Genetic variation of Azov and Black sea herring Alosa pontica (Eihwald, 1838), (Clupeiformes, Alosinae) in Danube river: analysis of biochemical gene markers

Genetic variation and structure of Danube stock of Aloca pontica pontica were investigated during the spawning moving by means of biochemical genetic marking. The level of heterozygosity was Hobs = 0,009. It is essentially lower than the average level for populations of other Teleostei and Clupeidae representatives. Polymorphism was defined only for Es-D of 20 analyzed loci expressed in muscle tissues. The allele frequencies for this locus were reliably different in the early spawning and later spawning parts of the stock, as well as proportion of heterozygotes and genotype diversity which was higher at the beginning of spawning moving. These results are discussed from two points of view: genetic differences between subpopulations in the course of spawning moving and presence of two close species of herring which come for the spawning together and hybridize to each other.     

Genetic structure and differentiation in cultivated grape,Vitis vinifera L

222 cultivated (Vitis vinifera) and 22 wild (V. vinifera ssp. sylvestris) grape accessions were analysed for genetic diversity and differentiation at eight microsatellite loci. A total of 94 alleles were detected, with extensive polymorphism among the accessions. Multivariate relationships among accessions revealed 16 genetic groups structured into three clusters, supporting the classical eco-geographic grouping of grape cultivars: occidentalis, pontica and orientalis. French cultivars appeared to be distinct and showed close affinity to the wild progenitor, ssp. sylvestris from south-western France (Pyrenees) and Tunisia, probably reflecting the origin and domestication history of many of the old wine cultivars from France. There was appreciable level of differentiation between table and wine grape cultivars, and the Muscat types were somewhat distinct within the wine grapes. Contingency chi2 analysis indicated significant heterogeneity in allele frequencies among groups at all loci. The observed heterozygosities for different groups ranged from 0.625 to 0.9 with an overall average of 0.771. Genetic relationships among groups suggested hierarchical differentiation within cultivated grape. The gene diversity analysis indicated narrow divergence among groups and that most variation was found within groups (approximately 85%). Partitioning of diversity suggested that the remaining variation is somewhat structured hierarchically at different levels of differentiation. The overall organization of genetic diversity suggests that the germplasm of cultivated grape represents a single complex gene pool and that its structure is determined by strong artificial selection and a vegetative mode of reproduction.     

Genetic polymorphism of adenosine deaminase (ADA; E.C. 3.5.4.4.) in allis shad, Alosa alosa and twaite shad, Alosa fallax

A genetic polymorphism of adenosine deaminase (ADA), is described for the first time in European shad species, Alosa alosa and Alosa fallax . Significant heterogeneity in gene frequencies was found, both between species and within species.     

Biochemical genetic variation among populations of the greenshell mussel, Perna canaliculus, from New Zealand: preliminary findings

Seven polymorphic and four monomorphic allozyme loci were assayed from nine wild populations and one cultured population of the endemic New Zealand greenshell mussel, Perna canaliculus. Genetic variation was examined to determine the extent of intra-population subdivision and inter-population variability. Five of seven polymorphic loci exhibited significant heterozygote deficiencies compared to Hardy-Weinberg equilibrium. Population F-statistics indicated that significant genetic heterogeneity exists among populations, indicating that there is insufficient gene flow between geographically isolated populations to create panmixia. The observed genetic heterogeneity among populations is best explained by an isolation-by-distance model of gene flow, which is modified by localized hydrographic conditions. These preliminary findings are discussed in the context of the one previous survey of population genetic variation in P. canaliculus and how this information relates to the gene flow of the greenshell mussel in New Zealand, which is often mediated by human transport from the main collection site of Kaitaia to aquaculture sites throughout the country.     

