Allelic Heterozygosity Research Articles

Multiplex PCR Analysis of 17 (11 Novels) STR Markers Linked to Six Autosomal Recessive Intellectual Disability Genes in Iranian Population.

Non-syndromic autosomal recessive intellectual disability (NS-ARID) is a heterogeneous neurodevelopmental disease. More research is needed to study the NS-ARID genes. Using STR markers linked to a specific gene, we can perform homozygosity mapping and prenatal diagnosis. One approach to investigate the NS-ARID genes in large families is homozygosity mapping. In this study, we surveyed allele frequency and allele heterozygosity of 17 NS-ARID STR markers linked to the six NS-ARID genes in Iranian population. The test group consisted of 120 unrelated healthy individuals. STR markers were designed using SERV software. Also, genotyping was done using multiplex PCR. Data was analyzed by Gene Mapper software. Allele frequency and observed heterozygosity rates were estimated using PowerStatV12. Deviation from the Hardy-Weinberg equilibrium (HWE) was performed based on the Exact test. Out of 17 STR loci, 11 were novel. In total, 166 alleles were detected for the 17 markers. According to our study, the D9MAN1B1SD7.4, D19S872, D6GRIK2SI1.7, D19TECRSDI.8, D1ST3GAL3SIO.5, and D14ZC3H14SD5.3 STR loci were found to be the most informative and polymorphic STR markers for MAN1B1, ZNF526, GRIK2, TECR, ST3GAL3, and ZC3H14 genes, respectively. We also performed other statistical analyses on these STR markers and found that all of the 17 STRs were polymorphic and met the Hardy-Weinberg equilibrium. Finding novel STRs, with high allele heterozygosity, is one of the most significant outcomes of the present study. These findings can be useful for homozygosity mapping, PGD, and PND practices for the NS-ARID.

Characterization of Korean Native Cattle Breeds by Microsatellite Markers on Sex Chromosomes

This study aimed to identify allele variability and determine the frequencies of microsatellite (MS) markers specific to bovine sex chromosomes in Korean native cattle (KNC; Chikso, Hanwoo and Jeju Black). The three KNC breeds were characterized using 4 MS markers (INRA30, TGLA325, UMN0905 and UMN0929), and allelic richness, allele frequency, heterozygosity and polymorphism information content (PIC) per locus were calculated. The mean observed heterozygosity and PIC values for Chikso, Jeju Black and Hanwoo were 0.541 and 0.542, 0.406 and 0.377, and 0.61 and 0.6, respectively. The heterozygosity and the PIC values of Jeju Black breed were smaller than those of Chikso and Hanwoo. Thus, these genetic parameters were used for the characterization of the breeds and for determining their genetic relationships. The findings of this study might be useful for the conservation, management, and utilization of KNC breeds as genetic resources.

Low genetic diversity, restricted dispersal, and elevation-specific patterns of population decline in American pikas in an atypical environment

AbstractIn the face of climate change, there is a growing need for research into the ability of organisms to persist at the limits of their bioclimatic envelope. American pikas ( Ochotona princeps ) have emerged as a focal mammalian species for investigating extinction risk related to climate change; however, most studies have occurred in characteristic alpine talus habitat within the range core. In the Columbia River Gorge (CRG), Oregon, American pikas inhabit low-elevation talus slopes previously considered outside the species’ bioclimatic range. We used microsatellite genotypic data to reconstruct levels of genetic variation, population connectivity, and demographic history at 11 CRG sites spanning an elevational gradient (104–1,292 m). Sampled sites separated into 2 genetic clusters largely explained by elevation, topography, and geographic proximity, with pairwise estimates of differentiation and migration rates suggesting little gene flow may be occurring. Sites were characterized by levels of allelic richness and heterozygosity substantially lower than values reported at characteristic alpine sites from the range core. Evidence of recent demographic contraction was found almost exclusively at high-elevation sites despite these areas being considered refuges from climate warming in more typical habitat. Given their unique genetic characteristics and persistence in an atypical environment, the CRG pika populations likely constitute a significant component of intraspecific biodiversity with high conservation value.

Rapid genetic restoration of a keystone species exhibiting delayed demographic response.

