Population differences of aspartate aminotransferase and peptidase in the bay mussel Mytilus edulis

This investigation has demonstrated considerable heterogeneity among populations and some heterogeneity within populations in the distribution of alleles at two variant loci of Mytilus edulis. Although the causes of this variation remain obscure, some speculations have been made on the basis of available data. A cline for aspartate aminotransferase (AAT) alleles has been observed on the Pacific Coast. An immigration model has been proposed to explain the atypical ecological and genetic characteristics of large mussels found on Amchitka Island, Alaska. Marked differences were found in the distribution of peptidase alleles among collections from Southern California, the North Pacific Ocean, and New Jersey. Deviations from random distribution of phenotypes observed in comparisons made between large and small mussels from the New Jersey collection may reflect selection operating on these loci in this population.     

Allozyme frequencies in New Jersey and North Carolina populations of Atlantic white-cedar, Chamaecyparis thyoides (Cupressaceae)

The present study was conducted to assess the distribution of genetic variation within and among populations of Chamaecyparis thyoides in both marginal and centrally located populations. Allozyme frequency analyses of ten loci from foliage of four New Jersey populations and two North Carolina populations of C. thyoides showed polymorphic loci = 50%, mean number of alleles per locus = 2.8, effective number of alleles per locus = 1.17, and expected heterozygosity = 0.14. Diversity was highest in two populations from southern New Jersey. The isolated population at High Point, New Jersey had only two polymorphic loci and expected heterozygosity of 0.03. There was no correlation between genetic and geographic distances among populations, implying that cedar must have possessed some means of long-distance dispersal at the end of the last glacial period, rather than advancing northward step by step.     

Crop-to-weed introgression has impacted allelic composition of johnsongrass populations with and without recent exposure to cultivated sorghum

Sorghum halepense L. (johnsongrass) is one of the world's most noxious weeds, and a paradigm for the potential dangers of crop-weed hybridization. Introduced into the southeastern United States about 200 years ago, S. halepense is a close relative of cultivated sorghum (Sorghum bicolor). Both artificial crossing and experimental field studies have demonstrated the potential for S. halepensex S. bicolor hybrid formation, but no prior study has addressed the long-term persistence of sorghum genes in johnsongrass populations. We surveyed 283 loci (on all 10 sorghum linkage groups) to identify 77 alleles at 69 loci that are found in US sorghum cultivars but are absent from a worldwide sampling of johnsongrass genotypes. These putatively cultivar-specific alleles were present in up to 32.3% of individuals in johnsongrass populations adjacent to long-term sorghum production fields in Texas and Nebraska. Lower frequencies of cultivar-specific alleles at smaller numbers of loci are found in johnsongrass populations from New Jersey and Georgia with no recent exposure to cultivated sorghum, suggesting that introgressed sorghum alleles may be dispersed across long distances. The number of cultivar-specific alleles and extensive multilocus patterns of cultivar-specific allelic composition observed at both linked and unlinked loci in the johnsongrass populations, are inconsistent with alternatives to introgression such as convergence, or joint retention of ancestral polymorphisms. Naturalized johnsongrass populations appear to provide a conduit by which transgenes from sorghum could become widely disseminated.     

Genetic Population Structure and Gene Flow in the Atlantic Cod Gadus Morhua: A Comparison of Allozyme and Nuclear RFLP Loci

High levels of gene flow have been implicated in producing uniform patterns of allozyme variation among populations of many marine fish species. We have examined whether gene flow is responsible for the limited population structure in the Atlantic cod, Gadus morhua L., by comparing the previously published patterns of variation at 10 allozyme loci to 17 nuclear restriction fragment length polymorphism (RFLP) loci scored by 11 anonymous cDNA clones. Unlike the allozyme loci, highly significant differences were observed among all populations at the DNA markers in a pattern consistent with an isolation-by-distance model of population structure. The magnitude of allele frequency variation at the nuclear RFLP loci significantly exceeded that observed at the protein loci (χ(2) = 24.6, d.f. = 5, P < 0.001). Estimates of gene flow from the private alleles method were similar for the allozymes and nuclear RFLPs. From the infinite island model, however, estimates of gene flow from the DNA markers were fivefold lower than indicated by the proteins. The discrepancy between gene flow estimates, combined with the observation of a large excess of rare RFLP alleles, suggests that the Atlantic cod has undergone a recent expansion in population size and that populations are significantly displaced from equilibrium. Because gene flow is a process that affects all loci equally, the heterogeneity observed among populations at the DNA level eliminates gene flow as the explanation for the homogeneous allozyme patterns. Our results suggest that a recent origin of cod populations has acted to constrain the extent of population differentiation observed at weakly polymorphic loci and implicate a role for selection in affecting the distribution of protein variation among natural populations in this species.     

