History vs. current demography: explaining the genetic population structure of the common frog (Rana temporaria)

The amount of genetic variability at neutral marker loci is expected to decrease, and the degree of genetic differentiation among populations to increase, as a negative function of effective population size. We assessed the patterns of genetic variability and differentiation at seven microsatellite loci in the common frog (Rana temporaria) in a hierarchical sampling scheme involving three regions (208-885 km apart), three subregions within regions and nine populations (5-20 km apart) within subregions, and related the variability and differentiation estimates to variation in local population size estimates. Genetic variability within local populations decreased significantly with increasing latitude, as well as with decreasing population size and regional site occupancy (proportion of censured localities occupied). The positive relationship between population size and genetic variability estimates was evident also when the effect of latitude (cf. colonization history) was accounted for. Significant genetic differentiation was found at all hierarchical levels, and the degree of population differentiation tended to increase with increasing latitude. Isolation by distance was evident especially at the regional sampling level, and its strength increased significantly towards the north in concordance with decreasing census and marker-based neighbourhood size estimates. These results are in line with the conjecture that the influence of current demographic factors can override the influence of historical factors on species population genetic structure. Further, the observed reductions in genetic variability and increased degree of population differentiation towards the north are in line with theoretical and empirical treatments suggesting that effective population sizes decline towards the periphery of a species' range.     

The effects of ecological and genetic neighbourhood size on the evolution of two competing species

Summary Individual-based simulations were conducted to examine the effect of a small ecological neighbourhood (an area in which ecological processes such as density-dependent factors operate) and the genetic neighbourhood size (the size of an area from which the parents may be assumed to be drawn at random) on the coevolution of two competing species. For the simulations, individuals of two consumer species compete for two types of food organisms. Different genotypes (one locus and two alleles) have different efficiencies of food acquisition for different food types. Individual consumer organisms search for food within their home ranges and reproduce depending on the amount of food eaten. The dispersal distance of the offspring follows a normal distribution with a zero mean and _d standard deviation. Simulations were conducted by varying the home range size, mating area (area from where individuals choose their mates), standard deviation of dispersal distance, food generation time, the reproductive rates of food populations and the sizes and number of independent food populations. Food organisms reproduce either within one population or independently within 16 spatially divided populations. For all the simulations, competitive exclusion was the most frequent outcome and character displacement was the least frequent outcome. Through a 200-generation simulation, the two consumer species could co-exist longer and maintain a polymorphic resource use longer when the home range and mating size were small in 16 spatially divided populations than when random mating and homogeneous interaction occurred within a community (perfect mixing population). For perfect mixing populations, the frequency of character displacement increased as the food generation time became short and the reproductive rates of food decreased. It follows from the results that the sizes of the genetic and ecological neighbourhoods and the mode of resource dynamics can affect the evolution of two competing species.     

When are genetic methods useful for estimating contemporary abundance and detecting population trends?

The utility of microsatellite markers for inferring population size and trend has not been rigorously examined, even though these markers are commonly used to monitor the demography of natural populations. We assessed the ability of a linkage disequilibrium estimator of effective population size (N_e) and a simple capture-recapture estimator of abundance (N) to quantify the size and trend of stable or declining populations (true N = 100–10,000), using simulated Wright–Fisher populations. Neither method accurately or precisely estimated abundance at sample sizes of S = 30 individuals, regardless of true N. However, if larger samples of S = 60 or 120 individuals were collected, these methods provided useful insights into abundance and trends for populations of N = 100–500. At small population sizes (N = 100 or 250), precision of the N_e estimates was improved slightly more by a doubling of loci sampled than by a doubling of individuals sampled. In general, monitoring N_e proved a more robust means of identifying stable and declining populations than monitoring N over most of the parameter space we explored, and performance of the N_e estimator is further enhanced if the N_e/N ratio is low. However, at the largest population size (N = 10,000), N estimation outperformed N_e. Both methods generally required ≥ 5 generations to pass between sampling events to correctly identify population trend.     

