Neutral Genetic Patterns for Expanding Populations with Nonoverlapping Generations

We investigate the inside dynamics of solutions to integrodifference equations to understand the genetic consequences of a population with nonoverlapping generations undergoing range expansion. To obtain the inside dynamics, we decompose the solution into neutral genetic components. The inside dynamics are given by the spatiotemporal evolution of the neutral genetic components. We consider thin-tailed dispersal kernels and a variety of per capita growth rate functions to classify the traveling wave solutions as either pushed or pulled fronts. We find that pulled fronts are synonymous with the founder effect in population genetics. Adding overcompensation to the dynamics of these fronts has no impact on genetic diversity in the expanding population. However, growth functions with a strong Allee effect cause the traveling wave solution to be a pushed front preserving the genetic variation in the population. In this case, the contribution of each neutral fraction can be computed by a simple formula dependent on the initial distribution of the neutral fractions, the traveling wave solution, and the asymptotic spreading speed.     

Spatial Patterns of Rhizoplane Populations of Pseudomonas fluorescens

Geostatistical analysis was used to compare rhizoplane colonization patterns of an antibiotic-producing biological control bacterium versus a non-antibiotic-producing mutant strain. Pea seeds were inoculated with Pseudomonas fluorescens 2-79RN(inf10) or P. fluorescens 2-79-B46 (a phenazine-deficient Tn5 mutant of P. fluorescens 2-79RN(inf10)) (10(sup8) CFU/pea), planted in sterile sand, and incubated at 20(deg)C. After 3 days, seedlings were prepared for scanning electron microscopy. Photomicrographs (x1,000) of the root surface were taken at the seed-root junction and at 0.5-cm intervals to the root tip. Bacterial counts on the root surface were made in 5- by 5-(mu)m sample units over an area which was 105 by 80 (mu)m. Coordinates and number of bacteria were recorded for each sample unit. Spatial statistics were calculated by covariance for the following directions: omnidirectional, 0, 45, 90, and 135(deg). The ranges of spatial influence and nugget (estimator of spatially dependent variation) were determined. For both P. fluorescens 2-79RN(inf10) and P. fluorescens 2-79-B46, spatial structure was evident along the entire root, particularly in the 0(deg) direction (along the root length) (e.g., range = 24 (mu)m, nugget = 0.52). The degree of spatial dependence observed indicated aggregation of bacterial cells. No differences were detected in the spatial patterns of colonies of P. fluorescens 2-79RN(inf10) and P. fluorescens 2-79-B46, indicating that the lack of phenazine production did not influence spatial patterns on the rhizoplane.     

Spatial Genetic Structure and Mitochondrial DNA Phylogeography of Argentinean Populations of the Grasshopper Dichroplus elongatus

Many grasshopper species are considered of agronomical importance because they cause damage to pastures and crops. Comprehension of pest population dynamics requires a clear understanding of the genetic diversity and spatial structure of populations. In this study we report on patterns of genetic variation in the South American grasshopper Dichroplus elongatus which is an agricultural pest of crops and forage grasses of great economic significance in Argentina. We use Direct Amplification of Minisatellite Regions (DAMD) and partial sequences of the cytochrome oxydase 1 (COI) mitochondrial gene to investigate intraspecific structure, demographic history and gene flow patterns in twenty Argentinean populations of this species belonging to different geographic and biogeographic regions. DAMD data suggest that, although genetic drift and migration occur within and between populations, measurable relatedness among neighbouring populations declines with distance and dispersal over distances greater than 200 km is not typical, whereas effective gene flow may occur for populations separated by less than 100 km. Landscape analysis was useful to detect genetic discontinuities associated with environmental heterogeneity reflecting the changing agroecosystem. The COI results indicate the existence of strong genetic differentiation between two groups of populations located at both margins of the Paraná River which became separated during climate oscillations of the Middle Pleistocene, suggesting a significant restriction in effective dispersion mediated by females and large scale geographic differentiation. The number of migrants between populations estimated through mitochondrial and DAMD markers suggest that gene flow is low prompting a non-homogeneous spatial structure and justifying the variation through space. Moreover, the genetic analysis of both markers allows us to conclude that males appear to disperse more than females, reducing the chance of the genetic loss associated with recent anthropogenic fragmentation of the D. elongatus studied range.     

