Hybrid zone structure and the potential role of selection in hybridizing populations of native westslope cutthroat trout (Oncorhynchus clarki lewisi) and introduced rainbow trout (O. mykiss)

Introgressive hybridization is a common feature of many zones of contact between divergent lineages of fishes. This is particularly common when taxa that are normally allopatric come into artificial (human-induced) secondary contact. We examined 18 native populations of westslope cutthroat trout (Oncorhynchus clarki lewisi, WCT) to determine the extent of introgressive hybridization with introduced rainbow trout (O. mykiss, RBT) and the genetic structure of hybridizing populations in the upper Kootenay River, southeastern British Columbia, Canada. Using four diagnostic nuclear loci we calculated a hybrid index, inbreeding coefficient, FIS, and the linkage disquilibrium correlation coefficient, Rij, for each locality to determine the distribution of genotypes in each population. We also categorized the 142 hybrid individuals found across localities into four hybrid classes based on their genotypes. The majority of localities (11/18) showed a unimodal distribution of genotypes skewed towards genotypes of WCT. Two localities, however (lower Gold Creek and Lodgepole Creek) showed a flat to bimodal distribution and one site (lower Bull River) showed a unimodal distribution skewed towards RBT genotypes. The majority of hybrid individuals were classified genotypically as WCT backcrosses (59%) and post-F1 individuals (24%). We found a skewed ratio of pure WCT to pure RBT (17:1) and only four F1 hybrids (3%), suggesting that the spread of RBT alleles may be facilitated by hybrids straying to neighbouring populations. We also tested for the action of selection in one population using cohort analyses, but found little evidence of differential selection between pure WCT and hybrid individuals. Pooled across age classes there were significant differences in genotypic frequencies among loci suggesting differential introgression. There was no asymmetry to the hybridization between rainbow trout and westslope cutthroat trout because both species' mitochondrial DNA haplotypes were observed at similar frequencies in the hybrids. Our analyses suggest that hybrid swarms are likely to form in the upper Kootenay River drainage and that certain native WCT populations in British Columbia are at risk of local genomic extinction.     

Hard selection in haploid species

The formulation of hard selection is reviwed in the context of haploid viabilities and the criteria for stability of the fixation states are given. In contrast to soft selection, both fixation states can be simultaneously stable. However, this is not possible if the migration matrix is positive definite. In the case of only two demes there is at most one polymorphic equilibrium as occurs under soft selection, but the internal equilibrium may be unstable in contrast to the soft selection case. The question of hard versus soft protection is posed in the context of haploid viabilities and the principle hard protection implies soft protection holds with a similar degree of generality as in the diploid case.     

Social transmission of migratory knowledge: quantifying the risk of losing migratory behavior

When migration is a learned behavior, small populations have a significant problem of maintaining migratory knowledge across generations. These populations risk losing migratory behavior entirely, which may exacerbate existing stressors on population size. Here we investigated the success of various behavioral, demographic, and social factors towards maintaining migration within small populations. Using a discrete-time probabilistic model to simulate repeated migrations, we found that migratory group size plays an important role in maintaining migratory knowledge within the population. Rare, large groups allow for migratory knowledge to be spread to many individuals at once. When a population learns migration information incrementally, the presence of individuals that can learn quickly, therefore transitioning rapidly into leaders, has a profound impact on migrational persistence. Furthermore, small populations are better able to maintain migratory behavior when groups rely on informed leaders as compared to using collective group knowledge, even when that collective knowledge is heavily weighted towards knowledgeable individuals. Finally, we found that both species with short lifespans and species that migrate with fixed group compositions are at especially high risk of losing their migration behavior at small population sizes.     

Evolution of dispersal in density regulated populations: A haploid model

The evolution of dispersal is explored in a density-dependent framework. Attention is restricted to haploid populations in which the genotypic fitnesses at a single diallelic locus are decreasing functions of the changing number of individuals in the population. It is shown that migration between two populations in which the genotypic response to density is reversed can maintain both alleles when the intermigration rates are constant or nondecreasing functions of the population densities. There is always a unique symmetric interior equilibrium with equal numbers but opposite gene frequencies in the two populations, provided the system is not degenerate. Numerical examples with exponential and hyperbolic fitnesses suggest that this is the only stable equilibrium state under constant positive migration rates (m) less than . Practically speaking, however, there is only convergence after a reasonable number of generations for relatively small migration rates ( ). A migration-modifying mutant at a second, neutral locus, can successfully enter two populations at a stable migration-selection balance if and only if it reduces the intermigration rates of its carriers at the original equilibrium population size. Moreover, migration modification will always result in a higher equilibrium population size, provided the system approaches another symmetric interior equilibrium. The new equilibrium migration rate will be lower than that at the original equilibrium, even when the modified migration rate is a nondecreasing function of the population sizes. Therefore, as in constant viability models, evolution will lead to reduced dispersal.     

