Gene Flow Distance Research Articles

Genetic diversity of fragmented populations of Polygala reinii (Polygalaceae), a perennial herb endemic to Japan.

Genetic variation at 10 allozyme loci was analyzed in 14 populations of Polygala reinii (Polygalaceae), a perennial herb endemic to central Honshu, Japan, with a fragmented geographical distribution. The levels of genetic variation within species ( P=80.0, A=3.10, H(E)=0.303) and within populations ( P=42.1, A=1.61, H(E)=0.163) were considerably higher than the mean for other endemic plants or short-lived perennial herbs. Genetic differentiation among populations was also high ( G(ST)=0.404). The genetic distance phenogram tended to show a clustering of the populations reflecting the fragmentation of the species range. A principal component analysis revealed the same tendency, as well as three groupings of populations in the Tokai district, on the Kii Peninsula and in the northern Kinki district. A negative correlation was obtained between the levels of gene flow and geographical distance among the populations ( r=-0.745, P<0.0001). These results indicated limited gene flow among populations in P. reinii, presumably due to the geographical isolation accompanying the fragmented distribution. On the other hand, the geographical differentiation between the Japan Sea and Pacific Ocean sides was found in P. reinii, suggesting the influence of postglacial migration on the establishment of the genetic structure of this species.

Allozyme variation in five populations of mopane, Colophospermum mopane (Fabaceae)

Ecological variants and morphological ecotypes are known in Colophospermum mopane which suggest phenotypic plasticity and possible genetic differentiation within the species. Five populations of C . mopane were studied to determine the levels of allozyme variation within and among them. Average heterozygosity values at 19 enzyme-coding loci in four populations varied little (H = 1.2% to 2.1%) with a much higher value (6.1%) in the Messina population. Polymorphism levels were the same for all populations as measured by the average number of alleles per locus (1.2) and the percentage of polymorphic loci (15.8%). Pair-wise fixation index ( F ST = 0.001 to 0.004), gene flow ( N em = 39.840 to 159.840) and genetic distance (D = 0.0002 to 0.0003) values indicate that four of the populations can be considered a single panmictic group, but that Messina is sufficiently diverged to regard it as a separate population. Results are discussed with specific reference to the conservation of the genetic integrity of C . mopane due to extensive exploitation by man.

Gene flow from cultivated rice to the wild species Oryza rufipogon under experimental field conditions.

• Here, the gene flow from a cultivated rice variety (Minghui-63) to common wild rice (Oryza rufipogon) was investigated to assess the biosafety risk associated with the environmental release of transgenic varieties. • Four experimental designs differing in the spatial arrangement of the Minghui-63 and O. rufipogon plants were used in experiments conducted in an isolated rice field in Hunan Province, southern China, where O. rufipogon occurs naturally. • Natural hybridization events between the two species were detected by scoring a simple sequence repeat (SSR) molecular marker. A total of 296 hybrids were identified from 23776 seedlings that were randomly germinated from >80000 seeds collected from O. rufipogon. The occurrence of the crop-to-wild gene flow was significantly associated with wind direction and frequencies of the gene flow, which decreased significantly with distance from the pollen sources. The maximum observed distance of gene flow was 43.2m. • The results indicated that gene flow from cultivated rice to O. rufipogon occurred at a considerable rate. Therefore, isolation measures should be considered when deploying transgenic rice in the sympatric regions of the wild rice, and when establishing in situ conservation of O. rufipogon. The experimental system in this study can be used for biosafety assessment of transgene escape of other wind-pollinated crops.

Larval settlement rates and gene flow of broadcast-spawning (Acropora tenuis) and planula-brooding (Stylophora pistillata) corals

