ISOLATION BY DISTANCE

The Role of Geographic Analysis in Locating, Understanding, and Using Plant Genetic Diversity

The genetic structure of an organism is shaped by various factors, many of which vary significantly over space. In this chapter, we provide insight on how studying geographic patterns may contribute to an improved understanding of variability in genetic structure. We first review the theoretical background on how differences in genetic structure may be generated through processes that are inherently variable over space. We then present novices with some basics on how geographic information systems (GIS) may be adopted to study this variation, including advice on software, data, and the type of research questions that might be addressed. The chapter finishes with a brief review of how spatial analysis has contributed to the conservation and use of plant genetic resources, through an understanding of spatial patterns in species distribution and genetic structure. We conclude that spatial variation is a factor often overlooked in genetic studies and one that merits greater consideration. With the advent of functional genomics and improved quantification of adaptive traits, spatial analysis may be key in understanding variation in genetic structure through careful analysis of genotype-environment interactions.

Craniometric variation and population history of the prehistoric Tewa

Although the population history and social organization of the prehistoric Pueblo Indians of the American Southwest have received attention in the archaeological literature, little research on this topic has been conducted by biological anthropologists. Here, we examine postmarital residence at two ancestral Tewa Indian pueblos located in north-central New Mexico using determinant ratio analysis. In addition, we examine genetic relationships among pueblos, as well as levels of within-pueblo heterogeneity due to gene flow from extraregional sources, or regional aggregation. Results from determinant ratio analysis indicate greater within-pueblo male variation, consistent with matrilocal residence for at least one Tewa pueblo. Less than expected heterogeneity at two pueblos suggests that endogamy might have been practiced among some prehistoric Tewa pueblos. Gene flow from extraregional sources is indicated for two different pueblos by greater than expected within-group heterogeneity. Distance matrix correlation analyses indicate little if any relationship between phenotypic and geographic distances, suggesting that geography was not the primary basis of gene flow or mate exchange. The weak relationship between phenotypic and geographic distances may be the combined effects of endogamy at some pueblos, nonrandom extraregional gene flow or migration at other pueblos, and limited nonproximity-dependent regional gene flow or migration among pueblos, possibly structured on ritual exchange networks based on medicine society affiliation.

Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps

Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Population structure, whether created by pooling samples from divergent populations or by the mating pattern in a mixed population, is accurately bioassayed from genotype frequencies. The effective bottleneck time for Eurasians is substantially less than for migration out of Africa, reflecting later bottlenecks. The classical dependence of allele frequency on mutation age does not hold for the generally shorter time span of inbreeding and LD. Limitation of the classical theory to mutation age justifies the assumption of constant time in a LD map, except for alleles that were rare at the effective bottleneck time or have arisen since. This assumption is derived from the Malecot model and verified in all samples. Tested measures of relative efficiency, support intervals, and localization error determine the operating characteristics of LD maps that are applicable to every sexually reproducing species, with implications for association mapping, high-resolution linkage maps, evolutionary inference, and identification of recombinogenic sequences.

Recent trends in population genetics: more data! More math! Simple models?

Recent developments in population genetics are reviewed and placed in a historical context. Current and future challenges, both in computational methodology and in analytical theory, are to develop models and techniques to extract the most information possible from multilocus DNA datasets. As an example of the theoretical issues, five limiting forms of the island model of population subdivision with migration are presented in a unified framework. These approximations illustrate the interplay between migration and drift in structuring gene genealogies, and some of them make connections between the fairly complicated island-model genealogical process and the much simpler, unstructured neutral coalescent process which underlies most inferential techniques in population genetics.

Molecular and ecological evidence for small-scale isolation by distance in an endangered damselfly, Coenagrion mercuriale

Coenagrion mercuriale (Charpentier) (Odonata: Zygoptera) is one of Europe's most threatened damselflies and is listed in the European Habitats directive. We combined an intensive mark-release-recapture (MRR) study with a microsatellite-based genetic analysis for C. mercuriale from the Itchen Valley, UK, as part of an effort to understand the dispersal characteristics of this protected species. MRR data indicate that adult damselflies are highly sedentary, with only a low frequency of interpatch movement that is predominantly to neighbouring sites. This restricted dispersal leads to significant genetic differentiation throughout most of the Itchen Valley, except between areas of continuous habitat, and isolation by distance (IBD), even though the core populations are separated by less than 10 km. An urban area separating some sites had a strong effect on the spatial genetic structure. Average pairwise relatedness between individual damselflies is positive at short distances, reflecting fine-scale genetic clustering and IBD both within- and between-habitat patches. Damselflies from a fragmented habitat have higher average kinship than those from a large continuous population, probably because of poorer dispersal and localized breeding in the former. Although indirect estimates of gene flow must be interpreted with caution, it is encouraging that our results indicate that the spatial pattern of genetic variation matches closely with that expected from direct observations of movement. These data are further discussed with respect to possible barriers to dispersal within the study site and the ecology and conservation of C. mercuriale. To our knowledge, this is the first report of fine-scale genetic structuring in any zygopteran species.

