Greater Genetic Differentiation Research Articles

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.

A biochemical genetic comparison of four populations of Breviceps adspersus (Anura: Microhylidae)

Four populations of the bushveld rain frog, Breviceps adspersus, representing three northern populations (B. adspersus adspersus), and a southern population (B. adspersus pentheri), were analysed by electrophoresis to assess the extent of genetic variation and differentiation amongst them. Eighteen protein-coding loci were resolved of which 11 loci (61 %) displayed polymorphism. A low mean heterozygosity ranging between H = 0.009 to H = 0.062 was estimated. Greater genetic differentiation was observed between the B. adspersus pentheri and B. adspersus adspersus populations, than between the three B. adspersus adspersus populations. This supports the subspecific status of both taxa.Key words: allozymes, anura, speciation, taxonomy.

RAPD variation within and between natural populations of the wild rice oryza rufipogon from china and brazil

Genetic variation within and between eight natural populations of Oryza rufipogon from China and Brazil was investigated at the DNA level by analysis of RAPD fragments. Out of 60 random primers, which were initially screened against DNA from four individuals, 20 generated highly reproducible RAPD fragments which were then used for further population analysis. With these primers, 95 discernible DNA fragments were produced and 78 (82.1%) were polymorphic, which indicated that high levels of genetic variation existed in these natural populations. In addition, the Chinese populations showed greater polymorphism than those from Brazil at both the population and regional levels. This is noteworthy considering that the Chinese populations are from a relatively restricted area of China. The factors responsible for these findings include the contrasting mating systems in the Brazilian and Chinese populations, and gene flow from annual cultivated rice to perennial natural populations in China. An Analysis of Molecular Variance (AMOVA) was used to apportion the variation between individuals within populations, between populations within regions, and between regions. Results showed that 61.8% of the total genetic diversity resided between the two continents, whereas only 14.9% and 23.3% was attributable to population differences within regions and to individual differences within a population, respectively. The great genetic differentiation between the Chinese and Brazilian populations is in agreement with recent treatment of the American form of O. rufipogon as a separate species, O. glumaepatula.

High amounts of genetic differentiation between populations of the malaria vector Anopheles arabiensis from West Africa and eastern outer islands.

Polymorphism at nine microsatellite loci was examined to assess the level of genetic differentiation between four Anopheles arabiensis populations from Senegal, the high plateau of Madagascar, and Reunion and Mauritius islands. Eight of nine loci showed great polymorphism (2-16 alleles/locus) and significant genetic differentiation was revealed between all four populations by F- and R-statistics, with Fst estimates ranging from 0.080 to 0.215 and equivalent Rst values ranging between 0.022 and 0.300. These high amounts of genetic differentiation are discussed in relation to geographic distance including large bodies of water, and history of mosquito settlement, and insecticide use on the islands. The results suggest that historical events of drift rather than mutation are probably the forces generating genetic divergence between these populations, with homogenization of the gene pool by migration being drastically restricted across the ocean.

Allozyme and DNA sequence data support speciation of Northern and Southern populations of silver catfish, Schilbe intermedius (Rüppel, 1832)

Patterns of genetic variation in Schilbe intermedius were investigated due to morphological differences and taxonomic uncertainties regarding the Southern African schilbeids. A total of three populations, two Southern populations representing the former Eutropius depressirostris and a Northern population representing S. mystus, were electrophoretically analysed to determine the extent of genetic differentiation among these populations. The Northern and Southern populations were fixed for different alleles at the G3PDH-2 protein coding locus and allozyme differentiation between populations, using the 0.95 criterion, were also encountered at the PGDH-2 locus. Genetic distance values indicate greater genetic differentiation between the Northern and Southern populations compared to the two Southern populations. DNA sequence analysis of 900–1000 nucleotides of the cytochrome b gene revealed distances of 3.2–3.5% between the Schilbe/Eutropius complex. This finding, together with ingroup and outgroup analysis of evolutionary relationships, is congruent with the results from the electrophoretic analysis of the taxa. Sufficient differentiation exist between the Northern and Southern populations to regard them as distinct species.

