Indirect Estimates Of Gene Flow Research Articles

A comparison of Direct and Indirect Measures of Gene Flow in the Bat‐Pollinated TreeHymenaea courbarilin the Dry Forest Life Zone of Southwestern Puerto Rico

Gene flow was estimated in the tropical tree Hymenaea courbaril using indirect measures based on the proportion of total genetic diversity from differences among populations (FST) and using direct paternity analyses. Outcrossing estimates ($$t_{\mathrm{m}\,}=1.07$$) are consistent with indications that H. courbaril is self‐incompatible. Direct estimates of pollen gene flow into two small ($$n< 6$$) stands of trees indicate that 42% and 62% of the pollen came from outside the stand. Despite this level of external gene flow, genetic drift is expected to cause divergence of populations over time (migration rate $$N_{\mathrm{e}\,}m=0.40$$ and 0.63), mainly because of the small number of adult trees within each population. Indirect estimates of gene flow based on nine larger populations of 21–48 trees gave estimates of 2.91 migrants per generation, but the absence of migration‐drift equilibrium renders this estimate unreliable. Analysis of pollen movement among 21 adult trees indicated that the effective number of fathers was only 6.9, with the majority of pollinations coming from just three trees. Asynchronous flowering, and perhaps restricted use of flowering resources by bats, the primary pollinators of H. courbaril, is the likely cause of this low number. Genetic diversity values based on 31 allozyme loci were lower than those reported for other outcrossing, gravity‐dispersed tree species. Few effective fathers, and a relatively low population density, are the likely reasons.

How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles.

The traditional view that species are held together through gene flow has been challenged by observations that migration is too restricted among populations of many species to prevent local divergence. However, only very low levels of gene flow are necessary to permit the spread of highly advantageous alleles, providing an alternative means by which low-migration species might be held together. We re-evaluate these arguments given the recent and wide availability of indirect estimates of gene flow. Our literature review of F(ST) values for a broad range of taxa suggests that gene flow in many taxa is considerably greater than suspected from earlier studies and often is sufficiently high to homogenize even neutral alleles. However, there are numerous species from essentially all organismal groups that lack sufficient gene flow to prevent divergence. Crude estimates on the strength of selection on phenotypic traits and effect sizes of quantitative trait loci (QTL) suggest that selection coefficients for leading QTL underlying phenotypic traits may be high enough to permit their rapid spread across populations. Thus, species may evolve collectively at major loci through the spread of favourable alleles, while simultaneously differentiating at other loci due to drift and local selection.

Genetic diversity of Hibiscus tiliaceus (Malvaceae) in China assessed using AFLP markers.

Amplified fragment length polymorphism (AFLP) markers were used to investigate the genetic variations within and among nine natural populations of Hibiscus tiliaceus in China. DNA from 145 individuals was amplified with eight primer pairs. No polymorphisms were found among the 20 samples of a marginal population of recent origin probably due to a founder effect. Across the other 125 individuals, 501 of 566 bands (88.5%) were polymorphic, and 125 unique AFLP phenotypes were observed. Estimates of genetic diversity agreed with life history traits of H. tiliaceus and geographical distribution. AMOVA analysis revealed that most genetic diversity resided within populations (84.8%), which corresponded to results reported for outcrossing plants. The indirect estimate of gene flow based on phiST was moderate (Nm=1.395). Long-distance dispersal of floating seeds and local environments may play an important role in shaping the genetic diversity of the population and the genetic structure of this species.

Patch quality and connectivity influence spatial dynamics in a dune wolfspider.

The spatial population dynamics of the wolfspider Pardosa monticola, inhabiting patchily distributed grasslands in the Flemish coastal dunes of Belgium and Northern France were investigated with incidence function models using field survey data from 1998 and 2000. Vegetation height and patch size were related to habitat quality. Mark-recapture experiments revealed maximum cursorial dispersal distances of 280 m for moss dunes and 185 m for higher dune grassland. Higher shrub vegetation appeared to be dispersal barriers. These habitat-dependant cursorial distances and the theoretically estimated ballooning distance were included with patch distances into a connectivity index for both dispersal modes. Forward multiple regression indicated that patch occurrence was influenced by habitat quality and ballooning connectivity. Habitat quality and cursorial connectivity explained patterns in short-term colonisation. Extinction appeared to be stochastic and not related to habitat quality and connectivity. Genetic differentiation and variability was low. The discrepancy between the estimated low dispersal capacity and the indirect estimate of gene flow ( F(ST)) indicates that historical population dynamics and/or historical ballooning dispersal influence the genetic structure in this species.

