Comments on lack of interference in the four strand model of crossing over

Summary Assuming a four strand model and no chromatid interference, lack of chiasma interference is known to be equivalent to the assumption that the formation of chiasmata follows a Poisson process. We prove that lack of chiasma interference is also equivalent to the assumption that a random gamete shows recombination on any given interval of a chromosome independently of recombination on all disjoint intervals. Both assumptions are sufficient, but not necessary, for Haldane's formula relating recombination to map distance to be true, as we demonstrate by specific counterexamples. These issues are discussed in the context of the theory of stochastic point processes.Research supported by: University of California at Los Angeles, NIH Special Resources Grant RR-3, and USPHS Predoctoral Traineeship GM 7104.     

Properties of a neutral allele model with intragenic recombination

An infinite-site neutral allele model with crossing-over possible at any of an infinite number of sites is studied. A formula for the variance of the number of segregating sites in a sample of gametes is obtained. An approximate expression for the expected homozygosity is also derived. Simulation results are presented to indicate the accuracy of the approximations. The results concerning the number of segregating sites and the expected homozygosity indicate that a two-locus model and the infinite-site model behave similarly for 4Nu less than or equal to 2 and r less than or equal to 5u, where N is the population size, u is the neutral mutation rate, and r is the recombination rate. Simulations of a two-locus model and a four-locus model were also carried out to determine the effect of intragenic recombination on the homozygosity test of Watterson (Genetics 85, 789-814; 88, 405-417) and on the number of unique alleles in a sample. The results indicate that for 4Nu less than or equal to 2 and r less than or equal to 10u, the effect of recombination is quite small.     

Selection on recombination in a multi-locus system

The model of Wills and Miller (1976) for selection on recombination rates in finite populations was studied by means of a computer model involving 80 selected loci and a linked or unlinked modifier gene affecting the map length occupied by the selected loci. The selected loci were subject to heterozygote advantage, and multiplicative fitness interactions between loci were assumed. In all cases studied, selection for reduction in recombination out-weighed any selection for increased recombination that may have been present.     

The use of recombinase proteins to generate transgenic large animals

The endogenous properties of recombinase proteins allow them to associate with and bind DNA to catalyze homologous recombination. These endogenous properties of cellular recombination enzymes may be useful to the field of transgenesis. The production of transgenic animals, in particular livestock, is an inefficient process by both conventional pronuclear microinjection techniques and nuclear transfer. Furthermore, the use of pronuclear microinjection is currently limited to the random addition of genes and does not allow for the replacement of an endogenous gene with a more desired one. The functions of cellular recombination enzymes have been exploited to develop a technique that is compatible with pronuclear microinjection and may make the process of generating transgenic livestock more efficient while also enabling the targeting of homologous chromosomal genes. In our hands, transgenic animals generated by the pronuclear microinjection of various recombinase protein-coated DNA fragments led to a higher than expected birth rate as well as transgene integration frequency. Most founder animals generated were likely mosaic, indicating that integration occurred after cell division. The presence of multiple related genes makes detection of any recombination event difficult. Overall, this technique is a straightforward, rapid, and efficient procedure that can be applied to any segment of DNA and any microinjection apparatus, and is less labor intensive than nuclear transfer.     

Population genetics of modifiers of meiotic drive. II. Linkage modification in the segregation distortion system

The conditions are found under which the frequency of a new gene altering the recombination fraction between two loci controlling meiotic drive will increase. When the model mimics the recombination reducing effects of a chromosomal rearrangement, such as an inversion or duplication, then the result is that the frequency of the chromosomal rearrangement in the population will increase. This may help explain the presence of inversions and duplications (or insertions) in the segregation-distorter system in Drosophila. In some cases it is found that if the new gene causes any alteration in the recombination fraction between the two loci, the frequency of the gene will increase.     

HOW MUCH HERITABLE VARIATION CAN BE MAINTAINED IN FINITE POPULATIONS BY MUTATION–SELECTION BALANCE?