Larval settlement rates, genetic structure, and gene flow of broadcast-spawning (Acropora tenuis) and planula-brooding (Stylophora pistillata) corals (Scleractinia) were compared within a 500 km range in the Ryukyu Archipelago. We conducted a laboratory experiment to investigate planula settlement rates, and a broad sampling survey to determine genetic variation in both species in the Archipelago. In the laboratory experiment, the planulae of S. pistillata settled a few hours after release, while those of A. tenuis started to settle at least 4 d after the release of gametes. The survival rates and competency periods of larvae were higher and longer for A. tenuis than for S. pistillata. These results suggest that broader dispersal is more likely for A. tenuis than for S. pistillata. In the population genetic analysis, we measured local (2 stations in a region) and regional (Okinawa, Kerama and Yaeyama) patterns of genetic variation with allozyme electrophoresis. We also inferred the levels of gene flow in the 2 species. In the study area, gene flow (N e m) and genetic distance (D) were, respectively, higher and smaller for the spawner A. tenuis (N e m = 3.5 to 16.4, D = 0.028 to 0.187) than for the brooder S. pistillata (N e m = 0.9 to 1.5, D = 0.026 to 0.309). Therefore, the planulae settlement rates were well in agreement with gene flow. In addition, for both species, N e m between the Okinawa and Kerama regions (30 to 150 km apart; N e m = 9.4 to 22.5 in A. tenuis and 1.4 to 3.3 in S. pistillata) was higher than that between the Okinawa-Kerama and Yaeyama regions (up to 500 km apart; N e m = 3.1 to 9.4 in A. tenuis and 0.5 to 1.4 in S. pistillata). The results suggest that coral populations in the Kerama Island are a major source of the coral planulae needed for the recovery of both brooding and spawning coral communities around the Okinawa Islands, after the mass-bleaching event in 1998.

Pollen dispersal and gene flow by pollen in Araucaria angustifolia

Araucaria angustifolia (Bert.) O.Ktze. is an economically important tree in southern Brazil. Indiscriminate exploitation is threatening this species with extinction. Conservation programs are urgently needed to save the remaining forest, and such programs must be guided by biological studies that genetically characterise the remaining populations. Pollen and seed dispersion patterns determine the distance of gene flow and directly influence genetic structure and effective population size. A. angustifolia is a wind-pollinated dioecious tree. For pollen-dispersal airflow, physical characteristics of pollen grain, such as size and shape, must be considered. The aim of this work was to determine the homogeneity of effective pollen clouds as well as to infer the physical characteristics of pollen. The homogeneity of pollen clouds of A. angustifolia was assessed for 70 trees of natural population in Brazil. Analysis of genetic variability and differentiation of the effective pollen clouds detected high diversity at the MDH-B and 6-PGDH-B loci. Heterogeneity G-tests indicated pollen pool heterogeneity in four of seven examined loci (GOT-B, PGM-A, SKDH-B and 6-PGDH-B). The pollen grains measured 61.50 μm. The floating rate ranged from 12.02 to 18.98 cm s–1. The physical characteristics of the pollen suggest that pollen dispersion is likely to be limited.

Nunatak survival of the high Alpine plant Eritrichium nanum (L.) Gaudin in the central Alps during the ice ages.

Polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) and sequence analysis of noncoding regions of chloroplast DNA were used to investigate 37 populations of Eritrichium nanum covering its total distribution area, the European Alps. There was no haplotypic variation within the populations, and most haplotypes were restricted to single sites or to neighbouring populations, suggesting low levels of long distance gene flow via seeds. The present geographical distribution of haplotypes probably reflects an ancient geographical pattern within two regions in the intensely glaciated western and eastern central Alps identified as genetic hotspot areas. These two regions contained seven of the total of 11 haplotypes, including many of the most derived ones. The divergent haplotypes formed closely related groups, which supported a separate evolution of these haplotypes in these two regions and, more importantly, gave strong evidence for the in situ survival of these populations on nunataks within the western and eastern central Alps during Pleistocene glaciation. This result is in concordance with a previous study on E. nanum using nuclear markers. Only one haplotype was common and widespread throughout the distributional range of E. nanum. At the same time, it was the evolutionarily basal-most and all other haplotypes were best described as its descendants. This haplotype is hypothesized to be genetically identical to a Tertiary Alpine colonizing ancestor, whose distribution was secondarily fragmented and infiltrated by derived haplotypes originating through local mutations.

Genetic variation and population structure in central and isolated populations of balsam fir,Abies balsamea(Pinaceae)

Genetic variation and spatial genetic structure in balsam fir (Abies balsamea) were examined in two isolated populations in Iowa and Minnesota thought to be paleorefugia and in two ecologically central populations in old-growth forests of Upper Michigan. Overall levels of genetic variability at 22 allozyme loci were lower than that found in most conifer species (H(o) values ranged from 0.005 in the isolated populations to 0.025 in the central populations). The mean F(IS) value (0.154) was larger than usually found in conifers and suggests moderate levels of inbreeding. The mean F(ST), an estimate of genetic diversity among populations, was 3.7% of the total diversity, a value lower than the mean for conifers. Nm, the number of migrants per generation, was 6.5, suggesting either some gene flow among populations or a lack of genetic differentiation. Spatial autocorrelation analysis revealed a moderately patchy structure, with gene flow distances of 30-70 m in the central populations and at least 10 m in the isolated populations. The future of the ecologically central populations depends on maintenance of an intact forest mosaic. The low genetic variability in the small, isolated populations suggests that habitat fragmentation has led to a reduction in evolutionary potential and that the future viability of these populations will likely require active management in the face of global climate change.