QUANTIFYING GENE FLOW FROM SPATIAL GENETIC STRUCTURE DATA IN A METAPOPULATION OF CHAMAECRISTA FASCICULATA (LEGUMINOSAE)

An extensive allozyme survey was conducted within a natural “meta” population of the native North American annual legume, Chamaecrista fasciculata (Leguminosae) to quantify genetic structure at different spatial scales. Gene flow was then estimated by a recently developed indirect method based on a continuous population model, using pairwise kinship coefficients between individuals. The indirect estimates of gene flow, quantified in terms of neighborhood size, with an average value on the order of 150 individuals, were concordant among different spatial scales (subpopulation, population, metapopulation). This gene-flow value lies within the range of direct estimates previously documented from observations of pollen and seed dispersal for the same metapopulation. Monte Carlo simulations using the direct measures of gene flow as parameters further demonstrated that the observed spatial pattern of allozyme variation was congruent with a model of isolation by distance. Combining previously published estimates of pollen dispersal distances with kinship coefficients from this study, we quantified biparental inbreeding relative to either a single subpopulation or the whole metapopulation. At the level of a neighborhood, little biparental inbreeding was observed and most departure from Hardy-Weinberg genotypic proportions was explained by self-fertilization, whereas both selfing and biparental inbreeding contributed to nonrandom mating at the metapopulation level. Gene flow was also estimated from indirect methods based on a discontinuous population structure model. We discuss these results with respect to the effect of a patchy population structure on estimation of gene flow.

Genetic structure and indirect estimates of gene flow in three taxa of Cucurbita (Cucurbitaceae) in western Mexico

Cultivated squash (Cucurbita argyrosperma ssp. argyrosperma and C. moschata) are important in the Mexican traditional agroecosystem. They are typically cultivated within maize fields where adjacent populations of a wild, close relative, C. argyrosperma ssp. sororia, occur. Consequently, there are ample opportunities for gene flow between domesticated and free-living Cucurbita populations. We used allozymes to examine genetic variation and gene flow among these three Cucurbita taxa in the state of Jalisco in Western Mexico. Twelve polymorphic allozyme loci were used to calculate genetic diversity for 16 populations of Cucurbita. We found high levels of genetic variation: polymorphism of 0.96, mean allelic diversity of 2.08, average expected heterozygosity 0.407, and little differentiation among conspecific populations (D = 0.081; F(ST) = 0.087; N(e)m = 5.22). These findings indicate that Cucurbita possess a high pollen dispersal potential, a somewhat surprising result considering they have specialist pollinators. Unweighted pair group method with arithmetic means (UPGMA) analysis of allozymes suggests the existence of at least two distinct groups of populations, one consisting of both subspecies of C. argyrosperma and another consisting of C. moschata.

RAPD Marker Diversity Within and Among Natural Populations of the Clonal Tree Cryptomeria japonica D. Don.

The Japanese cedar, Cryptomeria japonica D. Don., is one of the most important endemic species in Japan. A long history of heavy logging has resulted in natural populations being discontinuously distributed and scattered among small, restricted areas. An understanding of the patterns of genetic variability among and within populations of C. japonica is important for conserving the genetic resources of this economically important species. We studied genetic variation by random amplified polymorphic DNA (RAPD) markers in C. japonica of Kyoto prefecture, western Japan. A total of 398 plants sampled from six natural populations were analyzed by ten arbitrarily chosen decamer primers, resulting in 50 highly reproducible RAPD bands. Analysis of molecular variance partitionated the RAPD variation into the among- and within population components. The within-population component accounted for 93.75% of the variation. The among-population component accounted for only 6.25%. Indirect estimates of gene flow indicated that the average number of migrants exchanged among six populations per generation was 3.72. A Mantel test for each population did not yield significant correlations between geographic and genetic distances. The extent and distribution of C. japonica diversity in the Kyoto prefecture is in agreement with the conclusion that long-lived, wind-pollinated, out-crossing species with wide ranges retain a considerable amount of genetic diversity within populations and exhibit little genetic differentiation among populations.