The joint effects of stabilizing selection, mutation, recombination, and random drift on the genetic variability of a polygenic character in a finite population are investigated. A simulation study is performed to test the validity of various analytical predictions on the equilibrium genetic variance. A new formula for the expected equilibrium variance is derived that approximates the observed equilibrium variance very closely for all parameter combinations we have tested. The computer model simulates the continuum-of-alleles model of Crow and Kimura. However, it is completely stochastic in the sense that it models evolution as a Markov process and does not use any deterministic evolution equations. The theoretical results are compared with heritability estimates from laboratory and natural populations. Heritabilities ranging from 20% to 50%, as observed even in lab populations under a constant environment, can only be explained by a mutation-selection balance if the phenotypic character is neutral or the number of genes contributing to the trait is sufficiently high, typically several hundred, or if there are a few highly variable loci that influence quantitative traits.     

In silico analysis of disease-association mapping strategies using the coalescent process and incorporating ascertainment and selection

We present a new method for simulating samples of marker haplotypes, genotypes, or diplotypes in case-control studies in which the markers are linked to a disease locus in any specified region of the genome. The method allows realistic features to be incorporated into the simulations, including selection acting on disease alleles, sample ascertainment of disease chromosomes and polymorphic markers, a genetic dominance model of disease expression that allows incomplete penetrance and phenocopies, and an accurate genetic map of recombination rates and hotspots for recombination in the human genome (or, alternatively, an improved method for simulating the distribution of hotspots). The new method uses an approach that combines simulation of the coalescent process for the sampled chromosomes with a diffusion process used to model the evolution of the disease-mutation frequency over time. Examples illustrate how the method may be used to study the expected power of a marker-disease association study.     

Effects of acquired immunity and mating strategy on the genetic structure of parasite populations

Although it may have profound effects on how researchers seek to tackle many infectious diseases, little is known of the genetic structure of many pathogen populations. Previous models have suggested that if levels of cross-protection are high, parasite populations may be structured into discrete strains with nonoverlapping antigenic repertoires, even among populations that reproduce sexually. Here, I consider a discrete model of the coevolution of parasites with host-acquired immunity. In this model, if the effective recombination rate is low, strain structure can be maintained for very high levels of cross-protection. However, if the effective recombination rate is higher, this strain structure can no longer be maintained. The effective recombination rate is affected by the actual recombination rate between immunologically selected loci, the proportion of individuals that reproduce sexually, whether recombination occurs inside or outside of the host or vector, and the level of cross-protection. The model predicts that for Plasmodium falciparum, where reproduction occurs inside of a vector, we expect to see strain structure in areas of low transmission but not in areas of high transmission. Strain structure is unlikely to be seen in parasites that reproduce outside of a host or vector, such as Strongyloides ratti.     

Mismatch repair of heteroduplex DNA intermediates of extrachromosomal recombination in mammalian cells.

Previous work indicated that extrachromosomal recombination in mammalian cells could be explained by the single-strand annealing (SSA) model. This model predicts that extrachromosomal recombination leads to nonconservative crossover products and that heteroduplex DNA (hDNA) is formed by annealing of complementary single strands. Mismatched bases in hDNA may subsequently be repaired to wild-type or mutant sequences, or they may remain unrepaired and segregate following DNA replication. We describe a system to examine the formation and mismatch repair of hDNA in recombination intermediates. Our results are consistent with extrachromosomal recombination occurring via SSA and producing crossover recombinant products. As predicted by the SSA model, hDNA was present in double-strand break-induced recombination intermediates. By placing either silent or frameshift mutations in the predicted hDNA region, we have shown that mismatches are efficiently repaired prior to DNA replication.     

