Significant Heterozygote Deficiency Research Articles

Genetic variation and population structure of endemic yellow catfish, Horabagrus brachysoma (Bagridae) among three populations of Western Ghat region using RAPD and microsatellite markers

Random amplified polymorphic DNA (RAPD) and microsatellite markers were applied to evaluate the genetic variation in endemic and endangered yellow catfish, Horabagrus brachysoma sampled from three geographic locations of Western Ghat, South India river systems. In RAPD, of 32 10-mer RAPD primers screened initially, 10 were chosen and used in a comparative analysis of H. brachysoma collected from Meenachil, Chalakkudy and Nethravathi River systems. Of the 124 total RAPD fragments amplified, 49 (39.51%) were found to be shared by individuals of all 3 populations. The remaining 75 fragments were found to be polymorphic (60.48%). In microsatellites, six polymorphic microsatellite loci were identified by using primers developed for Pangasius hypophthalmus, Clarias macrocephalus and Clarias gariepinus. The identified loci were confirmed as microsatellite by sequencing after making a clone. The nucleotide sequences of 6 loci were published in NCBI genbank. The number of alleles across the six loci ranged from 4 to 7 and heterozygosities ranged from 0.07 to 0.93. The mean number of alleles and effective number of alleles per locus were 5.00 and 3.314, respectively. The average heterozygosity across all investigated samples was 0.72, indicating a significant deficiency of heterozygotes in this species. RAPD and microsatellite methods reported a high degree of gene diversity and genetic distances depicted by UPGMA dendrograms among the populations of H. brachysoma.

Population Structure of Deep‐Sea and Oceanic Phenotypes of Deepwater Redfish in the Irminger Sea and Icelandic Continental Slope: Are They Cryptic Species?

AbstractThe deepwater redfish Sebastes mentella has a wide distribution in the North Atlantic Ocean. In the Irminger Sea, there is evidence for two phenotypes (deep‐sea and oceanic) of deepwater redfish. The two phenotypes have overlapping geographic distributions but differ in depth preferences. There are two hypotheses on deepwater redfish stock structure in the Irminger Sea. One suggests that mature individuals of a single stock segregate according to size and age and therefore that the phenotypes represent different life stages of the same stock. The other hypothesis suggests that there are two different stocks and that these stocks segregate mainly according to depth. Additionally, it is not clear whether the fish of the deep‐sea phenotype in the Irminger Sea and those on the Icelandic continental shelf represent one stock. Analysis of genetic variability at eight allozyme markers in 1,763 deepwater redfish from 26 samples collected at different depths in the Irminger Sea and the Icelandic continental slope showed a significant difference between deep‐sea and oceanic samples, suggesting the presence of two distinguishable stocks. This is supported by (1) significant heterozygote deficiency at most loci in pooled samples, (2) extensive allele frequency differences between samples classified as belonging to deep‐sea and oceanic phenotypes, and (3) clustering of deepwater redfish samples of the same phenotype in a neighbor‐joining dendrogram and in Bayesian analyses (STRUCTURE and the ΔK procedure for determining the number of clusters). The results indicate that deepwater redfish stock structure should be taken into account for sustainable fisheries management in the Irminger Sea and adjacent waters.

DNA-based parentage verification in two Australian goat herds

This study aimed to evaluate a set of DNA markers for their effectiveness in parentage inference, to quantify the level of pedigree errors in Australian Angora and Cashmere goat herds using different pedigree recording methods, and to investigate genotype mismatches between parent and offspring. The 14 microsatellite markers evaluated in this study provided a high level of power (probability of exclusion, PE >99.70%) for parentage testing. The extent of PE depended on polymorphic information content ( PIC) and number of alleles for each marker. The minimum number of MS markers essential for accurate determination of parentage was 12, when neither parent is known ( PE1) and 10, when one parent is known ( PE2). In both populations, the error rates of recorded sire and dam pedigree were significant, averaging around 12%. The error rates of sire and dam pedigree varied considerably between the two populations, reflecting management differences on the two properties. Of 14 MS markers, one locus, SRCRSP07, had null alleles present in the heterozygous state. This null allele was revealed by mismatches of genotypes of parent-offspring pairs. Highly significant deviation from Hardy–Weinberg Equilibrium and significant heterozygote deficiency was also observed at this locus.