The influence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis

Patterns of genetic diversity within populations of human pathogens, shaped by the ecology of host-microbe interactions, contain important information about the epidemiological history of infectious disease. Exploiting this information, however, requires a systematic approach that distinguishes the genetic signal generated by epidemiological processes from the effects of other forces, such as recombination, mutation, and population history. Here, a variety of quantitative techniques were employed to investigate multilocus sequence information from isolate collections of Neisseria meningitidis, a major cause of meningitis and septicemia world wide. This allowed quantitative evaluation of alternative explanations for the observed population structure. A coalescent-based approach was employed to estimate the rate of mutation, the rate of recombination, and the size distribution of recombination fragments from samples from disease-associated and carried meningococci obtained in the Czech Republic in 1993 and a global collection of disease-associated isolates collected globally from 1937 to 1996. The parameter estimates were used to reject a model in which genetic structure arose by chance in small populations, and analysis of molecular variation showed that geographically restricted gene flow was unlikely to be the cause of the genetic structure. The genetic differentiation between disease and carriage isolate collections indicated that, whereas certain genotypes were overrepresented among the disease-isolate collections (the "hyperinvasive" lineages), disease-associated and carried meningococci exhibited remarkably little differentiation at the level of individual nucleotide polymorphisms. In combination, these results indicated the repeated action of natural selection on meningococcal populations, possibly arising from the coevolutionary dynamic of host-pathogen interactions.

Nucleotide diversity in gorillas

Comparison of the levels of nucleotide diversity in humans and apes may provide valuable information for inferring the demographic history of these species, the effect of social structure on genetic diversity, patterns of past migration, and signatures of past selection events. Previous DNA sequence data from both the mitochondrial and the nuclear genomes suggested a much higher level of nucleotide diversity in the African apes than in humans. Noting that the nuclear DNA data from the apes were very limited, we previously conducted a DNA polymorphism study in humans and another in chimpanzees and bonobos, using 50 DNA segments randomly chosen from the noncoding, nonrepetitive parts of the human genome. The data revealed that the nucleotide diversity (pi) in bonobos (0.077%) is actually lower than that in humans (0.087%) and that pi in chimpanzees (0.134%) is only 50% higher than that in humans. In the present study we sequenced the same 50 segments in 15 western lowland gorillas and estimated pi to be 0.158%. This is the highest value among the African apes but is only about two times higher than that in humans. Interestingly, available mtDNA sequence data also suggest a twofold higher nucleotide diversity in gorillas than in humans, but suggest a threefold higher nucleotide diversity in chimpanzees than in humans. The higher mtDNA diversity in chimpanzees might be due to the unique pattern in the evolution of chimpanzee mtDNA. From the nuclear DNA pi values, we estimated that the long-term effective population sizes of humans, bonobos, chimpanzees, and gorillas are, respectively, 10,400, 12,300, 21,300, and 25,200.

New insights from fine-scale spatial genetic structure analyses in plant populations

Many empirical studies have assessed fine-scale spatial genetic structure (SGS), i.e. the nonrandom spatial distribution of genotypes, within plant populations using genetic markers and spatial autocorrelation techniques. These studies mostly provided qualitative descriptions of SGS, rendering quantitative comparisons among studies difficult. The theory of isolation by distance can predict the pattern of SGS under limited gene dispersal, suggesting new approaches, based on the relationship between pairwise relatedness coefficients and the spatial distance between individuals, to quantify SGS and infer gene dispersal parameters. Here we review the theory underlying such methods and discuss issues about their application to plant populations, such as the choice of the relatedness statistics, the sampling scheme to adopt, the procedure to test SGS, and the interpretation of spatial autocorrelograms. We propose to quantify SGS by an 'Sp' statistic primarily dependent upon the rate of decrease of pairwise kinship coefficients between individuals with the logarithm of the distance in two dimensions. Under certain conditions, this statistic estimates the reciprocal of the neighbourhood size. Reanalysing data from, mostly, published studies, the Sp statistic was assessed for 47 plant species. It was found to be significantly related to the mating system (higher in selfing species) and to the life form (higher in herbs than trees), as well as to the population density (higher under low density). We discuss the necessity for comparing SGS with direct estimates of gene dispersal distances, and show how the approach presented can be extended to assess (i) the level of biparental inbreeding, and (ii) the kurtosis of the gene dispersal distribution.

Identifying adaptive genetic divergence among populations from genome scans

The identification of signatures of natural selection in genomic surveys has become an area of intense research, stimulated by the increasing ease with which genetic markers can be typed. Loci identified as subject to selection may be functionally important, and hence (weak) candidates for involvement in disease causation. They can also be useful in determining the adaptive differentiation of populations, and exploring hypotheses about speciation. Adaptive differentiation has traditionally been identified from differences in allele frequencies among different populations, summarised by an estimate of FST. Low outliers relative to an appropriate neutral population-genetics model indicate loci subject to balancing selection, whereas high outliers suggest adaptive (directional) selection. However, the problem of identifying statistically significant departures from neutrality is complicated by confounding effects on the distribution of FST estimates, and current methods have not yet been tested in large-scale simulation experiments. Here, we simulate data from a structured population at many unlinked, diallelic loci that are predominantly neutral but with some loci subject to adaptive or balancing selection. We develop a hierarchical-Bayesian method, implemented via Markov chain Monte Carlo (MCMC), and assess its performance in distinguishing the loci simulated under selection from the neutral loci. We also compare this performance with that of a frequentist method, based on moment-based estimates of FST. We find that both methods can identify loci subject to adaptive selection when the selection coefficient is at least five times the migration rate. Neither method could reliably distinguish loci under balancing selection in our simulations, even when the selection coefficient is twenty times the migration rate.

Comparison of the fine-scale genetic structure of three dipterocarp species

We investigated the fine-scale genetic structure of three tropical-rainforest trees, Hopea dryobalanoides, Shorea parvifolia and S. acuminata (Dipterocarpaceae), in Peninsular Malaysia, all of which cooccurred within a 6-ha plot in Pasoh Forest Reserve. A significant genetic structure was found in H. dryobalanoides, weaker (but still significant) genetic structure in S. parvifolia and nonsignificant structure in S. acuminata. Seeds of all three species are wind dispersed, and their flowers are thought to be insect pollinated. The most obvious difference among these species is their height: S. parvifolia and S. acuminata are canopy species, whereas H. dryobalanoides is a subcanopy species. Clear differences were also found among these species in their range of seed dispersal, which depends on the height of the release point; so taller trees disperse their seed more extensively. The estimates of seed dispersal area were consistent with the degree of genetic structure found in the three species. Therefore, tree height probably had a strong influence on the fine-scale genetic structure of the three species.

