ISOLATION BY DISTANCE

Effects of metapopulation processes on measures of genetic diversity

Many species persist as a metapopulation under a balance between the local extinction of subpopulations or demes and their recolonization through dispersal from occupied patches. Here we review the growing body of literature dealing with the genetic consequences of such population turnover. We focus our attention principally on theoretical studies of a classical metapopulation with a 'finite-island' model of population structure, rather than on 'continent-island' models or 'source-sink' models. In particular, we concern ourselves with the subset of geographically subdivided population models in which it is assumed that all demes are liable to extinction from time to time and that all demes receive immigrants. Early studies of the genetic effects of population turnover focused on population differentiation, such as measured by F(ST). A key advantage of F(ST) over absolute measures of diversity is its relative independence of the mutation process, so that different genes in the same species may be compared. Another advantage is that F(ST) will usually equilibrate more quickly following perturbations than will absolute levels of diversity. However, because F(ST) is a ratio of between-population differentiation to total diversity, the genetic effects of metapopulation processes may be difficult to interpret in terms of F(ST) on its own, so that the analysis of absolute measures of diversity in addition is likely to be informative. While population turnover may either increase or decrease F(ST), depending on the mode of colonization, recurrent extinction and recolonization is expected always to reduce levels of both within-population and species-wide diversity (piS and piT, respectively). One corollary of this is that piS cannot be used as an unbiased estimate of the scaled mutation rate, theta, as it can, with some assumptions about the migration process, in species whose demes do not fluctuate in size. The reduction of piT in response to population turnover reflects shortened mean coalescent times, although the distribution of coalescence times under extinction colonization equilibrium is not yet known. Finally, we review current understanding of the effect of metapopulation dynamics on the effective population size.

Null expectation of spatial correlograms under a stochastic process of genetic divergence with small sample sizes

An Ornstein-Uhlenbeck process was used to simulate the exponential relationship between genetic divergence and geographic distances, as predicted by stochastic processes of population differentiation, such as isolation-by-distance, stepping-stone or coalescence models. These simulations were based only on the spatial coordinates of the local populations that defined a spatial unweighted pair-group method using arithmetic averages (UPGMA) link among them. The simulated gene frequency surfaces were then analyzed using spatial autocorrelation procedures and Nei's genetic distances, constructed with different numbers of variables (gene frequencies). Stochastic divergence in space produced strong spatial patterns at univariate and mutivariate levels. Using a relatively small number of local populations, the correlogram profiles varied considerably, with Manhattan distances greater than those defined by other simulation studies. This method allows one to establish a range of correlogram profiles under the same stochastic process of spatial divergence, thereby avoiding the use of unnecessary explanations of genetic divergence based on other microevolutionary processes.

Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept

Subspecies have been considered artificial subdivisions of species, pattern classes, or incipient species. However, with more data and modern phylogenetic techniques, some subspecies may be found to represent true species. Mitochondrial DNA analysis of the polytypic snake, Elaphe obsoleta, yields well-supported clades that do not conform to any of the currently accepted subspecies. Complete nucleotide sequences of the cytochrome b gene and the mitochondrial control region produced robust maximum-parsimony and maximum-likelihood trees that do not differ statistically. Both trees were significantly shorter than a most parsimonious tree in which each subspecies was constrained to be monophyletic. Thus, the subspecies of E. obsoleta do not represent distinct genetic lineages. Instead, the evidence points to three well-supported mitochondrial DNA clades confined to particular geographic areas in the eastern United States. This research underscores the potential problems of recognizing subspecies based on one or a few characters.

Phylogeography and population structure of an ecotonal marsupial, Bettongia tropica, determined using mtDNA and microsatellites

The northern bettong, Bettongia tropica, is an endangered species of Potoroidae with a restricted distribution in the wet tropics of north Queensland, Australia. The species is only found within a thin strip of sclerophyll forest along the western margin of rainforest. This tight association with rainforest boundaries is predicted to have resulted in population isolation as rainforest contracted during the Pleistocene, though some have proposed that the northern bettong was not present in the wet tropics until the late Pleistocene. The dispersal ability of the species, and of the family, is not known. This study examined gene flow among populations within areas of continuous habitat complemented by a broader analysis of phylogeography. Individuals trapped at each of the four known regions (one region was subsampled at three different sites), were sequenced for 547 base pairs of the mitochondrial DNA (mtDNA) control region and typed for seven microsatellite loci. The mtDNA phylogeny showed congruence with a biogeographical hypothesis, a relatively deep split suggesting historical isolation in separate northern and southern refugia. The two divergent clades were both present within the Lamb Range, indicating an expansion from these refuges and subsequent admixture at one site. mtDNA allele frequencies indicated relatively limited gene flow within the Lamb Range over distances as short as nine km. Tests of population divergence using microsatellites (FST and assignment tests) strongly supported this result. A molecular signal indicative of a recent bottleneck was unexpectedly detected in one of the Lamb Range subpopulations. This lead us to examine the behaviour of the statistics used in this bottleneck test under a linear stepping-stone model with varying migration rates. We found that it may be more difficult to detect molecular signatures for recent bottlenecks under conditions of very low migration rates than for isolated populations and, conversely, that 'false' bottleneck signatures may be observed at higher migration rates. The Lamb Range FST estimate clearly fell within the category of potentially 'false' bottleneck signals. Despite relatively limited gene flow, evidence for asymmetric dispersal suggests more complicated population dynamics than a simple linear stepping-stone model.

