Transposable element copy number and stable polymorphisms

We consider a simple and analytically solvable model for the spread of a transposable element which has deleterious effects on fitness. Two possible modes are treated, one in which transposition occurs in the newly fertilized zygote, and another in which transposition takes place only in the germ line. In effect, transposition precedes selection in the first case and follows it in the second. This has different long-term consequences depending on the rate of transposition and the values of the selection coefficients. Conditions are derived for the existence of a stable polymorphism with respect to element copy number; the conditions are more stringent in the first case than in the second. It is proved that a polymorphism is impossible unless the copy number decreases fitness in a more-than-muitiplicative fashion.     

Mutation-selection balance in mixed mating populations

An approximation to the average number of deleterious mutations per gamete, Q, is derived from a model allowing selection on both zygotes and male gametes. Progeny are produced by either outcrossing or self-fertilization with fixed probabilities. The genetic model is a standard in evolutionary biology: mutations occur at unlinked loci, have equivalent effects, and combine multiplicatively to determine fitness. The approximation developed here treats individual mutation counts with a generalized Poisson model conditioned on the distribution of selfing histories in the population. The approximation is accurate across the range of parameter sets considered and provides both analytical insights and greatly increased computational speed. Model predictions are discussed in relation to several outstanding problems, including the estimation of the genomic deleterious mutation rates (U), the generality of "selective interference" among loci, and the consequences of gametic selection for the joint distribution of inbreeding depression and mating system across species. Finally, conflicting results from previous analytical treatments of mutation-selection balance are resolved to assumptions about the life-cycle and the initial fate of mutations.     

Evolution of interactions in family-structured populations: mixed mating models

THE EFFECT OF INBREEDING ON SOCIALITY IS STUDIED THEORETICALLY FOR THE EVOLUTION OF INTERACTIONS BETWEEN SIBLINGS IN CERTAIN MIXED MATING SYSTEMS THAT GIVE RISE TO INBREEDING: sib with random mating and selfing with random mating. Two approaches are taken. First, specific models of altruism are studied for the various mating systems. In the case of the additive model, inbreeding facilitates the evolution of altruistic genes. Likewise, for the multiplicative model this is usually the case, as long as the costs of altruism are not too great. Second, the case of total altruism, in which the gene has zero individual fitness but increases the fitness of associates, is studied for a general fitness formulation. In this case, inbreeding often retards the ability of such genes to increase when rare, and the equilibrium frequency of those recessive genes that can increase is totally independent of the mating system and, consequently, of the amount of inbreeding. It appears from the results presented that inbreeding facilitates most forms of altruism, but retards extreme altruism. These results stem from the fact that inbreeding increases the within-family relatedness by increasing the between-family variance in allele frequency. In most cases this facilitates altruism. However, in the case of total altruism, only heterozygotes can pass on the altruistic allele, and inbreeding tends to decrease this heterozygote class. In either case, the important effect of inbreeding lies in altering the genotypic distribution of the interactions.     

Structure of populations under mixed random and sib mating

Summary The present investigation relates to various properties of population bred by mixture of breeding systems namely mixed random and sib mating. Expressions have been derived which give the genotypic frequencies in any given generation in terms of the initial values. Under the mating system considered the population will eventually become stable having a certain amount of heterozygosis depending upon the amounts of random and sib mating. The loss of heterozygosity in successive generations has been examined for varying amounts of sib mating in the population.The formulae have been derived giving the mean and genotypic variance in any given generation of continued mixed mating. The effect of the mating system considered on mean and genotypic variance in successive generations has been discussed in detail in case of (i) absence of dominance and (ii) complete dominance.

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Zusammenfassung Die vorliegende Untersuchung bezieht sich auf verschiedene Eigenheiten des Populationsverhaltens unter Einfluß einer Mischung von Paarungssystemen, nämlich der Panmixie und der Geschwisterpaarung. Es wurden Formeln abgeleitet, die die genotypischen Frequenzen in jeder beliebigen Generation in Beziehung zu den Ausgangswerten angeben. Unter dem betrachteten Paarungssystem kann die Population gegebenenfalls stabil werden mit einem bestimmten Heterozygotieanteil, der vom Ausmaß der Panmixie und der Geschwisterpaarung abhängt. Für verschiedene Anteile der Geschwisterpaarung wurde der Verlust der Heterozygotie in aufeinanderfolgenden Generationen untersucht.Die abgeleiteten Formeln liefern das Mittel und die genotypische Varianz in jeder beliebigen Generation fortgesetzter gemischter Paarung. Die Wirkung des betrachteten Paarungssystems auf Mittel und genotypische Varianz in aufeinanderfolgenden Generationen wurde (1) für den Fall der Abwesenheit der Dominanz und (2) den der vollständigen Dominanz ausführlich diskutiert.