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.

High genetic identities between three oil mallee taxa, Eucalyptus kochii ssp. kochii, ssp. plenissima and E. horistes, based on nuclear RFLP analysis

The eucalypt species Eucalyptus kochii ssp. kochii, E. kochii ssp. plenissima and E. horistes, are harvested for oil production. The genetic diversity in these taxa and their phylogenetic relationships were assessed using anonymous nuclear RFLP loci. Variation was determined for 20 individuals from 10 populations representing the three taxa. The level of diversity in the taxa was high compared to other species where RFLP surveys have been conducted, including another eucalypt species. The populations showed little differentiation, low genetic distance and high gene flow between them. Phylogenetic relationships reveal clustering of populations consistent with their geographical distribution. This analysis suggests that genetically these taxa represent a single widespread, variable species with some provenance delineation. Establishment of a breeding programme based on all populations would allow progress in genetic improvement for oil yield.

A population genetic analysis of chloroplast DNA in wild populations of Prunus avium L. in Europe.

A population genetic study of chloroplast DNA was carried out in 23 wild populations of Prunus avium sampled from several European deciduous forests. An analysis of approx. 9% of the chloroplast genome detected mostly insertion-deletion mutations and one point mutation. In all, 16 haplotypes were detected. Six haplotypes were shared by two or more populations and 10 were unique. One haplotype was present in 21 of the 23 populations and 161 of 211 individuals, which probably indicates its ancient origin. The level of population subdivision, using unordered and ordered alleles, was low, GSTC=0.29 and NSTC=0.33, respectively. The difference between GSTC and NSTC is nonsignificant, indicating an absence of correlation between haplotype phylogeny and geographical distribution. The absence of phylogeographic structure in wild cherry may be attributed to long distance gene flow among populations by birds, animals and anthropogenic activities. The minimum-length spanning tree depicting the phylogenetic relationships between the haplotypes indicates the possible existence of two lineages represented by the haplotypes H3 and H4. The information about homogeneity or heterogeneity of populations in terms of haplotype constitution and detection of rare haplotypes in some populations will be useful for formulation of conservation and management strategies of wild cherry.

Population genetics of the fissiparous holothurians Stichopus chloronotus and Holothuria atra (Aspidochirotida): a comparison between the Torres Strait and La Réunion

Collections of about 50 individuals from each of five populations of the fissiparous holothurian species Stichopus chloronotus and four populations of Holothuria atra were made in 1999. These populations were located in the Torres Strait (western Pacific) and La Reunion (western Indian Ocean). Allozyme electrophoretic surveys of five (S. chloronotus) and six (H. atra) loci were conducted to compare patterns of asexual reproduction and to investigate connectivity between regions separated by large geographic distances. Deviations from genotype frequencies expected under Hardy–Weinberg equilibrium, mostly heterozygote excesses, were observed in all populations of both species. The maximum contribution of sexual reproduction (calculated as the maximum number of sexually produced individuals: sample size=N*/Ni) was similar for all S. chloronotus (58–64%) and H. atra (76–92%) populations, and on the same level as previously reported for midshelf reefs of the Great Barrier Reef. The higher values in the latter species indicated greater contributions of asexual reproduction to S. chloronotus populations. Variability was strongly reduced in S. chloronotus populations at La Reunion, with only one locus being variable in that population. When the dataset was reduced to one representative per multi-locus genotype per population to reduce the effect of asexual reproduction on calculations on gene flow, FST values were not significantly different from zero, suggesting high gene flow between these regions. However UPGMA cluster analyses using Rogers' genetic distance, roughly clustered populations by region. In the case of H. atra, pooled populations within each region were significantly different from those of the other region. Thus, although some restrictions in gene flow and greater genetic distances between the regions may exist, those differences are distinctly less than those reported in previous studies on echinoderms over similar geographic scales. Despite the importance of asexual reproduction for the maintenance of local population size, this study also confirmed that the potential for widespread dispersal mediated by sexually produced larvae is large.

