ISOLATION BY DISTANCE

Indirect measures of gene flow and migration: FST not equal to 1/(4Nm + 1)

The difficulty of directly measuring gene flow has lead to the common use of indirect measures extrapolated from genetic frequency data. These measures are variants of FST, a standardized measure of the genetic variance among populations, and are used to solve for Nm, the number of migrants successfully entering a population per generation. Unfortunately, the mathematical model underlying this translation makes many biologically unrealistic assumptions; real populations are very likely to violate these assumptions, such that there is often limited quantitative information to be gained about dispersal from using gene frequency data. While studies of genetic structure per se are often worthwhile, and FST is an excellent measure of the extent of this population structure, it is rare that FST can be translated into an accurate estimate of Nm.

The evolutionary biology and population genetics underlying fungal strain typing

Strain typing of medically important fungi and fungal population genetics have been stimulated by new methods of tapping DNA variation. The aim of this contribution is to show how awareness of fungal population genetics can increase the utility of strain typing to better serve the interests of medical mycology. Knowing two basic features of fungal population biology, the mode of reproduction and genetic differentiation or isolation, can give medical mycologists information about the intraspecific groups that are worth identifying and the number and type of markers that would be needed to do so. The same evolutionary information can be just as valuable for the selection of fungi for development and testing of pharmaceuticals or vaccines. The many methods of analyzing DNA variation are evaluated in light of the need for polymorphic loci that are well characterized, simple, independent, and stable. Traditional population genetic and new phylogenetic methods for analyzing mode of reproduction, genetic differentiation, and isolation are reviewed. Strain typing and population genetic reports are examined for six medically important species: Coccidioides immitis, Histoplasma capsulatum, Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus, and A. flavus. Research opportunities in the areas of genomics, correlation of clinical variation with genetic variation, amount of recombination, and standardization of approach are suggested.

Consequences of a catadromous life-strategy for levels of mitochondrial DNA differentiation among populations of the Australian bass, Macquaria novemaculeata

The influence of a catadromous life-strategy on levels of spatial genetic structuring in fish is poorly understood. In an effort to gain a better appreciation of how this specialized life-strategy determines population genetic structuring, we assessed variation in the mitochondrial DNA (mtDNA) control region in a catadromous perciform, the Australian bass Macquaria novemaculeata. Nineteen putative haplotypes were resolved using temperature gradient gel electrophoresis from 10 geographically distinct populations. Significant heterogeneity was revealed in haplotype frequencies and their spatial distributions among many locales. Gene partitioning statistics (AMOVA) for both raw haplotype frequency data and frequency data with sequence divergences were concordant, indicating that M. novemaculeata populations were moderately genetically structured (phi ST = 0.05, 0.06; P < 0.001, respectively). Isolation by distance seems to be a strong structuring force in M. novemaculeata, culminating in no detectable phylogeographic structuring among haplotypes. Low sequence divergences were observed among many haplotypes and it is suggested that these are the result of pruning of maternal lineages by cyclical variations in female reproductive success. This study highlights the importance of life-history patterns and, in particular, spawning locality, in determining spatial structuring of mtDNA variation in catadromous species.

Mitochondrial and nuclear genetic relationships among Pacific Island and Asian populations

Mitochondrial and autosomal short tandem-repeat (STR) genetic distances among 28 Pacific Island and Asian populations are significantly correlated (r=.25, P<.01) but describe distinct patterns of relationships. Maternally inherited-mtDNA data suggest that Remote Oceanic Islanders originated in island Southeast Asia. In contrast, biparental STR data reveal substantial genetic affinities between Remote Oceanic Islanders and Near Oceanic populations from highland Papua New Guinea and Australia. The low correlation between maternal and biparental genetic markers from the same individuals may reflect differences in genome-effective population sizes or in sex-biased gene flow. To explore these possibilities, we have examined genetic diversity, gene flow, and correlations among genetic, linguistic, and geographic distances within four sets of populations representing potential geographic and cultural spheres of interaction. GST estimates (a measure of genetic differentiation inversely proportional to gene flow) from mtDNA sequences vary between 0.13 and 0.39 and are typically five times greater than GST estimates from STR loci (0.05-0.08). Significant correlations (r>.5, P<.05) between maternal genetic and linguistic distances are coincident with high mtDNA GST estimates (>0.38). Thus, genetic and linguistic distances may coevolve, and their correspondence may be preserved under conditions of genetic isolation. A significant correlation (r=.65, P<.01) between biparental genetic and geographic distances is coincident with a low STR GST estimate (0.05), indicating that isolation by distance is observed under conditions of high nuclear-gene flow. These results are consistent with an initial settlement of Remote Oceania from island Southeast Asia and with extensive postcolonization male-biased gene flow with Near Oceania.

