ISOLATION BY DISTANCE

Invasion of vacant niches and subsequent sympatric speciation

An individual-based simulation study was conducted to examine the population dynamics of 'invasion of a vacant niche' and subsequent speciation (by reproductive isolation) when food resources are randomly distributed spatially within the habitat and the frequencies of different food types are bimodally distributed (i.e. smaller and larger sizes of food being most abundant). The initially vacant niche was that of unused larger sizes of food. When phenotypic variation for resource use (i.e. food sizes) was small in the initial population, and each female could choose a mate from anywhere in the habitat, the population could not invade the vacant niche. But when the dispersal distance of the offspring and the area within which a female could choose a mate were small (i.e. the genetic neighbourhood size was small), the population could, in most cases, evolve to use both smaller and larger food sizes and form sister species sympatrically, with each species utilizing one of the two niches (small and large sizes of food). When phenotypic variation in resource use in the initial population was large, the population could, in most cases, invade the vacant niche by evolving to use both smaller and larger sizes of food. The probability of speciation increased as the dispersal distance of offspring decreased. The results indicate that populations whose individuals have small Wright's genetic neighbourhoods may often exploit a vacant niche and diversify sympatrically in the process.

Patterns of genetic and phenotypic variation in Iris haynei and I. atrofusca (Iris sect. Oncocyclus = the royal irises) along an ecogeographical gradient in Israel and the West Bank

Iris haynei and I. atrofusca are two closely related narrow endemics distributed vicariously along an ecogeographical north-south gradient in Israel and the West Bank. To obtain baseline information of the taxonomic status, conservation and population history of these taxa, we investigated patterns of phenotypic variation and the partitioning of genetic variation within and among populations using dominant random amplified polymorphic DNA (RAPD) markers. Multivariate (principal components analysis) and taxonomic distance analyses based on morphometric traits from eight populations revealed no unambiguous separation into two distinct groups. Results of genetic analyses for nine populations differed only slightly when either allele- or marker-based approaches were employed. Mean within-population diversity was high (0.258 for Nei's expected heterozygosity), but there was no significant relationship between genetic diversity and either population size or latitude. Although the range-wide estimate of GST ( approximately 0.20) revealed relatively high differentiation among populations this value was inflated because of a small, but significant, component of molecular variance among regions viz. taxa ( approximately 5%). Limited long-distance dispersal capabilities in conjunction with a linearized habitat distribution are proposed to contribute to the approximate isolation by distance pattern observed. It also appears that extant populations are currently deviating from equilibrium conditions because of primary divergence of a formerly more widespread ancestral population. Given the absence of deep genetic and phenotypic subdivision among northern (I. haynei) vs. central/southern (I. atrofusca) populations, we argue for a revision of their species status. Nonetheless, we recommend conservation attention to these geographically differentiated segments as separate management units, which can be seen as an instructive example of incipient species formation.

Pollen pool heterogeneity in shortleaf pine,Pinus echinataMill

Pollen is the dominant vector of gamete exchange for most temperate tree species. Because pollen movement influences the creation, maintenance and erosion of genetic structure in adult populations, it is important to understand what factors influence the process of pollen movement. Isolation by distance in pollen donor populations can create highly structured pollen polls by increased sampling of local fathers. Extrinsic factors, such as the intervening vegetative structure and local pollen donor densities, can also influence the genetic composition of local pollen pools. Using paternally inherited chloroplast microsatellite markers, we examined the structure and diversity of pollen pools in Pinus echinata Mill. in southern Missouri, USA. Our analysis is based on a multivariate AMOVA analysis of stands ( approximately 1 ha; six per region) nested within regions (approximately 800 ha; four each). Significant multilocus structure of the pollen pool within regions (phiSR = 0.095), but not among regions (phiRT = 0.010), indicates that pollen movement is relatively restricted. Furthermore, the significant correlation between pairwise genetic and physical distances (Mantel correlation; rho = 0.32) provided support for the isolation by distance hypothesis. Our results indicated that availability of pollen donors did not affect diversity of the pollen pool, measured by the number of unique multilocus genotypes at each stand. However, pollen pool diversity was negatively associated with vegetative structure, measured as total forest tree density. Our findings indicated that on-going pollen movement within continuous forest is relatively restricted as a result of both isolation by distance and vegetative structure.

Estimating the unbiased estimator theta for population genetic survey data

We consider a method of approximating Weir and Cockerham's theta, an unbiased estimator of genetic population structure, using values readily available from published studies using biased estimators (Wright's F(ST) or Nei's G(ST)). The estimation algorithm is shown to be useful for both model populations and real-world avian populations. However, the correlation between Wright's F(ST) and Weir and Cockerham's theta is strong when compared among 39 empirical avian datasets. Thus, the advantage of approximating an unbiased estimator is unclear considering the small actual effect of theta's bias-removing power on empirical datasets.