Spatial genetic structure within a metallicolous population of Arabidopsis halleri, a clonal, self-incompatible and heavy-metal-tolerant species

Arabidopsis halleri, a close wild relative of A. thaliana, is a clonal, insect-pollinated herb tolerant to heavy metals (Zn, Pd, Cd) and a hyperaccumulator of Zn and Cd. It is of particular interest in the study of evolutionary processes and phytoremediation. However, little is known about its population gene flow patterns and the structure of its genetic diversity. We used five microsatellite loci to investigate the genetic structure at a fine spatial scale (10 cm to 500 m) in a metallicolous population of A. halleri. We also studied the contributions made by clonal propagation and sexual reproduction (seed and pollen dispersal) to the genetic patterns. Clonal diversity was high (D(G) > 0.9). Clonal spread occurs only at short distances (< 1 m). Both clonal spread and limited dispersal, associated with sexual reproduction, contribute to the significant spatial genetic structure revealed by spatial autocorrelation analysis. The shape of the autocorrelogram suggests that seed dispersal is restricted and pollen flow extensive, which may be related to intense activity by insect pollinators. Clonal spread was more extensive in the lowly polluted zone than in the highly polluted zone. This cannot be interpreted as a strategy for promoting the propagation of adapted genotypes under the harshest ecological constraints (highest heavy metal concentrations). The higher fine-scale spatial genetic structure found in the lowly polluted zone can be ascribed to plant densities that were lower than in the highly polluted zone. No evidence of genetic divergence due to spatial heavy metal heterogeneity was found between lowly and highly polluted zones.

Theory predicts the uneven distribution of genetic diversity within species

Global efforts to conserve species have been strongly influenced by the heterogeneous distribution of species diversity across the Earth. This is manifest in conservation efforts focused on diversity hotspots. The conservation of genetic diversity within an individual species is an important factor in its survival in the face of environmental changes and disease. Here we show that diversity within species is also distributed unevenly. Using simple genealogical models, we show that genetic distinctiveness has a scale-free power law distribution. This property implies that a disproportionate fraction of the diversity is concentrated in small sub-populations, even when the population is well-mixed. Small groups are of such importance to overall population diversity that even without extrinsic perturbations, there are large fluctuations in diversity owing to extinctions of these small groups. We also show that diversity can be geographically non-uniform--potentially including sharp boundaries between distantly related organisms--without extrinsic causes such as barriers to gene flow or past migration events. We obtained these results by studying the fundamental scaling properties of genealogical trees. Our theoretical results agree with field data from global samples of Pseudomonas bacteria. Contrary to previous studies, our results imply that diversity loss owing to severe extinction events is high, and focusing conservation efforts on highly distinctive groups can save much of the diversity.

Estimates of gene flow from rare alleles in natural populations of medfly Ceratitis capitata (Diptera: Tephritidae)

Gene flow based on the spatial distribution of rare alleles at 25 gene loci was estimated in 15 populations of Ceratitis capitata (Wiedemann) from different parts of the world. Estimates of Nm, the number of migrants exchanged per generation among populations in different regions of the world, appeared to be quite similar, ranging from 3.36 in tropical Africa to 2.94 in the New World and 2.72 in Mediterranean basin populations. This suggests that gene flow among neighbouring populations of medfly is quite extensive. The genetic differentiation in American, Mediterranean and African populations was related to major climatic differences between North and South. These differences arise mainly from five loci that showed gene frequency patterns suggestive of latitudinal clines in allele frequencies. The clinal variation was such that tropical-subtropical populations were more heterozygous than temperate populations. It was concluded that gene flow, counteracting the forces of natural selection and genetic drift, determines the extent to which geographical populations of C. capitata are differentiated.

Brownian models and coalescent structures

Brownian motions on coalescent structures have a biological relevance, either as an approximation of the stepwise mutation model for microsatellites, or as a model of spatial evolution considering the locations of individuals at successive generations. We discuss estimation procedures for the dispersal parameter of a Brownian motion defined on coalescent trees. First, we consider the mean square distance unbiased estimator and compute its variance. In a second approach, we introduce a phylogenetic estimator. Given the UPGMA topology, the likelihood of the parameter is computed thanks to a new dynamical programming method. By a proper correction, an unbiased estimator is derived from the pseudomaximum of the likelihood. The last approach consists of computing the likelihood by a Markov chain Monte Carlo sampling method. In the one-dimensional Brownian motion, this method seems less reliable than pseudomaximum-likelihood.