Patterns of genetic variability at individual minisatellite loci in minke whale Balaenoptera acutorostrata populations from three different oceans

The genetic variability at six cloned minisatellite loci was analyzed in minke whale populations from the North Atlantic, North Pacific, and Antarctic Oceans. Three loci displayed only a few different alleles in each of the three populations, with heterozygosity ranging from 0.00 to 0.47, and three loci revealed many different alleles in at least two fo the three populations, with heterozygosity ranging up to 0.98. Using small sample sizes, samples from two adjacent Antarctic Management Areas were not found to differ significantly in allele frequencies at any of the six loci. The use of principal coordinate analysis to detect multilocus disequilibria was explored. No significant evidence was found of intrapopulation heterogeneity within the pooled Antarctic sample. Pronounced interoceanic differences were observed at every locus, confirming the existence of genetic isolation found earlier using more conventional marker systems. The populations from the three oceans appear to have diverged to such a degree that the hypervariable loci have had time to evolve independently and arrive at different evolutionary stages in different populations. The frequency of undetected "null" alleles is remarkably high in minke whale populations compared to human populations and is probably a result of the cloning protocol used. Minisatellite loci are shown to provide a powerful population genetic tool, supplying levels of resolution appropriate to different degrees of evolutionary divergence.      

Allozyme and microsatellite DNA markers of toothfish population structure in the Southern Ocean

Toothfish represent a major finfish resource in the Southern Ocean, where there has been a rapid increase in exploitation of the Patagonian toothfish Dissostichus eleginoides. Molecular genetic methods have been applied to address questions relating to stock discrimination in D. eleginoides. Eight microsatellite loci were tested in population samples from the Atlantic, Indian, and Pacific Ocean sectors of the Southern Ocean. Some loci were characterised by a large number of alleles, but no alleles were restricted to specific ocean basins. However there was a significant allelic heterogeneity in the total data indicative of population differentiation, and a high level of genetic sub-division was measured with F _ST and R _ST. Seven polymorphic allozyme loci revealed no significant heterogeneity among Pacific and Indian Ocean sector samples. The microsatellite DNA heterogeneity suggests that there is restricted gene flow through the Southern Ocean, and that the different fishing grounds may support independent stocks.     

Strong founder effect in Drosophila pseudoobscura colonizing New Zealand from North America

The North American native species Drosophila pseudoobscura was first identified in New Zealand in the last few decades. Here, we have studied the genetic consequences of its spread across the Pacific Ocean. Using 10 microsatellites that are highly variable in North American populations, we found that the New Zealand population has substantially fewer alleles, a much lower average heterozygosity, and significantly different allele frequencies at these loci. We have discussed the relative sensitivity of these parameters for detecting the founding event. X-linked loci were more strongly differentiated between continents than autosomal loci, as reflected by larger changes in allele frequencies and greater reductions in numbers of alleles and average heterozygosity. The severity of the genetic diversity loss supports a scenario of a few D. pseudoobscura females being introduced to New Zealand from North America.     

Genetic variation at twentythree microsatellite loci in sixteen human populations

We have analysed genetic variation at 23 microsatellite loci in a global sample of 16 ethnically and geographically diverse human populations. On the basis of their ancestral heritage and geographic locations, the studied populations can be divided into five major groups, viz. African, Caucasian, Asian Mongoloid, American Indian and Pacific Islander. With respect to the distribution of alleles at the 23 loci, large variability exists among the examined populations. However, with the exception of the American Indians and the Pacific Islanders, populations within a continental group show a greater degree of similarity. Phylogenetic analyses based on allele frequencies at the examined loci show that the first split of the present-day human populations had occurred between the Africans and all of the non-African populations, lending support to an African origin of modern human populations. Gene diversity analyses show that the coefficient of gene diversity estimated from the 23 loci is, in general, larger for populations that have remained isolated and probably of smaller effective sizes, such as the American Indians and the Pacific Islanders. These analyses also demonstrate that the component of total gene diversity, which is attributed to variation between groups of populations, is significantly larger than that among populations within each group. The empirical data presented in this work and their analyses reaffirm that evolutionary histories and the extent of genetic variation among human populations can be studied using microsatellite loci.     