The discovery of single-nucleotide polymorphisms--and inferences about human demographic history

A method of historical inference that accounts for ascertainment bias is developed and applied to single-nucleotide polymorphism (SNP) data in humans. The data consist of 84 short fragments of the genome that were selected, from three recent SNP surveys, to contain at least two polymorphisms in their respective ascertainment samples and that were then fully resequenced in 47 globally distributed individuals. Ascertainment bias is the deviation, from what would be observed in a random sample, caused either by discovery of polymorphisms in small samples or by locus selection based on levels or patterns of polymorphism. The three SNP surveys from which the present data were derived differ both in their protocols for ascertainment and in the size of the samples used for discovery. We implemented a Monte Carlo maximum-likelihood method to fit a subdivided-population model that includes a possible change in effective size at some time in the past. Incorrectly assuming that ascertainment bias does not exist causes errors in inference, affecting both estimates of migration rates and historical changes in size. Migration rates are overestimated when ascertainment bias is ignored. However, the direction of error in inferences about changes in effective population size (whether the population is inferred to be shrinking or growing) depends on whether either the numbers of SNPs per fragment or the SNP-allele frequencies are analyzed. We use the abbreviation "SDL," for "SNP-discovered locus," in recognition of the genomic-discovery context of SNPs. When ascertainment bias is modeled fully, both the number of SNPs per SDL and their allele frequencies support a scenario of growth in effective size in the context of a subdivided population. If subdivision is ignored, however, the hypothesis of constant effective population size cannot be rejected. An important conclusion of this work is that, in demographic or other studies, SNP data are useful only to the extent that their ascertainment can be modeled.

Determinants of effective population size for loci with different modes of inheritance

Here we report an assessment of the determinants of effective population size (N(e)) in species with overlapping generations. Specifically, we used a stochastic demographic model to investigate the influence of different life-history variables on N(e)/N (where N = population census number) and the influence of sex differences in life-history variables on N(e) for loci with different modes of inheritance. We applied an individual-based modeling approach to two datasets: one from a natural population of savannah baboons (Papio cynocephalus) in the Amboseli basin of southern Kenya and one from a human tribal population (the Gainj of Papua New Guinea). Simulation-based estimates of N(e)/N averaged 0.329 for the Amboseli baboon population (SD = 0.116, 95% CI = 0.172 - 0.537) and 0.786 for the Gainj (SD = 0.184, 95% CI = 0.498 - 1.115). Although variance in male fitness had a substantial impact on N(e)/N in each of the two primate populations, ratios of N(e) values for autosomal and sex-linked loci exhibited no significant departures from Poisson-expected values. In each case, similarities in sex-specific N(e) values were attributable to the unexpectedly high variance in female fitness. Variance in male fitness resulted primarily from age-dependent variance in reproductive success, whereas variance in female fitness resulted primarily from stochastic variance in survival during the reproductive phase.

Gene genealogies in a metapopulation

A simple genealogical process is found for samples from a metapopulation, which is a population that is subdivided into a large number of demes, each of which is subject to extinction and recolonization and receives migrants from other demes. As in the migration-only models studied previously, the genealogy of any sample includes two phases: a brief sample-size adjustment followed by a coalescent process that dominates the history. This result will hold for metapopulations that are composed of a large number of demes. It is robust to the details of population structure, as long as the number of possible source demes of migrants and colonists for each deme is large. Analytic predictions about levels of genetic variation are possible, and results for average numbers of pairwise differences within and between demes are given. Further analysis of the expected number of segregating sites in a sample from a single deme illustrates some previously known differences between migration and extinction/recolonization. The ancestral process is also amenable to computer simulation. Simulation results show that migration and extinction/recolonization have very different effects on the site-frequency distribution in a sample from a single deme. Migration can cause a U-shaped site-frequency distribution, which is qualitatively similar to the pattern reported recently for positive selection. Extinction and recolonization, in contrast, can produce a mode in the site-frequency distribution at intermediate frequencies, even in a sample from a single deme.

Craniometric variation and the settlement of the Americas: testing hypotheses by means of R-matrix and matrix correlation analyses

New archaeological findings and the incorporation of new South American skull samples have raised fundamental questions for the classical theories of the Americas' settlement. The aim of this study was to estimate craniometric variability among several Asian and Native American populations in order to test goodness of fit of the data to different models of ancient population entries and dispersions into the New World. Our data set includes Howells' variables recorded on East Asian, North American, and South American natives (except for Na-Dene speakers). Five Fuego-Patagonian samples and one Paleoamerican sample were also included. A multivariate extension of the R-matrix method for quantitative traits was used to obtain Fst values, which were considered estimations of intergroup variation. Three main models for the peopling of the New World were represented in hypothetical design matrices. Matrix permutation tests were performed to quantify the fit of the observed data with 1) geographical separation of the samples and 2) three ways of settlement, which were the Three Migration Model (TMM), the Single Wave Migration model (SWM), and the Two Components Settlement Model (TCS). R-matrix results showed high levels of heterogeneity among Native Americans. Matrix permutation analyses suggested that the model involving high Amerindian heterogeneity and two different morphological patterns or components (derived "Mongoloid" vs. generalized "non-Mongoloid") explains better the variation observed, even when the effects of geographical separation are removed. Whether these patterns arose as a result of two separate migration events or by local evolution from Paleoamericans to Amerindians remains unresolved.

Using Restriction Fragment Length Polymorphisms to Assess Temporal Variation and Estimate the Number of Ascospores that Initiate Epidemics in Field Populations of Mycosphaerella graminicola

ABSTRACT Restriction fragment length polymorphisms (RFLPs) and DNA fingerprints were used to assess temporal variation and estimate the effective population size of the wheat pathogen Mycosphaerella graminicola over a 6-year period. In each year, the fungal population was founded by ascospores originating from outside the sampled fields. A total of 605 fungal isolates were included in this study. Our results indicate that the genetic structure of these M. graminicola populations were stable over the 6-year period. The common alleles at each RFLP locus were present at similar frequencies each year. More than 99% of gene diversity was distributed within populations sampled from the same year and less than 1% was attributed to differences among years. The lack of population differentiation among collections taken in different years indicated that the effective size of the source population was sufficiently large that genetic drift was insignificant in this location. It also suggests that the initial colonists from ascospore founder populations were a fair reflection of the source population. We estimate that the effective sizes of these field populations ranged from 3,400 to 700,000 individuals, depending on the size of the field sampled and assumptions about mutation rates. Estimates of the number of ascospores initiating epidemics of leaf blotch disease in each field plot and factors that contribute to the large effective population size of M. graminicola are discussed.