Partitioning nuclear and chloroplast variation at multiple spatial scales in the neotropical epiphytic orchid, Laelia rubescens

Insights into processes that lead to the distribution of genetic variation within plant species require recognition of the importance of both pollen and seed movement. Here we investigate the contributions of pollen and seed movement to overall gene flow in the Central American epiphytic orchid, Laelia rubescens. Genetic diversity and structure were examined at multiple spatial scales in the tropical dry forest of Costa Rica using nuclear (allozymes) and chloroplast restriction fragment length polymorphism (RFLP) markers, which were found to be diverse (allozymes, P = 73.3%; HE = 0.174; cpDNA, HE = 0.741). Nuclear genetic structure (FSTn) was low at every spatial scale (0.005-0.091). Chloroplast markers displayed more structure (0.073-0.254) but relatively similar patterns. Neither genome displayed significant isolation-by-distance. Pollen and seed dispersal rates did not differ significantly from one another (mp/ms = 1.40) at the broadest geographical scale, among sites throughout Costa Rica. However, relative contributions of pollen and seeds to gene flow were scale-dependent, with different mechanisms determining the dominant mode of gene flow at different spatial scales. Much seed dispersal is highly localized within the maternal population, while some seeds enter the air column and are dispersed over considerable distances. At the intermediate scale (10s to 100s of metres) pollinators are responsible for substantial pollen flow. This species appears capable of distributing its genes across the anthropogenically altered landscape that now characterizes its Costa Rican dry forest habitat.

Spatial genetic structure in populations ofQuercus mongolicavar.grosseserrata(Fagaceae) from southern Korea

Multilocus, putative allozyme genotypes were mapped and sampled from two local populations of Quercus mongolica Fischer ex Turcz var. grosseserrata (Bl.) Rehder & Wilson (Fagaceae) (each area is 100 m × 100 m, one with Sasa cover (N = 62) versus a second without it (N = 384)) occurring in undisturbed forests near Nogodan, Mount Jiri in southern Korea. Ripley's L-statistics and spatial autocorrelation analysis (a coancestry coefficient, fij) were used to test the prediction that because of low seedling establishment in a population with dense Sasa cover, there would be no spatial aggregation or hyperdispersion of individual trees and little evidence of fine-scale genetic structure in the population. As predicted, the Sasa-covered population showed no evidence of significant aggregation of individuals (P < 0.01) up to an interplant distance of 50 m and a random distribution of putative genotypes in the population. By contrast, the L-statistics conducted in the Sasa-free population indicated significant aggregation of individuals at interplant distances extending from 4 to 50 m. Spatial autocorrelation analysis revealed small but significant (P < 0.01), positive, fine-scale genetic structure extending from 10 to 30 m. A very similar result was obtained from 100 replicates each consisting of 62 trees in the Sasa-free populations by applying rarefaction and bootstrapping. These findings support the hypothesis that ground vegetation such as Sasa spp. has an impact on fine-scale genetic structure. The weak spatial genetic structure found in the Sasa-free population may primarily be due to limited acorn dispersal coupled with overlapping seed shadows and (or) secondary acorn dispersal by rodents.Key words: allozymes, Fagaceae, ground cover, Quercus mongolica var. grosseserrata, Sasa spp., spatial genetic structure.

Landscape connectivity influences gene flow in a roe deer population inhabiting a fragmented landscape: an individual-based approach

Changes in agricultural practices and forest fragmentation can have a dramatic effect on landscape connectivity and the dispersal of animals, potentially reducing gene flow within populations. In this study, we assessed the influence of woodland connectivity on gene flow in a traditionally forest-dwelling species--the European roe deer--in a fragmented landscape. From a sample of 648 roe deer spatially referenced within a study area of 55 x 40 km, interindividual genetic distances were calculated from genotypes at 12 polymorphic microsatellite loci. We calculated two geographical distances between each pair of individuals: the Euclidean distance (straight line) and the 'least cost distance' (the trajectory that maximizes the use of wooded corridors). We tested the correlation between genetic pairwise distances and the two types of geographical pairwise distance using Mantel tests. The correlation was better using the least cost distance, which takes into account the distribution of wooded patches, especially for females (the correlation was stronger but not significant for males). These results suggest that in a fragmented woodland area roe deer dispersal is strongly linked to wooded structures and hence that gene flow within the roe deer population is influenced by the connectivity of the landscape.

Fine-scale genetic structure and gene dispersal in Centaurea corymbosa (Asteraceae) I. Pattern of pollen dispersal

Pollen dispersal was characterized within a population of the narrowly endemic perennial herb, Centaurea corymbosa, using exclusion-based and likelihood-based paternity analyses carried out on microsatellite data. Data were used to fit a model of pollen dispersal and to estimate the rates of pollen flow and mutation/genotyping error, by developing a new method. Selfing was rare (1.6%). Pollen dispersed isotropically around each flowering plant following a leptokurtic distribution, with 50% of mating pairs separated by less than 11 m, but 22% by more than 40 m. Estimates of pollen flow lacked precision (0-25%), partially because mutations and/or genotyping errors (0.03-1%) could also explain the occurrence of offspring without a compatible candidate father. However, the pollen pool that fertilized these offspring was little differentiated from the adults of the population whereas strongly differentiated from the other populations, suggesting that pollen flow rate among populations was low. Our results suggest that pollen dispersal is too extended to allow differentiation by local adaptation within a population. However, among populations, gene flow might be low enough for such processes to occur.

Diversity analysis of commensal porcine Escherichia coli - associations between genotypes and habitat in the porcine gastrointestinal tract

Diversity studies of enteric Escherichia coli have relied almost entirely on faecal isolations on the assumption that they are representative of flora found throughout the gastrointestinal tract. The authors have addressed this belief by analysing isolates obtained from the duodenum, ileum, colon and faeces of pigs. E. coli isolates were obtained from eight pigs and characterized using multi-locus enzyme electrophoresis and PCR-based screening for a range of factors thought to be associated with intestinal and extra-intestinal disease. There are four main genetic groups of commensal E. coli (A, B1, B2, D). Group A strains represented 76 % of the isolates from the duodenum, ileum and colon compared to 58 % of the strains isolated from faeces. A nested molecular analysis of variance based on the allozyme and virulence factor screening results showed that differences among individual pigs accounted for 6 % of the observed genetic diversity, whilst 27 % of the genetic variation could be explained by clonal composition differences among gut regions. Finally, the absence of virulence genes in these commensals indicates that they may be suitable as a probiotic consortium, particularly if they also display increased adherence to enterocytes and antagonistic activity against pathogenic strains of E. coli.

