Populational interactions among underdominant chromosome rearrangements help them to persist in small demes

Populational interactions among unlinked chromosomal rearrangements with partial heterozygote sterility and multiplicative fitness were studied to verify whether they help such rearrangements to persist in small populations, in spite of a considerable migration rate with a large population. A deterministic island-continent model was studied by exact recurrence relations connecting gametic frequencies in successive generations. The increase in the number of chromosomal rearrangements with the same sterility rate (s) causes an increase in the critical value of the migration rate (m_c) over which the chromosomal rearrangements are eliminated from the small population, mainly for medium s values (0.2 ≤ s ≤ 0.5) (“reciprocal stabilization” of the chromosomal rearrangements). A comparison was made between the velocities of the fixation of a few rearrangements with high heterozygote sterility (low n/high s) and that of many rearrangements with low heterozygote sterility (high n/low s), to reach a given level of populational stability of the rearranged karyotype measured by m_c. The former process was shown to be more rapid in small demes, the latter in large ones. However, the increase in the number of unlinked chromosomal rearrangements is more efficient in reducing the neutral gene flow than in increasing the populational stability of the rearranged karyotype.     

Partial male sterility and the evolution of nuclear gynodioecy in plants

Gynodioecy, a genetic dimorphism of females and hermaphrodites, is pertinent to an understanding of the evolution of plant gender, mating and genetic variability. Classical models of nuclear gynodioecy attribute the maintenance of the dimorphism to frequency-dependent selection in which the female phenotype has a fitness advantage at low frequency owing to a doubled ovule fertility. Here, I analyse explicit genetic models of nuclear gynodioecy that expand on previous work by allowing partial male sterility in combination with either fixed or dynamically evolving mutational inbreeding depression. These models demonstrate that partial male sterility causes fitness underdominance at the mating locus, which can prevent the spread of females. However, if partial male sterility is compensated by a change in selfing rate, overdominance at the mating locus can cause the spread of females. Overdominance at introduction of the male sterility allele can be caused by high inbreeding depression and a lower selfing rate in the heterozygote, by purging of mutations by a higher selfing rate in the heterozygote, and by low inbreeding depression and a higher selfing rate in the heterozygote. These processes might be of general importance in the maintenance of mating polymorphisms in plants.     

Using molecular markers with high mutation rates to obtain estimates of relative population size and to distinguish the effects of gene flow and mutation: a demonstration using data from endemic Mauritian skinks

We propose a method of analysing genetic data to obtain separate estimates of the size (N(p)) and migration rate (m(p)) for the sampled populations, without precise prior knowledge of mutation rates at each locus ( micro(L)). The effects of migration and mutation can be distinguished because high migration has the effect of reducing genetic differentiation across all loci, whereas a high mutation rate will only affect the locus in question. The method also takes account of any differences between the spectra of immigrant alleles and of new mutant alleles. If the genetic data come from a range of population sizes, and the loci have a range of mutation rates, it is possible to estimate the relative sizes of the different N(p) values, and likewise the m(p) and the micro(L). Microsatellite loci may also be particularly appropriate because loci with a high mutation rate can reach mutation-drift-migration equilibrium more quickly, and because the spectra of mutants arriving in a population can be particularly distinct from the immigrants. We demonstrate this principle using a microsatellite data set from Mauritian skinks. The method identifies low gene flow between a putative new species and populations of its sister species, whereas the differentiation of two other populations is attributed to small population size. These distinct interpretations were not readily apparent from conventional measures of genetic differentiation and gene diversity. When the method is evaluated using simulated data sets, it correctly distinguishes low gene flow from small population size. Loci that are not at mutation-migration-drift equilibrium can distort the parameter estimates slightly. We discuss strategies for detecting and overcoming this effect.     

GENETIC HITCHHIKING AND THE DYNAMIC BUILDUP OF GENOMIC DIVERGENCE DURING SPECIATION WITH GENE FLOW

A major issue in evolutionary biology is explaining patterns of differentiation observed in population genomic data, as divergence can be due to both direct selection on a locus and genetic hitchhiking. “Divergence hitchhiking” (DH) theory postulates that divergent selection on a locus reduces gene flow at physically linked sites, facilitating the formation of localized clusters of tightly linked, diverged loci. “Genome hitchhiking” (GH) theory emphasizes genome‐wide effects of divergent selection. Past theoretical investigations of DH and GH focused on static snapshots of divergence. Here, we used simulations assessing a variety of strengths of selection, migration rates, population sizes, and mutation rates to investigate the relative importance of direct selection, GH, and DH in facilitating the dynamic buildup of genomic divergence as speciation proceeds through time. When divergently selected mutations were limiting, GH promoted divergence, but DH had little measurable effect. When populations were small and divergently selected mutations were common, DH enhanced the accumulation of weakly selected mutations, but this contributed little to reproductive isolation. In general, GH promoted reproductive isolation by reducing effective migration rates below that due to direct selection alone, and was important for genome‐wide “congealing” or “coupling” of differentiation (F_ST) across loci as speciation progressed.     

