Differentiation Of Gene Frequencies Research Articles

Genetic diversity of Prunus sibirica L. superior accessions based on the SSR markers developed using restriction-site associated DNA sequencing

Prunus sibirica (Siberian apricot) has ecological, economic, and social benefits that makes it an important fruit-bearing tree in China. However, current fruit yields are low and unstable, thus restricting development of Prunus sibirica industry. To provide a scientific basis for successful breeding research aimed at developing superior cultivars, 98 screened SSR markers were first used in our study, developed by restriction-site associated DNA sequencing, to assess the genetic diversity of 66 Prunus sibirica accessions collected from four populations. The average number of alleles per locus (9.910) and the number of effective alleles (5.445) showed high polymorphism in the entire population, and the polymorphism information content (0.675) indicated that these markers were highly polymorphic. There was gene flow among the Prunus sibirica accessions, however the genetic differentiation coefficient showed 15.4% gene frequency differentiation among the provenances. Meanwhile, extensive linkage disequilibrium (D′ > 0.5, P < 0.01) was found, however the overall level was low (r2 < 0.5, p < 0.01). Additionally, the 66 accessions clustered into four groups, and these groups were extremely significantly correlated with the provenances classification. The clustering results showed that geographical distribution and genetic diversity changed from high to low as the geographic separation between provenances increased. Furthermore, population structure analysis supported these findings as genetic structure and provenances were extremely significantly correlated (p < 0.01). Additionally, the relationships between the geographical and genetic distances of the provenances and of the individuals were significantly correlated, indicating that geographical isolation importantly influenced Prunus sibirica evolution. The geographic and genetic effects underlying the superior accessions which we selected provide a reference for future molecular marker assisted breeding of Prunus sibirica.

The influence of partial panmixia on neutral models of spatial variation

Partial panmixia can be regarded as the limiting case of long-distance migration. The effect of incorporating partial panmixia into neutral models of geographical variation is investigated. The monoecious, diploid population is subdivided into randomly mating colonies that exchange gametes independently of genotype. The gametes fuse wholly at random, including self-fertilization. Generations are discrete and nonoverlapping; the analysis is restricted to a single locus; every allele mutates to new alleles at the same rate. Introducing some panmixia intensifies sufficiently weak migration. A general formula is derived for the migration effective population number, N e , and N e is evaluated explicitly in a number of models with nonconservative migration. Usually, N e increases as the panmictic rate, b , increases; in particular, this result holds for two demes, and generically if the underlying migration is either sufficiently weak or panmixia is sufficiently strong. However, in an analytic model, there exists an open set of parameters for which N e decreases as b increases. Migration is conservative in the island and circular-habitat models, which are studied in detail. In the former, including some panmixia simply alters the underlying migration rate, increasing (decreasing) it if it is less (greater) than the panmictic value. For the circular habitat, the probability of identity in allelic state at equilibrium is calculated in a nonlocal, continuous-space, continuous-time approximation. In both models, by an efficient, general method, the expected homozygosity, effective number of alleles, and differentiation of gene frequencies are evaluated and discussed; their monotonicity properties with respect to all the parameters are determined; and in the model of infinitely many sites, the mean coalescence times and nucleotide diversities are studied similarly. For the probability of identity at equilibrium in the unbounded stepping-stone model in arbitrarily many dimensions, introducing some panmixia merely replaces the mutation rate by a larger parameter. If the average probability of identity is initially zero, as for identity by descent, then the same conclusion holds for all time.

Developing microsatellite markers for insect population structure: complex variation in a checkerspot butterfly.

We isolated and characterized two microsatellite markers from the genome of the endangered checkerspot butterfly Melitaea cinxia L. In Finland, this species only survives on the Aland islands, where it exhibits a highly fragmented metapopulation structure on small meadows. Four alleles were observed at the locus CINX1 and nine at CINX4; the total gene diversities at the two loci were HT = 0.34 and 0.80, respectively. A pilot survey showed moderate gene frequency differentiation among meadows (local populations; FLM = 0.1) and among metapopulations c. 30 km apart (FMT = 0.2). Contrary to prior expectation, distinct feeding larval groups collected in the spring did not represent offspring of single females. There was a conspicuous excess of homozygotes within local populations (FIL = 0.35), which can hardly be attributed to population structure alone; this urges caution in straightforward interpretation of microsatellite phenotype data.