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Journal paper No. J-6127, of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa. Project No. 1669. This work was supported by the National Institutes of Health, Grant No. GM-13827.     

Pollinator-mediated assortative mating in mixed ploidy populations of Chamerion angustifolium (Onagraceae)

Establishment of polyploid individuals within diploid populations is theoretically unlikely unless polyploids are reproductively isolated, pre-zygotically, through assortative pollination. Here, we quantify the contribution of pollinator diversity and foraging behaviour to assortative pollen deposition in three mixed-ploidy populations of Chamerion angustifolium (Onagraceae). Diploids and tetraploids were not differentiated with respect to composition of insect visitors. However, foraging patterns of the three most common insect visitors (all bees) reinforced assortative pollination. Bees visited tetraploids disproportionately often and exhibited higher constancy on tetraploids in all three populations. In total, 73% of all bee flights were between flowers of the same ploidy (2x–2x, 4x–4x); 58% of all flights to diploids and 83% to tetraploids originated from diploid and tetraploid plants, respectively. Patterns of pollen deposition on stigmas mirrored pollinator foraging behaviour; 73% of all pollen on stigmas (70 and 75% of pollen on diploid and tetraploid stigmas, respectively) came from within-ploidy pollinations. These results indicate that pollinators contribute to high rates of pre-zygotic reproductive isolation. If patterns of fertilization track pollen deposition, pollinator–plant interactions may help explain the persistence and spread of tetraploids in mixed-ploidy populations.     

Transposable elements and microevolutionary changes in natural populations

Transposable elements (TEs) usually represent the most abundant and dynamic fraction of genomes in almost all living organisms. The overall capacity of such ‘junk DNA’ to induce mutations and foster the reorganization of functional genomes suggests that TE may be of central evolutionary significance. However, to what extent TE dynamics drive and is driven by the evolutionary trajectory of host taxa remains poorly known. Further work addressing the fate of TE insertions in natural populations is necessary to shed light on their impact on microevolutionary processes. Here, we highlight methodological approaches (i.e. transposon displays and high‐throughput sequencing), tracking TE insertions across large numbers of individuals and discuss their pitfalls and benefits for molecular ecology surveys.     

Inbreeding depression and mixed mating in Leptosiphon jepsonii: a comparison of three populations

BACKGROUND AND AIMS: Inbreeding depression is thought to play a central role in the evolution and maintenance of cross-fertilization. Theory indicates that inbreeding depression can be purged with self-fertilization, resulting in positive feedback for the selection of selfing. Variation among populations of Leptosiphon jepsonii in the timing and rate of self-fertilization provides an opportunity to study the evolution of inbreeding depression and mating systems. In addition, the hypothesis that differences in inbreeding depression for male and female fitness can stabilize mixed mating in L. jepsonii is tested. METHODS: In a growth room experiment, inbreeding depression was measured in three populations with mean outcrossing rates ranging from 0.06 to 0.69. The performance of selfed and outcrossed progeny is compared at five life history stages. To distinguish between self-incompatibility and early inbreeding depression, aborted seeds and unfertilized ovules were counted in selfed and outcrossed fruits. In one population, pollen and ovule production was quantified to estimate inbreeding depression for male and female fitness. KEY RESULTS: Both prezygotic barriers and inbreeding depression limited self seed set in the most outcrossing population. Cumulative inbreeding depression ranged from 0.297 to 0.501, with the lowest value found in the most selfing population. Significant inbreeding depression for early life stages was found only in the more outcrossing populations. Inbreeding depression was not significant for pollen or ovule production. CONCLUSIONS: The results provide modest support for the hypothesized relationship between inbreeding depression and mating systems. The absence of early inbreeding depression in the more selfing populations is consistent with theory on purging. Differences in male and female expression of inbreeding depression do not appear to stabilize mixed mating in L. jepsonii. The current estimates of inbreeding depression for L. jepsonii differ from those of previous studies, underscoring the effects of environmental variation on its expression.     