Absence of evidence for isolation by distance in an expanding cane toad (Bufo marinus) population: an individual-based analysis of microsatellite genotypes

The cane toad (Bufo marinus) was introduced in 1935 in Australia, where it spread rapidly. We have tested for isolation by distance by analysing at a local geographical scale a continuous population using seven microsatellite markers and an individual-based method. The matrix of pairwise individual differentiation was not significantly correlated with that of geographical distance. Regression analyses gave a low positive slope of 0.00072 (all individuals) or a negative slope of 0.0017 (individuals with a distance higher than the previously estimated mean dispersal distance). The absence of evidence for isolation by distance favours the hypothesis that the substantial differentiation and autocorrelation previously observed at enzyme loci, mainly results from discontinuities in the colonization process with founder effects occurring at the time of the establishment of new populations.

Genetic microstructure in two Spanish cat populations. I: genic diversity, gene flow and selection

The genetic microstructure of two Spanish cat populations (in Barcelona and Alicante) was studied. These populations were in Hardy-Weinberg equilibrium at the locus O . There was significant genetic heterogeneity for most of the loci studied at the colony level, especially, and the subpopulation level in Barcelona, and at the subpopulation level in Alicante, although the amount of heterogeneity was relatively small compared with that found in other mammal species. Therefore, the major part of the gene diversity found was at the level of the small population structure (colonies). This agrees quite well with high theoretical gene flow estimates. The Lewontin-Krakauer test showed, in some cases, significant F tests, which appears to indicate the presence of several selective events on some of the loci studied (diversifying and/or unifying), although some other causes, such as differential gene flow, some different historical and demographic parameters at the time of the introduction of the different alleles within the cities studied, as well as different mutation rates of the loci analyzed, could produce significant Lewontin-Krakauer test values, as well.

Population structure of Hydropsyche exocellata. Genetic homogeneity in a zone of fragmented distribution

Using four allozymic loci, we analysed the genetic structure and differentiation of Hydropsyche exocellata (Trichoptera; Hydropsychidae) larvae in seven sites along the Upper Loire River (France). The genetic differentiation is low for this species despite distribution patchiness, and only due to one locus in one study site. No trend relating genetic differentiation to geographic distance (isolation by distance) was observed. Significant deviations from Hardy-Weinberg equilibrium were observed at most sites and loci. The population genetics analysis of an amphibiotic insect such as H. exocellata in light of current ecological and population genetics knowledge is discussed following two main factors: 1) sampling of partially reproductively isolated, genetically distinct subpopulations, and 2) form of selection. Despite knowledge on several aspects of the ecology of H. exocellata in the River Loire, numerous points limit genetic data interpretation. These points are underlined and discussed with reference to studies on other amphibiotic insects.

Spatial pattern and genetic diversity estimates are linked in stochastic models of population differentiation

In the present study, we used both simulations and real data set analyses to show that, under stochastic processes of population differentiation, the concepts of spatial heterogeneity and spatial pattern overlap. In these processes, the proportion of variation among and within a population (measured by G ST and 1 - G ST, respectively) is correlated with the slope and intercept of a Mantel's test relating genetic and geographic distances. Beyond the conceptual interest, the inspection of the relationship between population heterogeneity and spatial pattern can be used to test departures from stochasticity in the study of population differentiation.

Glacial vicariance and historical biogeography of rock ptarmigan (Lagopus mutus) in the Bering region

In this paper, we address alternative hypotheses for the evolution of subspecies of rock ptarmigan (Lagopus mutus) endemic to the Aleutian Archipelago. To do this we examined patterns of genetic differentiation among populations of rock ptarmigan in the Aleutian Islands and parts of both Alaska and Siberia. Variation in mitochondrial control region sequences of 105 rock ptarmigan from 10 subspecies within the Bering region revealed three major phylogenetic lineages, two of which are endemic to the Aleutian Islands. Accordingly, haplotype and nucleotide diversities of rock ptarmigan within the archipelago are much higher than within mainland Alaska or Siberia. For Aleutian rock ptarmigan, analyses of molecular variance indicated significant genetic structuring and low estimates of gene flow among populations, despite small interisland distances within the archipelago. However, isolation by distance did not describe the pattern of gene flow or differentiation at this scale. Our estimates of divergence times of lineages suggest that Aleutian rock ptarmigan became isolated prior to the most recent Pleistocene glaciation event (late Wisconsin Stade) and that current patterns of genetic variation reflect the postglacial redistribution of divergent lineages and subsequent limited gene flow. In addition, genetic divergence among lineages was concordant with the distribution of plumage types among subspecies. The patterns of genetic variation described here for rock ptarmigan provide evidence for the role of glacial vicariance in contributing to genetic diversity within this and other Bering region species.