Incipient species formation in salamanders of the Ensatina complex.

The Ensatina eschscholtzii complex of plethodontid salamanders, a well-known "ring species," is thought to illustrate stages in the speciation process. Early research, based on morphology and coloration, has been extended by the incorporation of studies of protein variation and mitochondrial DNA sequences. The new data show that the complex includes a number of geographically and genetically distinct components that are at or near the species level. The complex is old and apparently has undergone instances of range contraction, isolation, differentiation, and then expansion and secondary contact. While the hypothesis that speciation is retarded by gene flow around the ring is not supported by molecular data, the general biogeographical hypothesis is supported. There is evidence of a north to south range expansion along two axes, with secondary contact and completion of the ring in southern California. Current research targets regions once thought to show primary intergradation, but which molecular markers reveal to be zones of secondary contact. Here emphasis is on the subspecies E. e. xanthoptica, which is involved in four distinct secondary contacts in central California. There is evidence of renewed genetic interactions upon recontact, with greater genetic differentiation within xanthoptica than between it and some of the interacting populations. The complex presents a full array of intermediate conditions between well-marked species and geographically variable populations. Geographically differentiated segments represent a diversity of depths of time of isolation and admixture, reflecting the complicated geomorphological history of California. Ensatina illustrates the continuing difficulty in making taxonomic assignments in complexes studied during species formation.

Genetic structure of continental and island Populations of the Mediterranean Endemic Cyclamen Balearicum (Primulaceae)

Cyclamen balearicum is a self-compatible perennial herb endemic to the western Mediterranean Basin. This species occurs in five geographically isolated terrestrial islands in southern France and on four Balearic islands. In this study, we compare genetic variability and differentiation within and among 11 terrestrial island populations and 17 true island populations. Of nine readable enzyme loci, five were polymorphic in both terrestrial and true islands. F statistics showed a significant heterozygote deficiency in all populations, probably due to high levels of autonomous selfing, restricted gene flow, and subsequent genetic drift. Genetic diversity was higher in terrestrial islands than on the Balearic islands, suggesting that the Balearic islands were colonized when they were in contact with the continent. Population differentiation was greater among terrestrial islands (Fst = 0.417 and Gst = 0.344) than among true islands (Fst = 0.112 and Gst = 0.093). Furthermore, differentiation among populations on the Basses Cévennes terrestrial island was greater (Fst = 0.254) than among populations on the true island of Mallorca (Fst = 0.163). The greater genetic differentiation among terrestrial islands could have been caused by genetic bottlenecks associated with changes in climate and human land use that may have reduced population sizes more severely in terrestrial islands in southern France than on the Balearic islands.

Low Genetic Variation but High Population Differentiation in a Common Tropical Forest Tree Species

Genetic variation and population differentiation were studied in an abundant, outcrossing tropical tree species, Pentaclethra macroloba, in Costa Rica. Population differentiation was analyzed on two spatial scales by collecting leaf material from 7 locations within a 1800‐ha biological reserve and from 11 additional sites up to 70 km from the reserve. Genetic differences between age classes were investigated by collecting leaves from adults and seedlings at six locations within the reserve. Measures of genetic variation were determined using protein electrophoresis of leaf material. Five polymorphic and nine monomorphic loci were identified. The mean heterozygosity of P. macroloba populations was 0.074. Heterozygosity varied among populations, ranging from 0.045 to 0.135, with the lowest value found in the reserve and the highest in a distant population. Low variation in the reserve was largely due to fixation at two loci that were polymorphic outside the reserve. Within the reserve, seedling populations were less differentiated than adult populations, with multilocus Fst, values of 0.0189 and 0.0384, respectively. On larger geographic scales, however, population differentiation accounted for 21.9% of the total genetic variation. Nm, calculated from multilocus Fsv was negatively correlated with geographic distance among pairs of populations within the reserve (r = 0.53) and among populations throughout Costa Rica (r = −0.47). In combination, these results suggest that while P. macroloba may be panmitic within the reserve, gene flow is relatively restricted among sites that are scattered over a deforested landscape. Furthermore, in spite of the abundance of this species, genetic neighborhoods may be small due to asynchronous reproduction and isolation by distance. Allelic diversity is higher outside the reserve, and continuing deforestation may result in loss of genetic diversity, greater genetic differentiation, and genetic isolation of these populations.