Paternal population history of East Asia: sources, patterns, and microevolutionary processes

Asia has served as a focal point for human migration during much of the Late Pleistocene and Holocene. Clarification of East Asia's role as a source and/or transit point for human dispersals requires that this region's own settlement history be understood. To this end, we examined variation at 52 polymorphic sites on the nonrecombining portion of the Y chromosome (NRY) in 1,383 unrelated males, representing 25 populations from southern East Asia (SEAS), northern East Asia (NEAS), and central Asia (CAS). The polymorphisms defined 45 global haplogroups, 28 of which were present in these three regions. Although heterozygosity levels were similar in all three regions, the average pairwise difference among haplogroups was noticeably smaller in SEAS. Multidimensional scaling analysis indicated a general separation of SEAS versus NEAS and CAS populations, and analysis of molecular variance produced very different values of Phi(ST) in NEAS and SEAS populations. In spatial autocorrelation analyses, the overall correlogram exhibited a clinal pattern; however, the NEAS populations showed evidence of both isolation by distance and ancient clines, whereas there was no evidence of structure in SEAS populations. Nested cladistic analysis demonstrated that population history events and ongoing demographic processes both contributed to the contrasting patterns of NRY variation in NEAS and SEAS. We conclude that the peopling of East Asia was more complex than earlier models had proposed-that is, a multilayered, multidirectional, and multidisciplinary framework is necessary. For instance, in addition to the previously recognized genetic and dental dispersal signals from SEAS to NEAS populations, CAS has made a significant contribution to the contemporary gene pool of NEAS, and the Sino-Tibetan expansion has left traces of a genetic trail from northern to southern China.

Habitat structure and population persistence in an experimental community

Understanding spatial population dynamics is fundamental for many questions in ecology and conservation. Many theoretical mechanisms have been proposed whereby spatial structure can promote population persistence, in particular for exploiter-victim systems (host-parasite/pathogen, predator-prey) whose interactions are inherently oscillatory and therefore prone to extinction of local populations. Experiments have confirmed that spatial structure can extend persistence, but it has rarely been possible to identify the specific mechanisms involved. Here we use a model-based approach to identify the effects of spatial population processes in experimental systems of bean plants (Phaseolus lunatus), herbivorous mites (Tetranychus urticae) and predatory mites (Phytoseiulus persimilis). On isolated plants, and in a spatially undivided experimental system of 90 plants, prey and predator populations collapsed; however, introducing habitat structure allowed long-term persistence. Using mechanistic models, we determine that spatial population structure did not contribute to persistence, and spatially explicit models are not needed. Rather, habitat structure reduced the success of predators at locating prey outbreaks, allowing between-plant asynchrony of local population cycles due to random colonization events.

Field and allozyme studies investigating optimal mating success in two sympatric spring-ephemeral plants, Trillium erectum and T. grandiflorum

A combination of field experiments and allozyme studies was used to test whether two spring-ephemeral plants growing in eastern North America, Trillium erectum and T. grandiflorum (Liliaceae), exhibited an optimal outcrossing distance for fruit and seed production. Furthermore, the spatial genetic structure of the Trillium populations was examined in light of the outcrossing results. In field experiments, recipient plants were pollinated with either self pollen or with pollen from donors growing 1 m, 10 m, 100 m, and 1500 m away. These distances represented crosses between individuals growing within the same population (1 m, 10 m, and 100 m crosses) and between individuals growing in different populations (1500 m crosses). Self-pollinated T. erectum and T. grandiflorum produced 71% and 89% fewer seeds, respectively, than all other outcrossing treatments. However, there were no significant differences among outcrossing treatments for fruit or seed production. As neither T. erectum nor T. grandiflorum exhibited an optimal outcrossing distance for fruit or seed production, it was predicted that populations of the two would not demonstrate strong spatial genetic structure or isolation by distance. The allozyme results only partially supported the patterns revealed in the outcrossing treatments. Populations of T. erectum and T. grandiflorum showed moderate spatial genetic differentiation based on F-statistics, and only T. grandiflorum exhibited significant isolation by distance based on spatial autocorrelation analyses. The lack of optimal outcrossing distances and the patterns of allozyme variation in T. erectum and T. grandiflorum populations may be attributed to a number of factors, including active seed dispersal by ants, rare long-distance gene-flow events, post-pollination and post-fertilization selection, and/or the severity of inbreeding depression.

Genetic evidence for mixed origin of recolonized sea trout populations

Anadromous brown trout along the Norwegian Skagerrak coast are genetically differentiated among streams, and there are indications of further substructuring within some streams. Among presumably long-standing populations there is a pattern of increased genetic differentiation with distance, indicating an isolation-by-distance effect. For trout that inhabit streams that have recently been recolonized after the extinction of trout because of acidification, we find evidence for a mixed origin of the recolonizing trout. Both the high levels of gametic phase disequilibrium and the clear deviation from the general pattern of increased genetic differentiation with distance that are seen in recolonized streams, are consistent with recent population admixture, and confirm the loss of the original populations of these acid streams.

