population History ◽  
Balance Model ◽  
Data Set ◽  
Stochastic Force ◽  
Drift Estimation ◽  
Human Genes

Abstract The fate of alleles in the human population is believed to be highly affected by the stochastic force of genetic drift. Estimation of the strength of natural selection in humans generally necessitates a careful modeling of drift including complex effects of the population history and structure. Protein-truncating variants (PTVs) are expected to evolve under strong purifying selection and to have a relatively high per-gene mutation rate. Thus, it is appealing to model the population genetics of PTVs under a simple deterministic mutation–selection balance, as has been proposed earlier (Cassa et al. 2017). Here, we investigated the limits of this approximation using both computer simulations and data-driven approaches. Our simulations rely on a model of demographic history estimated from 33,370 individual exomes of the Non-Finnish European subset of the ExAC data set (Lek et al. 2016). Additionally, we compared the African and European subset of the ExAC study and analyzed de novo PTVs. We show that the mutation–selection balance model is applicable to the majority of human genes, but not to genes under the weakest selection.

scholarly journals Sewall Wright, 21 December 1889 - 3 March 1988

1990 ◽  
Vol 36 ◽  
pp. 567-579 ◽  
Keyword(s):  
Population Genetics ◽  
Evolutionary Biology ◽  
Natural Populations ◽  
Coat Colour ◽  
Balance Theory ◽  
Theory Of Evolution ◽  
Shifting Balance Theory ◽  
Sewall Wright ◽  
Shifting Balance ◽  
Active Research

Sewall Wright's active life spanned the development of genetics from a new discipline when the principles of inheritance were still being elucidated to the technology of recombinant gene construction and insertion. He was one of the major pioneers of population genetics, which gave a quantitative basis to the studies of evolution, of variation in natural populations and of animal and plant breeding. He contributed most significantly to methods and ideas over a long period, indeed his four volume treatise was written long after he formally ‘retired’ and his last paper (211) was published a few days before his death at the age of 98. In the field of population genetics Wright developed the method of path coefficients, which he used to analyse quantitative genetic variation and relationship, but which has been applied to subjects as diverse as economics, the ideas of inbreeding coefficient and F -statistics which form the basis of analysis of population structure, the theory of variation in gene frequency among populations, and the shifting balance theory of evolution, which remains a topic of active research and controversy. Wright contributed to physiological genetics, notably analysis of the inheritance of coat colour in the guinea pig, and in particular the epistatic relationships among the genes involved. There was a critical interplay between his population and physiological work, in that the analysis of finite populations on the one hand and of epistatic interactions on the other are the bases of Wright’s development of the shifting balance theory. A full and enlightening biography of Sewall Wright which traces his influence on evolutionary biology and his interactions with other important workers was published recently (Provine 1986) and shorter appreciations have appeared since his death, notably by Crow (1988), Wright’s long-time colleague. This biography relies heavily on Provine’s volume, and does no more than summarize Wright’s extensive contributions. Many of his important papers have been reprinted recently (1986).

scholarly journals A Killer–Rescue system for self-limiting gene drive of anti-pathogen constructs

2008 ◽  
Vol 275 (1653) ◽  
pp. 2823-2829 ◽  
Author(s):  
Fred Gould ◽  
Yunxin Huang ◽  
Mathieu Legros ◽  
Alun L Lloyd
Keyword(s):  
Gene Action ◽  
Natural Populations ◽  
Gene Drive ◽  
Fitness Costs ◽  
Molecular Approaches ◽  
Genetic Mechanisms ◽  
Rescue System ◽  
Near Term ◽  
Killer Gene ◽  
Over Time

A number of genetic mechanisms have been suggested for driving anti-pathogen genes into natural populations. Each of these mechanisms requires complex genetic engineering, and most are theoretically expected to permanently spread throughout the target species' geographical range. In the near term, risk issues and technical limits of molecular methods could delay the development and use of these mechanisms. We propose a gene-drive mechanism that can be self-limiting over time and space, and is simpler to build. This mechanism involves one gene that codes for toxicity (killer) and a second that confers immunity to the toxic effects (rescue). We use population-genetic models to explore cases with one or two independent insertions of the killer gene and one insertion of the rescue gene. We vary the dominance and penetrance of gene action, as well as the magnitude of fitness costs. Even with the fitness costs of 10 per cent for each gene, the proportion of mosquitoes expected to transmit the pathogen decreases below 5 per cent for over 40 generations after one 2 : 1 release (engineered : wild) or after four 1 : 2 releases. Both the killer and rescue genes will be lost from the population over time, if the rescue construct has any associated fitness cost. Molecular approaches for constructing strains are discussed.

scholarly journals Pervasive Purifying Selection Characterizes the Evolution of I2 Homologs

2006 ◽  
Vol 19 (3) ◽  
pp. 288-303 ◽  
Author(s):  
Brett C. Couch ◽  
Russ Spangler ◽  
Christine Ramos ◽  
Georgiana May
Keyword(s):  
Amino Acid ◽  
Gene Family ◽  
General Pattern ◽  
Purifying Selection ◽  
Gene Family Evolution ◽  
Death Process ◽  
Phylogenetic Distance ◽  
R Gene ◽  
The Family ◽  
Codon Positions

We sampled 384 sequences related to the Solanum pimpinel-lifolium (=Lycopersicon pimpinellifolium) disease resistance (R) gene I2 from six species, potato, S. demissum, tomato, eggplant, pepper, and tobacco. These species represent increasing phylogenetic distance from potato to tobacco, within the family Solanaceae. Using sequence data from the nucleotide binding site (NBS) region of this gene, we tested models of gene family evolution and inferred patterns of selection acting on the NBS gene region and I2 gene family. We find that the I2 family has diversified within the family Solanaceae for at least 14 million years and evolves through a slow birth-and-death process requiring approximately 12 million years to homogenize gene copies within a species. Analyses of selection resolved a general pattern of strong purifying selection acting on individual codon positions within the NBS and on NBS lineages through time. Surprisingly, we find nine codon positions strongly affected by positive selection and six pairs of codon positions demonstrating correlated amino acid substitutions. Evolutionary analyses serve as bioinformatic tools with which to sort through the vast R gene diversity in plants and find candidates for new resistance specificities or to identify specific amino acid positions important for biochemical function. The slow birth-and-death evolution of I2 genes suggests that some NBS-leucine rich repeat-mediated resistances may not be overcome rapidly by virulence evolution and that the natural diversity of R genes is a potentially valuable source for durable resistance.

Sign in / Sign up

Export Citation Format

Share Document