Morphometric, meristic character and electrophoretic analyses of two Irish populations of twaite shad, Alosa fallax (Lacépède)

Since 1911 a rare lacustrine form of twaite shad, Alosa fallax killarnensis Regan (1916), has been known to occur in the Killarney Lakes. During the summers of 1985 and 1986 a gill netting programme in Lough Leane for brown trout, Salmo trutta L., yielded 32 shad (1985) and 64 shad (1986) as a by-catch. These fish were deep frozen and compared with a sample of 59 marine twaite shad, taken on rod and line from St Mullin's, Co. Carlow, which had entered the River Barrow to spawn.
Morphometric, meristic and electrophoretic character analyses were carried out on the two populations. The three analyses, particularly the isoelectric focusing, confirmed a high degree of genetic similarity. The two major differences found were the dwarfed size of the Killarney shad and the increased numbers of gill rakers carried on the first branchial arch. The merits and demerits of assigning the term subspecies to the Killarney shad are discussed in the light of the available evidence produced.     

A Comprehensive Study of Genic Variation in Natural Populations of Drosophila Melanogaster. VI. Patterns and Processes of Genic Divergence between D. Melanogaster and Its Sibling Species, Drosophila Simulans

We present here an extensive set of data on allelic differences between homologous proteins of Drosophila melanogaster and its sibling species, Drosophila simulans, obtained by nondenaturing one-dimensional, and denaturing two-dimensional gel electrophoresis. The data suggest that, for these two species, (1) approximately 10% of protein-coding loci have no alleles in common in our sample, (2) the extent of genic variation at a locus (mean heterozygosity) within a species is not correlated with the extent of divergence (Nei's genetic distance) at that locus between species, and (3) significant heterogeneity of divergence rates exists for different structural/functional classes of loci. These results are discussed in the context of the dynamics of genetic variation within and between species.     

A two-step test for the heterogeneity of Fst values at different loci

Under genetic drift and in the absence of selection, the Fst values are expected to be equal at all loci, and heterogeneity among such values is considered as an evidence for different systematic pressures affecting the different genetic systems considered. A two-step test is here proposed. Fst values at various loci are classified into two nonarbitrary groups through the analysis of the association between pairs of genetic and environmental variables; the heterogeneity is then assessed by Wilcoxon's two-sample test. Estimation of the theoretical variance of Fst, which causes major shortcomings in the test proposed by Lewontin and Krakauer in 1973, is thus avoided.     

Small-scale clinal variation, genetic diversity and environmental heterogeneity in the marine gobies Pomatoschistus minutus and P. lozanoi (Gobiidae, Teleostei)

Genetic variation was assayed at 14 allozyme loci in estuarine, coastal and offshore samples of lozano's goby, Pomatoschistus lozanoi and the sand goby, P. minutus. Samples were taken from locations on the Belgian Continental Shelf and in the Schelde estuary with a range of environmental heterogeneity. We evaluate whether any differences in (1) the degree of genetic variation and (2) allele frequencies at the various loci exist within samples occurring in various habitats on the BCS and in the Schelde estuary. No significant differences in levels of genetic diversity were recorded between estuarine, coastal and offshore samples in either species. A temporally stable clinal gradient in allele frequencies at the two-allele locus GPI-A(*) was observed in P. lozanoi, differentiating the samples in an estuarine, coastal and offshore group. We suggest that these differences might be maintained by balancing selection at locus GPI-A(*).     

Electrophoretic identity between allis shad, Alosa alosa (L.), and twaite shad, A.fallax (Lacépède)

Morphological characteristics as well as electrophoretic polymorphism have been analysed in eight samples of allis shad, Alosa alosa (L.) and twaite shad, Alosa fallax (Lacepede), collected in the Loire basin and the Gironde-Dordogne system. The morphological characteristics showed that allis and twaite shad were present in these samples. Moreover, specimens with intermediate characteristics were found in the Loire and assumed to be hybrids between the two forms. By contrast, the two species were monomorphic and electrophoretically indistingishable at the 22 loci analysed. Therefore, it cannot be excluded that these two forms correspond to a single species.     