Mating system and genetic variance in a polygynous mustelid, the European polecat

The population genetic implications of mating system were investigated in European polecat Mustela putorius populations from western France, combining radiotracking survey and allozyme variation analysis. Mating period occurred from February to June and polecats showed a strategy of successive polygyny, a male consorting with 1.44 females during a brief period (2.9 days). Relatedness was largely sex biased, females (21%) being almost twice more related than males (13%) suggesting a natal philopatry. Nonetheless, breeding dispersal pattern appeared relatively complex. Males were the sex dispersing but the main strategy for male polecats consisted of short-term mating excursions in adjacent females ranges whereas long-distance dispersal only constituted an alternative breeding strategy. Despite their allozymic polymorphism level reaching 24% at p<0.05 for 38 scored loci, populations showed a high heterozygote deficiency as revealed by the F(IS) index averaging F(IS) = 0.383. Thus the mating system of such solitary mustelids may be poorly efficient to prevent inbreeding within populations.

"Neighbourhood" size, dispersal and density estimates in the prickly forest skink (Gnypetoscincus queenslandiae) using individual genetic and demographic methods

Dispersal, or the amount of dispersion between an individual's birthplace and that of its offspring, is of great importance in population biology, behavioural ecology and conservation, however, obtaining direct estimates from field data on natural populations can be problematic. The prickly forest skink, Gnypetoscincus queenslandiae, is a rainforest endemic skink from the wet tropics of Australia. Because of its log-dwelling habits and lack of definite nesting sites, a demographic estimate of dispersal distance is difficult to obtain. Neighbourhood size, defined as 4piDsigma2 (where D is the population density and sigma2 the mean axial squared parent-offspring dispersal rate), dispersal and density were estimated directly and indirectly for this species using mark-recapture and microsatellite data, respectively, on lizards captured at a local geographical scale of 3 ha. Mark-recapture data gave a dispersal rate of 843 m2/generation (assuming a generation time of 6.5 years), a time-scaled density of 13 635 individuals * generation/km2 and, hence, a neighbourhood size of 144 individuals. A genetic method based on the multilocus (10 loci) microsatellite genotypes of individuals and their geographical location indicated that there is a significant isolation by distance pattern, and gave a neighbourhood size of 69 individuals, with a 95% confidence interval between 48 and 184. This translates into a dispersal rate of 404 m2/generation when using the mark-recapture density estimation, or an estimate of time-scaled population density of 6520 individuals * generation/km2 when using the mark-recapture dispersal rate estimate. The relationship between the two categories of neighbourhood size, dispersal and density estimates and reasons for any disparities are discussed.

Stable two-allele polymorphisms maintained by fluctuating fitnesses and seed banks: protecting the blues in Linanthus parryae

Motivated by data demonstrating fluctuating relative and absolute fitnesses for white- versus blue-flowered morphs of the desert annual Linanthus parryae, we present conditions under which temporally fluctuating selection and fluctuating contributions to a persistent seed bank will maintain a stable single-locus polymorphism. In L. parryae, blue flower color is determined by a single dominant allele. To disentangle the underlying diversity-maintaining mechanism from the mathematical complications associated with departures from Hardy-Weinberg genotype frequencies and dominance, we successively analyze a haploid model, a diploid model with three distinguishable genotypes, and a diploid model with complete dominance. For each model, we present conditions for the maintenance of a stable polymorphism, then use a diffusion approximation to describe the long-term fluctuations associated with these polymorphisms. Our protected polymorphism analyses show that a genotype whose arithmetic and geometric mean relative fitnesses are both less than one can persist if its relative fitness exceeds one in years that produce the most offspring. This condition is met by data from a population of L. parryae whose white morph has higher fitness (seed set) only in years of relatively heavy rain fall. The data suggest that the observed polymorphism may be explained by fluctuating selection. However, the yearly variation in flower color frequencies cannot be fully explained by our simple models, which ignore age structure and possible selection in the seed bank. We address two additional questions--one mathematical, the other biological--concerning the applicability of diffusion approximations to intense selection and the applicability of long-term predictions to datasets spanning decades for populations with long-lived seed banks.

Microsatellite variation in the yellowhammer Emberiza citrinella: population structure of a declining farmland bird

In recent years, there has been much concern in the UK about population declines of widespread species in agricultural habitats. Conservation-orientated research on declining birds has focused on vital rates of survival and productivity. However, the environmental factors which may influence movements between populations of widespread species is poorly understood. Population genetic structure is an indirect description of dispersal between groups of individuals. To attempt to develop an understanding of genetic structuring in a widespread, but declining, farmland bird, we therefore investigated the yellowhammer, Emberiza citrinella, population in England and Wales using microsatellite data. Our first aim was to investigate whether there was genetic substructuring in the population. A second aim was to investigate if there was a relationship between genetic distances and various environmental variables. Finally, we analysed the microsatellite data for evidence of loss of genetic variation due to population decline. Our data showed a slight but significant structure within the yellowhammer population. This therefore cannot be considered a panmictic population. Our example from South Cumbria implies that high-altitude barriers may have a slight influence on population structure. However, on the whole, genetic distances between sample sites were not significantly correlated with geographical distances, degrees of population connectivity, high altitudes, or differences in precipitation between sites. Finally, we detected departures from mutation-drift equilibrium (excess heterozygosity), which is indicative of a loss of genetic variation through recent decline.