Ancient Humans Influenced the Current Spatial Genetic Structure of Common Walnut Populations in Asia

Common walnut (Juglans regia L) is an economically important species cultivated worldwide for its wood and nuts. It is generally accepted that J. regia survived and grew spontaneously in almost completely isolated stands in its Asian native range after the Last Glacial Maximum. Despite its natural geographic isolation, J. regia evolved over many centuries under the influence of human management and exploitation. We evaluated the hypothesis that the current distribution of natural genetic resources of common walnut in Asia is, at least in part, the product of ancient anthropogenic dispersal, human cultural interactions, and afforestation. Genetic analysis combined with ethno-linguistic and historical data indicated that ancient trade routes such as the Persian Royal Road and Silk Road enabled long-distance dispersal of J. regia from Iran and Trans-Caucasus to Central Asia, and from Western to Eastern China. Ancient commerce also disrupted the local spatial genetic structure of autochthonous walnut populations between Tashkent and Samarkand (Central-Eastern Uzbekistan), where the northern and central routes of the Northern Silk Road converged. A significant association between ancient language phyla and the genetic structure of walnut populations is reported even after adjustment for geographic distances that could have affected both walnut gene flow and human commerce over the centuries. Beyond the economic importance of common walnut, our study delineates an alternative approach for understanding how the genetic resources of long-lived perennial tree species may be affected by the interaction of geography and human history.     

Y-chromosome Genotyping and Genetic Structure of Zhuang Populations

Zhuang, the largest ethnic minority population in China, is one of the descendant groups of the ancient Bai-Yue. Linguistically, Zhuang languages are grouped into northern and southern dialects. To characterize its genetic structure, 13 East Asian-specific Y-chromosome biallelic markers and 7 Y-chromosome short tandem repeat (STR) markers were used to infer the haplogroups of Zhuang populations. Our results showed that O*, O2a, and O1 are the predominant haplogroups in Zhuang. Frequency distribution and principal component analysis showed that Zhuang was closely related to groups of Bai-Yue origin and therefore was likely to be the descendant of Bai-Yue. The results of principal component analysis and hierarchical clustering analysis contradicted the linguistically derived north-south division. Interestingly, a west-east clinal trend of haplotype frequency changes was observed, which was supported by AMOVA analysis that showed that between-population variance of east-west division was larger than that of north-south division. O* network suggested that the Hongshuihe branch was the center of Zhuang. Our study suggests that there are three major components in Zhuang. The O* and O2a constituted the original component; later, O1 was brought into Zhuang, especially eastern Zhuang; and finally, northern Han population brought O3 into the Zhuang populations.     

壮族Y染色体分型及其内部遗传结构

壮族是中国最大的少数民族,与东南亚的泰老族群关系密切,在东亚人群的遗传结构研究中地位非常特殊。本研究调查了壮族各个支系的Y染色体多样性,通过主成分分析、聚类分析和分子方差分析,揭示壮族的内部父系遗传结构。结果发现,壮族的主要Y染色体单倍群为O%＊,O2a,O1。传统的对壮族按方言分为南北二组的分类方法在遗传上并没有依据,壮族支系体现出从东往西的梯度变化过程。这说明壮族的结构中有几个层次,最早的成分普遍出现在各个支系中,第二层是由东部来的百越核心成分,第三层是北方来的汉族成分。壮族内部遗传结构的分析将有助于对东亚人群的南来起源的研究。     

Genetic Demographic Structure of Rural Populations of Kyrgyzstan

The genetic demographic parameters of rural populations of Kyrgyzstan have been studied. The rural population of Kyrgyzstan has the following demographic characteristics: (1) it is demographically young (the population mean age is 25–28 years); (2) the sex ratio in reproductive age groups is unfavorable; (3) the fertility is high (5.78–7.68 pregnancies and 4.27–5.20 surviving children per woman of postreproductive age; (4) interethnic marriages are rare (1.0–5.9%), whereas consanguineous marriages are frequent (1.4–12%); (5) Crow's indices are relatively low (I _tot = 0.24–0.29, I _m = 0.05–0.13, I _f = 0.14–0.22); and (6) both male and female contributions of different regions of the republic make unequal contributions to the gametic structure of the population, with the gametic structure varying from generation to generation. Demographic parameters vary in rural populations of different geographic regions and with different ethnic compositions.     