Patterns of genetic differention between populations of the specialized herbivore Macrosiphoniella tanacetaria (Homoptera, Aphididae)

For herbivorous insects, studies of isolation by distance (IBD) are available for large spatial scales, whereas studies over small geographic distances are relatively rare, in particular for species where population turnover is high. In this study, we investigated IBD and population genetic structure in the aphid Macrosiphoniella tanacetaria, a specialist herbivore of tansy (Tanacetum vulgare). Owing to clonal growth, an individual plant (genet) has one to many shoots (ramets), which can host aphid colonies. Both at the level of ramets and genets, aphid persistence is short, in the order of weeks. Sampling of 17 populations was performed on a logarithmic scale, along the Saale River in Germany in June 2001, with distances between populations ranging from 1 m to 170 km. For the six microsatellites used, allelic and genotypic variability within aphid populations was high, and deviations from Hardy-Weinberg equilibrium and linkage disequilibrium were frequent. Most pairs of populations were significantly differentiated but there was no pattern of IBD. However, including into the analysis four additional populations from Alsace, France, collected at distances of, on average 470 km, resulted in a weak but significant IBD. Aphids are passive dispersers that are known to occasionally disperse over large distances, even though most dispersal is likely to occur over a small spatial scale. We suggest that for the host-specific M. tanacetaria, patterns of genetic variation among populations are, at an ecologically meaningful scale, governed by colonization/extinction dynamics and genetic drift rather than by a drift-dispersal equilibrium.

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.

Molecular population divergence and sexual selection on morphology in the banded demoiselle (Calopteryx splendens)

The importance of sexual selection in population divergence is of much interest, mainly because it is thought to cause reproductive isolation and hence could lead to speciation. Sexually selected traits have been hypothesized to diverge faster between populations than other traits, presumably because of differences in the strength, mechanism or dynamics of selection. We investigated this by quantifying population divergence in eight morphological characters in 12 south Swedish populations of a sexually dimorphic damselfly, the banded demoiselle (Calopteryx splendens). The morphological characters included a secondary sexual character, the male melanized wing spot, which has an important function in both inter- and intrasexual selection. In addition, we investigated molecular population divergence, revealed by amplified fragment length polymorphism (AFLP) analysis. Molecular population divergence was highly significant among these Northern European populations (overall F(st)=0.054; pairwise population F(st)'s ranged from approximately 0 to 0.13). We found evidence for isolation-by-distance (r=0.70) for the molecular markers and a significant correlation between molecular and phenotypic population divergence (r=0.39). One interpretation is that population divergence for the AFLP loci are affected by genetic drift, but is also indirectly influenced by selection, due to linkage with loci for the phenotypic traits. Field estimates of sexual and natural selection from two of the populations revealed fairly strong sexual selection on wing spot length, indicating that this trait has the potential to rapidly diverge, provided that variation is heritable and the observed selection is chronic.

The role of marriage rules in the structure of genetic relatedness

In this work, we take a forward in time approach to compute the probabilities of non-identity by descent for a population consisting of n sections obeying one of a class of marriage rules that is invariant under cyclical relabeling of sections. A perturbation method allows for exact asymptotics using the reciprocal of the section population as a small parameter. The analysis yields relatedness measures that generalize Wright's F-statistics.

Analysis of phylogenetic relationship among five mulberry (Morus) species using molecular markers

Species identification in mulberry (Morus) continues to be a point of great debate among scientists despite the number of criteria such as floral characters, wood, and leaf anatomical and biochemical characters used to identify the species within this genus. However, no consensus system of classification has emerged. Hence, an investigation was undertaken with inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) markers to find out the possibility of using these DNA markers to confirm the identity of genotypes in a particular species. Fifteen ISSR and 15 RAPD primers generated 86% and 78% polymorphism, respectively, among 19 mulberry genotypes. The polymorphism among the species varied from 50% to 57% in ISSR markers and 31% to 53% in RAPD markers. Similarity coefficients were higher among the genotypes of M. latifolia, M. bombycis and M. alba. Cluster analyses separated genotypes of M. laevigata and M. indica from those of the other species. Population structure analysis of these species further showed high genetic differentiation coefficients (GST), high heterozygosity between two species (DST), and total heterozygosity among populations (Ht) coupled with considerably low gene flow (Nm) when M. laevigata was paired with other species. Based on these parameters and the result of cluster analysis it is concluded that M. laevigata can be considered as a separate species of mulberry, whereas the other four species may be grouped together and treated as subspecies.Key words: Morus species, genetic marker, ISSR, RAPD, DNA polymorphism, genetic flow.