Genetic Diversity of Goats from Korea and China Using Microsatellite Analysis

Nine microsatellite loci were analyzed in 84 random individuals to characterize the genetic variability of three domestic goat breeds found in Korea and China: Korean goat, Chinese goat and Saanen. Allele diversity, heterozygosity, polymorphism information content, F-statistics, indirect estimates of gene flow (Nm) and Nei's standard distances were calculated. Based on the expected mean heterozygosity, the lowest genetic diversity was exhibited in Korean goat (H E =0.381), and the highest in Chinese goat (H E =0.669). After corrections for multiple significance tests, deviations from Hardy-Weinberg equilibrium were statistically significant over all populations and loci, reflecting the deficiencies of heterozygotes (global F I S =0.053). Based on pairwise F S T and Nm between different breeds, there was a great genetic differentiation between Korean goat and the other two breeds, indicating that these breeds have been genetically subdivided. Similarly, individual clustering based on the proportion of shared alleles showed that Korean goat individuals formed a single cluster separated from the other two goat breeds.

Spatial population structure in a patchily distributed beetle.

The dynamics and evolution of populations will critically depend on their spatial structure. Hence, a recent emphasis on one particular type of structure--the metapopulation concept of Levins--can only be justified by empirical assessment of spatial population structures in a wide range of organisms. This paper focuses on Aphodius fossor, a dung beetle specialized on cattle pastures. An agricultural database was used to locate nearly 50 000 local populations of A. fossor in Finland. Several independent methods were then used to quantify key processes in this vast population system. Allozyme markers and mitochondrial DNA (mtDNA) sequences were applied to examine genetic differentiation of local populations and to derive indirect estimates of gene flow. These estimates were compared to values expected on the basis of direct observations of dispersing individuals and assessments of local effective population size. Molecular markers revealed striking genetic homogeneity in A. fossor. Differentiation was only evident in mtDNA haplotype frequencies between the isolated Aland islands and the Finnish mainland. Thus, indirect estimates of gene flow agreed with direct observations that local effective population size in A. fossor is large (hundreds of individuals), and that in each generation, a substantial fraction (approximately one-fifth) of the individuals move between populations. Large local population size, extreme haplotype diversity and a high regional incidence of A. fossor all testify against recurrent population turnover. Taken together, these results provide strong evidence that the whole mainland population of A. fossor is better described as one large 'patchy population', with substantial movement between relatively persistent local populations, than as a classical metapopulation.

New markers-old questions: population genetics of seagrasses

Marine angiosperms, or seagrasses, continue to be a major focus of marine biologists because of their important ecological role in many coastal ecosystems. Seagrass population biology could benefit from a population genetic perspective because genetic data enable the extraction of useful demographic information such as isolation and gene flow between demes. Moreover, population genetic processes may contribute to the growing ecological risks of local population extinction. Progress in seagrass genetics is partly driven by novel genetic markers which detect variation at the DNA level and overcome the limited polymorphism of allozymes. Key results of studies in the past decade, mostly using RAPD and microsatellites, were (1) considerable genetic and genotypic (clonal) diversity is present in several species in contrast to earlier notions of low polymorphism detected at allozyme loci, and (2) genetic differentiation among populations seems to be the rule despite earlier reports of genetic uniformity. Pronounced genetic structure was detected between populations of 4 species examined thus far (Posidonia oceanica, P. australis, Zostera marina, Thalassia testudinum). The FST estimates varied widely and ranged from 0.01 to 0.623 across studies and species. Genetic differentiation at a systematic range of scales was only studied in eelgrass Zostera marina, where it was positively correlated with geographic distance. The high polymorphism of RAPD or microsatellite markers will allow the augmention of indirect estimates of gene flow by methods detecting individual immigration events through paternity analysis or assignment tests. Important conservation related issues such as the level of inbreeding and the effective population size have also been obtained from genetic marker data, but results are too scarce at the moment to allow generalizations. In Zostera marina and Posidonia australis, several population genetic attributes such as clonal diversity, mating system and effective population size varied among populations within species, highlighting that there is no Œtypical¹ population. An important gap in our knowledge is whether the effects of natural population fragmentation and patchiness enhance the genetic isolation of populations due to anthropogenic disturbances. It is also unclear whether genetic differentiation displayed at marker loci are correlated with fitness-related plant traits, and whether genetic or genotypic diversity is important for medium- to long-term meadow persistence. An assessment of the genetic and genotypic diversity at marker loci should be combined with experiments on the ecological plasticity and reaction norms of genotypes composing the populations in question. This way, the role of genetic diversity for seagrass population maintenance and growth in the face of changing environmental conditions can be evaluated.

