Analysis of STAT5A/AvaI Gene Polymorphism in Four Italian Cattle Breeds

The STAT5A/AvaI polymorphism was investigated with PCR-RFLP in a sample of 339 cattle belonging to four breeds: Italian Friesian, Jersey, Italian Brown, and Podolica reared in south Italy. All three possible genotypes for the C/T polymorphism were identified. In these breeds, PCR-RFLP showed the predominance of the TT genotype in Italian Brown and Jersey cows; in Podolica and Italian Friesian CT is the most frequent genotype. The frequency of the T allele ranged from 0.55 to 0.81 in the analyzed populations. The distribution of genotypic and allelic frequencies at this locus was significantly different among the four populations based on a χ² test (P < 0.001), suggesting that the molecular characteristics of the STAT5A gene could be significantly affected by the breed selection. Gene heterozygosity, gene homozygosity, effective allele number, fixation index, and polymorphism information content (PIC) were calculated. The observed heterozygosity, as well as the N _e and PIC values, indicates high genetic variability in the Podolica breed. Podolica could be considered an interesting reservoir of genetic diversity for a species under high selective pressure elsewhere.     

Genetic Divergence and Signatures of Natural Selection in Marginal Populations of a Keystone,Long-Lived Conifer,Eastern White Pine (Pinus strobus) from Northern Ontario

Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (N _e) and higher genetic differentiation than central populations. We tested these hypotheses using eastern white pine (Pinus strobus) as a model for keystone, long-lived widely-distributed plants. All 614 eastern white pine trees, in a complete census of two populations each of marginal old-growth, central old-growth, and central second-growth, were genotyped at 11 microsatellite loci. The central populations had significantly higher allelic and genotypic diversity, latent genetic potential (LGP) and N _e than the marginal populations. However, heterozygosity and fixation index were similar between them. The marginal populations were genetically diverged from the central populations. Model testing suggested predominant north to south gene flow in the study area with curtailed gene flow to northern marginal populations. Signatures of natural selection were detected at three loci in the marginal populations; two showing divergent selection with directional change in allele frequencies, and one balancing selection. Contrary to the general belief, no significant differences were observed in genetic diversity, differentiation, LGP, and N _e between old-growth and second-growth populations. Our study provides information on the dynamics of migration, genetic drift and selection in central versus marginal populations of a keystone long-lived plant species and has broad evolutionary, conservation and adaptation significance.     

DOES MATE LIMITATION IN SELF‐INCOMPATIBLE SPECIES PROMOTE THE EVOLUTION OF SELFING? THE CASE OF LEAVENWORTHIA ALABAMICA

Genetic diversity at the S‐locus controlling self‐incompatibility (SI) is often high because of negative frequency‐dependent selection. In species with highly patchy spatial distributions, genetic drift can overwhelm balancing selection and cause stochastic loss of S‐alleles. Natural selection may favor the breakdown of SI in populations with few S‐alleles because low S‐allele diversity constrains the seed production of self‐incompatible plants. We estimated S‐allele diversity, effective population sizes, and migration rates in Leavenworthia alabamica, a self‐incompatible mustard species restricted to discrete habitat patches in rocky glades. Patterns of polymorphism were investigated at the S‐locus and 15 neutral microsatellites in three large and three small populations with 100‐fold variation in glade size. Populations on larger glades maintained more S‐alleles, but all populations were estimated to harbor at least 20 S‐alleles, and mate availabilities typically exceeded 0.80, which is consistent with little mate limitation in nature. Estimates of the effective size (N_e) in each population ranged from 600 to 1600, and estimated rates of migration (m) ranged from 3 × 10⁻⁴ to nearly 1 × 10⁻³. According to theoretical models, there is limited opportunity for genetic drift to reduce S‐allele diversity in populations with these attributes. Although pollinators or resources limit seed production in small glades, limited S‐allele diversity does not appear to be a factor promoting the incipient breakdown of SI in populations of this species that were studied.     