Complex social organization reflects genetic structure and relatedness in the cooperatively breeding bell miner, Manorina melanophrys

The cooperatively breeding bell miner, Manorina melanophrys, differs from most other cooperative breeding species in the complexity of its social system, where discrete social organization occurs on at least three levels. Microsatellite markers were used to investigate the degree of genetic structure underlying the social organization of M. melanophrys by comparing colonies, coteries and nest contingents. The genetic data confirmed behavioural observations of M. melanophrys living in male kin-based groups between which females disperse short distances to breed. Estimates of FST revealed restricted gene flow between eight colonies located within 30 km that was significantly associated with geographical distance when the two most distant colonies were included. Within a high density colony significant differences were found between coteries; analysis of the degree of relatedness between coterie members showed that this is due to related individuals associating preferentially with each other. Similarly, the contingent of individuals attending a nest were generally close relatives of the young they were aiding, supporting models invoking kin selection as the selective agency mediating helping.

The Evolution of Plasticity and Nonplastic Spatial and Temporal Adaptations in the Presence of Imperfect Environmental Cues

A model for the evolution of plasticity is considered in which the phenotype, undergoing stabilizing selection, is modeled as a linear function of an environmental cue correlated with the phenotypic optimum, with the coefficients z₀ and z₁ evolving according to standard quantitative genetic theory. In contrast to previous theoretical models, as the rate of migration between demes or the rate of cyclic fluctuations in the optimum increases, the amount of plasticity [Formula: see text] at equilibrium is shown to increase gradually, in part accounting for the effect of reduced nonplastic adaptation and reaching a maximum equal to the squared correlation between the environmental cue and the phenotypic optimum. Given that information available to the organism is limited, this bias of the expressed phenotype toward the global optimum is still optimal, however, in a certain decision-theoretic sense. When genetic variation in the plastic component of the trait is small so that spatial or temporal differentiation in plasticity is small, the effect of plasticity on nonplastic adaptation is to reduce the effects of variation in the phenotypic optimum by a factor [Formula: see text] only. Information acquisition costs and joint evolution of sensory systems are discussed.

The effects of subdivision on the genetic divergence of populations and species

An island model of migration is used to study the effects of subdivision within populations and species on sample genealogies and on between-population or between-species measures of genetic variation. The model assumes that the number of demes within each population or species is large. When populations (or species), connected either by gene flow or historical association, are themselves subdivided into demes, changes in the migration rate among demes alter both the structure of genealogies and the time scale of the coalescent process. The time scale of the coalescent is related to the effective size of the population, which depends on the migration rate among demes. When the migration rate among demes within populations is low, isolation (or speciation) events seem more recent and migration rates among populations seem higher because the effective size of each population is increased. This affects the probability of reciprocal monophyly of two samples, the chance that a gene tree of a sample matches the species tree, and relative likelihoods of different types of polymorphic sites. It can also have a profound effect on the estimation of divergence times.

Microsatellite variation in Daphnia pulex from both sides of the Baltic Sea

Despite large genetic differentiation among neighbouring populations of many freshwater zooplankton species, a macrogeographical homogeneity of allozyme variation is generally observed. A study on breeding systems in Scandinavian populations of Daphnia pulex suggested a latitudinally related cline in breeding system with both diploid cyclic parthenogens and diploid obligate parthenogens at the latitude of 60-61 degrees N. Variation at neutral markers may be more affected by selection at linked loci in such species than in strictly sexual species. In this paper I present a study of variation at five microsatellite loci in a total of 34 populations from small ponds and rockpools on both sides of the Baltic Sea at 60-61 degrees N. Two major groups, which may represent different species of the D. pulex complex, are defined with the microsatellites. Neighbouring populations show both similar and well differentiated genetic composition. Populations separated by larger geographical distances show only a large differentiation and a macrogeographic pattern. The large differentiation observed at small distances can be explained with small effective population size: variation at the microsatellite loci has been shaped by population bottlenecks followed with expansion in size, and possibly by selection. No conclusive evidence is found for obligative parthenogenesis.

Joint effects of natural selection and recombination on gene flow between Drosophila ananassae populations

We estimated DNA sequence variation in a 5.7-kb fragment of the furrowed (fw) gene region within and between four populations of Drosophila ananassae; fw is located in a chromosomal region of very low recombination. We analyzed gene flow between these four populations along a latitudinal transect on the Indian subcontinent: two populations from southern, subtropical areas (Hyderabad, India, and Sri Lanka) and two from more temperate zones in the north (Nepal and Burma). Furthermore, we compared the pattern of differentiation at fw with published data from Om(1D), a gene located in a region of normal recombination. While differentiation at Om(1D) shows an isolation-by-distance effect, at fw the pattern of differentiation is quite different such that the frequencies of single nucleotide polymorphisms are homogenized over extended geographic regions (i.e., among the two populations of the northern species range from Burma and Nepal as well as among the two southern populations from India and Sri Lanka), but strongly differentiated between the northern and southern populations. To examine these differences in the patterns of variation and differentiation between the Om(1D) and fw gene regions, we determine the critical values of our previously proposed test of the background selection hypothesis (henceforth called F(ST) test). Using these results, we show that the pattern of differentiation at fw may be inconsistent with the background selection model. The data depart from this model in a direction that is compatible with the occurrence of recent selective sweeps in the northern as well as southern populations.