When can ecological speciation be detected with neutral loci?

It is not yet clear under what conditions empirical studies can reliably detect progress toward ecological speciation through the analysis of allelic variation at neutral loci. We use a simulation approach to investigate the range of parameter space under which such detection is, and is not, likely. We specifically test for the conditions under which divergent natural selection can cause a ‘generalized barrier to gene flow’ that is present across the genome. Our individual‐based numerical simulations focus on how population divergence at neutral loci varies in relation to recombination rate with a selected locus, divergent selection on that locus, migration rate and population size. We specifically test whether genetic differences at neutral markers are greater between populations in different environments than between populations in similar environments. We find that this expected signature of ecological speciation can be detected under part of the parameter space, most consistently when divergent selection is strong and migration is intermediate. By contrast, the expected signature of ecological speciation is not reliably detected when divergent selection is weak or migration is low or high. These findings provide insights into the strengths and weaknesses of using neutral markers to infer ecological speciation in natural systems.     

Neutral gene flow in the presence of a selected gene with random or assortative mating

Neutral gene flow in an island model in the presence of a gene subject to selection has been analysed. The selection regime on the gene is such that the maintenance of a stable interpopulation differentiation at this locus is allowed for very low values of the migration rate. Mating at this locus may be random or assortative. Many models of zygotic or prezygotic isolating mechanisms with unifactorial inheritance are represented by this genetic model. Two general solutions for migration rates tending toward zero have been obtained for the case of migration preceding selection and vice versa. It is found that the zygotic isolating mechanisms and one type of prezygotic isolating mechanisms have the same qualitative and quantitative effects for the same values of selection coefficients and of recombination frequencies between the selected gene and the neutral gene. A second type of prezygotic mechanism behaves in a different way: the reduction of gene flow caused by such mechanisms is also a function of the “mating coefficients” of the various genotypes.     

A two-locus model of speciation.

Speciation is considered as the evolution of partial or complete cross-incompatibility between the carriers of genes (at a locus called "object locus") that distinguish the prospective species populations. The mating relations at the object locus are modified by the alleles at a second mating modifier locus. Based on a widely applicable concept of fitness and mating preference, it is shown that heterozygote disadvantage in fitness at the object locus is necessary for speciation, which corroborates Wallace's hypothesis. It is pointed out that the difference between sympatric and parapatric speciation essentially lies in the mechanisms stabilizing the polymorphism required at the object locus as a prerequisite for speciation. In the presence of recombination between the object and mating modifier locus speciation may be prevented by forces maintaining gametic phase imbalance between these loci such as can result from unidirectional gene flow between parapatric populations.     

THE EFFICACY OF DIVERGENCE HITCHHIKING IN GENERATING GENOMIC ISLANDS DURING ECOLOGICAL SPECIATION

Genes under divergent selection flow less readily between populations than other loci. This observation has led to verbal “divergence hitchhiking” models of speciation in which decreased interpopulation gene flow surrounding loci under divergent selection can generate large regions of differentiation within the genome (genomic islands). The efficacy of this model in promoting speciation depends on the size of the region affected by divergence hitchhiking. Empirical evidence is mixed, with examples of both large and small genomic islands. To address these empirical discrepancies and to formalize the theory, we present mathematical models of divergence hitchhiking, which examine neutral differentiation around selected sites. For a single locus under selection, regions of differentiation do not extend far along a chromosome away from a selected site unless both effective population sizes and migration rates are low. When multiple loci are considered, regions of differentiation can be larger. However, with many loci under selection, genome‐wide divergence occurs and genomic islands are erased. The results show that divergence hitchhiking can generate large regions of differentiation, but that the conditions under which this occurs are limited. Thus, speciation may often require multifarious selection acting on many, isolated and physically unlinked genes. How hitchhiking promotes further adaptive divergence warrants consideration.     