Temporal Stability of Genetic Variability and Differentiation in the Three-Spined Stickleback (Gasterosteus aculeatus)

Temporal variation in allele frequencies, whether caused by deterministic or stochastic forces, can inform us about interesting demographic and evolutionary phenomena occurring in wild populations. In spite of the continued surge of interest in the genetics of three-spined stickleback (Gasterosteus aculeatus) populations, little attention has been paid towards the temporal stability of allele frequency distributions, and whether there are consistent differences in effective size (N_e) of local populations. We investigated temporal stability of genetic variability and differentiation in 15 microsatellite loci within and among eight collection sites of varying habitat type, surveyed twice over a six-year time period. In addition, N_es were estimated with the expectation that they would be lowest in isolated ponds, intermediate in larger lakes and largest in open marine sites. In spite of the marked differences in genetic variability and differentiation among the study sites, the temporal differences in allele frequencies, as well as measures of genetic diversity and differentiation, were negligible. Accordingly, the N_e estimates were temporally stable, but tended to be lower in ponds than in lake or marine habitats. Hence, we conclude that allele frequencies in putatively neutral markers in three-spined sticklebacks seem to be temporally stable – at least over periods of few generations – across a wide range of habitat types differing markedly in levels of genetic variability, effective population size and gene flow.     

Conservation genetic studies of the endangered Cape Fear Shiner, Notropis mekistocholas (Teleostei: Cyprinidae)

Genetic variation at ten microsatellite lociand one anonymous-nuclear locus was assayed forthree geographic samples of the criticallyendangered North American cyprinidNotropis mekistocholas (Cape Fear shiner). Despite low abundance of this species, therewas little suggestion of small populationeffects; allele diversity and heterozygositywere relatively high, F_IS values withinsamples were non-significant, and genotypeswere distributed in frequencies according toHardy-Weinberg expectations. Geneticdivergence among samples was minimal despitethe presence of dams, constructed in the early1900s, that separate the sample sites. Thissuggests that recent gene flow has beensufficient to inhibit genetic divergence orthat gene flow has been reduced but there hasbeen insufficient time for genetic divergenceto develop. Tests of heterozygosity excesswere non-significant, suggesting that N.mekistocholas in the localities sampledhave not undergone recent reductions ineffective population size. Future studiesemploying larger sample sizes to provide morerobust tests of population structure andtemporally separated samples to estimatecontemporaneous N _e are warranted.     

元江鲤种群遗传多样性

选择12对微卫星标记检测了于2011年采集自元江(红河上游中国江段)5个样点192尾鲤的群体遗传多样性.共检测到201个等位基因,每个位点等位基因2-27个.各群体各位点平均等位基因(NA)12.25-14.67个,平均有效等位基因(NE)8.28-9.73个,平均观察杂合度(Ho)o.7765-0.8037,平均期望杂合度(HE)0.7761-0.8080,平均多态信息含量(PIC)0.7534-0.7843.元江鲤种群192个个体各位点NA、NE、Ho、HE、PIC分别为16.50、11.26、0.7927、0.8049、0.7966,种群遗传多样性水平高.元江鲤群体之间遗传分化小,可作为一个种群管理单元进行管理.增殖放流要防止遗传多样性丧失.     

Genetic diversity of the endangered Chinese endemic herb Dayaoshania cotinifolia (Gesneriaceae) revealed by simple sequence repeat (SSR) markers

Dayaoshania cotinifolia W.T. Wang is a critically endangered perennial herb endemic to southern China. Simple sequence repeat (SSR) markers were employed to assess genetic diversity in two populations of D. cotinifolia. Eight primer pairs generated a total of 36 alleles, with a mean of 4.5 alleles per locus. The expected heterozygosity (H_e = 0.416) and observed heterozygosity (H_o = 0.508) indicated a moderate level of genetic diversity, though the genetic differentiation between the populations was low (F_st = 0.014), a result that was supported by a higher gene flow (N_m = 18.000). No severe bottleneck effect was detected in the two populations. Thus, the endangered status of this species is most likely due to anthropologic effects rather than a lack of genetic diversity. In situ conservation strategies should be promoted, and the sizes of the populations should be increased through artificial breeding.     