Twelve new polymorphic microsatellite loci and PCR multiplexing in the whitefly, Bemisia tabaci

Twelve new dinucleotide microsatellite loci of the whitefly, Bemisia tabaci, were obtained from enriched genomic libraries. Three polymerase chain reaction multiplex sets comprising three, five and four loci were optimized and characterized across 133 B. tabaci females from Israeli rearings and natural populations collected in four Mediterranean countries (Tunisia, France, Spain and Morocco). There were three to 24 alleles per locus and the observed heterozygosity was from 0.084 to 0.420. Deviation from Hardy-Weinberg equilibrium was detected at four loci associated with significant heterozygote deficiencies due to null alleles and presence of subpopulations that were mostly in the Tunisian sample. The 12 loci carried independent information.

Microsatellite analysis reveals high genetic diversity but low genetic structure in Ethiopian indigenous cattle populations

Ethiopian cattle are under threat from uncontrolled mating practices and are at high risk of becoming genetically homogeneous. Therefore, to evaluate genetic diversity, population structure and degree of admixture, 30 microsatellite markers were genotyped using 351 DNA samples from 10 Ethiopian cattle populations and the Holstein breed. The mean number of alleles per cattle population ranged from 6.93 +/- 2.12 in Sheko to 7.50 +/- 2.35 in Adwa. The mean observed and expected heterozygosities were 0.674 +/- 0.015 and 0.726 +/- 0.019 respectively. Ethiopian cattle populations have maintained a high level of within-population genetic differentiation (98.7%), the remainder being accounted for by differentiation among populations (1.3%). A highly significant deficiency in heterozygotes was detected within populations (F(IS) = 0.071; P < 0.001) and total inbreeding (F(IT) = 0.083; P < 0.001). The study populations were highly admixed but distinct from pure Bos taurus and Bos indicus breeds. The various levels of admixture and high genetic diversity make Ethiopian cattle populations suitable for future genetic improvement and utilization under a wide range of agro-ecologies in Ethiopia.

An analysis of genetic diversity and inbreeding in Wuchereria bancrofti: implications for the spread and detection of drug resistance.

Estimates of genetic diversity in helminth infections of humans often have to rely on genotyping (immature) parasite transmission stages instead of adult worms. Here we analyse the results of one such study investigating a single polymorphic locus (a change at position 200 of the β-tubulin gene) in microfilariae of the lymphatic filarial parasite Wuchereria bancrofti. The presence of this genetic change has been implicated in benzimidazole resistance in parasitic nematodes of farmed ruminants. Microfilariae were obtained from patients of three West African villages, two of which were sampled prior to the introduction of mass drug administration. An individual-based stochastic model was developed showing that a wide range of allele frequencies in the adult worm populations could have generated the observed microfilarial genetic diversity. This suggests that appropriate theoretical null models are required in order to interpret studies that genotype transmission stages. Wright's hierarchical F-statistic was used to investigate the population structure in W. bancrofti microfilariae and showed significant deficiency of heterozygotes compared to the Hardy-Weinberg equilibrium; this may be partially caused by a high degree of parasite genetic differentiation between hosts. Studies seeking to quantify accurately the genetic diversity of helminth populations by analysing transmission stages should increase their sample size to account for the variability in allele frequency between different parasite life-stages. Helminth genetic differentiation between hosts and non-random mating will also increase the number of hosts (and the number of samples per host) that need to be genotyped, and could enhance the rate of spread of anthelmintic resistance.

Microsatellite markers developed for a Swedish population of sand lizard (Lacerta agilis)

Populations of sand lizards (Lacerta agilis) are declining throughout its north-western range. Here we characterize fifteen new microsatellite markers developed specifically for parentage analysis in a small Swedish population of sand lizards. These loci were screened in the Asketunnan population and a much larger and genetically diverse Hungarian population, with heterozygosities ranging from (0.217–0.875) and (0.400–0.974), respectively. All loci were in Hardy-Weinberg Equilibrium in the Swedish population but eight loci had significant heterozygote deficiencies in the Hungarian population. Two loci were significantly linked in both populations. These microsatellite loci are likely to be applicable in research on other sand lizard populations throughout Europe.