VARIABLE QUEEN NUMBER IN ANT COLONIES: NO IMPACT ON QUEEN TURNOVER, INBREEDING, AND POPULATION GENETIC DIFFERENTIATION IN THE ANT FORMICA SELYSI

Variation in queen number alters the genetic structure of social insect colonies, which in turn affects patterns of kin-selected conflict and cooperation. Theory suggests that shifts from single- to multiple-queen colonies are often associated with other changes in the breeding system, such as higher queen turnover, more local mating, and restricted dispersal. These changes may restrict gene flow between the two types of colonies and it has been suggested that this might ultimately lead to sympatric speciation. We performed a detailed microsatellite analysis of a large population of the ant Formica selysi, which revealed extensive variation in social structure, with 71 colonies headed by a single queen and 41 by multiple queens. This polymorphism in social structure appeared stable over time, since little change in the number of queens per colony was detected over a five-year period. Apart from queen number, single- and multiple-queen colonies had very similar breeding systems. Queen turnover was absent or very low in both types of colonies. Single- and multiple-queen colonies exhibited very small but significant levels of inbreeding, which indicates a slight deviation from random mating at a local scale and suggests that a small proportion of queens mate with related males. For both types of colonies, there was very little genetic structuring above the level of the nest, with no sign of isolation by distance. These similarities in the breeding systems were associated with a complete lack of genetic differentiation between single- and multiple-queen colonies, which provides no support for the hypothesis that change in queen number leads to restricted gene flow between social forms. Overall, this study suggests that the higher rates of queen turnover, local mating, and population structuring that are often associated with multiple-queen colonies do not appear when single- and multiple-queen colonies still coexist within the same population, but build up over time in populations consisting mostly of multiple-queen colonies.

A new protocol for evaluating putative causes for multiple variables in a spatial setting, illustrated by its application to European cancer rates

We introduce a statistical protocol for analyzing spatially varying data, including putative explanatory variables. The procedures comprise preliminary spatial autocorrelation analysis (from an earlier study), path analysis, clustering of the resulting set of path diagrams, ordination of these diagrams, and confirmatory tests against extrinsic information. To illustrate the application of these methods, we present incidence and mortality rates of 31 organ- and sex-specific cancers in Europe; these rates vary markedly with geography and type of cancer. Additionally, we investigated three factors (ethnohistory, genetics, and geography) putatively affecting these rates. The five variables were correlated separately for the 31 cancers over European reporting stations. We analyzed the correlations by path analysis, k-means clustering, and nonmetric multidimensional scaling; coefficients of the 31 path diagrams modeling the correlations vary substantially. To simplify interpretation, we grouped the diagrams into five clusters, for which we describe the differential effects of the three putative causes on incidence and mortality. When scaled, the path coefficients intergrade without marked gaps between clusters. Ethnic differences make for differences in cancer rates, even when the populations tested are ancient and complex mixtures. Path analysis usefully decomposes a structural model involving effects and putative causes, and estimates the magnitude of the model's components. Smooth intergradation of the path coefficients suggests the putative causes are the results of multiple forces. Despite this continuity of the path diagrams of the 31 cancers, clustering offers a useful segmentation of the continuum. Etiological and other extrinsic information on the cancers map significantly into the five clusters, demonstrating their epidemiological relevance.

ESTIMATING SEX-SPECIFIC DISPERSAL RATES WITH AUTOSOMAL MARKERS IN HIERARCHICALLY STRUCTURED POPULATIONS

A recent study suggests that sex-specific dispersal rates can be quantitatively estimated on the basis of sex- and state-specific (pre- vs. postdispersal) F-statistics. In the present paper, we extend this approach to account for the hierarchical structure of natural populations, and we validate it through individual-based simulations. The model is applied to an empirical data set consisting of 536 individuals (males, females, and predispersal juveniles) of greater white-toothed shrews (Crocidura russula), sampled according to a hierarchical design and typed for seven autosomal microsatellite loci. From this dataset, dispersal is significantly female biased at the local scale (breeding-group level), but not at the larger scale (among local populations). We argue that selective pressures on dispersal are likely to depend on the spatial scale considered, and that short-distance dispersal should mainly respond to kin interactions (inbreeding or kin competition avoidance), which exert differential pressure on males and females.

Using genetic markers to estimate the pollen dispersal curve

Pollen dispersal is a critical process that shapes genetic diversity in natural populations of plants. Estimating the pollen dispersal curve can provide insight into the evolutionary dynamics of populations and is essential background for making predictions about changes induced by perturbations. Specifically, we would like to know whether the dispersal curve is exponential, thin-tailed (decreasing faster than exponential), or fat-tailed (decreasing slower than the exponential). In the latter case, rare events of long-distance dispersal will be much more likely. Here we generalize the previously developed TWOGENER method, assuming that the pollen dispersal curve belongs to particular one- or two-parameter families of dispersal curves and estimating simultaneously the parameters of the dispersal curve and the effective density of reproducing individuals in the population. We tested this method on simulated data, using an exponential power distribution, under thin-tailed, exponential and fat-tailed conditions. We find that even if our estimates show some bias and large mean squared error (MSE), we are able to estimate correctly the general trend of the curve - thin-tailed or fat-tailed - and the effective density. Moreover, the mean distance of dispersal can be correctly estimated with low bias and MSE, even if another family of dispersal curve is used for the estimation. Finally, we consider three case studies based on forest tree species. We find that dispersal is fat-tailed in all cases, and that the effective density estimated by our model is below the measured density in two of the cases. This latter result may reflect the difficulty of estimating two parameters, or it may be a biological consequence of variance in reproductive success of males in the population. Both the simulated and empirical findings demonstrate the strong potential of TWOGENER for evaluating the shape of the dispersal curve and the effective density of the population (d(e)).

Individual assignment test reveals differential restriction to dispersal between two salmonids despite no increase of genetic differences with distance

In many species genes move over limited distances, such that genetic differences among populations or individuals are expected to increase as a function of geographical distance. In other species, however, genes may move any distance over a single generation time, such that no increase of genetic differences is expected to occur with distance. Patterns of gene dispersal have been assessed typically using this theoretical property. In this study, this classical approach based on a Mantel test was compared to a new method using individual assignment to reveal contrasts in dispersal patterns between 15 populations of brook charr Salvelinus fontinalis and 10 populations of Atlantic salmon Salmo salar sampled in eastern Canada, where both species co-occur naturally. Based on the Mantel test, we found evidence for neither an increase of genetic differences with distance in either species nor a significant contrast between them. The individual-based method, in contrast, revealed that individual assignment in both species was non random, being significantly biased toward geographically proximate locations. Furthermore, brook charr were on average assigned to a closer river than were salmon, according to a priori expectations based on the dispersal behaviour of the two species. We thus propose that individual assignment methods might be a promising and more powerful alternative to Mantel tests when isolation by distance cannot be postulated a priori.