Quantitative genetics of allogamous F2: an origin of randomly fertilized populations

The quantitative genetic properties are derived for the bulk F2 originating from random fertilization (RF) amongst hybrid (F1) individuals. Only its mean appears to have been derived previously, and that definition is confirmed (by another method). New general equations are found also for all genotype frequencies, allele frequencies, inbreeding coefficient, the genotypic, additive-genetic and dominance variances, and broad-sense and narrow-sense heritabilities. The assumption that such an F2 is a classical RF population is shown to be correct. Indeed, the allogamous F2 is a natural origin for the RF population. The relationships are given between precedent RF populations (parents) and subsequent RF populations following hybridization (allogamous F2). The allogamous F2 is generally inbred with respect to its parental F1, the degree depending on the hybrid's parents' allele frequencies. At the same time, it is outbred with respect to those original parents, and not inbred at all with respect to the equivalent RF population. The genotypic variance is generally more than in the F1, and likewise for heritabilities. These findings make it possible to evaluate the genetic advance from selection and hybridization. The results depend on the allele frequencies of the original parents and the degree of overdominance, but generally, selection is more advantageous than hybrid vigour.

Genetic structure of Camellia japonica L. in an old-growth evergreen forest, Tsushima, Japan

The spatial genetic structure of Camellia japonica was investigated, using microsatellite markers, in a 4-ha permanent plot within an old-growth forest. Spatial distribution of individuals was also assessed to obtain an insight into spatial relationships between individuals and alleles. Morisita's index of dispersion showed that 518 C. japonica individuals in the plot were clumped, and Moran's I spatial autocorrelation coefficient revealed weak genetic structure, indicating a low level of allele clustering. Average I correlograms showed that there was stronger genetic structure over short-distance classes. The clumped distribution of individuals and the positive autocorrelation over short-distance classes may result from the limited seed dispersal and microsite heterogeneity of the stand, while the genetic structure may be weakened by overlapping seed shadow and extensive pollen flow, mediated by animal vectors, and the high outcrossing rate found in C. japonica.

Genetic analysis of a documented population bottleneck: introduced Bennett's wallabies (Macropus rufogriseus rufogriseus) in New Zealand

Few bottlenecks of wild populations are sufficiently well-documented to constitute models for testing theories about the impact of bottlenecks on genetic variation, and subsequent population persistence. Relevant details of the Bennett's wallaby (Macropus rufogriseus rufogriseus) introduction into New Zealand were recorded (founder number, source and approximate bottleneck duration) and suggest this may provide a rare opportunity to examine the efficacy of tests designed to detect recent bottlenecks in wild populations. We first assessed the accuracy of historic accounts of the introduction using genetic diversity detected in mitochondrial DNA (mtDNA) and at five microsatellite loci. Phylogenetic analyses of mtDNA D-loop sequence haplotypes were consistent with the reported origin of the founders as Tasmania, rather than one of the Bass Strait islands in which Bennett's wallabies are also found. Microsatellite allele frequencies from the Tasmanian source population were then used to seed bottleneck simulations encompassing varying sizes and numbers of generations, in order to assess the severity of bottleneck consistent with diversity observed in the New Zealand population. The results suggested that the founder number was unlikely to have been as small as the three animals suggested by the account of the introduction. Nonetheless, the bottleneck was probably severe; in the range of three to five pairs of wallabies for one to three generations. It resulted in significantly reduced levels of allelic diversity and heterozygosity relative to the source population. This bottleneck is only detectable under the infinite allele model (IAM) and not under the stepwise mutation model (SMM) or the two-phase model (TPM), and possible explanations for this are discussed.

Microevolutionary patterns and processes of the Native Hawaiian colonizing fern Odontosoria chinensis (Lindsaeaceae)

The vascular-plant flora of the Hawaiian Islands is characterized by one of the highest rates of species endemism in the world. Among flowering plants, approximately 89% of species are endemic, and among pteridophytes, about 76% are endemic. At the single-island level, however, rates of species endemism vary dramatically between these two groups with 80% of angiosperms and only 6% of pteridophytes being single-island endemics. Thus, in many groups of Hawaiian angiosperms, it is possible to link studies of phylogeny, evolution, and biogeographic history at the interspecific and interisland levels. In contrast, the low level of single-island species endemism among Hawaiian pteridophytes makes similar interspecific and interisland studies nearly impossible. Higher levels of interisland gene flow may account for the different levels of single-island endemism in Hawaiian pteridophytes relative to angiosperms. The primary question we addressed in the present study was: Can we infer microevolutionary patterns and processes among populations within widespread species of Hawaiian pteridophytes wherein gene flow is probably common? To address this broad question, we conducted a population genetic study of the native Hawaiian colonizing species Odontosoria chinensis. Data from allozyme analyses allowed us to infer: (1) significant genetic differentiation among populations from different islands; (2) historical patterns of dispersal between particular pairs of islands; (3) archipelago-level patterns of dispersal and colonization; (4) founder effects among populations on the youngest island of Hawaii; and, (5) that this species primarily reproduces via outcrossing, but may possess a mixed-mating system.

