Isonymy structure of USA population

The isonymy structure of the 48 states of the continental United States of America was studied using the surname distributions of 18 million telephone users, distributed in 247 towns. The shortest linear distance between nearest neighbor towns included in the sample was 12.0 km. The largest distance was 4,577 km. The number of different surnames found in the whole analysis was 899,585. Lasker's distance was found to be significantly but weakly correlated with the geographic distance, with r = 0.21 +/- 0.01. A dendrogram of the 48 states was built from the matrix of isonymy distances: it divides the US into several clusters, in general correlated with geography. A notable exception is California and New Jersey, which cluster together. Wisconsin is separated from all other states. An important cluster is formed by Texas, Colorado, New Mexico, Nevada, and Arizona, together with Illinois and Florida. It was observed that Hispanic surnames are among the most frequent in Illinois, as they are in New Jersey and California. No main distinction among the states clearly attributable to surnames of French origin was detected; however, New Hampshire, Vermont, and Maine which have a considerable number of these surnames belong to the same northeastern cluster. From the present analysis, the great mobility of the US population emerges clearly, and it seems relevant that the practical absence of isolation by distance is seen also considering only small towns. It appears that groups of different origin are well-mixed over the whole area of the United States. The values of isonymy indicate that the south-central area of the USA has the highest level of inbreeding. In fact, the heterogeneity in surname composition is greater in the coastal areas, particularly on the East Coast, than anywhere else in the USA.     

Isonymy, consanguinity and repeated pairs of surnames in Aromun populations

The Aromuns represent a small and almost unknown people that live scattered over the Balkan Peninsula. Due to their language, that is very similar to classical Latin, they are in a special position. The Aromuns settled only in more recent times. Until now they lived as shepherds, as caravan guides and merchants and lead a semi-nomadic life. We are currently carrying out studies to determine the genetic structure of this population. To facilitate the interpretation of these data, we are also trying to obtain other important parameters that pertain to migration processes and the genealogical structure of this populations. The data arise from three areas in Albania, the Republic of Macedonia and Romania. The inbreeding coefficient and the proportion of repeated pairs of surnames was calculated through the use of genealogies and the isonymy method. The difference between these three populations are due primarily to confounding by selection of mates and family composition.     

Herbivory modifies the genetic structure of birch populations

We studied the effects of selective herbivory on genetic diversity in seedling populations of silver birch ( Betula pendula ), a light-demanding pioneer tree species. The experimental populations consisted of 20 families competing with each other in dense stands. The seedling stands were randomly assigned to insect and vole exposure and fertilization treatments. The study covered the first two growing seasons, during which considerable thinning occurred within the experimental populations. We compared the observed mortality to a simulated control representing random mortality. Our results show that mortality resulted in decreased diversity compared to the simulated control. When insect and vole herbivory and nutrient enrichment treatments were compared to each other, taking into account differences in mortality due to the treatments, vole herbivory led to increased diversity among the tallest seedlings (i.e. canopy layer). This is noteworthy, since the canopy layer includes those with the best prospects of surviving in competition for light. When mortality was accounted for, 2-year natural exposure to insects had no effect on diversity; but cluster analysis showed that insect herbivory changed the genetic composition of the experimental populations. Our results demonstrate the importance of herbivores in shaping the genetic structure of plant populations during the thinning phase.     

Isozyme diversity and genetic structure of buckwheat populations

Genetic diversity of 35 Fagopyrum populations belonging to thirteen taxa was studied using isozyme variation at 16 loci for nine enzyme systems (ADH, α-AMY, EST, GDH, GOT, IDH, MDH, PGM, and POD). The mean number of alleles per locus (A_p) showed little variation, ranging from 1.38 to 1.71. The mean percentage of polymorphic (P) of the thirteen taxa was high, ranging from 68.75% to 93.75. The mean expected heterozygosity (H_e) ranged from 0.21 to 0.37. Obvious grouping of populations according to taxonomic species was found in the cluster analysis, confirmed that the thirteen taxa studied were independent, with a clear boundary. Based on the dendrogram, the phylogenic relationship of Fagopyrum species are in agreement with the achene size were found, and it was inferred that southwestern China should be the original center of cultivated buckwheat.     

