Isonymy and isolation by distance in the Netherlands

The isonymy structure of the Netherlands was studied using the surname distribution of 2.4 million private telephone users selected from a 1996 commercial CD-ROM containing the names of 6.3 million users in the country. The users were distributed in 226 towns selected on a geographic basis to form an approximately regular grid throughout the Netherlands. Names of telephone users in each town were downloaded from the CD-ROM, with private users being selected for inclusion in the analysis. The shortest linear distance between several nearest neighboring towns was less than 2 km (e.g., Kampen and Ijsselmuiden, Krommen and Zaandijk, Hendrikdo and Papendrecht) and the longest distance was 326 km (Delfzijl and Oostburg ZL). The number of different surnames revealed by the analysis was 126,485. Lasker's distance, the negative value of the logarithm of isonymy between localities, was found to be significantly correlated with linear geographic distance, with r = 0.47 +/- 0.006. A dendrogram built using the matrix of isonymy distances, using the nearest neighbor-joining method, separates the Dutch towns into several clusters, most of them correlated with traditional Dutch regions. Comparisons with the results of previous analyses of the structure of other European countries are given. From the present analysis, isolation by distance emerges clearly, and it is relevant, although much weaker than in Switzerland, Austria, Italy, and Germany. The random component of inbreeding estimated from isonymy indicates a considerable degree of homogeneity in the Netherlands.     

The trouble with isolation by distance

The genetic population structure of many species is characterised by a pattern of isolation by distance (IBD): due to limited dispersal, individuals that are geographically close tend to be genetically more similar than individuals that are far apart. Despite the ubiquity of IBD in nature, many commonly used statistical tests are based on a null model that is completely non-spatial, the Island model. Here, I argue that patterns of spatial autocorrelation deriving from IBD present a problem for such tests as it can severely bias their outcome. I use simulated data to illustrate this problem for two widely used types of tests: tests of hierarchical population structure and the detection of loci under selection. My results show that for both types of tests the presence of IBD can indeed lead to a large number of false positives. I therefore argue that all analyses in a study should take the spatial dependence in the data into account, unless it can be shown that there is no spatial autocorrelation in the allele frequency distribution that is under investigation. Thus, it is urgent to develop additional statistical approaches that are based on a spatially explicit null model instead of the non-spatial Island model.     

Endogamy and isolation by distance in the Tatarstan population

A total sample of 31 837 marriage records made in 13 raions (districts) of Tatarstan in 1990–2000 have been used to determine the endogamy index and parameters of Malecot’s isolation by distance model. The endogamy index varied from 0.45 in Pestrechinsky raion to 0.74 in Aktynashsky raion. The parameters of Malecot’s isolation by distance model varied in Tatars as follows: random inbreeding, from 0.00014 to 0.00076; root mean square migration, from 46 to 110 km.     

Nonsignificant isolation by distance implies limited dispersal

Understanding the scale of dispersal is an important consideration in the conservation and management of many species. However, in species in which the high‐dispersal stage is characterized by tiny gametes or offspring, it may be difficult to estimate dispersal directly. This is the case for many marine species, whose pelagic larvae are dispersed by ocean currents by several days or weeks before beginning a benthic, more sedentary, adult stage. As consequence of the high‐dispersal larval stage, many marine species have low genetic structure on large spatial scales (Waples 1998 ; Hellberg 2007 ). Despite the high capacity for dispersal, some tagging studies have found that a surprising number of larvae recruit into the population they were released from (self‐recruitment). However, estimates of self‐recruitment are not informative about mean dispersal between subpopulations. To what extent are limited dispersal estimates from tagging studies compatible with high potential for dispersal and low genetic structure? In this issue, a study on five species of coral reef fish used isolation by distance (IBD) between individuals to estimate mean dispersal distances (Puebla et al. 2012 ). They found that mean dispersal was unexpectedly small (<50 km), given relatively low IBD slopes and long pelagic durations. This study demonstrates how low genetic structure is compatible with limited dispersal in marine species. A comprehensive understanding of dispersal in marine species will involve integrating methods that estimate dispersal over different spatial and temporal scales. Genomic data may increase power to resolve these issues but must be applied carefully to this question.     