Analysis of F ST outliers at allozyme loci in Pacific salmon: implications for natural selection

Natural selection has been invoked to explain the observed geographic distribution of allozyme allele frequencies for a number of teleost species. The effects of selection on allozyme loci in three species of Pacific salmon were tested. A simulation-based approach to estimate the null distribution of population differentiation (F _ST) and test for F _ST outliers was used. This approach showed that a majority of allozyme loci conform to neutral expectations predicted by the simulation model, with relatively few F _ST outliers found. No consistent F _ST outlier loci were found across species. Analysis of population sub-groups based on geography and genetic identity reduced the number of outlier loci for some species, indicating that large geographic groups may include genetically divergent populations and/or that there is geographic heterogeneity in selection pressure upon allozyme loci. Two outlier allozyme loci found in this analysis, lactate dehydrogenase-B and malic enzyme, have been shown to be influenced by selection in other teleost species. This approach is also useful in identifying allozyme loci (or other genetic markers) that meet assumptions for population genetic study.     

A note on the frequency distribution of AB0 and rhesus blood groups in four Thai populations of Assam (India) and their position among the Mongoloids of this region

An attempt has been made to give a picture of the distribution of AB0 and Rhesus blood groups in four Thai populations of Assam, India. Intragroup heterogeneity and their position among the Mongoloid populations of this region have also been examined. In all of these groups the frequency of the 0-allele was found to be the most predominant one followed by B- and A-alleles, respectively. A similar trend is observed in some other populations of Asia. The populations under study show statistically similarity with none of the Mongoloid populations of Assam. The incidence of Rhesus-negatives in the populations under study ranges from complete absence to below 2%.     

Isolation and characterization of microsatellite loci in western North American Anodonta species

We have developed and characterized 13 microsatellite loci from a group of Anodonta species in western North America, and demonstrated their utility in populations representing two major clades in this genus. Allelic diversity and polymorphic information content were high for all loci, although these characteristics varied across populations. Deviations from Hardy-Weinberg genotypic ratios were not detected, although the estimated frequency of null alleles was high in one population for one locus. This is the first set of microsatellite loci to be developed for freshwater mussels in western North America, and will be useful for describing gene flow patterns among populations.     

Malate dehydrogenase types in the Asian-Pacific area,and a description of new phenotypes

A survey of more than 21 000 haemolysates from blood samples collected in various parts of south and southeast Asia, Australasia and the Western Pacific and examined in this laboratory has revealed several new alleles controlling variants of sMDH; in addition, further information has been provided on the distribution of sMDH3 in New Guinea. Two of the variant alleles, sMDH3 and sMDH6, achieve polymorphic frequency in various populations. sMDH3 is widely distributed in New Guinea, with highest frequencies in the Eastern Highlands. The pattern of its distribution suggests the mutant arose originally in a Papuan-speaking population. So far, sMDH6 has been detected only in Micronesians from a number of islands in the Carolines. A single example of another new variant, sMDH 5-1, and two examples of a slow variant, sMDH 7-1, were detected in samples from Iran and Singapore, respectively. No examples of mMDH variants were found in a total of 652 placental extracts from Papua New Guinea and Australia.     

Psorophora columbiae and Psorophora toltecum (Diptera: Culicidae) Colombian populations cannot be differentiated by isoenzymes

Two populations of the mosquito Psorophora columbiae from the central Andean area of Colombia and one population of Ps. toltecum from the Atlantic coast of Colombia were analyzed for 11 isoenzyme markers. Psorophora columbiae and Ps. toltecum are two of the main vectors of Venezuelan equine encephalitis. We found no conspicuous genetic differences between the two species. The relatively high gene flow levels among these populations indicate that these are not two different species or that there has been recent divergence between these taxa. In addition, no global differential selection among the loci was detected, although the alpha-GDH locus showed significantly less genetic heterogeneity than the remaining loci, which could mean that homogenizing natural selection acts at this locus. No isolation by distance was detected among the populations, and a spatial population analysis showed opposite spatial trends among the 31 alleles analyzed. Multiregression analyses showed that both expected heterozygosity and the average number of alleles per locus were totally determined by three variables: altitude, temperature and size of the human population at the locality. Individually, the expected heterozygosity is more related to these three variables than to the average number of alleles.     