Multilocus estimation of genetic structure within populations

Spatial structure of genetic variation within populations is well measured by statistics based on the distribution of pairs of individual genotypes, and various such statistics have been widely used in experimental studies. However, the problem of uncharacterized correlations among statistics for different alleles has limited the applications of multiallelic, multilocus summary measures, since these had unknown sampling distributions. Usually multiple alleles and/or multiple loci are required in order to precisely measure spatial structures, and to provide precise indirect estimates of the amount of dispersal in samples of reasonable size. This article examines the correlations among pair-wise statistics, including Moran I-statistics and various measures of conditional kinship, for different alleles of a locus. First the correlations are mathematically derived for random spatial distributions, which allow averages over alleles and loci to be used as more powerful yet exact test statistics for the null hypothesis. Then extensive computer simulations are conducted to examine the correlations among values for different alleles under isolation by distance processes. For loci with more than three alleles, the results show that the correlations are remarkably and perhaps surprisingly small, establishing the principle that then alleles behave as nearly independent realizations of space-time stochastic processes. The results also show that the correlations are largely robust with respect to the degree of spatial structure, and they can be used in a straightforward manner to form confidence intervals for averages. The results allow a precise connection between observations in experimental studies and levels of dispersal in theoretical models.     

The genetic structure of malaria parasite populations

The suggestion that a clonal population structure may typify Plasmodium populations has proved highly controversial. For the most part, existing population genetic data from wild populations contradict the idea and are consistent with randomly interbreeding populations. In this article, Andrew Read and Koren Day point out that these data could also be consistent with population subdivision and frequent nonrandom mating, which current sampling methods would be incapable of detecting.     

Adaptive genetic structure in phytophagous insect populations

Genetic variation in insect populations is frequently structured into discrete groups, or demes, that form in response to stochastic forces or natural selection. Because host-plant populations are often highly heterogeneous, phytophagous insects may form demes that are adapted to the unique traits of individual plants. Recent field experiments indicate that selection pressures imposed by host-plants can promote rapid adaptive evolution in natural insect populations at very fine spatial scales. Adaptive deme formation may be more common among endophagous insects, which feed and reside within plant tissue, than for externally feeding insects, because internal feeders experience stronger plant-mediated selection pressures.     

8个亚洲水牛群体的遗传结构分析

应用13个微卫星标记结合荧光–多重PCR技术, 对德昌水牛、兴隆水牛、富钟水牛、温州水牛、东流水牛、福安水牛和两个引进品种摩拉水牛、尼里－拉菲水牛进行遗传结构分析。结果表明: 8个水牛群体在13个微卫星座位中共检测到157个等位基因, 其中7个群体具有各自的特有等位基因, 其和为23; 8个群体的有效等位基因数在2.2908～4.2308之间, 杂合度在0.4951～0.7194之间, 多态信息含量在0.4495～0.6776之间; 有11个座位为高度多态座位, 是适合分析水牛遗传多样性的多态标记; 聚类分析表明富钟水牛和东流水牛先聚在一起, 再与兴隆水牛聚在一起, 然后与温州水牛和福安水牛聚在一起, 德昌水牛独自聚为一类; 两个引进品种聚为一类。     

Morphological differentiation and genetic structure in island lizard populations

Only some island populations of Podarcis sicula are hyperchromatic. The study of this phenomenon and its relationship with the lizards of the mainland and other islands, exhibiting a "normal" coloration, provides useful hints in our understanding of evolutionary mechanisms that have created the observed morphological variation. We performed a comparative morphological and genetic analysis of a hyperchromatic lizard population from Licosa Island, and compared the data with that obtained from normal-colored lizard populations both from Ustica and Cirella islands in the Tyrrhenian sea and from nearby mainland Italy. Morphological and microsatellite gene differentiation in the hyperchromatic Licosa population appears to have been much more rapid than the molecular evolution of the mtDNA. We discuss herein that the comparison of hyperchromatism and other types of morphological variation with molecular data in island populations of lizards may provide useful hints as to evolutionary mechanisms.     

Identifying the environmental factors that determine the genetic structure of populations

The study of population genetic structure is a fundamental problem in population biology because it helps us obtain a deeper understanding of the evolutionary process. One of the issues most assiduously studied in this context is the assessment of the relative importance of environmental factors (geographic distance, language, temperature, altitude, etc.) on the genetic structure of populations. The most widely used method to address this question is the multivariate Mantel test, a nonparametric method that calculates a correlation coefficient between a dependent matrix of pairwise population genetic distances and one or more independent matrices of environmental differences. Here we present a hierarchical Bayesian method that estimates F(ST) values for each local population and relates them to environmental factors using a generalized linear model. The method is demonstrated by applying it to two data sets, a data set for a population of the argan tree and a human data set comprising 51 populations distributed worldwide. We also carry out a simulation study to investigate the performance of the method and find that it can correctly identify the factors that play a role in the structuring of genetic diversity under a wide range of scenarios.     