Microsatellites can be misleading: an empirical and simulation study

Abstract. It has been long recognized that highly polymorphic genetic markers can lead to underestimation of divergence between populations when migration is low. Microsatellite loci, which are characterized by extremely high mutation rates, are particularly likely to be affected. Here, we report genetic differentiation estimates in a contact zone between two chromosome races of the common shrew ( Sorex araneus ), based on 10 autosomal microsatellites, a newly developed Y-chromosome microsatellite, and mitochondrial DNA. These results are compared to previous data on proteins and karyotypes. Estimates of genetic differentiation based on F - and R -statistics are much lower for autosomal microsatellites than for all other genetic markers. We show by simulations that this discrepancy stems mainly from the high mutation rate of microsatellite markers for F -statististics and from deviations from a single-step mutation model for R -statistics. The sex-linked genetic markers show that all gene exchange between races is mediated by females. The absence of male-mediated gene flow most likely results from male hybrid sterility.     

The coalescent process in models with selection, recombination and geographic subdivision

A population genetic model with a single locus at which balancing selection acts and many linked loci at which neutral mutations can occur is analysed using the coalescent approach. The model incorporates geographic subdivision with migration, as well as mutation, recombination, and genetic drift of neutral variation. It is found that geographic subdivision can affect genetic variation even with high rates of migration, providing that selection is strong enough to maintain different allele frequencies at the selected locus. Published sequence data from the alcohol dehydrogenase locus of Drosophila melanogaster are found to fit the proposed model slightly better than a similar model without subdivision.     

The Effect of Linkage on Establishment and Survival of Locally Beneficial Mutations

We study invasion and survival of weakly beneficial mutations arising in linkage to an established migration–selection polymorphism. Our focus is on a continent–island model of migration, with selection at two biallelic loci for adaptation to the island environment. Combining branching and diffusion processes, we provide the theoretical basis for understanding the evolution of islands of divergence, the genetic architecture of locally adaptive traits, and the importance of so-called “divergence hitchhiking” relative to other mechanisms, such as “genomic hitchhiking”, chromosomal inversions, or translocations. We derive approximations to the invasion probability and the extinction time of a de novo mutation. Interestingly, the invasion probability is maximized at a nonzero recombination rate if the focal mutation is sufficiently beneficial. If a proportion of migrants carries a beneficial background allele, the mutation is less likely to become established. Linked selection may increase the survival time by several orders of magnitude. By altering the timescale of stochastic loss, it can therefore affect the dynamics at the focal site to an extent that is of evolutionary importance, especially in small populations. We derive an effective migration rate experienced by the weakly beneficial mutation, which accounts for the reduction in gene flow imposed by linked selection. Using the concept of the effective migration rate, we also quantify the long-term effects on neutral variation embedded in a genome with arbitrarily many sites under selection. Patterns of neutral diversity change qualitatively and quantitatively as the position of the neutral locus is moved along the chromosome. This will be useful for population-genomic inference. Our results strengthen the emerging view that physically linked selection is biologically relevant if linkage is tight or if selection at the background locus is strong.     

Environmental heterogeneity enhances clonal interference

Clonal interference (CI) is a phenomenon that may be important in several asexual microbes. It occurs when population sizes are large and mutation rates to new beneficial alleles are of significant magnitude. Here we explore the role of gene flow and spatial heterogeneity in selection strength in the adaptation of asexuals. We consider a subdivided population of individuals that are adapting, through new beneficial mutations, and that migrate between different patches. The fitness effect of each mutation depends on the patch and all mutations considered are assumed to be unconditionally beneficial. We find that spatial variation in selection pressure affects the rate of adaptive evolution and its qualitative effects depend on the level of gene flow. In particular, we find that both low migration and high levels of heterogeneity lead to enhanced CI. In contrast, for high levels of migration the rate of fixation of adaptive mutations is higher when environmental heterogeneity is present. In addition, we observe that the level of fitness variation is higher and simultaneous fixation of multiple mutations tends to occur in the regime of low migration rates and high heterogeneity.     

The exact values of the probability of fixation of underdominant chromosomal rearrangements.

A numerical analysis of the probability of fixation of a chromosomal mutation with partial sterility of the heterozygote in a single population is performed. Three different genetic models are considered: the first model entails constant selection against the heterozygote and is the model almost universally used in previous works; in the other two models selection against the heterozygote depends on its frequency. The exact values of the fixation probability are found by iterating transition matrices with genotype specification. Differences in results among models are small. The exact values found in the first model are compared to estimates obtained from approximations. Solutions based on diffusion models give good approximations when selection against the heterozygote is low, especially if the population is very small. For the higher values of the selection coefficient against the heterozygote, the estimates are rather imprecise, especially when the populations are not very small.     