华山新麦草自然居群的遗传结构和种内遗传多态性研究

华山新麦草为我国特有种,公分布在陕西华山,应用5种酶系统共13个基因位点对采自华山13个亚居群的华山新麦草进行等位酶分析,研究结果发现,多态性位点的比例（P）为69％,个位点等位基因的平均数（A）为1．8,平均每个位点的预期杂合性（He)为0．344,Simpson指数为0．998,证明华山新麦草居群内有较高的遗传多态性和克隆多样性,固定指数（F）显示有意义的负值（－0．252),预期的随机交配相比较,居群内有过多的杂合体,这可能与华山新麦草的交酸系统和繁育方式有关,平均的遗传距离为0．046（变化范围：0－0．139）,大约有91％的遗传变异存在于亚居群内,应用间接法测得华山新麦草自然居群间的基因流（Nm)为2．77,明显你于一般风媒传粉植物（5．24）,暗示华山新麦草自然居群的基因流水平似乎正处于一种临界状太,有进一步分化的潜能,但受多种因素的影响。     

白檀自然居群遗传结构与遗传多样性研究

采用ISSR分子标记技术分析了湖南省5个地区6个居群白檀的遗传多样性水平和遗传结构。结果表明,9条ISSR引物对6个居群的149份白檀样品PCR扩增检测到122个扩增位点,其中多态性位点113个,多态性比率高达92.62%。Nei's基因多样性指数(He)为0.3264,Shannon多样性指数(I)为0.4873,居群之间产生较大的遗传变异(Gst=0.5215,Nm=0.4588),AMOVA分子差异分析表明白檀居群间遗传分化程度高,51.07%的变异存在于居群间,48.93%的变异存在于居群内;UPGMA聚类分析将6个白檀居群分为3大类:大围山和龙山居群为一类,岳阳和道县居群组成另一类;衡山居群单独成一类,聚类原则跟地理位置不一致,与海拔高度有一定的相关性。     

Genetic Analysis of Invasive Plant Populations at Different Spatial Scales

Measuring genetic diversity requires selection of a spatial scale of analysis. Different levels of genetic structuring are revealed at different spatial scales, however, and the relative importance of factors driving genetic structuring varies along the spatial scale continuum. Unequal gene flow is a major factor determining genetic structure in plant populations at the local level, while the effect of selection imposed by environmental heterogeneity increases with the spatial scale of analysis. At a continental and global scale genetic structure of invasive plant populations is significantly affected by founder effect and propagule transport via human vectors. Although genetic analysis at one spatial scale provides only partial information about the invasion process, little published research reports such data for the same species at multiple scales. A multi-faceted approach to investigating the genetic structure of invasive plant species that incorporates sampling at different spatial and temporal scales would provide a more complete picture of the role of genetic forces in invasion.     

The Genetic Structure of Natural Populations of DROSOPHILA MELANOGASTER. Xviii. Clinal and Uniform Genetic Variation over Populations

It has been reported in the previous papers of this series that in the eastern United States and Japan there is a north-to-south cline of additive genetic variance of viability and that the amount of the additive genetic variance in the northern population can be explained by mutation-selection balance. To determine whether or not the difference in the genetic variation in northern and southern populations can be explained by the differences in mutation rate and/or effective population size, numerical calculations were made using population genetic parameters. In addition, the average heterozygosities of the northern and southern populations at ten of 19 polymorphic structural loci surveyed were estimated in relation to the cline of additive genetic variance of viability, and the following findings were obtained. (1) The changes in mutation rate and population size cannot simultaneously explain the difference in additive genetic variance and inbreeding decline between the northern and southern populations. Thus, the operation of some kind of balancing selection, most likely diversifying selection, was suggested to explain the observed excess of additive genetic variance. (2) Estimates of the average heterozygosities of the southern population were not significantly different from those of the northern population. Thus, it was strongly suggested that the excess of additive genetic variance in the southern population cannot be caused by structural loci, but by factors outside the structural loci, and that protein polymorphisms are selectively neutral or nearly neutral.     

Genetic Structure and Differentiation of Three Chinese Indigenous Cattle Populations

Levels of genetic differentiation, gene flow, and genetic structure of three indigenous cattle populations (Luxi, Bohai, and Minnan) and two reference cattle populations (Chinese Holstein and Qinhai yak) in China were estimated using the information from 12 microsatellites, and 141 microsatellite alleles were identified. The mean number of alleles per locus ranged from 2.9005 in yak to 4.9722 in Holstein. The observed heterozygosity ranged from 0.5325 (yak) to 0.7719 (Holstein); 29 private alleles were detected. The global heterozygote deficit across all populations amounted to 58.5% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds amounted to 43.2%. The five cattle populations were highly differentiated (F _st = 26.9%, p < 0.001) at all loci. The heterozygote deficit within the population was highest in Luxi cattle and lowest in yak. The average number of effective migrants exchanged per generation was highest (1.149) between Luxi and Holstein, and lowest (0.509) between Luxi and yak. With the application of prior population information, cluster analysis achieved posterior probabilities from 91% to 98% of correctly assigning individuals to populations. Combining the information of cluster analysis, gene flow, and Structure analysis, the five cattle populations belong to three genetic clusters, a taurine (Luxi and Chinese Holstein), a zebu (Bohai and Minnan), and a yak cluster. This indicates that Bohai black is closer to Bos indicus than Luxi cattle. The evolution and development of three indigenous cattle populations are discussed.     