Formation of population genetic structure following the introduction and establishment of non-native American shad (<Emphasis Type="Italic">Alosa sapidissima</Emphasis>) along the Pacific Coast of North America

Biological invasions provide opportunities to examine contemporary evolutionary processes in novel environments. American shad, an anadromous fish native to the Atlantic Coast of North America, was introduced to California in 1871 and established spawning populations along the Pacific Coast that may provide insights into the dynamics of dispersal, colonization, and the establishment of philopatry. Using 13 neutral microsatellite loci we genotyped anadromous, freshwater resident and landlocked American shad from 14 locations along the US Pacific Coast to resolve population genetic structure. We observed significant differences in multilocus allele frequency distributions in nearly all (61/66; 92%) pairwise comparisons of non-native anadromous, freshwater resident and landlocked populations, and detected significant genetic differentiation for most (55/66; 83%) of these comparisons. Genetic divergence between landlocked and anadromous populations is due to genetic drift in isolation because of a physical migration barrier. However, some reproductive isolating mechanism maintains genetic differentiation between sympatric populations in the Columbia River exhibiting alternative life history strategies (i.e. anadromous vs. ‘freshwater-type’). Non-native populations possessed genetic variants that were not observed in the species’ native range and were strongly differentiated from Atlantic Coast populations (\({\text{G}}^{{\prime }}_{\text{ST}}\)?=?0.218). Our results indicate that philopatry became established shortly after dispersal and colonization along the Pacific Coast. This study contributes to our understanding of dynamic evolutionary processes during invasions.     

Analysis of biochemical genetic data on Jewish populations: II. Results and interpretations of heterogeneity indices and distance measures with respect to standards.

A nonparametric statistical methodology is used for the analysis of biochemical frequency data observed on a series of nine Jewish and six non-Jewish populations. Two categories of statistics are used: heterogeneity indices and various distance measures with respect to a standard. The latter are more discriminating in exploiting historical, geographical and culturally relevant information. A number of partial orderings and distance relationships among the populations are determined. Our concern in this study is to analyze similarities and differences among the Jewish populations, in terms of the gene frequency distributions for a number of genetic markers. Typical questions discussed are as follows: These Jewish populations differ in certain morphological and anthropometric traits. Are there corresponding differences in biochemical genetic constitution? How can we assess the extent of heterogeneity between and within groupings? Which class of markers (blood typings or protein loci) discriminates better among the separate populations? The results are quite surprising. For example, we found the Ashkenazi, Sephardi and Iraqi Jewish populations to be consistently close in genetic constitution and distant from all the other populations, namely the Yemenite and Cochin Jews, the Arabs, and the non-Jewish German and Russian populations. We found the Polish Jewish community the most heterogeneous among all Jewish populations. The blood loci discriminate better than the protein loci. A number of possible interpretations and hypotheses for these and other results are offered. The method devised for this analysis should prove useful in studying similarities and differences for other groups of populations for which substantial biochemical polymorphic data are available.     

The population-genetic structure of <Emphasis Type="Italic">Corbicula japonica</Emphasis> prime, 1864 (Bivalvia: Cyrenidae) in estuarine water bodies of the Primorsky Region

The population-genetic structure of the bivalve Corbicula japonica from ten estuarine localities in the Primorsky Region was investigated using nine allozyme loci as gene markers. This study revealed spatial genetic heterogeneity between the investigated populations (G _st = 0.05); its degree was dependent on the distance between populations. No linkage disequilibrium was found for any pair of loci. The index of genetic similarity between pairs of populations varied from 0.916 to 0.994. The genetic heterogeneity of the C. japonica populations is probably a result of genetic drift balanced by an irregular gene flow. Such an equilibrium may indicate a relatively recent expansion of C. japonica, which may have occurred during the Holocene climatic optimum (about 7500 years ago).     

Feeding chronology and habits of Alosa spp. (Clupeidae) juveniles from the lower Hudson River estuary, New York

Synopsis Feeding habits of juvenile alewife, A. pseudoharengus, blueback herring, A. aestivalis, and American shad, Alosa sapidissima, were examined over a 24 h period at an inshore location on the lower Hudson River. Feeding periodicity differed by species: alewives showed no diel differences, whereas shad fed least intensively near dawn and herring least intensively at night. Alewives fed primarily on chironomids and the amphipod Corophium lacustre, shad on Formicidae and larval chironomids, and herring on chironomids and copepods. Diel variation in prey selection was evident. Dietary overlap was generally greatest between alewife and herring and least between shad and herring.     