Perspective: Evolution of flower color in the desert annual Linanthus parryae: Wright revisited

Linanthus parryae, a diminutive desert annual with white or blue flowers, has been the focus of a long-standing debate among evolutionary biologists. At issue is whether the flower color polymorphism in this species is the product of random genetic drift, as Sewall Wright argued, or of natural selection, as proposed by Carl Epling and his colleagues. Our long-term studies of three polymorphic populations in the Mojave Desert demonstrate that flower color is subject to selection that varies in both time and space in its direction and magnitude. For all sites taken together, blue-flowered plants produced more seeds than white-flowered plants in years of relatively low seed production, whereas white-flowered plants had higher fitness in years of high seed production. Evidence of selection on flower color was found in two of the three study sites. Differences in fitness between the color morphs were sometimes large, with selection coefficients as high as 0.60 in some years. Our longest period of observations was at Pearblossom site 1, where plants reached appreciable densities in seven of the 11 years of study. Here we found significant differences in the seed production of the color morphs in six years, with three years of blue advantage and three years of white advantage. For all sites taken together, total spring precipitation (March and April) was positively correlated with both absolute and relative seed production of the color morphs. At Pearblossom site 1, blue-flowered plants typically had a fitness advantage in years of low spring precipitation, whereas white-flowered plants had a fitness advantage in years of high spring precipitation. This temporal variation in selection may contribute to the maintenance of the flower-color polymorphism at Pearblossom site 1, whereas gene flow from neighboring populations is proposed as the principal factor maintaining the polymorphism at the other study sites. We found no significant differences between the color morphs in pollinator visitation rate or in their carbon isotope ratio, a measure of water-use efficiency. Although the mechanism of selection remains elusive, our results refute Wright's conclusion that the flower color polymorphism in L. parryae is an example of isolation by distance, a key component of his shifting balance theory of evolution.

Fine-scale genetic structure in Pinus clausa (Pinaceae) populations: effects of disturbance history

Spatial autocorrelation analyses of 12 allozyme loci were used to compare genetic structure within populations of two varieties of Pinus clausa. P. clausa var. immuginata populations tend to be uneven-aged, with continuous recruitment in small gaps created by wind damage, whereas P. clausa var. clausa populations are more even-aged, with recruitment postdating periodic canopy fires. Three var. immuginata populations and three matched pairs of var. clausa populations, including both a mature and a nearby recently burned population, were examined. Aggregation of multilocus genotypes at small distances was evident in all young var. clausa populations. Little inbreeding was apparent among juveniles or adults in these populations; their genetic structure is likely to have resulted from limited seed dispersal. Genotypes were not significantly spatially structured in nearby matched mature populations. Genetic structure was less evident in var. immuginata populations. Aggregated genotypes were only apparent in the population where patches included juveniles of similar ages; dense juvenile clumps in the other two var. immuginata populations comprised a variety of ages. Interannual variability in allele frequencies of surviving seedlings may account for the absence of genetic structure in these populations.

Genetic differentiation in South Amerindians is related to environmental and cultural diversity: evidence from the Y chromosome

The geographic structure of Y-chromosome variability has been analyzed in native populations of South America, through use of the high-frequency Native American haplogroup defined by the DYS199-T allele and six Y-chromosome-linked microsatellites (DYS19, DYS389A, DYS389B, DYS390, DYS391, and DYS393), analyzed in 236 individuals. The following pattern of within- and among-population variability emerges from the analysis of microsatellite data: (1) the Andean populations exhibit significantly higher levels of within-population variability than do the eastern populations of South America; (2) the spatial-autocorrelation analysis suggests a significant geographic structure of Y-chromosome genetic variability in South America, although a typical evolutionary pattern could not be categorically identified; and (3) genetic-distance analyses and the analysis of molecular variance suggest greater homogeneity between Andean populations than between non-Andean ones. On the basis of these results, we propose a model for the evolution of the male lineages of South Amerindians that involves differential patterns of genetic drift and gene flow. In the western part of the continent, which is associated with the Andean area, populations have relatively large effective sizes and gene-flow levels among them, which has created a trend toward homogenization of the gene pool. On the other hand, eastern populations-settled in the Amazonian region, the central Brazilian plateau, and the Chaco region-have exhibited higher rates of genetic drift and lower levels of gene flow, with a resulting trend toward genetic differentiation. This model is consistent with the linguistic and cultural diversity of South Amerindians, the environmental heterogeneity of the continent, and the available paleoecological data.

Genetic consequences of polygyny and social structure in an Indian fruit bat, Cynopterus sphinx. I. Inbreeding, outbreeding, and population subdivision

Population subdivision into behaviorally cohesive kin groups influences rates of inbreeding and genetic drift and has important implications for the evolution of social behavior. Here we report the results of a study designed to test the hypothesis that harem social structure promotes inbreeding and genetic subdivision in a population with overlapping generations. Genetic consequences of harem social structure were investigated in a natural population of a highly polygynous fruit bat, Cynopterus sphinx (Chiroptera: Pteropodidae), in western India. The partitioning of genetic variance within and among breeding groups was assessed using 10-locus microsatellite genotypes for 431 individually marked bats. Genetic analysis of the C. sphinx study population was integrated with field data on demography and social structure to determine the specific ways in which mating, dispersal, and new social group formation influenced population genetic structure. Microsatellite data revealed striking contrasts in genetic structure between consecutive offspring cohorts and between generations. Relative to the 1998 (dry-season) offspring cohort, the 1997 (wet-season) cohort was characterized by a more extensive degree of within-group heterozygote excess (F(IS) = -0.164 vs. -0.050), a greater degree of among-group subdivision (F(ST) = 0.123 vs. 0.008), and higher average within-group relatedness (r = 0.251 vs. 0.017). Differences in genetic structure between the two offspring cohorts were attributable to seasonal differences in the number and proportional representation of male parents. Relative to adult age-classes, offspring cohorts were characterized by more extensive departures from allelic and genotypic equilibria and a greater degree of genetic subdivision. Generational differences in F-statistics indicated that genetic structuring of offspring cohorts was randomized by natal dispersal prior to recruitment into the breeding population. Low relatedness among harem females (r = 0.002-0.005) was primarily attributable to high rates of natal dispersal and low rates of juvenile survivorship. Kin selection is therefore an unlikely explanation for the formation and maintenance of behaviorally cohesive breeding groups in this highly social mammal.