Spatial and temporal aspects of the genetic structure of Juniperus communis populations

Juniperus communis is a dioecious, wind pollinated shrub or small tree that produces 'berries' (female cones) containing a small number of seeds that are thought to be dispersed by birds. The expectation, therefore, would be that populations of Juniper are genetically diverse with little structuring between them. In Britain, the species has two main centres of distribution: a highland zone in the north and west, in which populations are still large and sexually reproducing, and a southern zone on chalk downlands in which populations are small and fragmented and individuals suffer from a decline in fertility. Thus, one would expect the large sexually viable populations in the north to exhibit high levels of within-population genetic variation, while the declining southern populations would be genetically depauperate. The analysis of amplified fragment length polymorphisms (AFLPs) was used to test this hypothesis. Surprisingly, all populations studied showed high levels of genetic variation although there was clear structuring between populations. On the basis of the geographical structuring of the populations it was hypothesized that J. communis colonized Britain via three separate routes.     

Population structure and genetic diversity of four Henan pig populations

To investigate the population structure and genetic diversity of Henan indigenous pig breeds, samples from a total of 78 pigs of 11 breeds were collected, including four pig populations from Henan Province, three Western commercial breeds, three Chinese native pig breeds from other provinces and one Asian wild boar. The genotyping datasets were obtained by genotyping‐by‐sequencing technology. We found a high degree of polymorphism and rapid linkage disequilibrium decay in Henan pigs. A neighbor‐joining tree, principal component analysis and structure analysis revealed that the Huainan and Erhualian pigs were clustered together and that the Queshan black pigs were clearly grouped together but that the Nanyang and Yuxi pigs were extensively admixed with Western pigs. In addition, heterozygosity values might indicate that Henan indigenous pigs, especially the Queshan black and Huainan pigs, were subjected to little selection during domestication. The results presented here indicate that Henan pig breeds were admixed from Western breeds, especially Nanyang and Yuxi pigs. Therefore, establishment of purification and rejuvenation systems to implement conservation strategies is urgent. In addition, it is also necessary to accelerate genetic resources improvement and utilization using modern breeding technologies, such as genomic selection and genome‐wide association studies.     

Inbreeding rate and genetic structure of cat populations in Poland

The objective of the study was to analyze effective population size and inbreeding level in populations of cat breeds registered in the Polish Studbook. The Association of Purebred Cat Breeders in Poland provided access to pedigrees of 26725 cats from seven breeds. The most frequent breed was Persian, however increasing tendency in numbers of registered animals from other breeds was recorded in later years. Although the percentage of inbred individuals was increasing over time, mating of close relatives was avoided by most of the breeders, and the average inbreeding coefficient exceeded 5% only for Siberian and Russian breeds. Current analysis suggests that the Polish pedigree cat populations are not threatened by negative effects of inbreeding.     

Extinction,recolonization, and the genetic structure of tidepool copepod populations

Summary Extinction and recolonization in metapopulations may either increase or decrease genetic differentiation among populations, but recent genetic models predict increased differentiation under most circumstances of recolonization. I examine this prediction empirically using tidepool populations of the marine tidepool copepodTigriopus californicus. The probability of extinction of tidepool populations was sufficiently high to invoke the model's predictions, but varied among populations. Nearly 75% of colonizing groups consisted of 10 or fewer individuals. The genetic effective size of colonizing groups might be as high as 18, depending on assumptions, but colonists probably originated from a subset of local populations. In contrast to my predictions, genetic differentiation was smaller among younger tidepool populations than among older populations on each of three rock outcrops, suggesting that genetic differentiation was reduced by metapopulation dynamics. The discrepancy between the prediction and the results may be explained by the unmet assumptions of classical metapopulation structure underlying the genetic models.     

The genetic structure of Nautilus pompilius populations surrounding Australia and the Philippines

Understanding the distribution of genetic diversity in exploited species is fundamental to successful conservation. Genetic structure and the degree of gene flow among populations must be assessed to design appropriate strategies to prevent the loss of distinct populations. The cephalopod Nautilus pompilius is fished unsustainably in the Philippines for the ornamental shell trade and has limited legislative protection, despite the species' recent dramatic decline in the region. Here, we use 14 microsatellite markers to evaluate the population structure of N. pompilius around Australia and the Philippines. Despite their relative geographical proximity, Great Barrier Reef individuals are genetically isolated from Osprey Reef and Shark Reef in the Coral Sea (F_ST = 0.312, 0.229, respectively). Conversely, despite the larger geographical distances between the Philippines and west Australian reefs, samples display a small degree of genetic structure (F_ST = 0.015). Demographic scenarios modelled using approximate Bayesian computation analysis indicate that this limited divergence is not due to contemporary gene flow between the Philippines and west Australia. Instead, present‐day genetic similarity can be explained by very limited genetic drift that has occurred due to large average effective population sizes that persisted at both locations following their separation. The lack of connectivity among populations suggests that immigrants from west Australia would not facilitate natural recolonization if Philippine populations were fished to extinction. These data help to rectify the paucity of information on the species' biology currently inhibiting their conservation classification. Understanding population structure can allow us to facilitate sustainable harvesting, thereby preserving the diversity of genetically distinct stocks.