Y-chromosome diversity characterizes the Gulf of Oman

Arabia has served as a strategic crossroads for human disseminations, providing a natural connection between the distant populations of China and India in the east to the western civilizations along the Mediterranean. To explore this region's critical role in the migratory episodes leaving Africa to Eurasia and back, high-resolution Y-chromosome analysis of males from the United Arab Emirates (164), Qatar (72) and Yemen (62) was performed. The role of the Levant in the Neolithic dispersal of the E3b1-M35 sublineages is supported by the data, and the distribution and STR-based analyses of J1-M267 representatives points to their spread from the north, most likely during the Neolithic. With the exception of Yemen, southern Arabia, South Iran and South Pakistan display high diversity in their Y-haplogroup substructure possibly a result of gene flow along the coastal crescent-shaped corridor of the Gulf of Oman facilitating human dispersals. Elevated rates of consanguinity may have had an impact in Yemen and Qatar, which experience significant heterozygote deficiencies at various hypervariable autosomal STR loci.

Genetic Structure of Southern Appalachian “Sky Island” Populations of the Southern Red-backed Vole (Myodes gapperi)

Abstract Sequence data from a 597–base pair region of the mitochondrial DNA control region and data for 19 presumed allozyme loci were used to examine genetic structure and to detect gene flow among populations of southern red-backed voles (Myodes gapperi, formerly known as Clethrionomys gapperi) inhabiting spruce–fir “sky-islands” in the southern Appalachians. Allozyme data showed a significant heterozygote deficiency for most populations. Average individual heterozygosity varied among populations from 1.75% to 16.78% (X ± SE = 8.63% ± 2.03%). FST values between any 2 sites ranged from 0.100 to 0.517 (X ± SE = 0.296 ± 0.026), with a significant metapopulation FST value = 0.599. Nei's genetic distances (based on allozyme data) among spruce–fir habitats ranged from 0.037 to 0.310 (X ± SE = 0.139 ± 0.079). Analysis of molecular variance permitted determination of the extent of geographic subdivision of mitochondrial haplotypes for 3 hierarchically organized sampling regimes: 14 high-altitude sample sites...

Isolation and characterization of microsatellite loci from the endangered highlands scrub hypericum (Hypericum cumulicola)

AbstractWe report the isolation of 19 primer pairs for amplification of polymorphic microsatellite loci for Hypericum cumulicola. These markers were evaluated in 24 individuals from one population; two to four alleles were detected per locus, and observed heterozygosity ranged from 0 to 0.5. Two loci demonstrated significant heterozygote deficiencies, possibly due to null alleles, and significant linkage disequilibrium was found between six pairs of loci. The remaining microsatellite loci will help determine if genetic differentiation is responsible for life‐history differences between natural and anthropogenically disturbed populations of H. cumulicola.

Spatial and temporal population genetic survey of Bulinus globosus from Zanzibar: an intermediate host of Schistosoma haematobium

AbstractIn Zanzibar, the freshwater hermaphroditic snail Bulinus globosus is the intermediate host of the human parasite Schistosoma haematobium. To shed light on the patterns of genetic variation within Bu. globosus, variation at six polymorphic microsatellite loci was assessed to quantify spatial genetic structure within eight populations and temporal changes in a further four populations of the snails. Limited genetic variation was observed within populations, possibly reflecting both partial‐selfing and fluctuations in population size. Although a statistically significant heterozygote deficiency was observed, Bu. globosus appears to be a preferential out‐crosser, which was consistent with the absence of genotypic linkage disequilibria. Genetic variation across populations was substantial, illustrating significant isolation‐by‐distance on a regional scale and that gene flow was restricted to nearby populations. The temporal survey showed that levels of genetic variation and inbreeding changed over a 1‐year period, consistent with field observations of seasonal change. The results strongly support a snail demographic model of population expansion and contraction throughout the year with habitats re‐colonized by aestivating or surviving snails from local refugia. This model might help explain co‐evolution of snails and schistosomes in Zanzibar as local populations of Bu. globosus have varying degrees of susceptibility to S. haematobium.