Nuclear DNA microsatellite analysis of genetic diversity and gene flow in the Scandinavian brown bear (Ursus arctos)

In the 1930s, the Scandinavian brown bear was close to extinction due to vigorous extermination programmes in Norway and Sweden. Increased protection of the brown bear in Scandinavia has resulted in the recovery of four subpopulations, which currently contain close to 1000 individuals. Effective conservation and management of the Scandinavian brown bear requires knowledge of the current levels of genetic diversity and gene flow among the four subpopulations. Earlier studies of mitochondrial DNA (mtDNA) diversity revealed extremely low levels of genetic variation, and population structure that grouped the three northern subpopulations in one genetic clade and the southernmost subpopulation in a second highly divergent clade. In this study, we extended the analysis of genetic diversity and gene flow in the Scandinavian brown bear using data from 19 nuclear DNA microsatellite loci. Results from the nuclear loci were strikingly different than the mtDNA results. Genetic diversity levels in the four subpopulations were equivalent to diversity levels in nonbottlenecked populations from North America, and significantly higher than levels in other bottlenecked and isolated brown bear populations. Gene flow levels between subpopulations ranged from low to moderate and were correlated with geographical distance. The substantial difference in results obtained using mtDNA and nuclear DNA markers stresses the importance of collecting data from both types of genetic markers before interpreting data and making recommendations for the conservation and management of natural populations. Based on the results from the mtDNA and nuclear DNA data sets, we propose one evolutionarily significant unit and four management units for the brown bear in Scandinavia.

Population genetics of the Chilean frog Batrachyla Leptopus (Leptodactylidae)

Electrophoretic variation of proteins encoded by 14 loci was analyzed in eight (five continental and three insular) populations of the Chilean leptodactylid frog Batrachyla leptopus. The overall proportion of polymorphic loci was estimated to be 18.7% and the average number of alleles per locus, 1.2, while observed and expected heterozygosities were 1.7 and 5.1%, respectively. The estimated coefficient of genetic identity was 0.940; the corresponding figure for genetic distance was 0.063. F-statistics analysis showed a total inbreeding coefficient (Fit) of 0.855 and high levels of genetic subdivision (Fst = 0.596) as well as of inbreeding within populations (Fis = 0.640). However, there was only a moderate level of genetic differentiation (Fst = 0.181) between the insular group of populations and the continental group.

Her name is "Lucy", our three-million-year-old ancestor

Dental anthropology is a key discipline in studies to determine the evolutionary history of our hominid ancestors, to identify the origin and dispersal of modern humans, and to reconstruct the source of observed dental variation. A survey of hominid and modern human evolutionary history, emphasizing results from powerful multivariate dental morphometric methodologies, suggests a single African origin of modern humans > 150,000 years before present from a Homo heidelbergensis ancestor. A continuum among modern humanity is described, with, first, sub-Saharan Africans, then southeast Asian Negrito, and Australian aborigines at its extant root. Other interpretations of the available data are possible. Examinations of the progress of the evolution of teeth through time give significant insight into dental morphogenetics and variation, and the biology of dental evolution. The mechanisms of evolution which fashion a phenotype and the methods of molecular and dental phylogenetics are reviewed and evaluated. This is an exciting time for dental anthropology, with fascinating and challenging questions to address, but anthropologists, not dentists, dominate the field. The perspective of a dentist can meaningfully add to the dynamics of dental anthropology.

Nonequilibrium migration in human history

A nonequilibrium migration model is proposed and applied to genetic data from humans. The model assumes symmetric migration among all possible pairs of demes and that the number of demes is large. With these assumptions it is straightforward to allow for changes in demography, and here a single abrupt change is considered. Under the model this change is identical to a change in the ancestral effective population size and might be caused by changes in deme size, in the number of demes, or in the migration rate. Expressions for the expected numbers of sites segregating at particular frequencies in a multideme sample are derived. A maximum-likelihood analysis of independent polymorphic restriction sites in humans reveals a decrease in effective size. This is consistent with a change in the rates of migration among human subpopulations from ancient low levels to present high ones.