Conservation of rare and endangered bryophytes: Input from population genetics

Effective conservation of biological diversity, including bryophytes, depends upon adequate knowledge of the genetic structure of natural populations and of the processes that create and maintain genetic diversity. Overall, species of mosses display a range of values for genetic variation similar to that of other land plants, whereas liverworts show lower levels of polymorphism. Within Plagiomnium section Rosulata, levels of variation are lower in rare, narrowly distributed species than in common, widespread taxa. On a more local scale, populations of P. ciliare from disturbed, secondary forests in the Piedmont of the southeastern United States are less polymorphic than those undisturbed, primary forests in the Appalachian Mountains. This may reflect the effects of genetic drift in small, recently recolonized populations. Typically, bryophyte species are more widely distributed than their angiosperm counterparts, yet there is greater genetic differentiation among populations. Genetic differences between species also are much larger, on average, for mosses and liverworths. In some thallose liverworts, disjunct ‘species’ actually consist of a number of genetically highly distinct sibling species. Even in continuously distributed taxa, it appears that gene flow is highly restricted. The small size of bryophytes and their wide ranges, high degree of population differentiation, and low levels of gene flow must all be taken into account in making informed management decisions about rare and endangered bryophytes.

THE EFFECT OF HOST PLANT PATCH SIZE VARIATION ON THE POPULATION STRUCTURE OF A SPECIALIST HERBIVORE INSECT, TETRAOPES TETRAOPHTHALMUS.

The patchy local distribution of the common milkweed, Asclepias syriaca, organizes populations of a beetle that feeds on it, Tetraopes tetraophthalmus, into numerous local demes. Genetic and ecological characteristics of demes of adult milkweed beetles occupying two naturally occurring size classes of patches, defined as large and small, were studied in order to describe the effect of patch size variation on local population structure. Allele frequency variance in two of three protein polymorphisms was significantly greater in collections of beetles from an array of 13 small patches when compared to collections from an array of 11 large populations. A multivariate measure of variance using information from all 3 genetic markers confirmed that the small patches displayed greater overall genetic differentiation. This was further quantified by computing an Fst value, combined across loci, of 0.018 for the small patches and 0.004 for the large patches. No significant difference between patch size classes in mean allele frequency was detected. Mark and recapture studies of the adults found in five small and four large patches showed the residence times of adults in small patches to be less than half of those found in large patches. This was interpreted as resulting from higher emigration rates from small patches. It is proposed that greater genetic differentiation is found among demes from smaller patches because smaller patches support smaller population sizes and further because smaller patches act as net exporters of migrants while larger patches act as net migrant importers.

Gene diversity and female philopatry.

The effect of female philopatry on the apportionment of gene diversity within a population is evaluated. Even with random mate selection, the apportionment of gene diversity within and among social lineages (groups of related females) is inherently different than in classically defined demic groups. Considerable excess heterozygosity occurs within lineages without substantial changes in total or population heterozygosity. The proportion of genetic variance among lineages within the population was dependent on the lineage size and the number of male breeders per lineage. The greatest genetic differentiation among lineages was evident when there was one polygynous male breeding within a lineage of philopatric females, a common breeding tactic in mammalian social systems. The fixation indices depicting the genetic structure of the population were found to attain constant values after the first few generations despite the continuous loss of gene diversity within the population by genetic drift. Additionally, the change of gene correlations within individuals relative to the change within the population attains a state of dynamic equilibrium, as do the changes of gene correlations within lineages relative to the total and within individuals relative to within lineages. Comparisons of coancestries and fixation indices for philopatric versus randomly dispersing females indicate that philopatry and polygyny have probably not evolved independently and that promotion of gene correlations among adults rather than offspring has been of primary importance.