Genetic differentiation in Daphnia obtusa: a continental perspective

1. The restricted scale of most prior studies of genetic diversity in daphniid populations provides limited information on the geographical patterning of gene frequencies. The present study addresses this gap by examining allozymic divergence in populations of the most broadly distributed daphniid in the warm temperate regions of North America, Daphnia obtusa, across its range.2. Local populations of this species show the gene frequency differentiation typical of other daphniids. In contrast to other daphniids with broad distributions, however, further divergence is apparent at a larger geographical scale, with North American D. obtusa fragmented into three lineages showing largely allopatric distributions. The three lineages are based primarily on allele frequency shifts at three polymorphic loci and are represented by eastern, central and south‐western groupings.3. Because of this pattern of differentiation, there is no simple monotonic relationship between geographical distance and genetic divergence. Instead, local metapopulations belonging to a specific lineage show little genetic divergence over several thousand km, while marked shifts in gene frequency occur over a few hundred km in regions where different lineages are in contact.

Estimating relatedness in social groups

Genetic relatedness is a vital parameter in the evolution of social behaviour by kin selection. It can be easily estimated using genetic markers and calculating the genotypic correlation or regression of group members. Spatial gene frequency differentiation, due to population subdivision or isolation by distance, boosts the relatedness estimates. In such cases it may be useful to partition the estimate into components, the operational relatedness is normally that among individuals in social groups within the same subpopulation. Although it is straightforward to estimate the average relatedness in social groups, estimating values for specific individuals with the help of genetic markers is still problematic. Current estimators tend to give biased values and the sampling error is large. In spite of these shortcomings, studies of social behaviour combining relatedness and reproductive success are sorely needed.

Diffusion model for genotype-dependent migration

A diffusion model for the joint action of genotype-dependent migration and genotype-independent population regulation is derived and investigated. The diploid, monoecious population occupies a finite chain of equally spaced colonies; generations are discrete and nonoverlapping; mating is random in each colony. A boundary-value problem is deduced for the gene frequencies at a multiallelic locus in the absence of mutation, selection, and random drift. This problem is studied for two alleles and constant and uniform population density and drift and diffusion coefficients. All equilibria are shown to be monotone, and explicit conditions for a protected polymorphism are established. Two examples of asymptotically stable clines are presented. It is demonstrated that genotype dependence of the mean displacements is necessary to produce or maintain spatial differentiation of gene frequencies.

Genetic aspects of migration in a rhesus monkey population

Abstract Gene frequency distributions in subdivided populations are affected by migration of individuals between groups. This paper considers the effects of such migration on blood protein allele frequency distributions in social groups of the Cayo Santiago rhesus macaque colony. Gene frequencies for complete social groups and their migrant and natal segments were analyzed at four points within a four year period in the colony's history. Gene frequencies varied between the migrant segments of different groups. Gene frequencies of migrant segments of particular groups also varied substantially with time. Usually, but not always, the presence of migrants in groups reduced the levels of inter-group gene frequency differentiation. We suggest that our findings are explained by a model in which the recruitment of immigrants into social groups is largely random with respect to individual genotypes. Such a model implies that migration contributes to both stochastic and directed changes in gene frequencies in rhesus and similarly substructured populations.

Some Reproductive Parameters of Mallards in Relation to Age, Captivity, and Geographic Origin

Some Reproductive Parameters of Mallards in Relation to Age, Captivity, and Geographic Origin

ENZYME VARIABILITY IN NATURAL POPULATIONS OF DAPHNIA MAGNA I. POPULATION STRUCTURE IN EAST ANGLIA.