Analysis of genetic structure and dispersal patterns in a population of sea beet

A model of the migration pattern in a metapopulation of sea beet (Beta vulgaris L. ssp. maritima), based on the continuous distributions of seed and pollen movements, is fitted to gene frequency data at 12 isozyme and RFLP loci by maximum likelihood by using an approximation of the simultaneous equilibrium distribution of the gene frequencies generated by the underlying multivariate stochastic process of genetic drift in the population. Several alternative restrictions of the general model are fitted to the data, including the island model, a model of complete isolation, and a model in which the seed and pollen dispersal variances are equal. Several likelihood ratio tests between these alternatives are performed, and median bias in the estimated parameters is corrected by using parametric bootstrapping. To assess the fit of the selected model, the predicted covariances are compared with covariances computed from the data directly. The dependency of estimated parameters on the ratio between effective and absolute subpopulation sizes, which is treated as a known parameter in the analysis, is also examined. Finally, we note that the data also appear to contain some information about this ratio.

Allele-specific population structure of Drosophila melanogaster alcohol dehydrogenase at the molecular level

The history of the Drosophila melanogaster alcohol dehydrogenase (ADH) Fast/Slow polymorphism was studied by recording molecular variation and inversion polymorphism in 233 chromosomes from European and African populations. Silent molecular variation in the Slow allele was very different between standard chromosomes and chromosomes bearing the In(2L)t inversion. Within populations, inverted Slow haplotypes were more variable than standard Slow haplotypes. Between populations, geographical structure was almost nonexistent for inverted Slow haplotypes and highly significant for standard Slow. All Fast haplotypes occurred on standard chromosomes. They showed little variation within and between populations. They were highly significantly closer to standard Slow haplotypes from Europe. These results suggest that the current range of Fast and In(2L)t Slow haplotypes is recent and that an older genetic differentiation between populations was followed by allele-specific gene flow.

Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history

Since the 1920s, population geneticists have had measures that describe how genetic variation is distributed spatially within a species' geographical range. Modern genetic survey techniques frequently yield information on the evolutionary relationships among the alleles or haplotypes as well as information on allele frequencies and their spatial distributions. This evolutionary information is often expressed in the form of an estimated haplotype or allele tree. Traditional statistics of population structure, such as F statistics, do not make use of evolutionary genealogical information, so it is necessary to develop new statistical estimators and tests that explicitly incorporate information from the haplotype tree. One such technique is to use the haplotype tree to define a nested series of branches (clades), thereby allowing an evolutionary nested analysis of the spatial distribution of genetic variation. Such a nested analysis can be performed regarding the geographical sampling locations either as categorical or continuous variables (i.e. some measure of spatial distance). It is shown that such nested phylogeographical analyses have more power to detect geographical associations than traditional, nonhistorical analyses and, as a consequence, allow a broader range of gene-flow parameters to be estimated in a precise fashion. More importantly, such nested analyses can discriminate between phylogeographical associations due to recurrent but restricted gene flow vs. historical events operating at the population level (e.g. past fragmentation, colonization, or range expansion events). Restricted gene flow and historical events can be intertwined, and the cladistic analyses can reconstruct their temporal juxtapositions, thereby yielding great insight into both the evolutionary history and population structure of the species. Examples are given that illustrate these properties, concentrating on the detection of range expansion events.

Fixation indices in subdivided populations

Without restricting the evolutionary forces that may be present, the theory of fixation indices, or F-statistics, in an arbitrarily subdivided population is developed systematically in terms of allelic and genotypic frequencies. The fixation indices for each homozygous genotype are expressed in terms of the fixation indices for the heterozygous genotypes. Therefore, together with the allelic frequencies, the latter suffice to describe population structure. Possible random fluctuations in the allelic frequencies (which may be caused, e.g., by finiteness of the subpopulations) are incorporated so that the fixation indices are parameters, rather than random variables, and these parameters are expressed in terms of ratios of evolutionary expectations of heterozygosities. The interpretation of some measures of population differentiation is also discussed. In particular, F(ST) is an appropriate index of gene-frequency differentiation if and only if the genetic diversity is low.