Coupling Demographic and Genetic Variability from Archived Collections of European Anchovy (Engraulis encrasicolus)

It is well known that temporal fluctuations in small populations deeply influence evolutionary potential. Less well known is whether fluctuations can influence the evolutionary potentials of species with large census sizes. Here, we estimated genetic population parameters from as survey of polymorphic microsatellite DNA loci in archived otoliths from Adriatic European anchovy (Engraulis encrasicolus), a fish with large census sizes that supports numerous local fisheries. Stocks have fluctuated greatly over the past few decades, and the Adriatic fishery collapsed in 1987. Our results show a significant reduction of mean genetic parameters as a consequence of the population collapse. In addition, estimates of effective population size (N_e) are much smaller than those expected in a fishes with large population census sizes (N_c). Estimates of N_e indicate low effective population sizes, even before the population collapse. The ratio N_e/N_e ranged between 10⁻⁶ and 10⁻⁸, indicating a large discrepancy between the anchovy gene pool and population census size. Therefore, anchovy populations may be more vulnerable to fishery effort and environmental change than previously thought.     

Loss of historical immigration and the unsuccessful rehabilitation of extirpated salmon populations

Comprehensive evaluations of multiple genetic factors are rarely undertaken in rehabilitation attempts of extirpated populations, despite a growing need to address why some rehabilitation projects succeed and others fail. Using temporally-spaced samples of microsatellite DNA, we tested several genetic hypotheses that might explain an unsuccessful attempt to re-establish Atlantic salmon populations (Salmo salar) in two rivers of the inner Bay of Fundy, Canada. Census sizes (N) in both populations plummeted to near zero from initial increases after reintroduction/human-mediated recolonization occurred. Over the same period (1974–1996), both populations were characterized by low or relatively low effective sizes (N _e ) and temporally unstable genetic structuring, whereas neighbouring populations, known historically for their significant salmon production, were not. Despite evidence for genetic bottlenecking and continual linkage disequilibrium over time in both populations, neither exhibited detectable inbreeding or a significant loss of allelic diversity or heterozygosity relative to known donor/source populations. Ratios of N _e to N also increased with decreasing N in both populations, implying a buffering capacity against losses of genetic diversity at depressed abundances. Most significantly, multiple lines of evidence were consistent with the hypothesis that there has been substantial and recurrent asymmetric migration (migration rate, m) from neighbouring areas into both populations even after initial rehabilitation. This included migration from a historically productive population that became extirpated during the course of rehabilitation efforts, indicating that both populations might have naturally depended on immigration from neighbouring areas for persistence. Our results highlight the value of incorporating temporal genetic data beyond commonly used metrics of neutral genetic diversity (F _ST, allelic richness, heterozygosity) to evaluate rehabilitation successes or failures. They also illustrate how the joint evaluation of multiple genetic concerns in rehabilitation attempts, at spatial scales beyond donor and rehabilitated populations, is useful for focusing future rehabilitation efforts.     

EFFECTIVE POPULATION SIZE AND GENETIC DRIFT IN TRISTYLOUS EICHHORNIA PANICULATA (PONTEDERIACEAE)