HIERARCHICAL PATTERNS OF GENETIC POPULATION STRUCTURE IN BLACK RAT SNAKES (ELAPHE OBSOLETA OBSOLETA) AS REVEALED BY MICROSATELLITE DNA ANALYSIS

We investigated the distribution of variation at six microsatellite loci in the black rat snake (Elaphe obsoleta obsoleta). Sampling occurred at three hierarchical scales ranging from communal hibernacula to regional populations, with most locales situated within the Frontenac Axis region of eastern Ontario. We detected no statistically significant pairwise differentiation (F_ST and R_ST ) between hibernacula within the same subpopulations (interhibernaculum distance <6 km). However, isolation-by-distance was evident among locales within the Frontenac Axis (maximum of 50 km) and among regional populations (maximum of 1500 km). Conservative estimates of N_c derived from heterozygosity values ranged from approximately 600 to 2000. These values suggest relatively large genetic neighborhoods encompassing many communal hibernacula. Our results considered together suggest viscosity of gene flow over relatively short distances (tens of kilometers), but substantial genetic exchange among local hibernacula.

Genetic Structure of Cronartium ribicola Populations in Eastern Canada

ABSTRACT The genetic structure of populations of Cronartium ribicola was studied by sampling nine populations from five provinces in eastern Canada and generating DNA profiles using nine random amplified polymorphic DNA markers. Most of the total gene diversity (H(t) = 0.386) was present within populations (H(w) = 0.370), resulting in a low level of genetic differentiation among populations in northeastern North America (F(st) = 0.062). A hierarchical analysis of genetic structure using an analysis of molecular variance (AMOVA) revealed no statistically significant genetic differentiation among provinces or among regions. Yet, genetic differentiation among populations within regions or provinces was small (AMOVA phi(st) = 0.078) but statistically significant (P < 0.001) and was several orders of magnitude larger than differentiation among provinces. This is consistent with a scenario of subpopulations within a metapopulation, in which random drift following migration and new colonization are major evolutionary forces. A phenetic analysis using genetic distances revealed no apparent correlation between genetic distance and the province of origin of the populations. The hypothesis of isolation-by-distance in the eastern populations of C. ribicola was rejected by computing Mantel correlation coefficients between genetic and geographic distance matrices (P > 0.05). These results show that eastern Canadian provinces are part of the same white pine blister rust epidemiological unit. Nursery distribution systems are controlled provincially, with virtually no seedling movement among provinces; therefore, infected nursery material may not play an important role in the dissemination of this disease. Long-distance spore dispersal across provincial boundaries appears to be an epidemiologically important factor for this pathogen.

The peopling of sub-Saharan Africa: the case study of Cameroon

This study analyzes the distribution of ten protein genetic polymorphisms in eighteen populations from the most densely inhabited areas of Cameroon. The languages spoken belong to three different linguistic families [Afro-Asiatic (AA), Nilo-Saharan (NS) and Niger-Kordofanian (NK)]. The analysis of variation of allele frequencies indicates that the level of genetic interpopulation differentiation is rather low (F(st) = 0.011 +/- 0.006) but statistically significant (p < 0.001). This result is not unexpected because of the relatively small geographic area covered by our survey. This value is also significantly lower than the one estimated for other groups of African populations. Among the factors responsible for this, we discuss the possible role of gene flow. There is a considerable genetic differentiation among the AA populations of north Cameroon as is to be expected because they all originated from the first agriculturists of the farming "savanna complex." The Podowko and Uldeme are considerably different from all the other AA groups, probably due to the combined effect of genetic drift and isolation. In the case of the Wandala and Massa, our analyses suggest that genetic admixture with allogeneous groups (especially with the Kanuri) played an important role in determining their genetic differentiation from other AA speaking groups. The Bantu speaking populations (Bakaka, Bamileke Bassa and Ewondo, NK family, Benué Congo subfamily) settled in western and southern Cameroon are more tightly clustered than AA speaking groups. This result shows that the linguistic affinity among these four populations coincides with a substantial genetic similarity despite their different origin. Finally, the Fulbe are genetically distinct from all the populations that belong to their same linguistic phylum (NK), and closer to the neighboring Fali and Tupuri, eastern Adamawa speaking groups of north Cameroon.

The genetic structure of enteric bacteria from Australian mammals

A total of 246 isolates representing five species of the family Enterobacteriaceae, taken from a variety of Australian mammal species, were characterized using multi-locus enzyme electrophoresis. Genome diversity estimates varied significantly among species, with the Klebsiella pneumoniae sample exhibiting the lowest diversity and the Citrobacter freundii sample the highest. Multi-locus linkage disequilibrium estimates revealed that alleles were non-randomly associated in all five species samples, but the magnitude of the estimates differed significantly among species. Escherichia coli had the lowest linkage disequilibrium estimate and Klebisella oxytoca the largest. Molecular analyis of variance was used to determine the extent to which population structure explained the observed genetic variation in a species. Two population levels were defined: the taxonomic family of the host from which the isolate was collected and the geographical locality where the host was collected. The amount of explained variation varied from 0% for K. oxytoca to 22% for K. pneumoniae. Host locality explained a significant amount of the genetic variation in the C. freundii (12%), E. coli (5%), Hafnia alvei (17%) and K. pneumoniae (22%) samples. Host family explained a significant fraction of the variation in E. coli (6%) H. alvei (7%) and K. pneumoniae (20%). Estimates of effective population size for all five species, based on the probability that two randomly chosen isolates will be identical, failed to reveal any relationship between the effective population size and the genetic diversity of a species.