Microsatellite markers reveal spatial genetic structure of Tetranychus urticae (Acari: Tetranychidae) populations along a latitudinal gradient in Europe

The genetic structure of populations of the two-spotted spider mite Tetranychus urticae was investigated along a south-north European transect spanning from southern France to The Netherlands. Mites were collected on Urtica dioica in 6 sampling zones. Microsatellite variation at 5 loci revealed considerable genetic variation with an average heterozygozity of 0.49. Significant heterozygote deficiency was found in 7 populations out of the 18 samples analyzed and one of them was completely monomorphic. Tetranychus urticae populations show some level of genetic structuring. First, genetic differentiation between localities (F (ST) estimates) was significant for all comparisons. Second, the analysis of molecular variance, AMOVA, indicates that there is an effect, albeit low (9%), of the locality in accounting for allele frequency variance. Geographic distance emerges as a factor responsible for this genetic structure. The results are discussed in relation to the biological features of the species and the known patterns of migration. Related agronomical issues are addressed.

Development and characterization of new microsatellite markers for ginseng (Panax ginseng C. A. Meyer)

Panax ginseng C.A. Meyer, commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. Its roots are highly prized for several medicinal properties. The present study describes development and characterization of twenty- two polymorphic microsatellite markers for this spe- cies. A total of 99 alleles were detected with an average of 4.5 alleles per locus across 20 accessions. Values for observed (HO) and expected (HE) heterozygosities ranged from 0.05 to 1.00 and from 0.18 to 0.73, respectively. Eleven loci deviated from Hardy-Wein- berg equilibrium (P < 0.001). Significant (P < 0.05) heterozygote deficiency was observed at 13 loci. Exact test for linkage disequilibrium showed significant val- ues (P < 0.05) between 12 pairs of loci. These micro- satellite markers provide powerful tools for understanding population and conservation genetics of this species and also for genetic differentiation and authentication of different Panax species being used in commercial ginseng products.

Identification and characterization of eight microsatellite loci in Aster amellus L. (Asteraceae)

AbstractEight polymorphic microsatellites were developed in the perennial herbaceous Aster amellus L. (Asteraceae) and characterized on three populations from France and Switzerland. The number of alleles ranged between four and 30 depending on the locus, and the mean number of effective alleles was 5.8. The average gene diversity equalled 0.744 (range: 0.419–0.957) and the overall differentiation was found significant (θ = 0.092, P &lt; 0.01). Three loci displayed significant heterozygote deficiencies, which might indicate the presence of null alleles. Amplifications were detected on eight loci in Aster alpinus L.

Systematics and evolution of the Dactylorhiza romana/sambucina polyploid complex (Orchidaceae)

The European–Mediterranean–Oriental Dactylorhiza romana/sambucina polyploid complex was studied with regard to genetic and morphological variation patterns. Allozyme and morphometric data were collected from 24 and 19 populations, respectively, initially identified as D. flavescens, D. insularis, D. markusii, D. romana, D. sambucina, and an indeterminate taxon. Genetic distances were calculated and illustrated by an unweighted pair-group method using arithmetic averages (UPGMA) dendrogram, and principal components analyses (PCAs) were used to summarize morphological variation patterns. Another PCA was performed on combined allozyme and morphometric data. On the basis of the dendrogram and the PCA plots, main groups of populations were delimited, and the probability that each morphological character would distinguish correctly between these groups was estimated. After combining morphometric interpretations with studies of herbarium material and information from the literature, the following taxa were confidently accepted: D. romana ssp. romana, D. romana ssp. guimaraesii (comb. et stat. nov.), D. romana ssp. georgica, D. sambucina, D. cantabrica (sp. nov.), and D. insularis. Levels of genetic diversity suggest that D. romana s.s. is the least derived member of the complex. The evolutionary divergence of the diploid species, D. romana and D. sambucina, was probably the outcome of vicariant speciation, whereas D. romana ssp. georgica and D. romana ssp. guimaraesii appear to have evolved from D. romana s.s. through incomplete vicariant and peripheral isolate speciation events, respectively. In some populations of the diploid taxa, a significant deficiency in heterozygotes was found at one to three loci. It is proposed that this pattern may indicate a Wahlund effect, hypothesizing that local populations are subdivided into demes determined by the commonly sympatric occurrence of two distinct colour morphs combined with partial morph constancy of individual pollinators (bumblebees). Several pathways are possible for the origin of the allotriploid D. insularis and the apparently allotetraploid D. cantabrica. A taxonomic revision is provided. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society, 2006, 152, 405–434.