Genetic structure of the Iberian chub,Leuciscus pyrenaicus,in the Tejo drainage

The pattern of genetic variation in 38 samples of Leuciscus pyrenaicus, from seven sites in the Tejo drainage sampled on six occasions (over 19 months), were examined electrophoretically at 12 variable loci. Significant levels of spatial subdivision were observed. In general, the genetic distances in a river, were smaller than those between rivers. The differences observed suggest that isolation-by-distance is one important factor responsible for the spatial genetic differentiation. Moreover, the genetic diversity of this species in the Tejo drainage seems to be influenced by habitat heterogeneity, i.e., upland and lowland rivers. In opposition to other cyprinid species inhabiting the same drainage, the disruption of connectivity between populations above and below dams was not confirmed. This revised version was published online in July 2006 with corrections to the Cover Date.     

The genetic structure of populations of the sea urchin Strongylocentrotus intermedius from the northwestern Sea of Japan in connection with a shift in spawning time

Usin seven allozyme loci as gene markers, we studied the genetic structure of ten natural populations of the sea urchin Strongylocentrotus intermedius in the northwestern Sea of Japan that differ in the proportion of individuals with different spawning seasonality (early spawning at the end of May?CJune and late spawning in September-early October). This study revealed the spatial genetic heterogeneity of the sea-urchin populations (F _st = 0.051); its degree was independent of the geographic distance between populations. Out of the seven loci that were surveyed, four loci (peptidase Pep-1, Pep-2, mannose phosphate isomerase Mpi, and inorganic pyrophosphatase Ipp) accounted for the differences between pairs of samples; different loci contributed to the variation in each sample pair. The genetic similarity between pairs of populations ranged from 0.905 to 0.988. The genetic heterogeneity of the sea-urchin populations seems to be a result of both genetic drift and natural selection. At the same time, no significant genetic differences were found between specimens of S. intermedius with different spawning times (the genetic similarity was 0.988?C0.991). The shift in spawning season from autumn to early summer in the populations of S. intermedius inhabiting the areas of Peter the Great Bay adjacent to Vladivostok city can be explained by a phenotypic response of this species to environmental changes caused by chronic anthropogenic pollution of the bay.     

Ontogeny, diet shifts, and nutrient stoichiometry in fish

Most stoichiometric models do not consider the importance of ontogenetic changes in body nutrient composition and excretion rates. We quantified ontogenetic variation in stoichiometry and diet in gizzard shad, Dorosoma cepedianum , an omnivorous fish with a pronounced ontogenetic diet shift; and zebrafish, Danio rerio, grown in the lab with a constant diet. In both species, body stoichiometry varied considerably along the life cycle. Larval gizzard shad and zebrafish had higher molar C:P and N:P ratios than larger fish. Variation in body nutrient ratios was driven mainly by body P, which increased with size. Gizzard shad body calcium content was highly correlated with P content, indicating that ontogenetic P variation is associated with bone formation. Similar trends in body stoichiometry of zebrafish, grown under constant diet in the laboratory, suggest that ontogeny (e.g. bone formation) and not diet shift is the main factor affecting fish body stoichiometry in larval and juvenile stages. The N:P ratio of nutrient excretion also varied ontogenetically in gizzard shad, but the decline from larvae to juveniles appears to be largely associated with variation in the N:P of alternative food resources (zooplankton vs detritus) rather than by fish body N:P. Furthermore, the N:P ratio of larval gizzard shad excretion appears to be driven more by the N:P ratio at which individuals allocate nutrients to growth, more so than static body N:P, further illustrating the need to consider ontogenetic variation. Our results thus show that fish exhibit considerable ontogenetic variation in body stoichiometry, driven by an inherent increase in the relative allocation of P to bones, whereas ontogenetic variation in excretion N:P ratio of gizzard shad is driven more by variation in food N:P than by body N:P.     