Phylogeography and conservation genetics of the Iowa pleistocene snail

The Iowa Pleistocene snail, Discus macclintocki, is an endangered species that survives only in relictual populations on algific (cold-air) talus slopes in northeast Iowa and northwest Illinois in the central region of the USA. These populations are believed to have been isolated since the temperatures began to warm at the end of the last glacial period around 16 500 years ago. DNA sequencing of the 16s rRNA gene of the mitochondria was used to determine the genetic relationship among 10 populations and the genetic diversity within these populations. Genetic diversity is extremely high within this species with 40 haplotypes spread across the 10 populations sampled within a 4000 km2 region. Phylogenetic analyses showed that haplotypes formed monophyletic groups by the watershed on which they were found, suggesting that watersheds were important historical avenues of gene flow. Genetic distances were strongly related to the geographical distance among all populations, but this relationship was dependent on the scale being considered.

Interethnic genetic differentiation: HLA class I antigens in the population of Mongolia

A total of 1668 individuals representing 10 major Mongolian ethnic groups were serologically typed for HLA-A, -B, and -C antigens. Antigens A2, A24, B61, B51, B58, Cw3, Cw7, and Cw6 were the most frequent specificities in Mongolians and no case of B42 was noted in all ethnic groups. The cluster analysis of Principal Components I and II shows that Mongolian speaking groups form one cluster vs Turkic-speaking Kazakhs. The analysis reveals a low, but significant differentiation of Mongolian ethnic groups as measured by F(ST) = 0.0100 (P < 0.001). Gene diversity analysis shows that the genetic diversity of the Mongolian population can be attributed largely to its ethnic component, which makes up 64% of total genetic variation. The low degree of interpopulation variation and high level of intrapopulation diversity can be explained by the nomadic way of life of this indigenous population. Three-locus haplotypes A24-B61-Cw3, A33-B58-Cw3 are the most common haplotypic associations in Mongolians. The presence of antigens characteristic of Mongoloid, Caucasoid, and Negroid populations in Mongolians suggests a unique genetic background of this indigenous population. The three-locus haplotype distribution among Mongolians relative to other world populations supports the migration of ancient people from Central Asia to the New World, Korean Peninsula, and Southeast Asia. Am. J. Hum. Biol. 11:603-618, 1999. Copyright 1999 Wiley-Liss, Inc.

Gene genealogies in geographically structured populations

Population genetics theory has dealt only with the spatial or geographic pattern of degrees of relatedness or genetic similarity separately for each point in time. However, a frequent goal of experimental studies is to infer migration patterns that occurred in the past or over extended periods of time. To fully understand how a present geographic pattern of genetic variation reflects one in the past, it is necessary to build genealogy models that directly relate the two. For the first time, space-time probabilities of identity by descent and coalescence probabilities are formulated and characterized in this article. Formulations for general migration processes are developed and applied to specific types of systems. The results can be used to determine the level of certainty that genes found in present populations are descended from ancient genes in the same population or nearby populations vs. geographically distant populations. Some parameter combinations result in past populations that are quite distant geographically being essentially as likely to contain ancestors of genes at a given population as the past population located at the same place. This has implications for the geographic point of origin of ancestral, "Eve," genes. The results also form the first model for emerging "space-time" molecular genetic data.

Population genetics of the yellow fever mosquito in Trinidad: comparisons of amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers

Recent development of DNA markers provides powerful tools for population genetic analyses. Amplified fragment length polymorphism (AFLP) markers result from a polymerase chain reaction (PCR)-based DNA fingerprinting technique that can detect multiple restriction fragments in a single polyacrylamide gel, and thus are potentially useful for population genetic studies. Because AFLP markers have to be analysed as dominant loci in order to estimate population genetic diversity and genetic structure parameters, one must assume that dominant (amplified) alleles are identical in state, recessive (unamplified) alleles are identical in state, AFLP fragments segregate according to Mendelian expectations and that the genotypes of an AFLP locus are in Hardy-Weinberg equilibrium (HWE). The HWE assumption is untestable for natural populations using dominant markers. Restriction fragment length polymorphism (RFLP) markers segregate as codominant alleles, and can therefore be used to test the HWE assumption that is critical for analysing AFLP data. This study examined whether the dominant AFLP markers could provide accurate estimates of genetic variability for the Aedes aegypti mosquito populations of Trinidad, West Indies, by comparing genetic structure parameters using AFLP and RFLP markers. For AFLP markers, we tested a total of five primer combinations and scored 137 putative loci. For RFLP, we examined a total of eight mapped markers that provide a broad coverage of mosquito genome. The estimated average heterozygosity with AFLP markers was similar among the populations (0.39), and the observed average heterozygosity with RFLP markers varied from 0.44 to 0.58. The average FST (standardized among-population genetic variance) estimates were 0.033 for AFLP and 0.063 for RFLP markers. The genotypes at several RFLP loci were not in HWE, suggesting that the assumption critical for analysing AFLP data was invalid for some loci of the mosquito populations in Trinidad. Therefore, the results suggest that, compared with dominant molecular markers, codominant DNA markers provide better estimates of population genetic variability, and offer more statistical power for detecting population genetic structure.