A formula for the mean lifetime of metapopulations in heterogeneous landscapes

We present a formula for the mean lifetime of metapopulations in heterogeneous landscapes. This formula provides new insights into the effect of the spatial structure of habitat networks on metapopulation survival, with consequences for modeling, landscape evaluation, and metapopulation management. In the whole study, the spatially realistic metapopulation model of Frank and Wissel is taken as a basis. First, as a key result on the way toward the desired formula, it is shown that a simple nonspatial (Levins-type) model is able to reproduce the behavior of the complex spatial model considered regarding the mean lifetime, provided its parameters appropriately summarize all the relevant details of spatial heterogeneity. Second, the formula presented reveals how data from species and landscape have to be combined to estimate the survival chance of a metapopulation without having to run any simulation or to solve numerically any model equation. Third, by taking the formula as a basis, landscape measures are derived that allow dissimilar habitat networks to be evaluated, compared, and ranked in terms of their effect on metapopulation survival. Fourth, a combination of analytical, nonlinear regression as well as aggregation techniques was used to deduce the formula presented. The potential of these techniques for simplifying (meta)population models that are complex due to spatial heterogeneity is discussed.     

Quantifying the Nongeminate Recombination Dynamics in Nonfullerene Bulk Heterojunction Organic Solar Cells

In this study, a comprehensive analytical model to quantify the total nongeminate recombination losses, originating from bimolecular as well as bulk and surface trap‐assisted recombination mechanisms in nonfullerene‐based bulk heterojunction organic solar cells is developed. This proposed model is successfully employed to obtain the different contributions to the recombination current of the investigated solar cells under different illumination intensities. Additionally, the model quantitatively describes the experimentally measured open‐circuit voltage versus light intensity dependence. Most importantly, it is possible to calculate the experimental results with the same fitting parameter values from the presented model. The validity of this model is also proven by a combination of other independent, steady‐state, and transient experimental techniques. This new powerful analytical tool will enable researchers in the photovoltaic community to take into account the synergetic contribution from all relevant types of nongeminate recombination losses in different optoelectronic systems and target their analysis of recombination dynamics at any operating voltage.     

Extrachromosomal DNA substrates in pre-B cells undergo inversion or deletion at immunoglobulin V-(D)-J joining signals

Sequences encoding immunoglobulin variable domains are known to be assembled from variable (V), diversity (D), and joining (J) segments by site-specific recombination. We present a sensitive and rapid assay for V-(D)-J recombination that uses plasmid DNA transiently introduced into transformed pre-B cells, and demonstrates that the recombination is independent of any unique chromosomal context. Sequences sufficient to constitute recombination sites are contained within the 84 and 42 bp flanking, respectively, the murine J kappa 1 and V kappa L8 segments, which include the known heptamer-nonamer V-(D)-J joining signals. Deletion and inversion occur at comparable frequencies. Thus, V-(D)-J recombination may be relatively insensitive to the topological arrangement of sites, and events at the two novel junctions produced by the reaction may be coupled.     

Effects of misspecifying genetic parameters in lod score analysis

The lod score method is widely used to test linkage and to estimate the recombination fraction between a disease locus and a marker locus. The parameters (gene frequency, penetrance, and degree of dominance) are assumed to be known at each locus. This condition may not be fulfilled at the disease locus. In this paper, we evaluate the errors due to the use of wrong parameters. The power of the linkage test is sensitive to the degree of dominance, and slightly to the penetrance, but not to the gene frequency. In contrast, the estimation of the recombination fraction may be strongly affected by an error on any genetic parameter.     

The joint effects of background selection and genetic recombination on local gene genealogies

Background selection, the effects of the continual removal of deleterious mutations by natural selection on variability at linked sites, is potentially a major determinant of DNA sequence variability. However, the joint effects of background selection and genetic recombination on the shape of the neutral gene genealogy have proved hard to study analytically. The only existing formula concerns the mean coalescent time for a pair of alleles, making it difficult to assess the importance of background selection from genome-wide data on sequence polymorphism. Here we develop a structured coalescent model of background selection with recombination and implement it in a computer program that efficiently generates neutral gene genealogies for an arbitrary sample size. We check the validity of the structured coalescent model against forward-in-time simulations and show that it accurately captures the effects of background selection. The model produces more accurate predictions of the mean coalescent time than the existing formula and supports the conclusion that the effect of background selection is greater in the interior of a deleterious region than at its boundaries. The level of linkage disequilibrium between sites is elevated by background selection, to an extent that is well summarized by a change in effective population size. The structured coalescent model is readily extendable to more realistic situations and should prove useful for analyzing genome-wide polymorphism data.     