Allozyme Loci Selection in the Pacific Mussel Mytilus trossulus under Stressful Conditions

The allozyme variability for 15 loci in two samples of the Pacific mussel Mytilus trossulus collected from a single giant cluster was investigated using the method of gel electrophoresis. One sample was subjected to short-term anaerobic stress and then to a longer aerobic stress, leading to the death of about 85% of the individuals. At some of the loci, significant differences in the genotypic and allele frequencies were found between the samples. The results are suggestive of the differential survival of mussels with different genotypes and alleles at some of the surveyed loci under stress. Our data are in agreement with the hypothesis of the adaptive significance of allozyme polymorphism.     

Assessing the allozyme variation in cultivars and Swedish landraces of rye (Secale cereale L.)

Genetic interpretation and diversity of 9 isozyme loci have been estimated in 7 improved varieties and 19 landraces from Sweden by means of starch gel electrophoresis. The isozyme systems were ACO, DIA, GPI, MDH, PGD and PGM. For the statistic analysis we used the following measures: average number of alleles per locus, percentage of polymorphic loci, average heterozygosity direct count and average heterozygosity Hardy-Weinberg expected unbiased estimate. The measures were made on species and population levels. The distribution of the total genetic diversity among populations was also calculated. To illustrate the genetic relationships among populations, genetic distances were measured and principal component analysis performed. As expected in a cross-pollinated crop we found high genetic diversity and a larger variation within than among the populations. Somewhat unexpectedly, however, we found that the currently used varieties have the same high level of heterozygosity as the landraces but in the dendrogram the two groups are separated. The dendrogram showed three main clusters. The large cluster included 21 populations and the two small clusters were clearly distinguishable from the rest. The landrace spring-type could not be separated from the landraces winter-type, but we did detect a difference between different spring types. A few populations had unique alleles for certain loci.     

Ancestral alleles and population origins: inferences depend on mutation rate.

Previous studies have found that at most human loci, ancestral alleles are "African," in the sense that they reach their highest frequency there. Conventional wisdom holds that this reflects a recent African origin of modern humans. This paper challenges that view by showing that the empirical pattern (of elevated allele frequencies within Africa) is not as pervasive as has been thought. We confirm this African bias in a set of mainly protein-coding loci, but find a smaller bias in Alu insertion polymorphisms, and an even smaller bias in noncoding loci. Thus, the strong bias that was originally observed must reflect some factor that varies among data sets--something other than population history. This factor may be the per-locus mutation rate: the African bias is most pronounced in loci where this rate is high. The distribution of ancestral alleles among populations has been studied using 2 methods. One of these involves comparing the fractions of loci that reach maximal frequency in each population. The other compares the average frequencies of ancestral alleles. The first of these methods reflects history in a manner that depends on the mutation rate. When that rate is high, ancestral alleles at most loci reach their highest frequency in the ancestral population. When that rate is low, the reverse is true. The other method--comparing averages--is unresponsive. Average ancestral allele frequencies are affected neither by mutation rate nor by the history of population size and migration. In the absence of selection and ascertainment bias, they should be the same everywhere. This is true of one data set, but not of 2 others. This also suggests the action of some factor, such as selection or ascertainment bias, that varies among data sets.     