Plant dispersal, neighbourhood size and isolation by distance

A theoretical relationship between isolation by distance or spatial genetic structure (SGS) and seed and pollen dispersal is tested using extensive spatial-temporal simulations. Although for animals Wright's neighbourhood size N(e) = 4pisigma(2)(t) has been ascertained also, where sigma(2)(t) is the axial variance of distances between parents and offspring, and it was recently confirmed that N(e) = 4pi(sigma(2)(f) + sigma(2)(m))/2 when dispersal of females and males differ, the situation for plants had not been established. This article shows that for a very wide range of conditions, neighbourhood size defined by Crawford's formula N(e) = 4pi(sigma(2)(s) + sigma(2)(p)/2) fully determines SGS, even when dispersal variances of seed (sigma(2)(s)) and pollen sigma(2)(p)) differ strongly. Further, self-fertilization with rate s acts as zero-distance pollen dispersal, and N(e) = 4pi[sigma(2)(s) + sigma(2)(p)(1 - s)/2] fully determines SGS, for most cases where there are both likely parameter values and substantial SGS. Moreover, for most cases, there is a loglinear relationship, I(1) = 0.587 - 0.117 ln(N(e)), between SGS, as measured by I(1), Moran's coefficient for adjacent individuals, and N(e). However, there are several biologically significant exceptions, namely for very low or large N(e), SGS exceeds the loglinear values. There are also important exceptions to Crawford's formula. First, plants with low seed dispersal, high outcross pollen dispersal and high selfing rate show larger SGS than predicted. Second, in plants with very low (near zero) seed dispersal, selfing decreases SGS, opposite expectations. Finally, in some cases seed dispersal is more critical than pollen dispersal, in a manner inconsistent with Crawford's formula.     

Disruption of historical patterns of isolation by distance in coastal steelhead

When natural populations exchange migrants at a rate proportional to their geographic distance, population genetics theory leads to the expectation of a pattern of isolation-by-distance (IBD), whereby geographic and genetic distance are correlated. However, the presence or absence of such patterns in modern populations may not fully reflect the historical relationships among those populations. Thus, historical samples, collected prior to modern human impacts, can often provide a critical baseline for comparison with modern populations. Steelhead, the anadromous form of rainbow trout, Oncorhynchus mykiss, are native to western North America and are endangered or threatened throughout most of California, near the southern extent of their native range. Population samples of steelhead collected in 1897 and 1909 in Central California rivers provided the opportunity to evaluate the historical genetic composition and population structure of these threatened fish. Here we show that these steelhead populations had a historically strong correlation between genetic and geographic distance that has been virtually erased in modern populations, suggesting that current relationships among modern steelhead populations are no longer reflective of natural migratory pathways. This demonstrates the critical role of migration in maintaining population relationships of threatened species and highlights the importance of natural history museums in providing historical baseline information.     

A likelihood-based approach to estimating and testing for isolation by distance

Simple regression of genetic similarities between pairs of populations on their corresponding geographic distances is frequently used to detect the presence of isolation by distance (IBD). However, these pairwise values are obviously not independent and there is no parametric procedure for estimating and testing for the IBD intercepts and slopes based on standard regression theory. Nonparametric tests, such as the Mantel test, and resampling techniques, such as bootstrapping, have been exploited with limited success. Here, I describe a likelihood-based analysis to allow for simultaneously detecting patterns of correlated residuals and estimating and testing for the presence of IBD. It is shown, through the analysis of two molecular datasets in pine species, that different covariance structures of the residuals exist. More over, the likelihood ratio tests under these covariance structures are less sensitive to the presence of IBD than the Mantel test and the simple regression analysis but more sensitive than the bootstrap and jackknife samples over independent populations or population pairs. Because the likelihood analysis directly models and accounts for nonindependence of residuals, it should legitimately detect the presence of IBD, thereby allowing for accurate inferences about evolutionary and demographic processes influencing the extent and patterns of IBD.     