Cytonuclear dynamics in selfing populations under selection

We develop a mathematical model to delimit the role of natural selection in maintaining nuclear and cytoplasmic polymorphisms in selfing populations. We provide explicit time-dependent solutions for joint cytonuclear frequencies under any combination of constant fertility, viability, and gametic selection and exact analytical conditions for the maintenance of polymorphisms under joint cytonuclear selection. The equilibrium structure is determined by the relative magnitude of echo fitnesses, defined as the rate at which individuals survive and produce offspring with their own genotype. Both nuclear and cytoplasmic polymorphisms can be maintained under biologically meaningful conditions, although the majority of the parameter combinations will lead to fixation. The theoretical framework developed here should be very useful in formally dissecting the form and strength of selection on cytonuclear genotypes in populations with negligible levels of outcrossing.     

The population genetics of reinforcing selection

A common outcome of disruptive selection experiments between two differentiated populations which produce disadvantageous hybrids is an increase in homogamy. Experiments reported here result in another outcome when ‘classical’ selection experiments are redesigned. In these modified experiments, frequencies of genotypes in the mating population were not artificially maintained at parity but were instead determined from progeny proportions in the previous generation. In these selection lines another outcome, apart from an increase in homogamy, was demonstrated. Under a high selection coefficient against heterozygotes, elimination of a homozygote and the corresponding fixation of the other was observed. No selection line demonstrated the maintenance of two differentiated populations concurrently with the selection process of heterozygote disadvantage. A high number of generations of selection under this population genetical process is necessary to increase differences between two populations. However, the instability of gene frequencies which results in fixation or elimination of a homozygote is shown to be extremely rapid by comparison. Classical experiments were repeated and after 21 generations of selection there was no increase in divergence. For lower selection coefficients, high levels of introgression are apparent, and hence the genetical distinctness of the two populations decreases over time. This is in addition to the problem of an unstable equilibrium under selection against heterozygotes. Both aspects are important but not previously considered in experimental evidence for speciation models for which their implications are discussed.     

Multilocus selection in subdivided populations I. Convergence properties for weak or strong migration

The dynamics and equilibrium structure of a deterministic population-genetic model of migration and selection acting on multiple multiallelic loci is studied. A large population of diploid individuals is distributed over finitely many demes connected by migration. Generations are discrete and nonoverlapping, migration is irreducible and aperiodic, all pairwise recombination rates are positive, and selection may vary across demes. It is proved that, in the absence of selection, all trajectories converge at a geometric rate to a manifold on which global linkage equilibrium holds and allele frequencies are identical across demes. Various limiting cases are derived in which one or more of the three evolutionary forces, selection, migration, and recombination, are weak relative to the others. Two are particularly interesting. If migration and recombination are strong relative to selection, the dynamics can be conceived as a perturbation of the so-called weak-selection limit, a simple dynamical system for suitably averaged allele frequencies. Under nondegeneracy assumptions on this weak-selection limit which are generic, every equilibrium of the full dynamics is a perturbation of an equilibrium of the weak-selection limit and has the same stability properties. The number of equilibria is the same in both systems, equilibria in the full (perturbed) system are in quasi-linkage equilibrium, and differences among allele frequencies across demes are small. If migration is weak relative to recombination and epistasis is also weak, then every equilibrium is a perturbation of an equilibrium of the corresponding system without migration, has the same stability properties, and is in quasi-linkage equilibrium. In both cases, every trajectory converges to an equilibrium, thus no cycling or complicated dynamics can occur.      