Characterization of novel microsatellite markers from the Yesso scallop Mizuhopecten yessoensis

AbstractTwelve polymorphic and informative microsatellite markers were isolated and characterized for the Yesso scallop, Mizuhopecten yessoensis. We characterized these loci by genotyping 48 individuals; the number of alleles ranged from two to eight, and the values of observed heterozygosity and expected heterozygosity varied from 0 to 0.8333 and from 0.2546 to 0.8231, respectively. No significant linkage disequilibrium between pairs of loci was found and three loci showed significant heterozygote deficiency from the Hardy–Weinberg equilibrium. These markers are potential for studies of the population structure, individual or hybrid identification of the species.

Population genetic structure of the common warthog (Phacochoerus africanus) in Uganda: evidence for a strong philopatry among warthogs and social structure breakdown in a disturbed population

AbstractFine‐scale genetic structure of large mammals is rarely analysed. Yet it is potentially important in estimating gene flow between the now fragmented wildlife habitats and in predicting re‐colonization following local extinction events. In this study, we examined the extent to which warthog populations from five localities in Uganda are genetically structured using both mitochondrial control region sequence and microsatellite allele length variation. Four of the localities (Queen Elizabeth, Murchison Falls, Lake Mburo and Kidepo Valley) are national parks with relatively good wildlife protection practices and the other (Luwero), not a protected area, is characterized by a great deal of hunting. In the total sample, significant genetic differentiation was observed at both the mtDNA locus (FST = 0.68; P &lt; 0.001) and the microsatellite loci (FST = 0.14; P &lt; 0.001). Despite the relatively short geographical distances between populations, significant genetic differentiation was observed in all pair‐wise population comparisons at the two marker sets (mtDNA FST = 0.21–0.79, P &lt; 0.001; microsatellite FST = 0.074–0.191, P &lt; 0.001). Significant heterozygote deficiency was observed at most loci within protected areas while no significant deviation from Hardy–Weinberg expectation was observed in the unprotected Luwero population. We explain these results in terms of: (i) a strong philopatry among warthogs, (ii) a Wahlund effect resulting from the sampling regime and (iii) break down of social structure in the disturbed Luwero population.

Multilocus allozyme heterozygote deficiencies in Crepidula onyx: geographic and temporal patterns among adult snails in Mission Bay, California

Although the phenomenon of multilocus heterozygote deficiencies in numerous taxonomically diverse molluscs has been studied for over 30 years it has resisted general explanation. Here we describe a case in Crepidula onyx Sowerby, a common protandrous slipper limpet on the Pacific coast of southern California. Spatial and temporal differentiation at 16 polymorphic allozyme loci were examined in samples of adult snails from three or four seasons and six localities in Mission Bay, San Diego. The populations were highly polymorphic (proportion of polymorphic loci PL=0.65–0.69; mean individual heterozygosity HO=0.13–0.29) and although there were slightly more changes in allele frequency between autumn and winter than between winter and spring, statistically significant spatial and temporal change or patterning was not detected. If the larvae are passive dispersers the lack of population structure is attributable to the fact that during any three-week period that they are in the plankton, the waters of Mission Bay are completely mixed by tidal currents. In marked contrast, statistically significant heterozygote deficiencies were found in all samples (locality and season) and subsamples (males and females). At each locality and season, deficiencies were as pronounced in males as in females. Furthermore, at each locality, there was no increase in level of multilocus deficiency between males in one season and females in a subsequent season. We conclude that the heterozygotes had been lost in the larval planktonic stage or at the time of metamorphosis and settlement. Several hypotheses to explain the heterozygote deficiencies in adults are discussed: inbreeding, self-fertilization, presence of null alleles, allele scoring bias, aneuploidy, parental imprinting, spatial and temporal Wahlund effects, age-effects, and direct natural selection on the marker loci. Although we can reject some of these hypotheses, others like inbreeding, require testing with markers with greater statistical power. Wahlund effects due to inadvertent mixing of two cryptic species and/or micro-spatial population genetic structuring due to reproductive asynchronies appear unlikely causes. Natural selection against heterozygotes in the larval phase of life may account for the observations, but selection does not appear to operate directly on any of the individual loci studied. An hypothesis is offered to explain the general selection against heterozygotes during the pelagic larval stage, and for the reverse during the sessile adult stage. Selection coefficients would, however, have to be unusually high and we conclude that we are unable satisfactorily to explain our observations.

