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.     

Isonymy and isolation by distance in Italy

The isonymy structure of Italy was studied using the surname distribution of 5,043,580 private telephone users selected from a 1996 commercial CD-ROM that contains all 24 million users in the country. The users were distributed in 123 towns selected on a geographic basis. The 123 towns were either on the main communication roads of the country or at the ends of such roads. The shortest distance between nearest neighbor towns was 5.3 km (Carrara and Massa), and the largest distance was 1,136 km (Aosta and Castrignano del Capo). The number of different surnames found in the whole analysis was 215,623. Lasker's distance, the negative value of the logarithm of random isonymy between localities, was linearly and significantly correlated with the logarithm of geographic distance, with r = 0.63 +/- 0.008. A dendrogram was built from the matrix of isonymy distances, using UPGMA. It separates the Italian towns into 5 main clusters: 1 in the southern portion of the country, a second cluster toward the center, and 3 in the northern area of Italy. Within each cluster small subclusters with specific geographic distributions could be related to regional borders. Comparisons with the results of a previous analysis of Switzerland and Germany's structures are given. From the present analysis isolation by distance emerges clearly, although it is less strong than in Switzerland and stronger than in Germany. The random component of inbreeding estimated from isonymy indicates that the southern area of Italy is on average more inbred than the northern area. In fact, the heterogeneity is greater in the northern area, particularly in the plain of the Po River, than anywhere else in Italy.     

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.     

The influence of dispersal and diet breadth on patterns of genetic isolation by distance in phytophagous insects

To determine the effects of dispersal ability and diet breadth on population-genetic structure, we reviewed the allozyme literature and estimated genetic isolation by distance (IBD) for 43 species/host races of phytophagous insects. Subsequently, we tested two opposing hypotheses regarding the influence of dispersal ability on IBD: that IBD slopes do not vary with mobility, but that intercepts increase with mobility, and, alternatively, that IBD slopes vary with dispersal ability. We found that from tens of kilometers to more than 1,000 km, IBD is weak in sedentary and highly mobile species but pronounced in moderately mobile species. We attribute the weak IBD in strong dispersers to the homogenizing effects of gene flow, whereas in sedentary species, limited gene flow allows nearly all populations to diverge. In intermediate dispersers, genetic homogeneity is achieved at small spatial scales, but limited dispersal promotes genetic divergence over long distances. We also tested the hypothesis that IBD increases with decreasing diet breadth. We discovered no such pattern, casting doubt on the supposition that specialization promotes speciation by influencing population-genetic subdivision. Finally, we found that the number of populations is a more important consideration than the number of polymorphic loci in studies of IBD.     

Absence of isolation by distance patterns at the regional scale in the fungal plant pathogen Leptosphaeria maculans

Outcomes of host-pathogen coevolution are influenced by migration rates of the interacting species. Reduced gene flow with increasing spatial distance between populations leads to spatial genetic structure, as predicted by the isolation by distance (IBD) model. In wind-dispersed plant-pathogenic fungi, a significant spatial genetic structure is theoretically expected if local spore dispersal is more frequent than long-distance dispersal, but this remains to be documented by empirical data. For 29 populations of the oilseed rape fungus Leptosphaeria maculans sampled from two French regions, genetic structure was determined using eight minisatellite markers. Gene diversity (H = 0.62-0.70) and haplotypic richness (R = 0.96-1) were high in all populations. No linkage disequilibrium was detected between loci, suggesting the prevalence of panmictic sexual reproduction. Analysis of molecular variance showed that > 97% of genetic diversity was observed within populations. Genetic differentiation was low among populations (F(st) < 0.05). Although direct methods previously revealed short-distance dispersal for L. maculans, our findings of no correlation between genetic and geographic distances among populations illustrate that the IBD model does not account for dispersal of the fungus at the spatial scale we examined. These results indicate high gene flow among French populations of L. maculans, suggesting high dispersal rates and/or large effective population sizes, two characteristics giving the pathogen high evolutionary potential against the deployment of resistant oilseed rape cultivars.     

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.     

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.     