Evidence for genetic hitchhiking effect associated with insecticide resistance in Aedes aegypti

Information on genetic variation within and between populations is critical for understanding the evolutionary history of mosquito populations and disease epidemiology. Previous studies with Drosophila suggest that genetic variation of selectively neutral loci in a large fraction of genome may be constrained by fixation of advantageous mutations associated with hitchhiking effect. This study examined restriction fragment length polymorphisms of four natural Aedes aegypti mosquito populations from Trinidad and Tobago, at 16 loci. These populations have been subjected to organophosphate (OP) insecticide treatments for more than two decades, while dichlor-diphenyltrichlor (DDT) was the insecticide of choice prior to this period. We predicted that genes closely linked to the OP target loci would exhibit reduced genetic variation as a result of the hitchhiking effect associated with intensive OP insecticide selection. We also predicted that genetic variability of the genes conferring resistance to DDT and loci near the target site would be similar to other unlinked loci. As predicted, reduced genetic variation was found for loci in the general chromosomal region of a putative OP target site, and these loci generally exhibited larger F(ST) values than other random loci. In contrast, the gene conferring resistance to DDT and its linked loci show polymorphisms and genetic differentiation similar to other random loci. The reduced genetic variability and apparent gene deletion in some regions of chromosome 1 likely reflect the hitchhiking effect associated with OP insecticide selection.

Fine-scale spatial genetic structure with nonuniform distribution of individuals

This paper presents the first theoretical study of spatial genetic structure within nonuniformly distributed continuous plant populations. A novel individual-based model of isolation by distance was constructed to simulate genetic evolution within such populations. We found larger values of spatial genetic autocorrelations in highly clumped populations than in uniformly distributed populations. Most of this difference was caused by differences in mean dispersal distances, but aggregation probably also produced a slight increase in spatial genetic structure. Using an appropriate level of approximation of the continuous distribution of individuals in space, we assessed the potential effects of density, seed and pollen dispersal, generation overlapping, and overdominance selection at an independent locus, on fine-scale genetic structure, by varying them separately in a few particular cases with extreme clumping. When selfing was allowed, all these input variables influenced both aggregation and spatial genetic structure. Most variations in spatial genetic structure were closely linked to variations in clumping and/or local density. When selfing was not allowed, spatial genetic structure was lower in most cases.

Out of Africa? What do genes tell us?

Genetic diversity patterns in nuclear versus mitochondrial systems and in low versus high mutation rate systems do not support the hypothesis of a recent African origin for all of humanity following a split between Africans and non-Africans 100,000 years ago, nor do genetic distance data. Geographical analyses of nuclear and mitochondrial gene trees do not support the hypothesis of a recent global replacement of humans coming out of Africa, although a local replacement event in Europe is indicated by these analyses and recent studies on Neandertal DNA. The gene tree analyses instead indicate that genetic interchanges have ensured that all of humanity has evolved as a single evolutionary lineage with no major splits.

Effective size and F-statistics of subdivided populations. I. Monoecious species with partial selfing

Assuming discrete generations and autosomal inheritance involving genes that do not affect viability or reproductive ability, we have derived recurrence equations for the inbreeding coefficient and coancestry between individuals within and among subpopulations for a subdivided monoecious population with arbitrary distributions of male and female gametes per family, variable pollen and seed migration rates, and partial selfing. From the equations, formulas for effective size and expressions for F-statistics are obtained. For the special case of a single unsubdivided population, our equations reduce to the simple expressions derived by previous authors. It is shown that population structure (subdivision and migration) is important in determining the inbreeding coefficient and effective size. Failure to recognize internal structures of populations may lead to considerable bias in predicting effective size. Inbreeding coefficient, coancestry between individuals within and among subpopulations accrue at different and variable rates over initial generations before they converge to the same asymptotic rate of increase. For a given population, the smaller the pollen and seed migration rates, the more generations are required to attain the asymptotic rate and the larger the asymptotic effective size. The equations presented herein can be used for the study of evolutionary biology and conservation genetics.