Density dependent selection in parthenogenetic and self-mating populations

The consequences of density dependent selection on genetically heterogeneous, diploid populations reproducing by self-mating or various parthenogenetic mechanisms is investigated. A logistic fitness function that depends upon both the genotype of an individual and the density of the population is used. Such a fitness function simultaneously determines the population size and the genotype frequencies. The equilibrium solutions to a one locus and two locus model are given as well as some generalizations to n loci and nonlogistic fitness functions. Conditions are found that maintain several different genotypes simultaneously in the equilibrium population. The interaction of such selection with the genetic mechanisms which determine mode of reproduction in parthenogenetic populations is also discussed.     

Linkage Disequilibrium in Subdivided Populations

The linkage disequilibrium in a subdivided populaton is shown to be equal to the sum of the average linkage disequilibrium for all subpopulations and the covariance between gene frequencies of the loci concerned. Thus, in a subdivided population the linkage disequilibrium may not be 0 even if the linkage disequilibrium in each subpopulation is 0. If a population is divided into two subpopulations between which migration occurs, the asymptotic rate of approach to linkage equilibrium is equal to either r or 2(m(1) + m(2)) - (m(1) + m(2))(2), whichever is smaller, where r is the recombination value and m(1) and m(2) are the proportions of immigrants in subpopulations 1 and 2, respectively. Thus, if migration rate is high compared with recombination value, the change of linkage disequilibrium in subdivided populations is similar to that of a single random mating population. On the other hand, if migration rate is low, the approach to lnkage equilibrium may be retarded in subdivided populations. If isolated populations begin to exchange genes by migration, linkage disequilibrium may increase temporarily even for neutral loci. If overdominant selection operates and the equilibrium gene frequencies are different in the two subpopulations, a permanent linkage disequilibrium may be produced without epistasis in each subpopulation.     

Mathematical model of active migrations as feeding strategy in trophic communities

Models of spatial and temporal dynamics of trophic communities are considered and numerically investigated. Stability of equilibriums of two trophic levels models is analytically studied. Active migrations are described on the bases of idea that acceleration of directed migration of predators is pro-rate the density gradient of prey populations. High migration activity of predators ensures the stability of complex non-uniform spatial regimes even when the abundance of predators is constant. In this case both summarized consumption of preys by predators and total number of preys considerably exceed equilibrium meanings of homogeneous regime, that takes place when predators are not able to migrate directionally. In three levels trophic system plant resource-pest-predator the increase in migration activity of predator leads to the increase of its abundance and the abundance of pest while the biomass of the resource decreases. This result is interpreted as an example of non-effective biological control when predators with high searching ability are used.     

VNTR loci reveal differentiation between and structure within populations of the eastern barred bandicoot Perameles gunnii

The Eastern Barred Bandicoot Perameles gunnii has declined in abundance within mainland south-eastern Australia, to a relict wild population of less than 100 individuals in Hamilton, Victoria. It is more common, but is also declining in Tasmania. Genomic DN A variability was compared within and between surviving populations of P. gunnii using variable number of tandem repeat (VNTR) markers in one of two ways. First, average percentage differences (APDs) were determined between profiles for two VNTR probe—endonuclease combinations. Secondly, because one of these combinations revealed two multiallelic VNTR loci, genotypes were assigned and analysed for homogeneity of allele frequencies among subpopulations, for deviation of heterozygosity from Hardy-Weinberg equilibrium within populations and for genetic structuring among individuals from different subpopulations. The results of both the APD and defined locus approaches showed consistent trends within and between populations. Genetic variability was higher among mainland P. gunnii than in Tasmanian populations (higher APDs, number of alleles, and heterozygosity at one locus), despite the known decline and subdivision of the Hamilton population. Eleven per cent of the variability detected in Hamilton was attributed to genetic differentiation between east and west subdivisions of the population. Departure from random mating indicating local inbreeding within collecting localities was evident for one locus in both north and south Tasmania, particularly at one locality. AH alleles at both loci were unique to either Hamilton or Tasmanian P. gunnii. The initial captive colony contains high heterozygosity for these loci. It is concluded that VNTR markers can be of benefit for use in studies of population differentiation and for conservation management.     