The patchy distribution of freshwater ponds would seem to provide ideal opportunities for deme formation and enhancement of evolutionary rates due to selective and stochastic exploration of genetic variation (Wright, 1940, 1960). In actual fact, however, pond dwelling organisms show evidence of slow evolutionary differentiation. The zoogeographical uniformity of pond life, particularly of those groups which rely on passive dispersal, has long been recognized (Darwin, 1859; Belt, 1874); global distributions are frequent at the generic level, while species usually have large ranges over which they show little evidence of subspeciation. Bayley (1967), for example, points out that many of the cyclopoid copepods found in Australia are phenotypically indistinguishable from North American species. This apparent lack of genetic differentiation has generally been related to high vagility (Mayr, 1963). The cladoceran crustacean, Daphnia magna, possesses many of the characteristics typical of passively dispersing pond organisms. The range of the species is extensive: D. magna occurs throughout the Palearctic, over much of the Nearctic and in the southern portion of the Ethiopian region as well (Richard, 1896; Sars, 1916). Over this area the species is subject to little phenotypic variation. Brooks (1957) mentions that European and North American populations can be distinguished only with difficulty. If gene flow is responsible for maintaining phenotypic uniformity over this large range, then one might expect microgeographical differentiation of gene frequencies to be minimal. Yet in an

Genetic structure of a population occupying a circular habitat.

The geographical structure of a finite population distributed continuously and homogeneously along a circular habit is explored. Selection is supposed to be absent, and the analysis is restricted to a single locus with discrete, non-overlapping generations. Assuming every mutant is new to the population, the rate of decay of genetic variability is obtained, and the probability that two homologous genes separated by a given distance are different alleles is calculated. If moments of the migration function higher than second are neglected, the eigenvalue equation is shown to be a simple trigonometric one, and the Fourier series giving the transient and stationary probabilities of allelism are summed in terms of elementary functions. The proportion of homozygotes, the effective number of alleles maintained in the population, and the amount of local differentiation of gene frequencies are discussed.

The decay of genetic variability in geographically structured populations.

The geographical structure of a population distributed continuously and homogeneously along an infinite linear habitat is explored. The analysis is restricted to a single locus in the absence of selection, and every mutant is assumed to be new to the population. An explicit formula is derived for the probability that two homologous genes separated by a given distance at any time t are the same allele. The ultimate rate of approach to equilibrium is shown to be t(-3/2)e(-2ut), where u is the mutation rate. An approximation is given for the stationary probability of allelism in an infinite two-dimensional population, which, unlike previous expressions, is finite everywhere. For a finite habitat of arbitrary shape and any number of dimensions, it is proved that if the population density is very high, then asymptotically the transient part of the probability of allelism is spatially uniform and decays at the rate e(-[2u+1/(2N)]t), where N is the total population size. Thus, in this respect the population behaves as if it were panmictic. The dependence of the amount of local gene frequency differentiation on population density and habitat size and dimensionality is discussed.

The rate decay of genetic variability in a geographically structured finite population

The asymptotic rate of decay of genetic variability in a (one-dimensional) geographically structured population is proportional to the variance of dispersal distances when the habitat is large, and it is proportional to the reciprocal of the population size when the population density is large or the migration distances are large. The rate is independent of the migration pattern except for its variance. The theory is applied to the problems of the speed of gene substitution and of the local differentiation of gene frequencies.

Pattern of neutral polymorphism in a geographically structured population.

SUMMARYIn a two-dimensional stepping-stone model of finite size, if a pair of alleles happen to segregate in the whole population, marked local differentiation of gene frequencies can occur only if migration between colonies is sufficiently rare so thatNm&lt; 1, whereNis the effective size of each colony andmis the rate at which each colony exchanges individuals with four surrounding colonies each generation. On the other hand, ifNm≥ 4, the whole population behaves as if it were panmictic and the allelic frequencies become uniform over the entire distribution range unless mutation is unusually high. Tendency toward local differentiation is much weaker in two-dimensional than in one-dimensional habitats.