Populations of the tristylous, annual Eichhornia paniculata are markedly differentiated with respect to frequency of mating types. This variation is associated with evolutionary changes in mating system, from predominant outcrossing to high self-fertilization. To assess the potential influence of genetic drift acting on this variation, we estimated effective population size in 10 populations from northeastern Brazil using genetic and demographic methods. Effective size (N_e) was inferred from temporal changes in allele frequency at two to eight isozyme loci and also calculated using five demographic variables: 1) the number of flowering individuals (N); 2) temporal fluctuations in N; 3) variance in flower number; 4) frequency of mating types; and 5) selfing rate. Average N_e based on isozyme data was 15.8, range 3.4–70.6, and represented a fraction (mean N_e/N = 0.106) of the census number of individuals (mean N = 762.8; range: 30.5–5,040). Temporal variation in N and variance in flower number each reduced N_e to about a half of N whereas mating type frequencies and selfing rate caused only small reductions in N_e relative to N. All estimates of N_e based on demographic variables were considerably larger than those obtained from genetic data. The two kinds of estimates were in general agreement, however, when all demographic variables were combined into a single measure. Monte Carlo simulations indicated that effective size must be fewer than about 40 for drift to overcome the frequency-dependent selection that maintains the polymorphism for mating type. Applying the average N_e/N value to 167 populations censused in northeastern Brazil indicated that 72% had effective sizes below this number. This suggests that genetic drift is likely to play a dominant role in natural populations of E. paniculata.     

Reconciling Genetic and Demographic Estimators of Effective Population Size in the Anuran Amphibian Bufo Calamita

We used genetic and demographic methods to estimate the variance effective population sizes (N _e) of three populations of natterjack toads Bufo calamita in Britain. This amphibian breeds in temporary pools where survival rates can vary among families. Census population sizes (N) were derived from spawn string counts. Point and coalescent-based maximum likelihood estimates of N _e based on microsatellite allele distributions were similar. N _e/N ratios based on genetic estimates of N _e ranged between 0.02 and 0.20. Mean demographic estimates of N _e were consistently higher (2.7–8.0-fold) than genetic estimates for all three populations when variance in breeding success was evaluated at the point where females no longer influence their progeny. However, discrepancies between genetic and demographic estimators could be removed by using a model that included extra variance in survivorship (above to Poisson expectations) among families. The implications of these results for the estimation of N _e in wild populations are discussed.     

Effective population size in eusocial Hymenoptera with worker-produced males

In many eusocial Hymenoptera, a proportion of males are produced by workers. To assess the effect of male production by workers on the effective population size N_e, a general expression of N_e in Hymenoptera with worker-produced males is derived on the basis of the genetic drift in the frequency of a neutral allele. Stochastic simulation verifies that the obtained expression gives a good prediction of N_e under a wide range of conditions. Numerical computation with the expression indicates that worker reproduction generally reduces N_e. The reduction can be serious in populations with a unity or female-biased breeding sex ratio. Worker reproduction may increase N_e in populations with a male-biased breeding sex ratio, only if each laying worker produce a small number of males and the difference of male progeny number among workers is not large. Worker reproduction could be an important cause of the generally lower genetic variation found in Hymenoptera, through its effect on N_e.     

Sexual recombination under the joint effects of mutation,selection, and random sampling drift

The advantage or disadvantage of sexual reproduction or recombination for the accumulation of mutant genes in a population is studied under the joint effects of recurrent mutations, selection, and random sampling drift. To obtain the rate at which mutant genes are incorporated three different methods are used; numerical integration of Kolmogorov backward equations, simulation of stochastic difference equations, and Monte Carlo experiments. The first two methods are used in a two-locus system to obtain the fixation probability of double mutants and other related quantities under five different selection models. The third one is conducted for a multiple-locus system and the rate of accumulation of mutant genes per locus is studied. Comparison of the results between sexual and asexual populations shows that the effect of recombination depends on initial linkage disequilibrium, mutation rate v, selection intensity s, and population size N_e. The mode of selection is also an important factor and the large effect of recombination is observed when mutant genes are individually deleterious but collectively favorable. Under a given model of selection, the great advantage or disadvantage of recombination is achieved when a large extent of genetic polymorphism is produced not by mutation but by recombination. Extreme values of N_es and N_ev make the effect insignificant. The results of Monte Carlo experiments also reveal the presence of interaction between selection and sampling drift even when the loci segregate independently and selection is multiplicative. Although this interaction is usually small, there are cases in which one locus theory cannot be used freely. In those cases, the effect of recombination is prominent and one locus theory gives an overestimate of the rate.     