Genotypic diversity of the cotton-melon aphid Aphis gossypii (Glover) in Tunisia is structured by host plants

The study of intraspecific variation with respect to host plant utilization in polyphagous insects is crucial for understanding evolutionary patterns of insect-plant interactions. Aphis gossypii (Glover) is a cosmopolitan and extremely polyphagous aphid species. If host plant species or families constitute selective regimes to these aphids, genetic differentiation and host associated adaptation may occur. In this study, we describe the genetic structure of A. gossypii collected in six localities in Tunisia on different vegetable crops, on citrus trees and on Hibiscus. The aim was to determine if the aphid populations are structured in relation to the host plants and if such differentiation is consistent among localities. The genetic variability of A. gossypii samples was examined at eight microsatellite loci. We identified only 11 multilocus genotypes among 559 individuals. Significant deviations from Hardy-Weinberg equilibrium, linkage disequilibria and absence of recombinant genotypes, confirmed that A. gossypii reproduces by continuous apomictic parthenogenesis. Genetic differentiation between localities was not significant, whereas a strong differentiation was observed between host plant families (0.175相似文献   

Some circumstances assuring monomorphism in subdivided populations

It is well known that in a subdivided population subject to soft selection with two alleles at one locus, instability of both fixation states (a “protected polymorphism”) entails at least one stable polymorphic equilibrium. Although stable polymorphic and monomorphic equilibria can coexist in general, a stable fixation state (monomorphic equilibrium) precludes the existence of any polymorphic equilibrium under the circumstances of haploid or submultiplicative diploid viabilities. This provides that a stable monomorphism is robust against random fluctuations in allele frequencies. It also increases the known circumstances where there is a unique globally attracting stable equilibrium, i.e., where allele frequencies are determined by the selection-migration structure independent of the history of the system.     

Ecological genetics of adaptive color polymorphism in pocket mice: geographic variation in selected and neutral genes

Patterns of geographic variation in phenotype or genotype may provide evidence for natural selection. Here, we compare phenotypic variation in color, allele frequencies of a pigmentation gene (the melanocortin-1 receptor, Mc1r), and patterns of neutral mitochondrial DNA (mtDNA) variation in rock pocket mice (Chaetodipus intermedius) across a habitat gradient in southern Arizona. Pocket mice inhabiting volcanic lava have dark coats with unbanded, uniformly melanic hairs, whereas mice from nearby light-colored granitic rocks have light coats with banded hairs. This color polymorphism is a presumed adaptation to avoid predation. Previous work has demonstrated that two Mc1r alleles, D and d, differ by four amino acids, and are responsible for the color polymorphism: DD and Dd genotypes are melanic whereas dd genotypes are light colored. To determine the frequency of the two Mc1r allelic classes across the dark-colored lava and neighboring light-colored granite, we sequenced the Mc1r gene in 175 individuals from a 35-km transect in the Pinacate lava region. We also sequenced two neutral mtDNA genes, COIII and ND3, in the same individuals. We found a strong correlation between Mc1r allele frequency and habitat color and no correlation between mtDNA markers and habitat color. Using estimates of migration from mtDNA haplotypes between dark- and light-colored sampling sites and Mc1r allele frequencies at each site, we estimated selection coefficients against mismatched Mc1r alleles, assuming a simple model of migration-selection balance. Habitat-dependent selection appears strong but asymmetric: selection is stronger against light mice on dark rock than against melanic mice on light rock. Together these results suggest that natural selection acts to match pocket mouse coat color to substrate color, despite high levels of gene flow between light and melanic populations.     

Genome-enabled hitchhiking mapping identifies QTLs for stress resistance in natural Drosophila

Identification of genes underlying complex traits is an important problem. Quantitative trait loci (QTL) are mapped using marker-trait co-segregation in large panels of recombinant genotypes. Most frequently, recombinant inbred lines derived from two isogenic parents are used. Segregation patterns are also studied in pedigrees from multiple families. Great advances have been made through creative use of these techniques, but narrow sampling and inadequate power represent strong limitations. Here, we propose an approach combining the strengths of both techniques. We established a mapping population from a sample of natural genotypes, and applied artificial selection for a complex character. Selection changed the frequencies of alleles in QTLs contributing to the selection response. We infer QTLs with dense genotyping microarrays by identifying blocks of linked markers undergoing selective changes in allele frequency. We demonstrated this approach with an experimental population composed from 20 isogenic strains. Selection for starvation survival was executed in three replicated populations with three control non-selected populations. Three individuals per population were genotyped using Affymetrix GeneChips. Two regions of the genome, one each on the left arms of the second and third chromosomes, showed significant divergence between control and selected populations. For the former region, we inferred allele frequencies in selected and control populations by pyrosequencing. We conclude that the allele frequency difference, averaging approximately 40% between selected and control lines, contributed to selection response. Our approach can contribute to the fine scale decomposition of the genetics of direct and indirect selection responses, and genotype by environment interactions.     