Genetic variation between and within populations of Engelmann spruce and subalpine fir

The genetic structure of Engelmann spruce (Picea engelmannii) and subalpine fir (Abies lasiocarpa) in two adjacent sites in the Colorado Front Range was examined using allozyme data from 21 loci in spruce and 18 loci in fir. The genetic diversity measures of alleles per locus, percent loci polymorphic, and mean heterozygosity did not differ significantly between or within species. However, the observed heterozygosity (0.126 spruce, 0.081 fir) values suggest that Engelmann spruce is more genetically variable than subalpine fir. Mean inbreeding coefficients were twice as high in fir as in spruce (FIS = 0.154 spruce, 0.341 fir). There were significant differences in allele frequencies in both species between and within sites, and among age-classes, with spatial differences greater than temporal differences. F-statistics showed greater genetic differentiation within (FST = 2.3–2.6% spruce, 2.0–2.8% fir) than between sites (FST = 1.7% spruce, 1.3% fir). Both species had higher FST and genetic distance values, yet lower FIS values, for spatial subdivisions within rather than between sites. This pattern suggests that the size of a spatial subdivision, where maximum gene flow is 54 m, approximates the size of the largest panmictic unit. In contrast with studies on other conifers, these results suggest that factors such as differential selection pressures, seed dispersal patterns, and clumped spatial distribution have resulted in genetic differentiation at the microhabitat level in Engelmann spruce and subalpine fir.Key words: genetic variation, genetic structure, allozymes, Engelmann spruce, subalpine fir, microgeographic differentiation.

Genetic variability and differentiation in a species complex of troglobitic beetles based on isozyme data

Abstract To reconstruct phylogenetic relationships, methods are described for the resolution of troglobitic Coleoptera enzymes by horizontal starch gel and vertical polyacrylamide gel electrophoresis. An electrophoretic survey of 18 loci distributed among 15 enzyme systems revealed that 23, 25 and 41% of the loci are polymorphic in Speonomus hydrophilus, S. zophosinus and S. colluvii . A comparison of the genetic structure of populations of the three endemic and closely related species is given and a significant deficiency of heterozygotes was noted at all loci in all populations. The very great genetic differentiation between populations in the complex of three species and the fixation of different alleles at eight loci indicate an absence of gene flow between the species at present. Our data support a close relationship between S. hydrophilus and S. zophosinus.

Genetic Variation in a Dwarfed Lineage, the Mexican Salamander Genus Thorius (Amphibia: Plethodontidae): Taxonomic, Ecologic and Evolutionary Implications

Patterns of genetic relationship and taxonomic identity are examined in Thorius, an enigmatic genus of minute neotropical salamanders that represent the smallest tailed tetrapods. Data comprise an electrophoretic analysis of 16 protein loci in 69 population samples from 55 localities throughout the range of the genus in southern Mexico. Eight of the nine described species are genetically distinct: Nei's D commonly exceeds 0.9. There is no biochemical evidence of more than a single species at Zoquitlan, Pue., type locality of T. schmidti and T. maxillabrochus. Genetic differentiation between disjunct subspecies of T. pennatulus is less than the mean pairwise value between described species, but exceeds that observed between some sympatric species pairs. Seven additional as yet undescribed species are identified, based either on their sympatric occurrence with, or great genetic differentiation from, described species. Most species initially identified by electrophoresis are morphologically distinct. Electrophoretic data fail to resolve the taxonomic affinity of a few remaining populations, although they do provide clearcut and distinguishable hypotheses of relationship that can be tested using other sources, such as morphology. The 15 species constitute three faunal units: Veracruz and eastern Puebla; Sierra de Juarez, Oaxaca; southern and western Oaxaca, and Guerrero. Local endemism is observed within each region, in which sympatry involving two or three species is common. Species frequently demonstrate narrow elevational zonation and distinct habitat and microhabitat preference (e.g., arboreal vs terrestrial). The distribution of four species on Cerro Pelon, Oax., is examined in detail.