Stochastic Dispersal Processes in Plant Populations

A dispersal model for airborne pollen based on assumptions about wind directionality, gravity, and a wind threshold at which pollen is taken by the wind is developed, using a three dimensional diffusion approximation. The bivariate probability distribution of pollen receipt by flowers at the same height as the pollen source is derived. Gravity, vertical random movements, and vegetation density turn out to have similar effects on this distribution. Maximum likelihood methods for estimating the combined parameters from data with multiple point or continuous pollen sources, and one or more plant varieties, are developed. Using an example data set from the literature, it is shown that our model gives a better fit than more traditional descriptive dispersal models of the form e-ar b. We also show that estimates of important properties of the dispersal distribution, such as the variances, become considerably smaller using our model than for the more traditional models. Finally, we discuss potential extensions and evolutionary implications of these types of models. Copyright 1997 Academic Press

Centaurea corymbosa, a cliff-dwelling species tottering on the brink of extinction: a demographic and genetic study

Centaurea corymbosa (Asteraceae) is endemic to a small area (< or = 3 km2), and < 500 individuals reproduce in any given year. Nevertheless, enzyme polymorphism was found within and among the six local extant populations, the most distant at 2.3 km. Levels of gene flow among populations and seed and pollen dispersal data indicated very low dispersal capacity. Rarity of long distance dispersal events coupled with traits such as prolonged juvenile period, monocarpy, and self-incompatibility precludes the establishment of new populations and thus the evolution toward colonization ability through increased dispersal rate, polycarpy, or self-compatibility. The species thus appears to be trapped on an evolutionary dead-end toward extinction, even though, from a preliminary introduction experiment, we conclude that several nearby unoccupied sites would be suitable for the species.

Female-biased dispersal in the monogamous mammal Crocidura russula: evidence from field data and microsatellite patterns

We investigated dispersal patterns in the monogamous Crocidura russula, based both on direct field observations (mark-recapture data) and on genetic analyses (microsatellite loci). Natal dispersal was found to be low. Most juveniles settled within their natal territory or one immediately adjacent. Migration rate was estimated to two individuals per year and per population. The correlation between genetic and geographical distances over a 16 km transect implies that migration occurs over short ranges. Natal dispersal was restricted to first-litter juveniles weaned in early May; this result suggests a direct dependence of dispersal on reproductive opportunities. Natal dispersal was highly female biased, a pattern unusual among mammals. Its association with monogamy provides support for the resource-competition model of dispersal. Our results demonstrate that a state-biased dispersal can be directly inferred from microsatellite genotype distributions, which opens new perspectives for empirical studies in this area.

Models of the evolution of some genetic systems

This paper reviews models of two aspects of genome evolution. The first is the problem of the conditions for establishment of chromosome rearrangements, as a result of their suppression of recombination between polymorphic genes that interact in their effects on fitness. The second is the spread of genomic elements either by their differential contributions to gametes, or by their ability to replicate and transpose themselves to new sites within the genome.

Inferring patterns of migration from gene frequencies under equilibrium conditions

A new maximum likelihood method to simultaneously estimate the parameters of any migration pattern from gene frequencies in stochastic equilibrium is developed, based on a model of multivariate genetic drift in a subdivided population. Motivated by simulations of this process in the simplified case of two subpopulations, problems related to the nuisance parameter q, the equilibrium gene frequency, are eliminated by conditioning on the observed mean gene frequency. The covariance matrix of this conditional distribution is calculated by constructing an abstract process that mimics the behavior of the original process in the subspace of interest. The approximation holds as long as there is limited differentiation between subpopulations. The bias and variance of estimates of long-range and short-range migration in a finite stepping stone model are evaluated by fitting the model to simulated data with known values of the parameters. Possible ecological extensions of the model are discussed.