DISPERSAL OF INVERTEBRATES AMONG TEMPORARY PONDS: ARE GENETIC ESTIMATES ACCURATE?

Dispersal is difficult to quantify in most temporary pond invertebrates. As a consequence, researchers often infer the movement of individuals from indirect estimates of gene flow. Here, we review the assumptions associated with the most common gene flow estimate, which approximates migration using a simple island model and assumes equilibrium. Particular attention is focused on empirical studies of temporary pond invertebrates, where nonequilibrium conditions may be particularly important. When populations have not reached a long-term equilibrium between the migration of genes and random drift, estimates of movement can be biased dramatically. Eight comparative and theoretical tests for ascertaining these biases are described here. In some cases, specific hypotheses regarding contemporary and historical processes can also be tested statistically using computer simulations. Although the accuracy of gene flow estimates in temporary pond species varies widely, empirical and theoretical methods for assessing...

Genetic Diversity and Population Structure of Juniperus rigida (Cupressaceae) and Juniperus coreana

Enzyme electrophoresis was used to estimate genetic diversity and population structure of Juniperus rigida (Cupressaceae) and Juniperus coreana in Korea. In J. rigida, 16 of the 22 loci (72.7%) showed detectable polymorphism. Genetic diversity (0.224) was higher than average values for species with similar life history traits. The endemic species (J. coreana) was found to have fewer alleles per locus (1.39 vs. 1.61), fewer alleles per polymorphic locus (2.42 vs. 2.63), lower percent polymorphic locus (54.6 vs. 72.7%), and lower diversity (0.199 vs. 0.224) than J. rigida. These genetic diversity parameters indicated that J. coreana was genetically depauperate relative to its presumptive progenitor, J. rigida. Analysis of fixation indices showed a substantial deficiency of heterozygotes relative to Hardy–Weinberg expectations suggesting inbreeding in J. coreana. The G ST values of J. rigida and J. coreana were 0.173 and 0.118 respectively. The indirect estimate of gene flow based on mean G ST was moderate (Nm = 1.19 for J. rigida and 1.86 for J. coreana).

Genetic differentiation and structure of Hippocrepis valentina (Leguminosae) populations.

We present an analysis of isozyme variability in natural populations of the plant species Hippocrepis valentina (Leguminosae), which is endemic to the eastern Mediterranean coast of Spain and currently has endangered species status. Our results, obtained by starch-gel electrophoresis of 15 loci, show normal levels of variability for species with similar biology. The comparison with the patterns of genetic variability of two closely related species, H. balearica and H. grosii, confirms the taxonomic status of H. valentina as a proper species, independent of H. balearica, as previously suggested. The analysis of population subdivision shows that substantial variation among populations is present, and a hierarchical analysis demonstrates that when zones are defined according to their geographic location, a higher differentiation among populations within zones than among zones is found. Indirect estimates of gene flow indicate that levels of migration per generation are relatively low, except for a group composed of four populations, three of which are in close proximity. For the remaining populations, there is evidence of substantial differentiation. These results have implications for the design of a conservation strategy for this species.