Genetic population structure of turbot (Scophthalmus maximus L.) supports the presence of multiple hybrid zones for marine fishes in the transition zone between the Baltic Sea and the North Sea

Genetic population structure of turbot (Scophthalmus maximus L.) in the Northeast Atlantic was investigated using eight highly variable microsatellite loci. In total 706 individuals from eight locations with temporal replicates were assayed, covering an area from the French Bay of Biscay to the Aaland archipelago in the Baltic Sea. In contrast to previous genetic studies of turbot, we found significant genetic differentiation among samples with a maximum pairwise FST of 0.032. Limited or no genetic differentiation was found among samples within the Atlantic/North Sea area and within the Baltic Sea, suggesting high gene flow among populations in these areas. In contrast, there was a sharp cline in genetic differentiation going from the low saline Baltic Sea to the high saline North Sea. The data were explained best by two divergent populations connected by a hybrid zone; however, a mechanical mixing model could not be ruled out. A significant part of the genetic variance could be ascribed to variation among years within locality. Nevertheless, the population structure was relatively stable over time, suggesting that the observed pattern of genetic differentiation is biologically significant. This study suggests that hybrid zones are a common phenomenon for marine fishes in the transition area between the North Sea and the Baltic Sea and highlights the importance of using interspecific comparisons for inferring population structure in high gene flow species such as most marine fishes.

Population genetics of the potentially invasive African fruit fly species, Ceratitis rosa and Ceratitis fasciventris (Diptera: Tephritidae)

A set of 10 microsatellite markers was used to survey the levels of genetic variability and to analyse the genetic aspects of the population dynamics of two potentially invasive pest fruit fly species, Ceratitis rosa and C. fasciventris, in Africa. The loci were derived from the closely related species, C. capitata. The degree of microsatellite polymorphism in C. rosa and C. fasciventris was extensive and comparable to that of C. capitata. In C. rosa, the evolution of microsatellite polymorphism in its distribution area reflects the colonization history of this species. The mainland populations are more polymorphic than the island populations. Low levels of differentiation were found within the Africa mainland area, while greater levels of differentiation affect the islands. Ceratitis fasciventris is a central-east African species. The microsatellite data over the Uganda/Kenya spatial scale suggest a recent expansion and possibly continuing gene flow within this area. The microsatellite variability data from C. rosa and C. fasciventris, together with those of C. capitata, support the hypothesis of an east African origin of the Ceratitis spp.

Spatial structure and genetic diversity of two tropical tree species with contrasting breeding systems and different ploidy levels

Analyses of the spatial distribution pattern, spatial genetic structure and of genetic diversity were carried out in two tropical tree species with contrasting breeding systems and different ploidy levels using a 50-ha demographic plot in a lowland dipterocarp forest in Peninsular Malaysia. Shorea leprosula is a diploid and predominantly outcrossed species, whereas S. ovalis ssp. sericea is an autotetraploid species with apomictic mode of reproduction. Genetic diversity parameters estimated for S. leprosula using microsatellite were consistently higher than using allozyme. In comparisons with S. leprosula and other tropical tree species, S. ovalis ssp. sericea also displayed relatively high levels of genetic diversity. This might be explained by the lower pressure of genetic drift due to tetrasomic inheritance, and for autotetraploids each locus can accommodate up to four different alleles and this allows maintenance of more alleles at individual loci. The observed high levels of genetic diversity in S. ovalis ssp. sericea can also be due to a random retention of more heterogeneous individuals in the past, and the apomictic mode of reproduction might be an evolutionary strategy, which allows the species to maintain high levels of genetic diversity. The spatial distribution pattern analyses of both species showed significant levels of aggregation at small and medium but random distribution at the big diameter-class. The decrease in magnitude of spatial aggregation from small- to large-diameter classes might be due to compensatory mortality during recruitment and survival under competitive thinning process. Spatial genetic structure analyses for both species revealed significant spatial genetic structure for short distances in all the three diameter-classes. The magnitude of spatial genetic structure in both species was observed to be decreasing from smaller- to larger-diameter classes. The high spatial genetic structuring observed in S. ovalis ssp. sericea at the small-diameter class is due primarily to limited seed dispersal and apomictic mode of reproduction. The similar observation in S. leprosula, however, can be explained by limited seed and pollen dispersal, which supports further the fact that the species is pollinated by weak fliers, mainly of Thrips and Megalurothrips in the lowland dipterocarp forest.

Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnypetoscincus queenslandiae

To examine the effects of recent habitat fragmentation, we assayed genetic diversity in a rain forest endemic lizard, the prickly forest skink (Gnypetoscincus queenslandiae), from seven forest fragments and five sites in continuous forest on the Atherton tableland of northeastern Queensland, Australia. The rain forest in this region was fragmented by logging and clearing for dairy farms in the early 1900s and most forest fragments studied have been isolated for 50-80 years or nine to 12 skink generations. We genotyped 411 individuals at nine microsatellite DNA loci and found fewer alleles per locus in prickly forest skinks from small rain forest fragments and a lower ratio of allele number to allele size range in forest fragments than in continuous forest, indicative of a decrease in effective population size. In contrast, and as expected for populations with small neighbourhood sizes, neither heterozygosity nor variance in allele size differed between fragments and sites in continuous forests. Considering measures of among population differentiation, there was no increase in FST among fragments and a significant isolation by distance pattern was identified across all 12 sites. However, the relationship between genetic (FST) and geographical distance was significantly stronger for continuous forest sites than for fragments, consistent with disruption of gene flow among the latter. The observed changes in genetic diversity within and among populations are small, but in the direction predicted by the theory of genetic erosion in recently fragmented populations. The results also illustrate the inherent difficulty in detecting genetic consequences of recent habitat fragmentation, even in genetically variable species, and especially when effective population size and dispersal rates are low.