Local genetic structure within two rookeries of Chelonia mydas (the green turtle)

We used multilocus minisatellite DNA fingerprinting to examine the local genetic structure within nesting populations of green turtles (Chelonia mydas) in Tortuguero, Costa Rica and Melbourne, Florida, USA. In the Tortuguero population, there was a significant negative correlation between genetic similarity of pairs of nesting females and the distance between their nest sites both within years (r2 = 0.273; P < 0.001) and between years (r2 = 0.578; P < 0.001). Of the 122 female pairs scored for Tortuguero, 12.3 per cent had genetic similarity values resembling those of mother-offspring pairs. In the Melbourne population, however, no relationship between genetic similarity and distance was found (r2 = 0.017; P = 0.075). The distance-related genetic structure of the Tortuguero population indicates that these females exhibit low levels of dispersal from natal sites, and that nestmates return independently to nest near their natal sites. The lack of a similar structure in the Melbourne population suggests that females from this population may not return to natal sites with comparable precision. High levels of mortality among nests, hatchlings or maturing turtles produced in the Melbourne rookery may also be responsible for the absence of distance-related local genetic structure.

Stock structure and homing fidelity in Gulf of Mexico sturgeon (Acipenser oxyrinchus desotoi) based on restriction fragment length polymorphism and sequence analyses of mitochondrial DNA

Efforts have been proposed worldwide to restore sturgeon populations through the use of hatcheries to supplement natural reproduction and to reintroduce sturgeon where they have become extinct. We examined the population structure and inferred the extent of homing in the anadromous Gulf of Mexico (Gulf) sturgeon (Acipenser oxyrinchus desotoi). Restriction fragment length polymorphism and control region sequence analyses of mitochondrial DNA (mtDNA) were used to identify haplotypes of Gulf sturgeon specimens obtained from eight drainages spanning the subspecies' entire distribution from Louisiana to Florida. Significant differences in haplotype frequencies indicated substantial geographic structuring of populations. A minimum of four regional or river-specific populations were identified (from west to east): (1) Pearl River, LA and Pascagoula River, MS, (2) Escambia and Yellow rivers, FI, (3) Choctawbatchee River, FL and (4) Apalachicola Ochlockonee, and Suwannee rivers, FL. Estimates of maternally mediated gene flow between any pair of the four regional or river-specific stocks ranged between 0.15 to 1.2. Tandem repeats in the mtDNA control region of Gulf sturgeon were not perfectly conserved. This result, together with an absence of heteroplasmy and length variation in Gulf sturgeon mtDNA, indicates that the molecular mechanisms of mtDNA control region sequence evolution differ among acipenserids.

Measurement of genetic structure within populations using Moran's spatial autocorrelation statistics

Spatial structure of genetic variation within populations, an important interacting influence on evolutionary and ecological processes, can be analyzed in detail by using spatial autocorrelation statistics. This paper characterizes the statistical properties of spatial autocorrelation statistics in this context and develops estimators of gene dispersal based on data on standing patterns of genetic variation. Large numbers of Monte Carlo simulations and a wide variety of sampling strategies are utilized. The results show that spatial autocorrelation statistics are highly predictable and informative. Thus, strong hypothesis tests for neutral theory can be formulated. Most strikingly, robust estimators of gene dispersal can be obtained with practical sample sizes. Details about optimal sampling strategies are also described.

Spatial and temporal genetic structure of Asclepias verticillata (whorled milkweed) among prairie patches in a forested landscape

We examined the spatial scale of genetic structure of Asclepias verticillata L. (whorled milkweed) populations in a landscape where suitable habitat is fragmented by woodlands to determine if the distance between patches influences genetic differentiation. In addition, we sampled over 2 years to determine if there are temporal genetic differences. This forb is found in prairie habitat in the Edge of Appalachia Preserve System, Ohio. Prairie patches have a clumped distribution with patches within a region located < 150 m apart and regions located > 1.5 km apart. Allozyme electrophoresis was used to collect genetic data from reproductive individuals in nine patches representing four regions. Observed heterozygosity was not significantly different among patches or between years, even though population sizes varied. Rogers' genetic distance and hierarchical F-statistics indicated that there was little genetic differentiation among patches within a region. Although genetic differentiation was greater among regions, it was relatively low. Between years, genetic differentiation within a patch was as great as genetic differentiation between patches. Conditional allele frequencies suggest that loss of one patch within a region will increase genetic differentiation within a region. Data suggest that prairie management could focus on a few regions with large numbers of patches. Keywords: habitat fragmentation, allozyme, genetic diversity, prairie management.