Autocorrelação espacial das freqüências alélicas em subpopulações de cagaiteira (Eugenia dysenterica DC., Myrtaceae) no sudeste de Goiás

Among the many fruit trees from cerrado region that show large economic potential in traditional agricultural systems, the cagaiteira (Eugenia dysenterica DC.) deserves a special place. In this work, spatial autocorrelation analyses were used to evaluate spatial patterns of genetic variation among ten local populations from southeastern Goias State, Brazil. Six isoenzymatic markers (SKDH, 6-PGD, a-EST, MDH, PGI e PGM) were used to evaluate genetic variability, in a total of eight polymorphic loci. Moran’s I coefficients were estimated for four geographic distance classes, and correlograms thus obtained showed clinal patterns of variation for most alleles. Simulations of neutral evolution among local populations were performed using the Ornstein-Uhlenbeck process, both to establish null patterns to test this hypothesis and to define the limits of similarity among correlograms. These analyses showed that population differentiation in this species probably occurred under a neutral process in which local drift is counteracted by low geographic distance gene flow, as in isolation-by-distance or stepping-stone models.

Evidence for long-distance dispersal in a sedentary passerine, Gymnorhina tibicen (Artamidae)

Australian magpies (Gymnorhina tibicen) are group-living birds found across much of mainland Australia. Adults commonly remain in a breeding territory until death. Young of the year either remain on the natal (birth) site or are forced by their parents to disperse. Observational studies in south-eastern Australia suggest that most dispersing juveniles settle within 7 km of their natal territory. Therefore, despite potential for considerable gene flow (via flight), social organization predisposes magpies towards local population structuring. In this study, we measured genetic variation at both nuclear (allozyme) and mitochondrial loci and found evidence of substantial gene flow over very large distances (up to 1599 km). Thus, some juvenile magpies may disperse much greater distances than was previously thought. For mtDNA, geographic and genetic distance were strongly correlated, consistent with a pattern of isolation by distance. Therefore, although female gene flow is substantial it is apparently geographically restricted over large distances, in approximately a stepping-stone fashion. We conclude that a strong relationship between gene flow and geographic distance can develop even over large distances if populations have experienced no major historical disturbances to gene flow.

Patterns of genetic differentiation and gene flow in Central Italian populations of Dinocras cephalotes (Curtis, 1827) (Insecta, Plecoptera)

Dispersal is a crucial phenomenon which has a strong influence on the ecology and evolution of species, determining the extent of gene flow among conspecific populations. In this paper, we present data on the degree of genetic structuring in 11 populations of the stonefly Dinocras cephalotes, focusing our attention on three Central Italian rivers: Aniene, Nera and Velino. We studied the genetic variation at 28 enzymatic loci by means of starch gel electrophoresis: 19 loci were polymorphic in one population at least. The degree of genetic structuring and levels of gene flow were estimated by F-statistics using WEIR & COCKERHAM'S estimators. Relatively high levels of genetic differentiation were revealed, considerably higher than those obtained in other studies of stonefly species. Neighbour-joining analysis provided a geographic scheme of relationships of the study populations, grouping them according to the river of origin. This analysis was supported by bootstrap values. We were not able to detect an unequivocal relationship between gene flow and geographic distances between sites within each river; this led us to hypothesise that equilibrium has not been reached between genetic drift and gene flow.

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.

ISOLATION BY DISTANCE IN THE ATLANTIC COD, GADUS MORHUA, AT LARGE AND SMALL GEOGRAPHIC SCALES

Abstract 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 (< 1600 km) that mirror those previously detected over its entire geographic range (up to 7300 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 populat...

Low levels of genetic variation within and high levels of genetic differentiation among populations of species of Abies from southern Mexico and Guatemala

Populations of Abies in southern Mexico and Guatemala (A. flinckii, A. guatemalensis, A. hickeli, and A. religiosa) have a patchy distribution. This pattern is particularly clear in A. guatemalensis. Genetic diversity within populations, measured by average heterozygosity at 16 isozyme loci, is lower than the range reported for most conifers (mean H(o) ranging from 0.069 in A. guatemalensis to 0.113 in A. flinckii), while differentiation among populations is higher than that observed in most conifer species studied (θ = F(st) ranging from 0.073 in A. hickeli to 0.271 in A. flinckii). Estimated levels of gene flow are low (ranging from 0.672 in A. flinckii to 3.17 in A. hickeli). Populations in most cases had an excess of homozygosity over that expected under Hardy-Weinberg equilibrium, suggesting some inbreeding (F(is) ranging from 0.074 in A. flinckii to 0.235 in A. guatemalensis). A significant relationship between gene flow and geographic distance was observed in A. religiosa, but not in the other three taxa studied. The patterns of genetic variation appear to have been influenced by the distributions and histories of these species. Paleoclimatic evidence suggests that the ranges of these species retreated upwards during the Pleistocene glaciation and became fragmented during the warming period that followed. The populations could have passed through genetic bottlenecks that reduced genetic variation and led to interpopulation differentiation.