Interactions between environmental factors can hide isolation by distance patterns: a case study of Ctenomys rionegrensis in Uruguay

Identifying the factors responsible for the structuring of genetic diversity is of fundamental importance for biodiversity conservation. However, arriving at such understanding is difficult owing to the many factors involved and the potential interactions between them. Here, we present an example of how such interactions can preclude us from arriving at a complete characterization of the demographic history and genetic structure of a species. Ctenomys rionegrensis is a species with restricted dispersal abilities and, as such, should exhibit an isolation by distance (IBD) pattern, which previous studies were unable to uncover. It was therefore concluded that this species underwent a recent population expansion. Using a novel hierarchical Bayesian method, we show that the inability to detect the IBD pattern is due to the interaction between elevation and geographical distance. We posit that populations in low areas suffer periodic floods that may reduce local population sizes, increasing genetic drift, a process that masks the effect of distance on genetic differentiation. Our results do not refute the possibility that the populations of C. rionegrensis underwent a recent population expansion but they indicate that an alternative scenario described by a metapopulation model at or near migration-drift equilibrium cannot be excluded either.     

Concentration-dependent patterns of leucine incorporation by coastal picoplankton

Coastal pelagic environments are believed to feature concentration gradients of dissolved organic carbon at a microscale, and they are characterized by pronounced seasonal differences in substrate availability for the heterotrophic picoplankton. Microbial taxa that coexist in such habitats might thus differ in their ability to incorporate substrates at various concentrations. We investigated the incorporation patterns of leucine in four microbial lineages from the coastal North Sea at concentrations between 0.1 and 100 nM before and during a spring phytoplankton bloom. Community bulk incorporation rates and the fraction of leucine-incorporating cells in the different populations were analyzed. Significantly fewer bacterial cells incorporated the amino acid before (13 to 35%) than during (23 to 47%) the bloom at all but the highest concentration. The incorporation rate per active cell in the prebloom situation was constant above 0.1 nM added leucine, whereas it increased steeply with substrate concentration during the bloom. At both time points, a high proportion of members of the Roseobacter clade incorporated leucine at all concentrations (55 to 80% and 86 to 94%, respectively). In contrast, the fractions of leucine-incorporating cells increased substantially with substrate availability in bacteria from the SAR86 clade (8 to 31%) and from DE cluster 2 of the Flavobacteria-Sphingobacteria (14 to 33%). The incorporation patterns of marine Euryarchaeota were between these extremes (30 to 56% and 48 to 70%, respectively). Our results suggest that the contribution of microbial taxa to the turnover of particular substrates may be concentration dependent. This may help us to understand the specific niches of coexisting populations that appear to compete for the same resources.     

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.     

Fine-scale sampling reveals distinct isolation by distance patterns in chum salmon (Oncorhynchus keta) populations occupying a glacially dynamic environment

Populations with spatially restricted gene flow are characterized by genetic differentiation that may be positively correlated with the geographic distance separating populations, a pattern known as isolation by distance (IBD). Here we examined the fine-scale genetic structure of 66 chum salmon (Oncorhynchus keta) populations spawning in Alaska waterways and explored patterns of IBD using 90 nuclear and 3 mitochondrial single nucleotide polymorphisms. Estimating population structure of chum salmon in Alaska is of increasing concern because of fluctuating census sizes and the uncertain effects of harvest on specific populations. We hypothesized that IBD would be present because chum salmon spawn in coastal rivers that are distributed along a linear array and gene flow is spatially restricted due to homing. Evidence of very weak IBD was found throughout the region (R² = 0.06, p < 0.0001) but the strength of the IBD relationship varied greatly over different spatial scales and geographic regions. Decomposed pairwise regression analyses identified nine outlier populations to regional IBD patterns, suggesting that geographic distance is not the only factor influencing genetic differentiation in the region. Instead, population structure appears to be heavily influenced by glacial history of the region and the presence of a glacial refugium on Kodiak Island.     

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.     

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.     