Genetic diversity and parentage assignment in Dojo loach,Misgurnus anguillicaudatus based on microsatellite markers

In this study, genetic diversity and structure of three Misgurnus anguillicaudatus populations from three different geographical locations in China (Hunan, Hubei and Henan province) were investigated using microsatellite markers. High level of genetic diversity of all three populations was revealed by expected heterozygosity (H_e), observed heterozygosity (H_o) and allele number. Significant genetic differentiations were found between all pairs of populations. The efficiency of eight microsatellite markers in parentage assignment of 540 progeny from twenty full-sib families was evaluated. Simulation based on allele frequency data demonstrated that probabilities of exclusion per locus range from 0.313 to 0.825 when no parent information is available and 0.504 to 0.904 when one parent is known. The assignment success rate based on the real data using eight markers was 96.85%. This study indicates that these M. anguillicaudatus resources are valuable genetic and breeding material for aquaculture and the microsatellite markers will be useful for investigation of genetic background and molecular marker-assisted selective breeding in this species.     

Genetic divergence without spatial isolation in polecat Mustela putorius populations

Understanding how genetic divergence could exist without spatial isolation is a fundamental issue in biology. Although carnivores have previously been considered as having a weak genetic variability, polecats Mustela putorius from eight distinct populations exhibited both a strong polymorphism (17.5–22.5%) and a substantial allele effective number reaching N_e=1.12. Heterozygosity ranging from H_o=0.031–0.063 significantly differed among populations, while the mean F_IS averaging 0.388 stressed a real deficiency of heterozygotes. Observed heterozygosity levels among populations did not correlate with any habitat types but were clearly associated with habitat diversity index. The habitat structure in polecat home range corresponded to habitat mosaic structure in which discrete habitat types alternated causing multifactorial constraints that may favour heterozygosity. Allozymic frequencies within populations did not vary with dominant habitat. But in the Tyrosinase‐1, the rare homozygote BB, resulting in a ‘dark’ phenotype, was found much more in deciduous woods than the homozygote AA showing the ‘typical’ pattern. Thus, the genetic basis for a character differentiation was here evidenced in a remarkable situation without spatial isolation. Further, the very low proportion of heterozygotes for this locus suggests a disruptive effect and supports the prediction of intermediate phenotypes being at a disadvantage. This heterozygote deficit may also result from an assortative mating intra phenotype (homogamy). The divergence in polecat phenotypes showed that genetic differentiation can be induced by subtle variations in environment, a situation that is likely to be frequent in most natural populations, and emphasized the adaptive nature of habitat preference.     

Effective size of density‐dependent two‐sex populations: the effect of mating systems

Density dependence in vital rates is a key feature affecting temporal fluctuations of natural populations. This has important implications for the rate of random genetic drift. Mating systems also greatly affect effective population sizes, but knowledge of how mating system and density regulation interact to affect random genetic drift is poor. Using theoretical models and simulations, we compare N_e in short‐lived, density‐dependent animal populations with different mating systems. We study the impact of a fluctuating, density‐dependent sex ratio and consider both a stable and a fluctuating environment. We find a negative relationship between annual N_e/N and adult population size N due to density dependence, suggesting that loss of genetic variation is reduced at small densities. The magnitude of this decrease was affected by mating system and life history. A male‐biased, density‐dependent sex ratio reduces the rate of genetic drift compared to an equal, density‐independent sex ratio, but a stochastic change towards male bias reduces the N_e/N ratio. Environmental stochasticity amplifies temporal fluctuations in population size and is thus vital to consider in estimation of effective population sizes over longer time periods. Our results on the reduced loss of genetic variation at small densities, particularly in polygamous populations, indicate that density regulation may facilitate adaptive evolution at small population sizes.     