Microspatial genetic structure in the land snail helix aspersa (Gastropoda: helicidae)

The microspatial genetic structure of allele frequencies at seven isozyme loci was examined for 15 populations of the land snail Helix aspersa sampled in a village from Brittany (north-western France). Spatial heterogeneity of allele frequencies was highly significant (P < 0.001). Fixation indices reflected nonrandom mating within neighbourhoods and a slight but consistent differentiation between colonies (FST=0.044; P < 0.01). Analyses of gene flow or genetic distances failed to reveal a significant relationship with geographical distance, probably because of the complexity of environmental heterogeneity. However, matrix comparisons between genetic distances and connectivity networks among adjacent colonies (Gabriel-connected graph) yielded a significant correlation in every case, indicating a 'step-by-step' relationship between neighbouring localities. Moreover, most of the allozymes were spatially structured and showed (i) a gradual isolation of colonies with increasing geographical distances, and (ii), for some correlogram profiles, a circular gradient illustrating a multidirectional colonization of the village. The probable existence of disperser individuals allowed us to suggest a metapopulation model which would explain the maintenance of such animals in fragmented habitats where anthropogenic disturbances and extinction/recolonization events are commonly observed.

Genetic structure of natural populations of Castanea sativa in Turkey: evidence of a hybrid zone

Abstract This study points out the evidence of a hybrid zone between two groups of genetically differentiated populations of chestnut (Castanea sativa Mill.) in Turkey. Genetic structure, gene flow and introgression levels, based on 16 allozyme loci, were investigated on 34 population samples spanning the entire C. sativa distribution area in this country. The occurrence of the hybrid zone, located in the Bithynian region, was inferred in a group of populations showing the following genetic characteristics: (i) enhanced genetic variability and intermediate allelic frequencies between those of the Western and Eastern groups of populations; (ii) sharp and concordant changes in allele frequencies; (iii) decreased gene flow with the Western and Eastern populations. Starting from the cline width estimated to be 324 km, strength of selection was evaluated from the gene flow distance, as indicated from the degree of genetic structuring outside the hybrid zone. Evolutionary processes shaping the observed genetic differentiation and introgression are discussed on the basis of palynological data, palaeoclimatic events and evidence of hybridization found in other plant and animal species in the same region.

THE RELATIVE IMPORTANCE OF HISTORICAL EVENTS AND GENE FLOW ON THE POPULATION STRUCTURE OF A MEDITERRANEAN RAGWORT,SENECIO GALLICUS(ASTERACEAE)

Comparisons of cytoplasmic and nuclear diversity within and among natural plant populations have the potential to distinguish the relative influences of seed and pollen dispersal on contemporary gene flow, or alternatively, may permit inferences of the colonization history of a species via seed. We examined patterns of cpDNA and allozyme variation in Senecio gallicus, a diploid, annual plant that occurs in both coastal and ruderal inland areas of the Iberian Peninsula and southern France. The species appears to have a strong propensity for long-distance seed dispersal. Five cpDNA haplotypes were found by RFLP analysis among a sample of 111 individuals derived from 11 populations. Differences in haplotype frequencies across populations were most evident with respect to a dramatic increase in the frequency of a derived haplotype from coastal to inland localities. The level of cpDNA differentiation among populations within the inland group (θ0 = 0.07) was significantly less than that seen within the coastal group (θ0 = 0.41). In contrast, for allozymes, no significant difference in population structure was evident between collections from coastal and inland habitats. At the rangewide geographic scale, there was only a very weak association between inferred levels of gene flow and geographic distance for cpDNA, and no such association was found for allozymes. It appears that while seed movement in the species might be sufficiently great to disturb the pattern of isolation by distance for cpDNA, it cannot fully account for the nearly randomized spatial structure at polymorphic allozyme loci. It is suggested that isolation of populations in Atlantic-Mediterranean coastal refugia during previous glacial maxima, and the effects of subsequent colonization events in inland areas, have had an important effect on molding the present genetic structure of the species.