Structure of Sphingomyelin Bilayers: A Simulation Study

We have carried out a molecular dynamics simulation of a hydrated 18:0 sphingomyelin lipid bilayer. The bilayer contained 1600 sphingomyelin (SM) molecules, and 50,592 water molecules. After construction and initial equilibration, the simulation was run for 3.8 ns at a constant temperature of 50°C and a constant pressure of 1 atm. We present properties of the bilayer calculated from the simulation, and compare with experimental data and with properties of dipalmitoyl phosphatidylcholine (DPPC) bilayers. The SM bilayers are significantly more ordered and compact than DPPC bilayers at the same temperature. SM bilayers also exhibit significant intramolecular hydrogen bonding between phosphate ester oxygen and hydroxyl hydrogen atoms. This results in a decreased hydration in the polar region of the SM bilayer compared with DPPC. Since our simulation system is very large we have calculated the power spectrum of bilayer undulation and peristaltic modes, and we compare these data with similar calculations for DPPC bilayers. We find that the SM bilayer has significantly larger bending modulus and area compressibility compared to DPPC.     

Genetic Structure of Daphnia galeata Populations in Eastern China

This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial correspondence analysis, and UPGMA clustering consistently showed that populations from two neighbouring lakes were genetically separated from a mixture of genotypes found in other lakes, which formed another two subgroups. Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity. Overall, populations did not cluster by geographical origin. Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes.     

Population Dynamic and Genetic Consequences of Spatial Density-Dependent Dispersal in Patchy Populations

Predictions about sex-specific, spatial density-dependent dispersal and their demographic and genetic consequences were tested in experimental populations of root voles (Microtus oeconomus). Each population consisted of two demes inhabiting equal-sized habitat patches imbedded in a barren matrix area. We used a neutral two-allele allozyme marker to monitor gene flow. Initially, the two demes were genetically distinct and had different densities so that the size of a high-density deme (genotype bb) was four times larger than that of a low-density deme (genotype aa). The sex-specific dispersal pattern was in accordance with our prediction. Male dispersal was unconditional on deme-specific densities, and the majority of the first-generation males became dispersed from both demes, whereas female dispersal was strongly density dependent, so that dispersal took place exclusively from the high-density to the low-density deme. The demographic implication of this dispersal pattern was that the initial density difference between the demes was quickly canceled out. We built a mathematical model that predicted that the initially rare allele (a) would increase in frequency given the dispersal pattern, and this was supported by our experimental data. This result relies mostly on the density-independent male-dispersal strategy, which presumably stems from inbreeding avoidance. Our study highlights the importance of incorporating sex-specific dispersal strategies in population genetic models. Sex-biased dispersal may act as a deterministic force counteracting the tendency for stochastic loss of alleles in small and fragmented populations.     

Genetic Structure of the French Red Squirrel Populations: Implication for Conservation

The decline of the red squirrel (Sciurus vulgaris) in several European countries due to the introduction of the American grey squirrel (S. carolinensis) and the predicted arrival of the grey squirrel in France in the near future has lead to the development of a preventative conservation project in this country. In this study, we conducted an extensive survey of mitochondrial DNA variation in French red squirrels using a fragment of the mitochondrial D-loop and we compared the results with previously published data from other European populations. Our main aims were: (1) to determine whether genetically differentiated populations, which could represent prioritized units for conservation purposes, were present in France and (2) to determine whether the French population, which is currently largely undisturbed, could provide information on the postglacial recolonization history of the species. We found that French D-loop haplotypes show almost no tendency to cluster by geographic origin, be it region or country, suggesting that French red squirrels have not been isolated from other populations during an evolutionarily significant period and that they do not constitute an Evolutionary Significant Unit. The French red squirrels showed strong signals of population expansion, the opposite to what is observed in most other European populations, making them of particular interest to study the postglacial expansion history of the species.