Evolution of Ribosomal DNA (Rdna) Genetic Structure in Colonial Californian Populations of Avena Barbata

DNA samples from 980 plants of Avena barbata from 48 ecologically diverse sites in California and Oregon were assayed to determine their genotype for two duplicated loci governing rDNA variants. More than 40 different rDNA genotypes were observed among which 5 made up 96% of our sample in environmentally homogeneous sites; predominant genotypes were less frequent and recombinant genotypes were more frequent in environmentally heterogeneous sites. The spatial distribution of each predominant rDNA genotype was nearly an exact overlay on both macro- and microgeographical scales of a distinctive habitat and also of the distribution of an eight-locus morphological-allozyme variant genotype. In all, seven different habitat-genotype combinations (ecotypes) were distinguishable on the basis of their morphological-allozyme-rDNA genotypes. None of these seven genotypes has been found in ancestral Spanish populations; thus the above predominant multilocus genotypes (ecotypes) of the colonial populations evidently evolved subsequent to the recent introduction (within 150-200 generations) of A. barbata to California. The precise associations of specific alleles and genotypes of the morphological allozyme and rDNA loci with different specifiable habitats leads us to the conclusion that natural selection favoring particular multilocus combinations of alleles in different habitats was the main guiding force in shaping the internal genetic structure of local populations as well as the overall adaptive landscape of A. barbata over California and Oregon.     

Apparent Differential Selection at an Isozyme Locus between Queens and Workers of the Ant APHAENOGASTER RUDIS

The frequencies of two alleles at a cathodal malate dehydrogenase locus in populations of A. rudis were studied in 47 colonies from three localities in Georgia and one in New Jersey. The male gene frequencies of the New Jersey and one Georgia locality differ significantly. All the queens at one Georgia locality were heterozygotes. This genotypic distribution differs strongly from that of the workers, in which approximately equal numbers of heterozygotes and homozygotes were found. The heterozygote excess among queens but not their worker progeny suggests differential selection between these castes. This study also shows that rudis colonies consist of a single, once-mated queen and her worker progeny.     

Major Histocompatibility Complex (MHC) class II sequence polymorphism in long-finned pilot whale (Globicephala melas) from the North Atlantic

Determining how intra-specific genetic diversity is apportioned among natural populations is essential for detecting local adaptation and identifying populations with inherently low levels of extant diversity which may become a conservation concern. Sequence polymorphism at two adaptive loci (MHC DRA and DQB) was investigated in long-finned pilot whales (Globicephala melas) from four regions in the North Atlantic and compared with previous data from New Zealand (South Pacific). Three alleles were resolved at each locus, with trans-species allele sharing and higher levels of non-synonymous to synonymous substitution, especially in the DQB locus. Overall nucleotide diversities of 0.49?±?0.38% and 4.60?±?2.39% were identified for the DRA and DQB loci, respectively, which are relatively low for MHC loci in the North Atlantic, but comparable to levels previously described in New Zealand (South Pacific). There were significant differences in allele frequencies within the North Atlantic and between the North Atlantic and New Zealand. Patterns of diversity and divergence are consistent with the long-term effects of balancing selection operating on the MHC loci, potentially mediated through the effects of host-parasite coevolution. Differences in allele frequency may reflect variation in pathogen communities, coupled with the effects of differential drift and gene flow.     

Genetic structure of the global population of banana black leaf streak fungus, Mycosphaerella fijiensis

The genetic structure of Mycosphaerella fijiensis populations around the world was examined using DNA restriction fragment length polymorphism (RFLP) markers. Allele frequencies at 19 nuclear RFLP loci were estimated in a sample of 136 M. fijiensis isolates from five geographical populations representative of banana-producing areas (South-East Asia including the Philippines and Papua New Guinea, Africa, Latin America and Pacific Islands). Within each population, gametic disequilibrium tests between the 19 nuclear RFLP loci were mainly non significant ( P > 0.05), indicating that random sexual reproduction occurred in these populations. All M. fijiensis populations had a high level of genotypic and allelic diversity ( H , gene diversity: 0.25–0.59). The highest levels of gene diversity were found in the two South-East Asian populations ( H : 0.57 and 0.59). Most of the alleles (> 88%) detected in Africa, Latin America and Pacific Islands populations were also detected in South-East Asian populations. Furthermore, a high and significant ( P < 0.05) level of genetic differentiation was observed among M. fijiensis geographical populations (overall estimate of F_st : 0.32). These results were consistent with the hypothesis that M. fijiensis originated in South-East Asia and spread recently to other parts of the world. The level of allelic diversity in M. fijiensis populations from regions other than South-East Asia was drastically reduced, indicating founder effects. The data also suggested rare occurrence of migration of M. fijiensis between continents.