The reduction of gene exchange due to a prezygotic isolating mechanism with monogenic inheritance

The efficiency of an incomplete prezygotic reproductive isolating mechanism in one- and two-population models is studied. The isolating mechanism studied has a monogenic hereditary basis, and depends on the fact that the various genotypes "choose" different periods or sites to perform their reproductive activity. In the one-population models, the "neutral" gene exchange between the two morphs characterized by the alternative forms of the isolating mechanism decreases drastically only when there is an extremely low frequency of individuals with different genotypes reproducing in the same sites and during the same periods. Furthermore, the reduction in gene exchange caused by the prezygotic isolation is smaller with tight linkage between the gene-determining partial reproductive isolation and the neutral gene. In the two-population models the prezygotic isolation causes a reduction in gene exchange which is smaller with low migration rates, and is negligible for very low rates.     

Population differentiation and nuclear gene flow in the Dominican anole (Anolis oculatus)

Allele frequency data from nuclear microsatellite loci were used to investigate patterns of nuclear gene flow and population structure in the morphologically variable Dominican anole (Anolis oculatus). All six loci used proved to be highly polymorphic, with an average of 18.8 alleles per locus. Test for Hardy-Weinberg equilibrium revealed small numbers of heterozygote deficiencies at single loci in single populations and consistent patterns of increasingly significant heterozygote deficiency in global tests across populations and loci. No significant relationship between FST and patristic distances estimated from mitochondrial DNA sequences was detected and estimates of FIS were significantly higher in females than in males, indicating that gene flow may be sex-biased and mediated mainly by male migration. A highly significant correlation between linearized FST and loge (geographical distance) indicates that geographical proximity is a significant factor in the genetic structure of A. oculatus populations. However, levels of gene flow between morphologically differentiated parapatric populations are frequently seen to be relatively high. This supports the hypothesis of natural selection being the driving force behind the development and maintenance of morphological variation and shows that adaptive differentiation may be maintained despite the homogenizing influence of gene flow. Generally, the morphologically variable populations of A. oculatus are seen to be poor candidates for in situ speciation, but an exceptional case on the west coast of Dominica indicates that isolation resulting from vicariant events may lead to rapid differentiation at both mitochondrial and nuclear loci. This provides a possible mechanism for anole speciation on other Caribbean islands.     

Empirical phylogenies and species abundance distributions are consistent with preequilibrium dynamics of neutral community models with gene flow

Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modeled communities–that is with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities–from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual‐based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species‐abundance distribution), consistent with gene flow being a key process in macro‐evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in preequilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under preequilibrium conditions.     

Ty Element-Induced Temperature-Sensitive Mutations of Saccharomyces Cerevisiae

Temperature-sensitive mutants of Saccharomyces cerevisiae were isolated by insertional mutagenesis using the HIS3 marked retrotransposon TyH3HIS3. In such mutants, the TyHIS3 insertions are expected to identify loci which encode genes essential for cell growth at high temperatures but dispensable at low temperatures. Five mutations were isolated and named hit for high temperature growth. The hit1-1 mutation was located on chromosome X and conferred the pet phenotype. Two hit2 mutations, hit2-1 and hit2-2, were located on chromosome III and caused the deletion of the PET18 locus which has been shown to encode a gene required for growth at high temperatures. The hit3-1 mutation was located on chromosome VI and affected the CDC26 gene. The hit4-1 mutation was located on chromosome XIII. These hit mutations were analyzed in an attempt to identify novel genes involved in the heat shock response. The hit1-1 mutation caused a defect in synthesis of a 74-kD heat shock protein. Western blot analysis revealed that the heat shock protein corresponded to the SSC1 protein, a member of the yeast hsp70 family. In the hit1-1 mutant, the TyHIS3 insertion caused a deletion of a 3-kb DNA segment between the delta 1 and delta 4 sequences near the SUP4 locus. The 1031-bp wild-type HIT1 DNA which contained an open reading frame encoding a protein of 164 amino acids and the AGG arginine tRNA gene complemented all hit1-1 mutant phenotypes, indicating that the mutant phenotypes were caused by the deletion of these genes. The pleiotropy of the HIT1 locus was analyzed by constructing a disruption mutation of each gene in vitro and transplacing it to the chromosome. This analysis revealed that the HIT1 gene essential for growth at high temperatures encodes the 164-amino acid protein. The arginine tRNA gene, named HSX1, is essential for growth on a nonfermentable carbon source at high temperatures and for synthesis of the SSC1 heat shock protein.     