Genetic variation in populations of the endemicAchillea millefoliumssp.megacephalafrom the Athabasca sand dunes and the widespread ssp.lanulosain western North America

As part of an analysis of genetic diversity in endemic taxa of the Athabasca sand dunes in northern Saskatchewan, Canada, genetic variation was examined by starch gel electrophoresis in six populations of the endemic Achillea millefolium ssp. megacephala, and 13 populations of the closely related widespread taxon, A. millefolium ssp. lanulosa. Endemic populations had more alleles per locus, a higher percentage of polymorphic loci, and greater genetic diversity than did populations of the widespread taxon. At polymorphic loci, total gene diversity was comparable in both taxa, although within-population gene diversity was higher in the endemic taxon. Population differentiation (GST) was considerably lower in ssp. megacephala than in ssp. lanulosa, although GSTvalues were reduced when the parameter was calculated separately for geographic subdivisions of the widespread taxon. Our results differ from previous studies in which the endemic is typically depauperate of genetic variation relative to related widespread species. We suggest that obligate sexual reproduction and the absence of long-term asexual reproduction may be one of a number of factors that help populations of ssp. megacephala maintain higher levels of genetic variation on the Athabasca sand dunes. Keywords: genetic variation, endemic, rare species, Athabasca sand dunes, Achillea millefolium.

Hierarchical genetic structure and gene flow in three sympatric species of Amazonian rodents

The population genetic structure of three species of Amazonian rodents (Oligoryzomys microtis, Oryzomys capito, and Mesomys hispidus) is examined for mtDNA sequence haplotypes of the cytochrome b gene by hierarchical analysis of variance and gene flow estimates based on fixation indices (NST) and coalescence methods. Species samples are from the same localities along 1000 km of the Rio Juruá in western Amazonian Brazil, but each species differs in important life history traits such as population size and reproductive rate. Average haplotype differentiation, hierarchical haplotype apportionment, and gene flow estimates are contrasted in discussing the current and past population structure. Two species exhibit isolation by distance patterns wherein gene flow is largely limited to geographically adjacent localities. Mesomys exhibits this pattern throughout its range along the river. More than 75% of haplotype variation is apportioned among localities and regions, and estimates of Nm for pair-wise comparisons are nearly always less than 1. Oligoryzomys shows weak isolation by distance, but only over the largest geographical distances. Nm values for this species are nearly always above 1 and most (about 80%) of haplotype variation is contained within local populations. In contrast, Oryzomys exhibits no genetic structure throughout its entire distribution; Nm values average 17 and nearly 90% of the total haplotype variance is contained within local populations. Although gene flow estimates are high, the pattern of Nm as a function of geographical distance suggests that this species experienced a more recent invasion of the region and is still in genetic disequilibrium under its current demographic conditions.

Genetic structure and parasite compatibility of Bulinus globosus (Gastropoda: Planorbidae) from two areas of different endemicity of Schistosoma haematobium in Zimbabwe

A comparative study of the genetic structure of 8 populations of B.globosus from 2 areas of different endemicity of Schistosoma haematobium was done. Five populations were from Chiweshe (high endemicity) and three were from Plumtree (low endemicity). Genetic structure, as determined by allozyme genetics, revealed high levels of genetic variability in Chiweshe populations (Ho = 0.12-0.26) and low levels in Plumtree (Ho = 0.06-0.12). Populations from Chiweshe were genetically heterogeneous whereas in Plumtree the populations were uniform. There were significant deviations from Hardy-Weinberg proportions at different loci in Chiweshe populations. The observed excess of homozygotes was probably caused by partial selfing. The compatibility studies showed variation between allopatric and sympatric combinations of snails and parasites, and the Plumtree parasite had a significant influence on the compatibility parameters. This strain had a positive correlation (P < 0.01) of its infection rate with allele frequency of Est-2(100) and a negative correlation (P < 0.05) with allele Idh100.

Recombination and the multilocus structure of fungal populations

This review examines the relationship between recombination and the multilocus structure of populations. This discussion of population structure is based on the pattern of genetic variation within populations, especially the frequencies of multilocus genotypes, which can be used for making inferences about recombination. Three questions are addressed: Is population structure consistent with a random mating hypothesis? Is there evidence for recombination? How frequently does recombination occur?