Enzyme gene heterozygosity in small island populations of Philaenus spumarius (L.) (Homoptera)

Genetic polymorphism at about twenty enzyme loci in one mainland and in six differentially isolated island populations of Philaenus spumarius (L.) was studied by starch gel electrophoresis. The populations have different average degrees of heterozygosity, so that the most isolated population is the least polymorphic. The differences in heterozygosity seem to be correlated to the size of the population and the degree of isolation from other populations. With a single exception, the most common allele in each locus is the most common one everywhere. The results are compared with the differences observed in the color polymorphism of Philaenus island populations. The allele frequencies of enzyme loci are maintained by selection; the fact that the prevalent allele is the same in all populations may be due to selection and founder principle.Report no. 485 from the Tvärminne Zoological Station, University of Helsinki.     

Testing single-sample estimators of effective population size in genetically structured populations

The effective population size (N _e ) is a key parameter in evolutionary and population genetics. Single-sample N _e estimation provides an alternative to traditional approaches requiring two or more samples. Single-sample methods assume that the study population has no genetic sub-structure, which is unlikely to be true in wild populations. Here we empirically investigated two single-sample estimators (onesamp and L d N e) in replicated and controlled genetically structured populations of Drosophila melanogaster. Using experimentally controlled population parameters, we calculated the Wright–Fisher expected N _e for the structured population ( ^Total N _e ) and demonstrated that the loss of heterozygosity did not significantly differ from Wright’s model. We found that disregarding the population substructure resulted in ^Total N _e estimates with a low coefficient of variation but these estimates were systematically lower than the expected values, whereas hierarchical estimates accounting for population structure were closer to the expected values but had a higher coefficient of variation. Analysis of simulated populations demonstrated that incomplete sampling, initial allelic diversity and balancing selection may have contributed to deviations from the Wright–Fisher model. Overall the approximate-Bayesian onesamp method performed better than L d N e (with appropriate priors). Both methods performed best when dispersal rates were high and the population structure was approaching panmixia.     

Gene Frequency Distribution of the BoLA-DRB3 Locus in Saavedreño Creole Dairy Cattle

The objective of this study is to describe the gene frequency distribution of the bovine lymphocyte antigen (BoLA)-DRB3 locus in Saavedreño Creole dairy cattle and to compare it with previously reported patterns in other cattle breeds. One hundred and twenty-five Saavedreño Creole dairy cattle were genotyped for the BoLA-DRB3.2 allele by polymerase chain reaction and restriction fragment length polymorphism. Twenty-two out of 53 previously identified BoLA-DRB3.2 alleles were detected, with gene frequencies ranging from 0.4 to 16.8%. Seventy percent of the variation corresponded to the seven most frequent alleles (BoLA-DRB3.2*7, *8, *11, *16, *27, *36, and *37). The studied population exhibits a high degree of expected heterozygosity (h _e = 0.919). The F _IS index did not show significant deviation from Hardy-Weinberg equilibrium. However, the neutrality test showed an even gene frequency distribution. This result could be better explained assuming balancing selection instead of neutral or positive selection for one or a few alleles. In conclusion, the results of this study demonstrated that BoLA-DRB3.2 is a highly polymorphic locus in Saavedreño Creole dairy cattle, with significant variation in allele frequency among cattle breeds.     

A century-long genetic record reveals that protist effective population sizes are comparable to those of macroscopic species

Effective population size (N_e) determines the rate of genetic drift and the relative influence of selection over random genetic changes. While free-living protist populations characteristically consist of huge numbers of cells (N), the absence of any estimates of contemporary N_e raises the question whether protist effective population sizes are comparably large. Using microsatellite genotype data of strains derived from revived cysts of the marine dinoflagellate Pentapharsodinium dalei from sections of a sediment record that spanned some 100 years, we present the first estimates of contemporary N_e for a local population in a free-living protist. The estimates of N_e are relatively small, of the order of a few 100 individuals, and thus are similar in magnitude to values of N_e reported for multicellular animals: the implications are that N_e of P. dalei is of many orders of magnitude lower than the number of cells present (N_e/N ∼ 10⁻¹²) and that stochastic genetic processes may be more prevalent in protist populations than previously anticipated.