Allozyme Diversity in Populations of Cymbidium goeringii (Orchidaceae)

: Using 14 allozyme loci, we investigated levels of genetic diversity within populations, and degree of genetic divergence among 24 populations of Cymbidium goeringii (Orchidaceae) in Korea and Japan. Cymbidium goeringii maintains high levels of genetic diversity both at population (mean expected heterozygosity, He = 0.238) and species levels (0.260). Means of He found in 24 populations were not significantly different from each other. About 90 % of the total variation in the species is common to all populations (mean GST = 0.108). No unique allele was found in any population. The indirect estimate of gene flow based on the mean GST was high (Nm = 2.06). Nei's genetic identities for pairs of populations had high values (mean = 0.974 [SD = 0.013]). The Mantel-Z test showed a significant correlation between genetic distance and geographic distance. However, the mean GST value between 17 populations in Korea and seven Japanese populations was relatively low (0.029), even though the land connection between the southern Korean peninsula and southern Japanese archipelagos has not existed since the middle Pleistocene. Large numbers of small seeds of C. goeringii might travel long distances by wind from populations to populations both in Korea and Japan, increasing genetic diversity within populations and maintaining low genetic differentiation among populations.

Genetic variation within a fragmented population of swietenia humilis zucc

With large tracts of once continuous forest now modified by human use to leave reduced and highly fragmented stands of trees, the determination of the genetic consequences of forest fragmentation is a priority for ascertaining the conservation value of resultant stands, and in formulating sustainable management strategies. The levels and distribution of genetic diversity over 10 microsatellite loci were investigated within a fragmented population of the neotropical tree Swietenia humilis Zucc. High levels of genetic variation, typical of a highly outcrossing species, were found in all fragments at all loci (mean HE = 0.548). The majority of the variation was within rather than between fragments (RST = 0.032), giving high indirect estimates of gene flow (Nm = 8.9), probably reflecting the genetic structure of the trees present under more continuous forest. A high proportion of loci also showed significant departures from Hardy-Weinberg equilibrium with associated significant levels of FIS. The initial effects of fragmentation were, however, seen in the fragments through the loss of low-frequency alleles present in the continuous 'control' stand. The percentage of this allelic loss increased with a decrease in fragment size.

Allozyme Diversity in the Endangered Shrub Abeliophyllum distichum (Oleaceae): A Monotypic Korean Genus

Allozyme analyses for 433 individuals of the endangered monotypic genus Abeliophyllum distichum, endemic to the central Korean peninsula, assessed levels of genetic diversity for five known populations and the species as a whole. Allozyme analyses revealed higher levels of genetic variability compared with 26 other woody endemics (proportion of polymorphic loci, $$P_{S}=40$$% vs. 42.5% and $$P_{p}=35.2$$% vs. 26.3%; genetic diversity, $$H_{eS}=0.143$$ vs. 0.078 and $$H_{eP}=0.110$$ vs. 0.056). The high levels of genetic diversity in A. distichum indicate that anthropogenic disruption of habitats is recent (<100 yr) and has not yet greatly reduced the genetic variation in the species. In addition, populations of A. distichum harbor high levels of clonal diversity (mean $$D_{G}=0.992$$ and $$G/ N=0.68$$). A moderate genetic differentiation among five populations was observed (mean $$G_{ST}=0.141$$). Indirect estimates of gene flow (Nm) were 1.52 and 2.10, based on GST and a mean frequency of two private alleles (alleles detected in only one population), respectively. The variation may reflect the outcrossing mode of reproduction, clonal reproduction, and recentness of habitat loss.

SPATIAL SCALE OF GENETIC STRUCTURE AND AN INDIRECT ESTIMATE OF GENE FLOW IN EELGRASS, ZOSTERA MARINA.