The maintenance of reproductive isolation in a mosaic hybrid zone between the fire-bellied toads Bombina bombina and B. variegata

Mosaic hybrid zones arise when ecologically differentiated taxa hybridize across a network of habitat patches. Frequent interbreeding across a small-scale patchwork can erode species differences that might have been preserved in a clinal hybrid zone. In particular, the rapid breakdown of neutral divergence sets an upper limit to the time for which differences at marker loci can persist. We present here a case study of a mosaic hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae) near Apahida in Romania. In our 20 x 20 km study area, we detected no evidence of a clinal transition but found a strong association between aquatic habitat and mean allele frequencies at four molecular markers. In particular, pure populations of B. bombina in ponds appear to cause massive introgression into the surrounding B. variegata gene pool found in temporary aquatic sites. Nevertheless, the genetic structure of these hybrid populations was remarkably similar to those of a previously studied transect near Pescenica (Croatia), which had both clinal and mosaic features: estimates of heterozygote deficit and linkage disequilibrium in each country are similar. In Apahida, the observed strong linkage disequilibria should stem from an imperfect habitat preference that guides most (but not all) adults into the habitats to which they are adapted. In the absence of a clinal structure, the inferred migration rate between habitats implies that associations between selected loci and neutral markers should break down rapidly. Although plausible selection strengths can maintain differentiation at those loci adapting the toads to either permanent or temporary breeding sites, the divergence at neutral markers must be transient. The hybrid zone may be approaching a state in which the gene pools are homogenized at all but the selected loci, not dissimilar from an early stage of sympatric divergence.

Diversification of Sulawesi macaque monkeys: decoupled evolution of mitochondrial and autosomal DNA

In macaque monkeys, females are philopatric and males are obligate dispersers. This social system is expected to differently affect evolution of genetic elements depending on their mode of inheritance. Because of this, the geographic structure of molecular variation may differ considerably in mitochondrial DNA (mtDNA) and in autosomal DNA (aDNA) in the same individuals, even though these genomes are partially co-inherited. On the Indonesian island of Sulawesi, macaque monkeys underwent an explosive diversification as a result of range fragmentation. Today, barriers to dispersal have receded and fertile hybrid individuals can be found at contact zones between parapatric species. In this study, we examine the impact of range fragmentation on Sulawesi macaque mtDNA and aDNA by comparing evolution, phylogeography, and population subdivision of each genome. Our results suggest that mtDNA is paraphyletic in some species, and that mtDNA phylogeography is largely consistent with a pattern of isolation by distance. Autosomal DNA, however, is suggestive of fragmentation, in that interspecific differentiation across most contact zones is significant but intraspecific differentiation between contact zones is not. Furthermore, in mtDNA, most molecular variation is partitioned between populations within species but in aDNA most variation is partitioned within populations. That mtDNA has a different geographic structure than aDNA (and morphology) in these primates is a probable consequence of (1) a high level of ancestral polymorphism in mtDNA, (2) differences between patterns of ancestral dispersal of matrilines and contemporary dispersal of males, and (3) the fact that female philopatry impedes gene flow of macaque mtDNA.

Horse-mounted invaders from the Russo-Kazakh steppe or agricultural colonists from western Central Asia? A craniometric investigation of the Bronze Age settlement of Xinjiang

Numerous Bronze Age cemeteries in the oases surrounding the Täklamakan Desert of the Tarim Basin in the Xinjiang Uyghur Autonomous Region, western China, have yielded both mummified and skeletal human remains. A dearth of local antecedents, coupled with woolen textiles and the apparent Western physical appearance of the population, raised questions as to where these people came from. Two hypotheses have been offered by archaeologists to account for the origins of Bronze Age populations of the Tarim Basin. These are the "steppe hypothesis" and the "Bactrian oasis hypothesis." Eight craniometric variables from 25 Aeneolithic and Bronze Age samples, comprising 1,353 adults from the Tarim Basin, the Russo-Kazakh steppe, southern China, Central Asia, Iran, and the Indus Valley, are compared to test which, if either, of these hypotheses are supported by the pattern of phenetic affinities possessed by Bronze Age inhabitants of the Tarim Basin. Craniometric differences between samples are compared with Mahalanobis generalized distance (d2), and patterns of phenetic affinity are assessed with two types of cluster analysis (the weighted pair average linkage method and the neighbor-joining method), multidimensional scaling, and principal coordinates analysis. Results obtained by this analysis provide little support for either the steppe hypothesis or the Bactrian oasis hypothesis. Rather, the pattern of phenetic affinities manifested by Bronze Age inhabitants of the Tarim Basin suggests the presence of a population of unknown origin within the Tarim Basin during the early Bronze Age. After 1200 B.C., this population experienced significant gene flow from highland populations of the Pamirs and Ferghana Valley. These highland populations may include those who later became known as the Saka and who may have served as "middlemen" facilitating contacts between East (Tarim Basin, China) and West (Bactria, Uzbekistan) along what later became known as the Great Silk Road.