Correlates of genetic differentiation and isolation by distance in 17 congeneric Silene species

The contemporary pattern of intraspecific genetic variation can indicate the relative role of gene flow and local differentiation in shaping the evolutionary history and future trajectory of a species. To assess the recent influence of contrasting life history and demographic characteristics on genetic structure within a group of closely related species, patterns of genetic differentiation (F(ST) and related statistics) and isolation by distance (IBD) were compared among 17 congeneric herbaceous plant species. Data came from 35 published studies of 16 species, and a previously unpublished analysis of chloroplast genetic variation in the rare endemic Silene rotundifolia. Among-population genetic variance was most strongly influenced by the type of genetic marker used; cytoplasmic markers showed larger values than allozyme and anonymous nuclear markers. Other independently significant factors were geographical range size and, for allozyme studies, reproductive system; in particular, endemism and hermaphroditism were associated with higher among-population genetic variance, whereas large native geographical range and dioecy were associated with lower among-population variance. Over equivalent spatial scales, dioecious populations also showed weaker IBD than hermaphrodites, perhaps because increased population transience and/or variance in the spatial pattern of gene flow are more closely associated with dioecy in this genus. Invasive populations had both highly variable among-population genetic variance, and no evidence for IBD, consistent with nonequilibrium conditions. Other analysed factors including predominant pollinator had no discernable influence on genetic structure or patterns of IBD. In general, this comparative approach appears to be valuable for synthesizing the complementary information provided by F-statistics and IBD, and for indicating the relative importance of particular biological factors in shaping genetic variation within different species of a closely related plant group.     

Global isolation by distance despite strong regional phylogeography in a small metazoan

Background  

Small vagile eukaryotic organisms, which comprise a large proportion of the Earth's biodiversity, have traditionally been thought to lack the extent of population structuring and geographic speciation observed in larger taxa. Here we investigate the patterns of genetic diversity, amongst populations of the salt lake microscopic metazoan Brachionus plicatilis s. s. (sensu stricto) (Rotifera: Monogononta) on a global scale. We examine the phylogenetic relationships of geographic isolates from four continents using a 603 bp fragment of the mitochondrial COI gene to investigate patterns of phylogeographic subdivision in this species. In addition we investigate the relationship between genetic and geographic distances on a global scale to try and reconcile the paradox between the high vagility of this species and the previously reported patterns of restricted gene flow, even over local spatial scales.     

Global patterns of isolation by distance based on genetic and morphological data

The isolation-by-distance model predicts that genetic similarity between populations will decrease exponentially as the geographic distance between them increases, because of the limiting effect of geographic distance on rates of gene flow. Many studies of human populations have applied the isolation-by-distance model to genetic variation between local populations in a limited geographic area, but few have done so on a global level, and these few used different models and analytical methods. I assess genetic variation between human populations across the world using data on red blood cell polymorphisms, microsatellite DNA markers, and craniometric traits. The isolation-by-distance model provides an excellent fit to average levels of genetic similarity within geographic distance classes for all three data sets, and the rate of distance decay is the same in all three. These results suggest that a common pattern of global gene flow mediated by geographic distance is detectable in diverse genetic and morphological data. An alternative explanation is that the correspondence between genetic similarity and geographic distance reflects the history of dispersal of the human species out of Africa.     

Likelihood-based inferences under isolation by distance: two-dimensional habitats and confidence intervals

Likelihood-based methods of inference of population parameters from genetic data in structured populations have been implemented but still little tested in large networks of populations. In this work, a previous software implementation of inference in linear habitats is extended to two-dimensional habitats, and the coverage properties of confidence intervals are analyzed in both cases. Both standard likelihood and an efficient approximation are considered. The effects of misspecification of mutation model and dispersal distribution, and of spatial binning of samples, are considered. In the absence of model misspecification, the estimators have low bias, low mean square error, and the coverage properties of confidence intervals are consistent with theoretical expectations. Inferences of dispersal parameters and of the mutation rate are sensitive to misspecification or to approximations inherent to the coalescent algorithms used. In particular, coalescent approximations are not appropriate to infer the shape of the dispersal distribution. However, inferences of the neighborhood parameter (or of the product of population density and mean square dispersal rate) are generally robust with respect to complicating factors, such as misspecification of the mutation process and of the shape of the dispersal distribution, and with respect to spatial binning of samples. Likelihood inferences appear feasible in moderately sized networks of populations (up to 400 populations in this work), and they are more efficient than previous moment-based spatial regression method in realistic conditions.     

Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe

Arabidopsis thaliana provides a useful model system for functional, evolutionary and ecological studies in plant biology. We have analysed natural genetic variation in A. thaliana in order to infer its biogeographical and historical distribution across Eurasia. We analysed 79 amplified fragment length polymorphism (AFLP) markers in 142 accessions from the species' native range, and found highly significant genetic isolation by distance among A. thaliana accessions from Eurasia and southern Europe. These spatial patterns of genetic variation suggest that A. thaliana colonized central and northern Europe from Asia and from Mediterranean Pleistocene refugia, a trend which has been identified in other species. Statistically significant levels of multilocus linkage disequilibrium suggest intermediate levels of disequilibrium among subsets of loci, and analysis of genetic relationships among accessions reveal a star or bush-like dendrogram with low bootstrap support. Taken together, it appears that there has been sufficient historical recombination in the A. thaliana genome such that accessions do not conform to a tree-like, bifurcating pattern of evolution - there is no 'ecotype phylogeny.' Nonetheless, significant isolation by distance provides a framework upon which studies of natural variation in A. thaliana may be designed and interpreted.     

Isonymy and the genetic structure of Albanian populations

It is well known that in systems of surname transmission through the paternal line, surnames simulate neutral gene alleles belonging to the Y chromosome. This property of surnames was used to analyze the genetic structure of Albanian populations. Two large samples of surnames belonging to two different periods of time were analyzed. The analysis of indicators of population structure showed that geographical distance has an important effect on surname distribution. It seems that isolation by distance and genetic drift have been still important factors in the determination of the genetic structure of the Albanian population.     

First large-scale isolation of Prototheca zopfii from milk produced by dairy herds in Italy

A total of 1045 milk samples collected from infected and non infected quarters of 269 cows were investigated. This study showed that 4.7% of samples possessed cells of Prototheca spp. (10⁶cells/ml). The presence of other pathogenic microorganisms was also monitored. Prototheca spp. isolates were classified on the basis of current taxonomic guidelines and identified as P. zopfii. Susceptibility tests carried out in vitro by using 25 antibiotic compounds revealed that the strains of P. zopfii. were susceptible only to nystatin and amphotericin B (58 and 33% of total strains, respectively). The present study represents the first large-scale investigation carried out in Italy on the isolation of this achlorophyllous yeast-like microalga in milk samples produced by dairy herds.     

Clinal genetic variation and isolation by distance in the European eel Anguilla anguilla (L.)

The genetic variability and structure of the European eel ( Anguilla anguilla L.) in populations throughout Europe was reassessed using 15 allozymic loci, seven of which were polymorphic. Seven sites were sampled on a latitudinal gradient across the natural continental range, extending from southern France to southern Norway. Heterozygosity ( H _e = 0.05) and level of polymorphism (P = 0.43) were comparable to other marine fish. Populations were poorly differentiated ( G _ST = 0.014, F _ST = 0.002), which is not surprising considering the high dispersal capability of the European eel. However, a significant geographical cline was detected at two alleles ( IDH-1 * 100 and GPI-1 * 110 ), and genetic distances ( D _CE) were concordant with geographical coastal distances. Mantel tests, pairwise F _ST's and multidimensional scaling analyses identify three distinct groups: Northern Europe, Western Europe and the Mediterranean Sea. We propose that the clinal genetic structure in the European eel may be due to (1) isolation by distance (as recently detected with microsatellites), (2) temporal reproductive separation, (3) post-larval selective forces, (4) contact between formerly separated groups or (5) some combination thereof.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 509–521     

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.