In this study, the first investigation of population structure in an aquatic angiosperm, I show that populations of a marine angiosperm (eelgrass, Zostera marina) are genetically differentiated at a number of spatial scales. I find also that there is no correspondence between geographic and genetic distances separating subpopulations, an increasingly common result in spatially stratified studies of genetic structure in marine invertebrates. F-statistics, calculated for two years from electrophoretic variation at five polymorphic allozyme loci, indicate significant genetic differentiation among sampling quadrats within each of two bays (θ = 0.064-0.208), between tide zones within a bay (θ = 0.025-0.157) and between bays (θ = 0.079). Spatial autocorrelation analysis was used to explore genetic differentiation at smaller spatial scales; estimated patch sizes (within which genetic individuals are randomly associated) indicated no appeciable genetic structure at scales less than 20 m × 20 m. Calculated values of F-statistics were a function of the spatial scale from which samples were drawn: increasing the size of the "subpopulation" included in calculation of fixation indices for the same "total" sample resulted in an increase in the magnitude of f (e.g., from 0.092 to 0.181) and a decrease in θ (e.g., from 0.186 to 0.025). On the basis of the best estimate of the spatial scale of subpopulations, the effective number of migrants per generation (Ne m) ranges from 1.1 to 2.8. Genetic consequences of the disturbance regime in the eelgrass habitat sampled were extreme variation between years in the allele richness and proportion of heterozygotes in a sample and a positive relationship between the extinction probability of patches and the genetic variance among them. The changes in F-statistics as a function of sampling scale and the observation that θ among sampled quadrats was positively associated with the probability of extinction among quadrats indicated that indirect estimates of gene flow (Ne m) calculated from θ should be cautiously interpreted in populations that may not yet be in drift-migration equilibrium.

Spatial Scale of Genetic Structure and an Indirect Estimate of Gene Flow in Eelgrass, Zostera marina

Spatial Scale of Genetic Structure and an Indirect Estimate of Gene Flow in Eelgrass, Zostera marina

Hybridization and introgression in Carpobrotus spp. (Aizoaceae) in California II. Allozyme evidence

Morphological evidence has indicated that hybridization and introgression are occurring between Carpobrotus edulis L., a nonindigenous, invasive species in California (Bolus), and its putative native congener, C. chilensis. The identification of allozyme markers has enabled us to quantify hybridization and the extent of introgression between these species. Samples from 20 individuals of each of five morphological types (both parent species and three hybrid phenotypes) were collected from 39 populations along the coast of California from the Mexico to Oregon borders. Ten enzyme systems revealed a total of 17 resolvable loci, eight of which were polymorphic for the genus. Five of the polymorphic loci easily differentiate C. edulis and C. chilensis. Allele frequencies among the morphologically defined types are consistent with estimations of allele frequency changes due to first- and second-generation backcrossing. In comparison to long-lived, herbaceous perennials and widespread species, C. edulis and intermediate types have more variation in their populations (P = 41.73, Ap = 2.11, Ho = 0.246, and P = 38.13, Ap = 2.06, Ho = 0.216, respectively) than C. chilensis (P = 11.76, Ap = 2.00, Ho = 0.082). Indirect estimates of gene flow indicate four of the five morphological types are outcrossing. Gene flow between previously allopatric species may have broad implications if it results in an increase in fitness; further experimentation is needed to determine the ultimate ecological consequences of this phenomenon and its possible threat to limited, remaining natural habitat in California.

Genetic structure of two endangered pitcher plants, Sarracenia jonesii and Sarracenia oreophila (sarraceniaceae)

Sarracenia jonesii and S. oreophila arc insectivorous perennial plants of the southeastern United States. Both pitcher plant taxa arc rare and endangered. Allozyme diversity was assessed for eight of the ten extant populations of S. jonesii and 14 of the 35 remaining S. oreophila populations. Genetic diversity was low and comparable for both species (Hes = 0.086 and 0.082 for S. jonesii and S. oreophila, respectively). Mean population genic diversity (Hep) was 0.061 for S. jonesii and 0.060 for S. oreophila. Estimates of genetic diversity were typical of those commonly associated with endemic species. Small populations of each species and geographically disjunct populations tended to maintain less genetic diversity. Indirect estimates of gene flow were comparable for S. oreophila (Nm = 1.62) and S. jonesii (Nm = 1.07).