Population subdivision in marine environments: the contributions of biogeography, geographical distance and discontinuous habitat to genetic differentiation in a blennioid fish, Axoclinus nigricaudus

The relative importance of factors that may promote genetic differentiation in marine organisms is largely unknown. Here, contributions to population structure from a biogeographic boundary, geographical distance and the distribution of suitable habitat were investigated in Axoclinus nigricaudus, a small subtidal rock-reef fish, throughout its range in the Gulf of California. A 408-bp fragment of the mitochondrial control region was sequenced from 105 individuals. Variation was significantly partitioned between 28 of 36 possible combinations of population pairs. Phylogenetic analyses, hierarchical analyses of variance and a modified Mantel test substantiated a major break between two putative biogeographic regions. This genetic discontinuity coincides with an abrupt change in ecological characteristics, including temperature and salinity, but does not coincide with known oceanographic circulation patterns or any known historic barriers. There was an overall relationship of increasing genetic distance with increasing geographical distance between population pairs, in a manner consistent with isolation-by-distance. A significant habitat-by-geographical-distance interaction term indicated that, for a given geographical distance, populations separated by discontinuous habitat (sand) are more distinct genetically than are populations separated by continuous habitat (rock). In addition, populations separated by deep open waters were more genetically distinct than populations separated by continuous habitat (rock). These results indicate that levels of genetic differentiation among populations of A. nigricaudus cannot be explained by a single factor, but are due to the combined influences of biogeography, geographical distance and availability of suitable habitat.

Spatial patterns of genetic diversity in Posidonia oceanica, an endemic Mediterranean seagrass

Posidonia oceanica is an endemic seagrass species in the Mediterranean Sea. In order to assess levels of genetic structure in this species, the microsatellite polymorphism was analysed from meadows collected in several localities, along the coasts of the Tyrrhenian Sea (Mediterranean Sea). The existence of single population units and the recruitment of seedlings collected in some localities were investigated. Moreover, genetic structure at different spatial scales and biogeographic relationships among populations were also assessed. Our analysis showed the existence of clear patterns of genetic structure in P. oceanica in the area considered in the analysis. P. oceanica, in fact, is present in separate meadows that represent discrete populations, characterized by low genetic diversity. Comparable levels of genetic variability between mature meadows and seedlings were found. Patterns of genetic relatedness among populations seem to be in accord with direction of dominant current flux in the whole area, separating South Tyrrhenian from North Tyrrhenian populations. Moderate levels of gene flow between populations and genetic substructure within populations, together with the finding of the limited role of sexual reproduction in increasing genetic variability, should be a cause for concern for the persistence of this essential resource in the Mediterranean basin.

Population structure and dispersal in the Canary Island caddisfly Mesophylax aspersus (Trichoptera, Limnephilidae)

Population genetic structure of the circum-Mediterranean caddisfly Mesophylax aspersus (Trichoptera, Limnephilidae) on the Canary Islands was investigated by studying allozyme variation at nine putative loci in five populations. Genetic variability, population structure and gene flow were compared with data in the literature for continental taxa to assess the effect of isolation of island populations on the genetic structure. Larvae were collected from streams on the islands of Tenerife (one population), La Gomera (two populations in the same catchment) and La Palma (two populations in different catchments). Genetic variability within populations was high relative to that recorded previously for continental Trichoptera, e.g. mean heterozygosity was 0.119--0.336 (0.035--0.15 in continental taxa). Highly significant population structuring was observed (mean F(ST)=0.250), and there was significant within-population structuring (mean F(IS)=0.098). Populations from the same catchment or island were no more similar than populations from different islands, which suggests that occasional long-distance dispersal, both between and within islands, is the predominant influence on the population structure. This dispersal ability has contributed to the colonization of most permanent streams on the Canary Islands by M. aspersus.

Partnership

Individuals are called partners when it is in their best interest to help each other, if by doing so they increase the probability of being together in the future when, for similar reasons, they will continue to help each other. Kinsmen or individuals who often face (hedonic) situations in which helping is the dominating strategy are committed to help each other. Partnership may develop among them since the loss of the other means the loss of a guaranteed helper. Thus, they may be willing to take additional risks to help each other. Partnership may occur among unrelated individuals and with no hedonic situations. Partnership creates bonds between partners which may be much stronger than those between kinsmen; an individual may take more risks for his partner than he will ever take for a kin. Partnership may evolve without the sophistication and memory required for reciprocation altruism. Although kin selection, partnership and reciprocation are likely to appear fused as the causes for altruism, we argue that it may be possible to distinguish between them in some situations. We show that as the partners get older partnership may become less important to them. We also show that like cooperation, and for analogous reasons, malice may evolve among partners so that each will be willing to take additional risks in order to eliminate the other.