Inheritance Beyond Plain Heritability: Variance-Controlling Genes in Arabidopsis thaliana

The phenotypic effect of a gene is normally described by the mean-difference between alternative genotypes. A gene may, however, also influence the phenotype by causing a difference in variance between genotypes. Here, we reanalyze a publicly available Arabidopsis thaliana dataset [1] and show that genetic variance heterogeneity appears to be as common as normal additive effects on a genomewide scale. The study also develops theory to estimate the contributions of variance differences between genotypes to the phenotypic variance, and this is used to show that individual loci can explain more than 20% of the phenotypic variance. Two well-studied systems, cellular control of molybdenum level by the ion-transporter MOT1 and flowering-time regulation by the FRI-FLC expression network, and a novel association for Leaf serration are used to illustrate the contribution of major individual loci, expression pathways, and gene-by-environment interactions to the genetic variance heterogeneity.     

Weak population differentiation in northern European populations of the endangered anadromous clupeid Alosa fallax

Examination of genetic structure among different spawning populations of the endangered twaite shad Alosa fallax showed statistically significant but weak differentiation estimated using nine microsatellite loci. Results point to substantial gene flow among the majority of individual estuary/river spawning locations, and no evidence that habitat disruption has led to increased local genetic drift.     

Detecting linkage for genetically heterogeneous diseases and detecting heterogeneity with linkage data.

Interest in searching for genetic linkage between diseases and marker loci has been greatly increased by the recent introduction of DNA polymorphisms. However, even for the most well-behaved Mendelian disorders, those with clear-cut mode of inheritance, complete penetrance, and no phenocopies, genetic heterogeneity may exist; that is, in the population there may be more than one locus that can determine the disease, and these loci may not be linked. In such cases, two questions arise: (1) What sample size is necessary to detect linkage for a genetically heterogeneous disease? (2) What sample size is necessary to detect heterogeneity given linkage between a disease and a marker locus? We have answered these questions for the most important types of matings under specified conditions: linkage phase known or unknown, number of alleles involved in the cross at the marker locus, and different numbers of affected and unaffected children. In general, the presence of heterogeneity increases the recombination value at which lod scores peak, by an amount that increases with the degree of heterogeneity. There is a corresponding increase in the number of families necessary to establish linkage. For the specific case of backcrosses between disease and marker loci with two alleles, linkage can be detected at recombination fractions up to 20% with reasonable numbers of families, even if only half the families carry the disease locus linked to the marker. The task is easier if more than two informative children are available or if phase is known. For recessive diseases, highly polymorphic markers with four different alleles in the parents greatly reduce the number of families required.     

Genetic differences and similarities in the introduced population of European beaver (Castor fiber L., 1785) in the Kirov and Novosibirsk regions of Russia

Potential factors were analyzed that affected the formation of gene pools of two introduced beaver populations founded in the 1940s-1950s by releasing beavers from Voronezh oblast and Belarus into rivers of the Kirov and Novosibirsk oblasts. The populations from these two regions were shown to differ in four allozyme loci (Ahd-2, Gpi, Es-5, and Dia-2). Within Kirov oblast, the samples from three tributaries of the Vyatka River differed in three other loci (Ck-1, Gp-9, and Trf). It is suggested that these features of the allele distribution at these loci are explained by the history of the introduced populations, hybridization between beavers from Voronezh oblast and Belarus, and founder effect during the subsequent artificial and spontaneous migration. Generally, genetic differences between the populations in all studied loci were very small: D = 0.02 between populations from different regions and D = 0.01 between populations from the tributaries of third-order rivers of the Kirov oblast. At the same time, disequilibrium was detected for ten polymorphic loci in the combined sample from the populations of Kirov oblast, which indicates the existence of interpopulation heterogeneity at the level of local populations of fourth- and fifth-order rivers. The unexpected finding of a genetic similarity between one studied individual of Tuvinian beaver subspecies (Castor fiber tuvinicus) and C. f. orientoeuropeas was recorded.