Molecular characterization of novel reciprocal translocation t(6;14) in an Epstein-Barr virus-transformed B cell precursor.

An in vitro culture of FLEB14 cells, an Epstein-Barr virus-transformed B cell precursor containing the germ line immunoglobulin genes, gave rise to a uniclonally expanded variant, FLEB14 delta 3, which was rearranged at the immunoglobulin heavy-chain gene locus. Cytogenetic analysis showed that FLEB14 delta 3 had a novel reciprocal translocation, t(6;14)(q15;q32). Molecular cloning of the rearranged DNA fragments and determination of their nucleotide sequence revealed that the recombination event was reciprocal, imprecise, and nonhomologous and took place in the S mu region, like those found in Burkitt's lymphoma cells. We propose a molecular model to explain this genetic event which may be relevant to class switch recombination. The translocated sequence of chromosome 6 did not contain any known oncogenes, although the sequence is conserved among mammals. FLEB14 delta 3 did not show tumorigenicity.     

The impact of homologous recombination on the generation of diversity in bacteria

The imprint of demographic and selective processes on bacterial population structure needs to be evaluated as deviation from the expectations of an appropriate null neutral model. We explore the impact of varying the population mutation and recombination rates theta and rho on ideal populations, using a recently developed model of neutral drift at multiple loci. This model may be fitted to experimental data to provide estimates of these parameters, and we do so for seven bacterial species (Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes, Staphylococcus aureus, Helicobacter pylori, Burkholderia pseudomallei and Bacillus cereus), illustrating that bacterial species vary extensively in these fundamental parameters. Historically, the influence of recombination has often been estimated through its influence on the Index of Association I(A). We show that this may be relatively insensitive to changes in either mutation or recombination rates. It is known that biased sampling can lead to artificially high estimates of I(A). We therefore provide a method of precisely separating the effects of such bias and true linkage between alleles. We also demonstrate that by fitting the neutral model to experimental data, more informative and precise estimates of the relative roles of recombination and mutation may be obtained.     

THE EVOLUTION OF STRONG REPRODUCTIVE ISOLATION

Felsenstein distinguished two ways by which selection can directly strengthen isolation. First, a modifier that strengthens prezygotic isolation can be favored everywhere. This fits with the traditional view of reinforcement as an adaptation to reduce deleterious hybridization by strengthening assortative mating. Second, selection can favor association between different incompatibilities, despite recombination. We generalize this "two allele" model to follow associations among any number of incompatibilities, which may include both assortment and hybrid inviability. Our key argument is that this process, of coupling between incompatibilities, may be quite different from the usual view of reinforcement: strong isolation can evolve through the coupling of any kind of incompatibility, whether prezygotic or postzygotic. Single locus incompatibilities become coupled because associations between them increase the variance in compatibility, which in turn increases mean fitness if there is positive epistasis. Multiple incompatibilities, each maintained by epistasis, can become coupled in the same way. In contrast, a single-locus incompatibility can become coupled with loci that reduce the viability of haploid hybrids because this reduces harmful recombination. We obtain simple approximations for the limits of tight linkage, and strong assortment, and show how assortment alleles can invade through associations with other components of reproductive isolation.     

DNA oligonucleotide-assisted genetic manipulation increases transformation and homologous recombination efficiencies: Evidence from gene targeting of Dictyostelium discoideum

Artificial gene alteration by homologous recombination in living cells, termed gene targeting, presents fundamental and considerable knowledge of in vivo gene function. In principle, this method can possibly be applied to any type of genes and transformable cells. However, its success is limited due to a low frequency of homologous recombination between endogenous targeted gene and exogenous transgene. Here, we describe a general gene-targeting method in which co-transformation of DNA oligonucleotides (oligomers) could significantly increase the homologous recombination frequency and transformation efficiency. The oligomers were simply designed such that they were identical to both the ends of the homologous flanking regions of the targeting construct. Using this strategy, both targeted alleles of diploid cells were simultaneously replaced in a single transformation procedure. Thus, the simplicity and versatility of this method applicable to any type of cell may increase the application of gene targeting.