Temporal changes in allele frequency, genetic variation and inbreeding depression in small populations of the guppy, Poecilia reticulata

We established three closed lines of N = 10 for the guppy Poecilia reticulata, to evaluate the relationships among temporal changes in allele frequency, genetic variation and inbreeding depression for a fitness-related trait in small populations. Genetic variation at the allozyme loci, expressed by the proportion of polymorphic loci, number of alleles per locus and heterozygosity, decreased somewhat in two closed lines but it increased in one closed line over six generations. Effective population size (Ne) at each generation was estimated from the standardized variance in the allele frequencies. The average Ne was 24.4, 10.3 and 10.0 in the three closed lines. The inbreeding coefficient calculated from the Ne increased to 0.186, 0.321 and 0.414, respectively. As an index of the amount of inbreeding depression, changes in salinity tolerance were examined, because this trait is strongly sensitive to inbreeding depression and decreases linearly with an increase in inbreeding coefficient. The mean value of the salinity tolerance significantly decreased to 82.5%, 71.7% and 67.6% in the three closed lines during the six generations, suggesting inbreeding depression for salinity tolerance. Although a significant correlation was not observed between the amount of inbreeding depression and the genetic variation, the amount of inbreeding depression correlated with the inbreeding coefficient calculated from Ne. The regression line indicated an 8.4% decrease in the mean per 10% increase in the inbreeding coefficient and was similar to that obtained directly from full-sib matings. These results indicate that the temporal changes in the allele frequencies can provide an estimation of the amount of inbreeding depression during successive generations in small populations.

Testing multiregionality of modern human origins

In order to examine the possibility of multiple founding populations of anatomically modern Homo sapiens, we collected DNA sequence data from 10 X-chromosomal regions, 5 autosomal regions, and 1 Y-chromosomal region, in addition to mitochondrial DNA. Except for five regions which are genealogically uninformative and two other regions for which chimpanzee orthologs are not available, the ancestral sequence and population for each of the remaining regions were successfully inferred. Of these 10 ancestral sequences, 9 occurred in Africa and only 1 occurred in Asia during the Pleistocene. Computer simulation was carried out to quantify the multiregional hypothesis based solely on the premise that there was more than one founding population in the Pleistocene. Allowing the breeding size to vary among the founding populations, the hypothesis may account for the observed African ancestry in 90% of the genomic regions. However, it is required that the founding population in Africa was much larger than that outside Africa. Likelihood estimates of the breeding sizes in the founding populations were more than 9,000 in Africa and less than 1,000 in outside of Africa, although these estimates can be much less biased at the 1% significance level. If the number of African ancestral sequences further increases as more data accumulate in other genomic regions, the conclusion of a single founding population of modern H. sapiens is inevitable.

Population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at microsatellite loci

We report the population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at 10 microsatellite loci. Additionally, we compare heterozygosity and inbreeding estimates for continuous and fragmented populations and discuss the consequences for conservation. For a total of 314 individuals over 10 populations, the number of alleles per locus ranged from 20 to 27 and expected and observed heterozygosity varied from 0.129 to 0.924 and 0.067 to 1.000, respectively. Significant values of theta and R(ST) showed important genetic differentiation among populations. theta was much lower than R(ST), suggesting that identity by state and identity by descent have diverged in these populations. Although a significant amount of inbreeding was found under the identity by descent model (f = 0.11), an estimate of inbreeding for microsatellite markers based on a more adequate stepwise mutation model showed no evidence of nonrandom mating (R(IS) = 0.04). Differentiation (pairwise F(ST)) was positively correlated with geographical distance, as expected under the isolation by distance model. No effect of fragmentation on heterozygosity or inbreeding could be detected. This is most likely due to the fact that Cerrado fragmentation is a relatively recent event (approximately 60 years) compared to the species life cycle. Also, the populations surveyed from both fragmented and disturbed areas were composed mainly of adult individuals, already present prior to ecosystem fragmentation. Adequate hypothesis testing of the effect of habitat fragmentation will require the recurrent analysis of juveniles across generations in both fragmented and nonfragmented areas.

Group selection models in prebiotic evolution

The evolution of enzyme production is studied analytically using ideas of the group selection theory for the evolution of altruistic behavior. In particular, we argue that the mathematical formulation of Wilson's structured deme model [The Evolution of Populations and Communities (Benjamin-Cumings, Menlo Park, 1980)] is a mean-field approach in which the actual environment that a particular individual experiences is replaced by an average environment. That formalism is further developed so as to avoid the mean-field approximation and then applied to the problem of enzyme production in the prebiotic context, where the enzyme producer molecules play the altruists role while the molecules that benefit from the catalyst without paying its production cost play the nonaltruists role. The effects of synergism (i.e., division of labor) as well as of mutations are also considered and the results of the equilibrium analysis are summarized in phase diagrams showing the regions of the space of parameters where the altruistic, nonaltruistic, and the coexistence regimes are stable. In general, those regions are delimitated by discontinuous transition lines which end at critical points.