Genetic differences between Tunisian camel and sheep strains of the cestodeEchinococcus granulosusrevealed by SSCP

Ovine and dromedary Echinococcus granulosus isolates from Tunisia were identified as G1 and G6 strains based on polymorphism of the mitochondrial cytochrome C oxydase CO1. Single strand conformation polymorphism (SSCP) was used in order to examine the genetic variation within and between Tunisian G1 and G6 strains and to estimate the extent of selfing. The dromedary isolates are genetically distinct from sheep isolates (high value of genetic variation between populations: Fst= 0.46). No significant deficiency in heterozygotes was found in sheep isolates, whereas heterozygote deficiency (suggesting selfing) was found in a limited number of camel isolates.

Genetic structure of the European polecat (Mustela putorius) and its implication for conservation strategies

AbstractDuring the last century, the European polecat Mustela putorius populations in most of Europe declined and survived in fragmented patches, because of habitat alterations and direct persecution. To assess the genetic consequences of the demographic decline and to describe the spatial pattern of genetic diversity, 250 polecats sampled at seven localities from five European countries – Poland, Denmark (southern Denmark and northern Denmark), Spain, Belgium (eastern and western) and the Netherlands – were screened by means of nine microsatellite loci. Genetic diversity estimated by mean expected heterozygosity (HE) and allelic richness (AR) were moderately high within populations [range: 0.50 (northern Denmark) ≤HE≤0.64 (Poland) and 1.33≤AR≤7.80] as compared with other carnivores and mustelids. Bottleneck tests suggested that polecat populations in southern Denmark and Poland have declined recently and populations from northern Denmark and the Netherlands have expanded recently, whereas the remaining populations did not show any sign of demographic change. Recent demographic changes could suggest that some of the populations are still not in equilibrium, which could partly explain the relatively high genetic variability observed in polecat populations despite the drastic decline in population size observed in several European countries. A significant heterozygote deficiency [FIS=0.19; 0.01≤95% confidence interval (CI)≤0.32] suggests substructuring within the total European sample. Partitioning of the genetic variation among sampling locations (FST=0.14; 0.06≤95% CI≤0.23) and pairwise FST between localities (range: 0.01≤FST≤0.37) without any correlation with the geographic distances between localities were found, suggesting a recent divergence and a restriction of gene flow between populations and the action of genetic drift. An assignment test showed that the Polish and the northern Danish populations were the most unique, whereas the other populations were partially admixed. Factorial component analysis tests indicate a subdivision of the total sample into two distinct groups: one including the samples from Poland and the two Danish localities and the second group comprising the remaining localities investigated. The observed pattern of genetic differentiation is suggested to be due to two main routes of recolonization after the last glacial period. To compare the results obtained with microsatellite data, the most variable region of the mitochondrial DNA (d‐loop) was sequenced and different phylogenetic reconstructions and genetic diversity analyses based on nucleotide (π) and haplotype diversity (h) measures within populations were performed using a subsample of populations. The lack of well‐defined geographical structure, as well as the reduced level of mitochondrial DNA variability (π: 0.00274±0.00038; h: 0.876±0.028) that was found, has been previously reported in several studies on different carnivores and supports the hypothesis of post‐glacial recolonization from southern or eastern refugees of Europe as suggested by the microsatellite data. Implications for conservation strategies of the polecat at the European level are discussed.