Selection-migration regimes characterized by a globally stable equilibrium

The principle that a subdivided population subject to overdominance viability selection in each habitat will manifest a unique, globally attractng polymorphic equilibrium is posited. This follows as a corollary to the stronger principle that, if haploid selection or submultiplicative diploid selection (definition: the geometric mean of the homozygote viabilities is less than or equal to the heterozygote viability) is operating in each habitat,there is a unique, globally attracting stable equilibrium that may be monomorphic or polymorphic. These principles are proven for a broad spectrum of migration patterns. In all such migration selection systems, multiple fixation states cannot be simultaneously stable under submultiplicative viability regimes. Contrasting examples where submultiplicative viabilities are not in force are given.     

Cytonuclear disequilibria in a spatially structured hybrid zone

A hybrid zone model was developed that uses a stepping-stone model of population structure along with both nuclear and cytoplasmic genotypes to evaluate the effect that migration has on random mating organisms when no selection is present. Numerical simulations indicate that a number of different allele frequency and cytonuclear disequilibrium patterns can be found across the hybrid zone when it has reached equilibrium, and these results are discussed in the context of relative migration rates of the two sexes and the two source populations. The importance of numbers of subpopulations sampled, census time, and the persistence of pure species individuals into the hybrid zone are also discussed. Although this model does not consider selection or assortative mating in the hybrid zone, it should provide a useful baseline for evaluating joint cytonuclear genetic data from a structurally complex hybrid zone.     

Multinomial-Sampling Models for Random Genetic Drift

Three different derivations of models with multinomial sampling of genotypes in a finite population are presented. The three derivations correspond to the operation of random drift through population regulation, conditioning on the total number of progeny, and culling, respectively. Generations are discrete and nonoverlapping; the diploid population mates at random. Each derivation applies to a single multiallelic locus in a monoecious or dioecious population; in the latter case, the locus may be autosomal or X-linked. Mutation and viability selection are arbitrary; there are no fertility differences. In a monoecious population, the model yields the Wright-Fisher model (i.e., multinomial sampling of genes) if and only if the viabilities are multiplicative. In a dioecious population, the analogous reduction does not occur even for pure random drift. Thus, multinomial sampling of genotypes generally does not lead to multinomial sampling of genes. Although the Wright-Fisher model probably lacks a sound biological basis and may be inaccurate for small populations, it is usually (perhaps always) a good approximation for genotypic multinomial sampling in large populations.     

Characterization of ten polymorphic microsatellite markers for the protected Spanish moon moth <Emphasis Type="Italic">Graellsia isabelae</Emphasis> (Lepidoptera: Saturniidae)

Ten polymorphic microsatellite loci were developed for Graellsia isabelae. Polymorphism was assessed for 20 individuals from a Spanish population (Els-Ports-de-Beseit, Catalonia) and 39 more individuals from one population in the French Alps and six other Spanish localities. Overall, the number of alleles per locus ranged from 5 to 24. Els-Ports-de-Beseit showed an average number of alleles per locus of 9.80 (SD = 4.32), observed heterozygosity was 0.71 (SD = 0.226), and expected heterozygosity was 0.788 (SD = 0.146). Genotypic frequencies conformed to Hardy–Weinberg equilibrium at the Catalonian population, and no evidence for linkage disequilibrium was observed. Multilocus genotypes resulting from this set of markers will be useful to determine genetic diversity and differentiation within and among populations of this highly protected moth. Several loci amplified and resulted polymorphic in two related species: two loci in Actias neidhoeferi, and three loci in A. luna.     

Uniqueness of polymorphic equilibria under soft selection

Any two allele polymorphic equilibrium of a subdivided haploid population subject to soft selection is stable. This provides that for a two allele system in a subdivided haploid population there is a globally attracting equilibrium which is polymorphic if a polymorphic equilibrium exists, otherwise monomorphic. These results extend to diploid populations if within each habitat the heterozygote viability is greater than or equal to the geometric mean of the homozygote viabilities.