Genetic divergence and reproductive isolation between Anisakis brevispiculata and Anisakis physeteris (Nematoda: Anisakidae)s

In order to assess the taxonomic status of Anisakis brevispiculata Dollfus, 1966 population samples of this taxon from central and south-eastern Atlantic ocean were compared at 22 enzymatic loci with samples belonging to Anisakis physeteris Baylis, 1923 from the Mediterranean sea and central-eastern Atlantic ocean. Very low interpopulational genetic divergence was observed both within A. brevispiculata (average D(Nei) = 0.008) and within A. physeteris (D(Nei) = 0.009) despite the geographic distance among the samples, indicating high levels of gene flow in both taxa. On the other hand, the average genetic distance between A. brevispiculata and A. physeteris was found to be D(Nei) = 0.80, a value generally observed between well differentiated congeneric species. The reproductive isolation between A. brevispiculata and A. physeteris is indicated by the following observations: (1) no F(1) hybrids or recombinant genotypes were until now observed; and (2) the two Anisakis species do not seem to share their definitive hosts. The main definitive host of A. brevispiculata is the pygmy sperm whale (Kogia breviceps), while for A. physeteris it is the sperm whale (Physeter catodon). Only adult males differ slightly in spicule length, while females and larval stages are not differentiated morphologically. Both A. brevispiculata and A.physeteris show a type II larva. The correct recognition of A. brevispiculata from A. physeteris and from other Anisakis species studied, in either sexes and at any life stage, is made easy by allozyme markers (e.g. Icdh, Gapdh, Sod-1, Np, Aat-2, Adk-2, fEst-2, PepB, PepC-2, Mpi). Diagnostic keys, which can be used for routine identification in the field of these Anisakis worms, based on genetic markers, are given.

Nested clade analysis of the freshwater shrimp, Caridina zebra (Decapoda: Atyidae), from north-eastern Australia

The freshwater shrimp, Caridina zebra, is endemic to montane rainforest streams of the Atherton Tableland, north-eastern Australia. As the confluences of many of the headwater streams are in unsuitable habitat, dispersal is expected to be highly restricted. Results from a previous allozyme survey for this species suggested that historical dispersal between separate river drainages had occurred due to rearrangements of the drainage lines at some stage in the recent past. The aim of this study was to use temporal information from the mitochondrial cytochrome oxidase subunit I (CO-I) gene to determine whether the observed genetic structure was a result of historical processes, or alternatively, due to low levels of terrestrial dispersal. The mitochondrial DNA (mtDNA) data were analysed using nested clade analysis, which can differentiate between historical fragmentation and range expansion vs. contemporary restricted gene flow. The results displayed three divergent clades that were likely to have arisen in allopatry. One widespread clade, with individuals in more than one river drainage, reflected a pattern of restricted gene flow. This suggests that this species is capable of terrestrial dispersal.

Isolation by distance in the Atlantic cod, Gadus morhua, at large and small geographic scales

Genetic isolation by distance (IBD) has rarely been described in marine species with high potential for dispersal at both the larval and adult life-history stages. Here, we report significant relationships between inferred levels of gene flow and geographic distance in the Atlantic cod, Gadus morhua, at 10 nuclear restriction-fragment-length-polymorphism (RFLP) loci at small regional scales in the western north Atlantic region (< 1,600 km) that mirror those previously detected over its entire geographic range (up to 7,300 km). Highly significant allele frequency differences were observed among eight northwestern Atlantic populations, although the mean FST for all 10 loci was only 0.014. Despite this weak population structuring, the distance separating populations explained between 54% and 62% of the variation in gene flow depending on whether nine or 10 loci were used to estimate Nm. Across the species' entire geographic range, highly significant differences were observed among six regional populations at nine of the 10 loci (mean FST = 0.068) and seven loci exhibited significant negative relationships between gene flow and distance. At this large geographic scale, natural selection acting in the vicinity of one RFLP locus (GM798) had a significant effect on the correlation between gene flow and distance, and eliminating it from the analysis caused the coefficient of determination to increase from 17% to 62%. The role of vicariance was assessed by sequentially removing populations from the analysis and was found to play a minor role in contributing to the relationship between gene flow and distance at either geographic scale. The correlation between gene flow and distance detected in G. morhua at small and large spatial scales suggests that dispersal distances and effective population sizes are much smaller than predicted for the species and that the recent age of populations, rather than extensive gene flow, may be responsible for its weak population structure. Our results suggest that interpreting limited genetic differences among populations as reflecting high levels of ongoing gene flow should be made with caution.

Mississippians in motion? A population genetic analysis of interregional gene flow in West-Central Illinois

Population genetic and biological distance studies of Late Woodland and Mississippian populations from west-central Illinois have provided insight into a number of prehistoric demographic processes at the regional level. However, a formal analysis of diachronic interregional gene flow has not been attempted within a population genetics framework. In this study, cranial measurements of 489 individuals from 13 skeletal samples across the central and lower Illinois valleys are analyzed to address two central issues. First, the potential impact of Cahokia's decline and associated demographic events on the population structure of west-central Illinois Mississippians is examined. Second, the Mississippian and Late Woodland interregional migration patterns are compared to determine if geographic and/or cultural boundaries affected local population structure. Following Relethford and Blangero ([1990] Hum Biol 62:5-25), R matrix methods are utilized to calculate observed and expected phenotypic variances, minimum genetic distances, and F(ST) values in order to detect patterns of differential external gene flow over time. The results indicate that Late Woodland peoples had a larger sphere of biological interaction than Mississippians. In the Mississippian period, culturally imposed barriers paralleled geographic boundaries between regions such that the geographic distribution of biological variation closely adheres to a classic isolation-by-distance model. Further, intraregional population movement was a more significant contributor to Mississippian population structure than interregional gene flow, even during periods of sociopolitical strife. Small-scale intraregional shuffling is consistent with other recent studies of prehistoric Mississippian biocultural and geographic landscapes in the southeast United States.