Impacts of seed and pollen flow on population genetic structure for plant genomes with three contrasting modes of inheritance

The classical island and one-dimensional stepping-stone models of population genetic structure developed for animal populations are extended to hermaphrodite plant populations to study the behavior of biparentally inherited nuclear genes and organelle genes with paternal and maternal inheritance. By substituting appropriate values for effective population sizes and migration rates of the genes concerned into the classical models, expressions for genetic differentiation and correlation in gene frequency between populations can be derived. For both models, differentiation for maternally inherited genes at migration-drift equilibrium is greater than that for paternally inherited genes, which in turn is greater than that for biparentally inherited nuclear genes. In the stepping-stone model, the change of genetic correlation with distance is influenced by the mode of inheritance of the gene and the relative values of long- and short-distance migration by seed and pollen. In situations where it is possible to measure simultaneously Fst for genes with all three types of inheritance, estimates of the relative rates of pollen to seed flow can be made for both the short- and long-distance components of migration in the stepping-stone model.

Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure

Population genetic theory predicts that plant populations will exhibit internal spatial autocorrelation when propagule flow is restricted, but as an empirical reality, spatial structure is rarely consistent across loci or sites, and is generally weak. A lack of sensitivity in the statistical procedures may explain the discrepancy. Most work to date, based on allozymes, has involved pattern analysis for individual alleles, but new PCR-based genetic markers are coming into vogue, with vastly increased numbers of alleles. The field is badly in need of an explicitly multivariate approach to autocorrelation analysis, and our purpose here is to introduce a new approach that is applicable to multiallelic codominant, multilocus arrays. The procedure treats the genetic data set as a whole, strengthening the spatial signal and reducing the stochastic (allele-to-allele, and locus-to-locus) noise. We (i) develop a very general multivariate method, based on genetic distance methods, (ii) illustrate it for multiallelic codominant loci, and (iii) provide nonparametric permutational testing procedures for the full correlogram. We illustrate the new method with an example data set from the orchid Caladenia tentaculata, for which we show (iv) how the multivariate treatment compares with the single-allele treatment, (v) that intermediate frequency alleles from highly polymorphic loci perform well and rare alleles poorly, (vi) that a multilocus treatment provides clearer answers than separate single-locus treatments, and (vii) that weighting alleles differentially improves our resolution minimally. The results, though specific to Caladenia, offer encouragement for wider application.

Population structure and gene flow of the brazilian shrub helicteres brevispira

Helicteres brevispira is a pioneer species of the tropical riparian forest whose populations appear to cycle through episodes of extinction and recolonization. Therefore, genetic consequences of founding events may strongly affect the genetic structure of its populations. An analysis of F-statistics showed that the studied population of H. brevispira is genetically substructured with the highest values of FST found in areas of high plant densities. Spatial autocorrelation analysis showed that genetic patches have diameters of 3-6 m. Although pollinator movements are usually between plants which are 3-6 m apart, longer flights occur and the neighbourhood area is estimated to have a diameter of 15 m. This suggests that genetic patches are smaller than the neighbourhood area. Seed dispersal is limited, mostly less than 2 m from the mother plants. Thus, short seed dispersal, seed dormancy and founder effects in the seed bank may be the most important determinants of genetic structure in populations of H. brevispira. Factors such as drift and inbreeding may also increase the level of substructure in this population, but the equilibrium model of isolation by distance does not fit our data.

Major histocompatibility complex differentiation in Sacramento River chinook salmon

The chinook salmon of the Sacramento River, California, have been reduced to a fraction of their former abundance because of human impact and use of the river system. Here we examine the genetic variation at a major histocompatibility complex class II exon in the four Sacramento chinook salmon runs. Examination of the alleles found in these and other chinook salmon revealed nucleotide patterns consistent with selection for amino acid replacement at the putative antigen-binding sites. We found a significant amount of variation in each of the runs, including the federally endangered winter run. All of the samples were in Hardy-Weinberg proportions. A significant amount of genetic differentiation between runs was revealed by several measures of differentiation. Winter run was the most genetically divergent, while the spring, late-fall, and fall runs were less differentiated.

Allelic association between marker loci

Allelic association has proven useful to refine the location of major genes prior to positional cloning, but it is of uncertain value for genome scans in complex inheritance. We have extended kinship theory to give information content for linkage and allelic association. Application to pairs of closely linked markers as a surrogate for marker x oligogene pairs indicates that association is largely determined by regional founders, with little effect of subsequent demography. Sub-Saharan Africa has the least allelic association, consistent with settlement of other regions by small numbers of founders. Recent speculation about substantial advantages of isolates over large populations, of constant size over expansion, and of F1 hybrids over incrosses is not supported by theory or data. On the contrary, fewer affected cases, less opportunity for replication, and more stochastic variation tend to make isolates less informative for allelic association, as they are for linkage.