Self-organization and complexity in historical landscape patterns

Self‐organization describes the evolution process of complex structures where systems emerge spontaneously, driven internally by variations of the system itself. Self‐organization to the critical state is manifested by scale‐free behavior across many orders of magnitude (Bak et al. 1987, Bak 1996, Solé et al. 1999). Spatial scale‐free behavior implies fractal properties and is quantified by the fractal dimension. Temporal scale‐free behavior is evident in power spectra of fluctuations that obey power laws. Self‐organized criticality is a universal phenomenon that likely produces some of the fractals and power laws observed in nature. We investigated the historical landscape of southern Wisconsin (USA) (60,000 km²) for self‐organization and complexity. The landscape is patterned into prairies, savannas, and open and closed forests, using data from the United States General Land Office Surveys that were conducted during the 19th century, at a time prior to Euro‐American settlement. We applied a two‐dimensional cellular automaton model with one adjustable parameter. Model evolution replaces a cell that dies at random times by a cell chosen randomly from within a circular radius r, where r typically takes values between 1 (local) and 10 units (regional). Cluster probability is used to measure the degree of organization. The model landscape self‐organizes to a realistic critical state if neighborhoods of intermediate size (r=3) are chosen, indicating that (a) no particular time or space scale for the clusters is singled out, i.e. the spatial dependence is fractal, and temporal fluctuations in the cluster probability exhibit power laws; (b) a simple model suffices to replicate the landscape pattern resulting from complex spatial and temporal interactions. Measures of comparison between the observed and the simulated landscape show good agreement: fractal dimensions for simulated (1.6) and observed landscapes (1.64), cluster probabilities for simulated (32.3%) and observed (32.6%) landscapes, and algorithmic complexity for simulated (6792 bytes) and observed (6205 bytes) landscapes. The results are robust towards variation of initial and boundary conditions as well as perturbations.     

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.     

Seasonal patterns of urea regeneration by size-fractionated microheterotrophs in well-mixed temperate coastal waters

Urea regeneration by size-fractionated plankton was measuredover an annual cycle at a coastal station in the permanentlywell-mixed waters of the western English Channel. Rates of urearegeneration in the <200 µm fraction varied from 0.6to 20.6 nmol N L^–1 h^–1. Regeneration rates werelowest in winter and highest in summer. The ratio of the ratesof regeneration to uptake of urea was close to 1 on all time(seasonal and nycthemeral), and space (vertical) scales indicatingthat regeneration by microheterotrophs supplied the totalityof urea used by phytoplankton. On an annual basis, urea regeneratedby the microheterotrophs (0.98 mol N m^–2 year^–1)was equivalent to 33% of the total regenerated N (urea + ammonium).The major part of urea regeneration was due to the nanoplankton(51%) and microplankton fractions (36%). Regeneration of ureain the picoplankton was detectable only from April to Octoberand represented, on an average, 25% of the total urea regeneratedduring this period. Urea regeneration in micro- and nanoplanktonfractions was mainly associated with ciliates and in the picoplanctonfraction with bacteria.     

Adaptive trade-offs in juvenile salmonid metabolism associated with habitat partitioning between coho salmon and steelhead trout in coastal streams

1. Adaptive trade-offs are fundamental to the evolution of diversity and the coexistence of similar taxa and occur when complimentary combinations of traits maximize efficiency of resource exploitation or survival at different points on environmental gradients. 2. Standard metabolic rate (SMR) is a key physiological trait that reflects adaptations to baseline metabolic performance, whereas active metabolism reflects adaptations to variable metabolic output associated with performance related to foraging, predator avoidance, aggressive interactions or migratory movements. Benefits of high SMR and active metabolism may change along a resource (productivity) gradient, indicating that a trade-off exists among active metabolism, resting metabolism and energy intake. 3. We measured and compared SMR, maximal metabolic rate (MMR), aerobic scope (AS), swim performance (UCrit) and growth of juvenile hatchery and wild steelhead and coho salmon held on high- and low-food rations in order to better understand the potential significance of variation in SMR to growth, differentiation between species, and patterns of habitat use along a productivity gradient. 4. We found that differences in SMR, MMR, AS, swim performance and growth rate between steelhead trout and coho salmon were reduced in hatchery-reared fish compared with wild fish. Wild steelhead had a higher MMR, AS, swim performance and growth rate than wild coho, but adaptations between species do not appear to involve differences in SMR or to trade-off increased growth rate against lower swim performance, as commonly observed for high-growth strains. Instead, we hypothesize that wild steelhead may be trading off higher growth rate for lower food consumption efficiency, similar to strategies adopted by anadromous vs. resident brook trout and Atlantic salmon vs. brook trout. This highlights potential differences in food consumption and digestion strategies as cryptic adaptations ecologically differentiating salmonid species. 5. We hypothesize that divergent digestive strategies, which are common and well documented among terrestrial vertebrates, may be an important but overlooked aspect of adaptive strategies of juvenile salmonids, and fish in general.