Estimating Effective Population Size from Temporally Spaced Samples with a Novel,Efficient Maximum-Likelihood Algorithm

The effective population size N_e is a key parameter in population genetics and evolutionary biology, as it quantifies the expected distribution of changes in allele frequency due to genetic drift. Several methods of estimating N_e have been described, the most direct of which uses allele frequencies measured at two or more time points. A new likelihood-based estimator NB^ for contemporary effective population size using temporal data is developed in this article. The existing likelihood methods are computationally intensive and unable to handle the case when the underlying N_e is large. This article tries to work around this problem by using a hidden Markov algorithm and applying continuous approximations to allele frequencies and transition probabilities. Extensive simulations are run to evaluate the performance of the proposed estimator NB^, and the results show that it is more accurate and has lower variance than previous methods. The new estimator also reduces the computational time by at least 1000-fold and relaxes the upper bound of N_e to several million, hence allowing the estimation of larger N_e. Finally, we demonstrate how this algorithm can cope with nonconstant N_e scenarios and be used as a likelihood-ratio test to test for the equality of N_e throughout the sampling horizon. An R package “NB” is now available for download to implement the method described in this article.     

DNA “fingerprinting” and the genetic management of a captive chimpanzee population (Pan troglodytes)

DNA fingerprinting probes are cloned sequences which simultaneously detect a large number of similar hypervariable loci in the target DNA. The resulting highly polymorphic pattern visualized on an autoradiograph allows resolution of questions concerning individual identification and parentage. M13 bacteriophage has been used as a DNA fingerprinting probe for paternity ascertainment among captive chimpanzees housed in multi-male groups as part of the National Chimpanzee Breeding and Research Program. In 31 cases of unknown paternity where DNA samples for mother, offspring, and all potential sires were available, DNA fingerprinting with M13 resulted in the unambiguous assignment of paternity for all 31 infants. Knowledge of pedigrees among the captive-born animals is used to address several issues important in the genetic management of captive breeding colonies, including estimation of effective population size and of the rate of decline in genetic variability, variance in male and female reproduction, and the effect of social dominance on male reproductive success. Our analysis demonstrates the beneficial effects of genetic management by comparing the managed dedicated cohort to the Bastrop colony as a whole.     

杭州石荠苧的传粉、小坚果散布和邻群大小

作者在杭州葛岭对杭州石荠苧自然居群的传粉和小坚果散布进行了详细的观察和实验。结果显示 ,以 2 6 0个传粉昆虫的飞行距离推算的花粉绝对散布方差为 0 .0 82 m2 ,798个小坚果的亲子散布方差为0 .1587m2。在上述散布特点和异交率为 0 .92 5条件下的邻群面积为 2 .2 33m 2 ,在有效密度为 4 7.7株 / m 2的有效密度下的邻群大小为 10 6 .5株。杭州石荠以异交为主 ,非常有限的基因散布导致邻群面积很小 ,居群容易发生遗传分化。     

The effects of cyclic dynamics and mating system on the effective size of an island mouflon population

The Haute Island mouflon (Ovis aries) population is isolated on one small (6.5 km2) island of the remote Kerguelen archipelago. Given a promiscuous mating system, a cyclic demography and a strong female-biased sex ratio after population crashes, we expected a low effective population size (Ne). We estimated Ne using demographic and temporal genetic approaches based on genetic information at 25 microsatellite loci from 62 and 58 mouflons sampled in 1988 and 2003, respectively. Genetic Ne estimates were higher than expected, varying between 104 and 250 depending on the methods used. Both demographic and genetic approaches show the Haute Island Ne is buffered against population crashes. The unexpectedly high Ne likely results from the cyclic winter crashes that allow young males to reproduce, limiting the variance of male reproductive success. Based on individual-based simulations, we suggest that despite a strongly female-biased sex ratio, the effects of the mating system on the effective population size more closely resemble random mating or weak polygyny.     

The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus)

This study compares estimates of the census size of the spawning population with genetic estimates of effective current and long-term population size for an abundant and commercially important marine invertebrate, the brown tiger prawn (Penaeus esculentus). Our aim was to focus on the relationship between genetic effective and census size that may provide a source of information for viability analyses of naturally occurring populations. Samples were taken in 2001, 2002 and 2003 from a population on the east coast of Australia and temporal allelic variation was measured at eight polymorphic microsatellite loci. Moments-based and maximum-likelihood estimates of current genetic effective population size ranged from 797 to 1304. The mean long-term genetic effective population size was 9968. Although small for a large population, the effective population size estimates were above the threshold where genetic diversity is lost at neutral alleles through drift or inbreeding. Simulation studies correctly predicted that under these experimental conditions the genetic estimates would have non-infinite upper confidence limits and revealed they might be overestimates of the true size. We also show that estimates of mortality and variance in family size may be derived from data on average fecundity, current genetic effective and census spawning population size, assuming effective population size is equivalent to the number of breeders. This work confirms that it is feasible to obtain accurate estimates of current genetic effective population size for abundant Type III species using existing genetic marker technology.     