How likely is speciation in neutral ecology?

Patterns of biodiversity predicted by the neutral theory rely on a simple phenomenological model of speciation. To further investigate the effect of speciation on neutral biodiversity, we analyze a spatially explicit neutral model based on population genetics. We define the metacommunity as a system of populations exchanging migrants, and we use this framework to introduce speciation with little or no gene flow (allopatric and parapatric speciation). We find that with realistic mutation rates, our metacommunity model driven by neutral processes cannot support more than a few species. Adding natural selection in the population genetics of speciation increases the number of species in the metacommunity, but the level of diversity found in the Barro Colorado Island is difficult to reach.     

A MODEL FOR THE EVOLUTION OF ASYMMETRICAL MALE HYBRID STERILITY AND ITS IMPLICATIONS FOR SPECIATION

Chromosomal analysis of several cases of asymmetrical male hybrid sterility in Drosophila has implicated the X- or the Y-chromosome and one or more autosomes. Here, I develop a model for the evolution of this phenomenon. An autosomal locus is assumed to affect viability and to interact with a Y-linked or an X-linked locus to determine male fertility. In a new environment, selection for viability favors a new allele at the autosomal locus, but incompatibility of this new allele with the sex-chromosome-linked gene generates male sterility. The incompatibility can be resolved if a new allele at the sex-linked locus invades the population. This results in nonreciprocal male hybrid sterility, the direction of the nonreciprocity being determined by the dominance or recessiveness of the new autosomal gene in its effect on fertility. It is shown that stable polymorphism for the autosomal locus is possible and that, if the equilibrium frequency of the new allele is above a critical value, the population will be constantly at the verge of speciation, “waiting” for the sex-linked mutation to occur. The appearance of this mutation causes a runaway process leading to rapid fixation of the new autosomal and sex-linked alleles. If the equilibrium frequency of the new autosomal allele is less than the critical value, deterministic speciation is impossible, but random drift may increase the frequency above the critical value and predispose the population to the invasion of the new sex-linked allele. Thus, both deterministic and stochastic modes of speciation are possible. Because deterministic speciation requires large selection coefficients, which impose a severe genetic load on the population, and because stochastic speciation requires repeated population bottlenecks, it is concluded that relative to the number of successful speciation events there will be many more events of deme extinction.     

Genes in the first and fourth inversions of the mouse t complex synergistically mediate sperm capacitation and interactions with the oocyte

The t haplotypes (t) are recent evolutionary derivatives of an alternate form of the mouse t complex region located at the proximal end of chromosome 17. This variant form of approximately 1% of the mouse genome is a source of mutations altering numerous sperm functions crucial for fertilization. Males that carry two t haplotypes (t/t) are invariably sterile. t haplotypes contain four inversions relative to the wild-type t complex (+), so that in matings involving a +/t heterozygote, t is usually transmitted as a single unit. However, rare recombinants have been recovered, which carry only part of the t genotype and express only some of the t-dependent phenotypes. Use of these partial t haplotypes in genetic crosses has resulted in the general location of the two major t male sterility factors, S1 and S2, within inversions 1 and 4, respectively. Since sterility can result from a plethora of sperm defects, we have made a detailed study of various functional parameters of sperm from mice carrying S1 or S2 heterozygously or homozygously or in combination. Both S1 and S2 contain mutations altering sperm functions, including motility, capacitation, binding to the zona pellucida, binding to the oocyte membrane, and penetration of the zona pellucida-free oocyte. Therefore it seems clear that each of these factors contains multiple genes contributing to sterility. Furthermore, our results indicate that genes within S1 interact with genes in S2 for all sperm functions examined. However, S1 and S2 genes affecting motility interact in a purely additive fashion, while S1 and S2 genes affecting most other sperm characteristics interact in a synergistic manner. Additionally, the patterns of synergism between S1 and S2 for abnormalities in capacitation, sperm-oolemma binding, and zona-free oocyte penetration are nearly identical. This suggests that these three defects are caused by mutation of the same gene within each sterility factor. These findings will not only be instrumental in matching the various t haplotype sperm defects to candidate genes for S1 and S2, but will facilitate a more comprehensive understanding of the cellular and genetic mechanisms underlying t haplotype male sterility.