Transposable element origins of epigenetic gene regulation

Transposable elements (TEs) are massively abundant and unstable in all plant genomes, but are mostly silent because of epigenetic suppression. Because all known epigenetic pathways act on all TEs, it is likely that the specialized epigenetic regulation of regular host genes (RHGs) was co-opted from this ubiquitous need for the silencing of TEs and viruses. With their internally repetitive and rearranging structures, and the acquisition of fragments of RHGs, the expression of TEs commonly makes antisense RNAs for both TE genes and RHGs. These antisense RNAs, particularly from heterochromatic reservoirs of 'zombie' TEs that are rearranged to form variously internally repetitive structures, may be advantageous because their induction will help rapidly suppress active TEs of the same family. RHG fragments within rapidly rearranging TEs may also provide the raw material for the ongoing generation of miRNA genes. TE gene expression is regulated by both environmental and developmental signals, and insertions can place nearby RHGs under the regulation (both standard and epigenetic) of the TE. The ubiquity of TEs, their frequent preferential association with RHGs, and their ability to be programmed by epigenetic signals all indicate that RGHs have nearly unlimited access to novel regulatory cassettes to assist plant adaptation.     

Ancestry-related assortative mating in Latino populations

Background

While spouse correlations have been documented for numerous traits, no prior studies have assessed assortative mating for genetic ancestry in admixed populations.

Results

Using 104 ancestry informative markers, we examined spouse correlations in genetic ancestry for Mexican spouse pairs recruited from Mexico City and the San Francisco Bay Area, and Puerto Rican spouse pairs recruited from Puerto Rico and New York City. In the Mexican pairs, we found strong spouse correlations for European and Native American ancestry, but no correlation in African ancestry. In the Puerto Rican pairs, we found significant spouse correlations for African ancestry and European ancestry but not Native American ancestry. Correlations were not attributable to variation in socioeconomic status or geographic heterogeneity. Past evidence of spouse correlation was also seen in the strong evidence of linkage disequilibrium between unlinked markers, which was accounted for in regression analysis by ancestral allele frequency difference at the pair of markers (European versus Native American for Mexicans, European versus African for Puerto Ricans). We also observed an excess of homozygosity at individual markers within the spouses, but this provided weaker evidence, as expected, of spouse correlation. Ancestry variance is predicted to decline in each generation, but less so under assortative mating. We used the current observed variances of ancestry to infer even stronger patterns of spouse ancestry correlation in previous generations.

Conclusions

Assortative mating related to genetic ancestry persists in Latino populations to the current day, and has impacted on the genomic structure in these populations.     

Hardy-Weinberg equilibria in random mating populations

The structure of multiloci random mating populations is examined. Sufficient conditions for the existence of stable local Hardy-Weinberg equilibria for n loci and an arbitrary number of alleles per locus, are then derived for specified situations under the assumption of multiplicative gene action between loci. It is shown that a stable Hardy-Weinberg equilibrium can not be a local maximum of the mean fitness function with multiplicative gene action between loci. The stability of Hardy-Weinberg type border points and the condition for the increase of newly introduced genes are topics on which some n-loci results are also obtained for an arbitrary number of alleles per locus in systems that allow Hardy-Weinberg equilibria.     

Competitive divergence in non-random mating populations

A haploid model of frequency-dependent selection and assortative mating is introduced and analyzed for the case of a single multiallelic autosomal locus. Frequency-dependent selection is due to intraspecific competition mediated by a quantitative character under stabilizing or directional selection. Assortment is induced by the same trait. We analyze the equilibrium structure and the local stability properties of all possible equilibria. In the limit of weak selection we obtain global stability properties by finding a Lyapunov function. We provide necessary and sufficient conditions for the maintenance of polymorphism in terms of the strength of stabilizing selection, intraspecific competition and assortment. Our results also include criteria for the ability of extreme types to invade the population. Furthermore, we study the occurrence of disruptive selection and provide necessary and sufficient conditions for intraspecific divergence to occur.     

Transposable element derived DNaseI-hypersensitive sites in the human genome

Background  

Transposable elements (TEs) are abundant genomic sequences that have been found to contribute to genome evolution in unexpected ways. Here, we characterize the evolutionary and functional characteristics of TE-derived human genome regulatory sequences uncovered by the high throughput mapping of DNaseI-hypersensitive (HS) sites.     

Transposable elements in mendelian populations. I. A theory

Transposable elements are DNA sequences, found throughout eukaryotes, that transpose replicatively and cause numerous genetic and developmental effects on their hosts. A model of the evolution of transposable elements in Mendelian populations is proposed. From its analysis, formulas for the mean copy number and frequency spectrum are obtained.