Effective population size associated with self-fertilization: lessons from temporal changes in allele frequencies in the selfing annual Medicago truncatula

Despite its significance in evolutionary and conservation biology, few estimates of effective population size (N(e)) are available in plant species. Self-fertilization is expected to affect N(e), through both its effect on homozygosity and population dynamics. Here, we estimated N(e) using temporal variation in allele frequencies for two contrasted populations of the selfing annual Medicago truncatula: a large and continuous population and a subdivided population. Estimated N(e) values were around 5-10% of the population census size suggesting that other factors than selfing must contribute to variation in allele frequencies. Further comparisons between monolocus allelic variation and changes in the multilocus genotypic composition of the populations show that the local dynamics of inbred lines can play an important role in the fluctuations of allele frequencies. Finally, comparing N(e) estimates and levels of genetic variation suggest that H(e) is a poor estimator of the contemporaneous variance effective population size.     

Reproductive ecology of 21 coexisting Psychotria species (Rubiaceae): when is heterostyly lost?

Heterostyly is a genetic polymorphism in which plant populations are composed of two or more morphs that differ in stigma and anther heights. The polymorphism promotes intermorph pollen transfer, thus outcrossing. Heterostyly has been reported in 28 angiosperm families and is frequently lost in heterostylous lineages. To assess ecological factors related to shifts from heterostyly to monomorphy, we examined the reproductive ecology of heterostylous tropical shrubs of Psychotria . Among 21 species at Barro Colorado Island and the nearby Parque Nacional Soberania, Panama, 14 species were heterostylous while seven were monomorphic. A molecular phylogeny and the existence elsewhere of heterostylous populations indicated that the breakdown of heterostyly had occurred independently. Heterostylous and monomorphic species were visited by the same bee species, although visit frequencies were lower in monomorphic species. Monomorphic species had significantly lower population density and greater fruit set than did heterostylous species. Autonomous autogamy made a large contribution to fruit set in monomorphic species and was only rarely observed in heterostylous species. The results indicate monomorphic and heterostylous species produce more seeds through selfing and outcrossing, respectively. The limitation of outcrossing as a result of low population density may be related to the breakdown of heterostyly and the evolution of selfing.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 125–134.     

植物亲缘地理学的研究现状与发展趋势

新生代以来剧烈的地质和气候变化,特别是第四纪冰期和间冰期的反复交错对温带植物类群的地理分布格局、种群结构和物种分化造成了深刻影响。近20年来,随着分子标记技术的发展和分析方法的成熟,植物亲缘地理学利用基因谱系关系和在种群中的时空分布来追溯种群的进化历史,在探讨植物类群对地质气候变迁的响应以及种群分化的历史成因等方面开展了大量工作,取得了一些重要进展。在取得这些成绩的同时,作者也注意到了被研究者所忽略的一些问题。试图对这些问题进行初步的总结,着重于分析方法和几个常用软件的使用,并对今后的发展趋势进行了展望。     

Methods for minimizing the loss of genetic diversity in conserved populations with overlapping generations

Minimization of the average coancestry in a population has been theoretically proven to be the most efficient method to preserve genetic diversity. In the present study, based on a population genetic model, two methods to minimize the average coancestry in populations with overlapping generations were developed. For a given parental coancestry structure, the first method (OG) minimizes the average coancestry in the next generation, and the second method (LT) is designed to minimize the long-term accumulation of coancestry. The efficiencies of the two methods were examined by stochastic simulation. Compared to random choice of parents, the annual effective population sizes under the two proposed methods increased 2–3 folds. The difference among the two methods was small in a population with short generation interval. For populations with long generation intervals, the OG method showed a slightly larger annual effective size in an initial few years. However, in the subsequent years, the LT method gave a 5–15% larger annual effective size than the OG method. From these results, it is suggested that the LT method would be preferred to the OG method in most practical situations.