Genetic founder effects are often expected when animals colonize restored habitat in fragmented landscapes, but empirical data on genetic responses to restoration are limited. We examined the genetic response of banner-tailed kangaroo rats (Dipodomys spectabilis) to landscape-scale grassland restoration in the Chihuahuan Desert of New Mexico, USA. Dipodomys spectabilis is a grassland specialist and keystone species. At sites treated with herbicide to remove shrubs, colonization by D. spectabilis is slow and populations persist at low density for ≥10 years (≥6 generations). Persistence at low density and low gene flow may cause strong founder effects. We compared genetic structure of D. spectabilis populations between treated sites and remnant grasslands, and we examined how the genetic response to restoration depended on treatment age, area, and connectivity to source populations. Allelic richness and heterozygosity were similar between treated sites and remnant grasslands. Allelic richness at treated sites was greatest early in the restoration trajectory, and genetic divergence did not differ between recently colonized and established populations. These results indicated that founder effects during colonization of treated sites were weak or absent. Moreover, our results suggested founder effects were not mitigated by treatment area or connectivity. Dispersal is negatively density-dependent in D. spectabilis, and we hypothesize that high gene flow may occur early in the restoration trajectory when density is low. Our study shows genetic diversity can be recovered more rapidly than demographic components of populations after habitat restoration and that founder effects are not inevitable for animals colonizing restored habitat in fragmented landscapes.

TNF-α -238, -308, -863 polymorphisms, and brucellosis infection

BackgroundBrucella abortus is an intracellular bacterium that affects humans and domestic animals. Tumor necrosis factor-alpha (TNF-α) has been shown as a key player in the induction of cell-mediated resistance against Brucella infection. We aimed to evaluate the possible influence of the TNF-α promoter polymorphisms (-308 G/A, -238 G/A, and -863 C/A) on the susceptibility of human brucellosis. MethodologyA total of 153 patients with active brucellosis and 128 healthy individuals were recruited. All subjects were genotyped for the polymorphisms in the TNF-α gene by Allele-Specific polymerase chain reaction analysis. ResultsOur results showed that the TNF-α -308 GG genotype was significantly more frequently present in controls than in brucellosis patients (91% vs. 75%), thus was a protective factor against developing brucellosis (OR=0.313, p=0.001). In contrast, the -308 GA genotype (OR=3.026, p=0.002) and minor allele (A) (OR=3.058, p=0.001) as well as AAG haplotype (OR=4.014, p=0.001) conferred an increased risk of brucellosis. However, the -238 G/A and -863 C/A polymorphisms were not associated with the risk of brucellosis at both allelic and genotypic levels (p>0.05). ConclusionOur study revealed that the TNF-α -308 A allele or GA heterozygosity or AAG haplotype were associated with an increased risk of brucellosis in our population.

Origin and genetic structure of a recovering bobcat (Lynxrufus) population

Genetic analyses can provide important insights into the demographic processes that underlie recovering populations of mammals of conservation concern such as felid species. To better understand the recent and rapid recovery of bobcats (Lynx rufus (Schreber, 1777)) in Ohio, we analyzed samples from four states in the lower Great Lakes Region using 12 microsatellite DNA loci and a portion of the mtDNA control region. Our results showed that a newly established population of bobcats in the eastern part of Ohio was genetically distinct from a multistate population distributed across Kentucky, southern Ohio, West Virginia, and western Pennsylvania. There was no direct genetic evidence of a bottleneck or inbreeding in this population. A lack of private alleles and only slightly lower levels of allelic richness and heterozygosity compared with its neighbors suggest that the eastern Ohio population likely originated from the migration of relatively large numbers of individuals from a source population rather than re-emerging from an undetected residual population. We recommend that a management plan should define the areas occupied by the two populations in Ohio as separate management units at least for the near future.

Pregnancy-associated plasma protein A gene polymorphism in pregnant women with preeclampsia and intrauterine growth restriction

Preeclampsia (PE) and intrauterine growth restriction (IUGR) are still among the most commonly researched titles in perinatology. To shed light on their etiology, new prevention and treatment strategies are the major targets of studies. In this study, we aimed to investigate the relation between gene polymorphism of one of the products of trophoblasts, pregnancy-associated plasma protein A (PAPP-A) and PE/IUGR.A total of 147 women (IUGR, n = 61; PE, n = 47; IUGR + PE, n = 37; eclampsia, n = 2) were compared with 103 controls with respect to the sequencing of exon 14 of the PAPP-A gene to detect (rs7020782) polymorphism. Genotypes “AA” and “CC” were given in the event of A or C allele homozygosity and “AC” in A and C allele heterozygosity. Our findings revealed that the rate of AA, CC homozygotes, and AC heterozygotes did not differ between groups. Moreover, there was no difference in the distribution of PAPP-A genotypes among the patients with IUGR, PE, IUGR + PE, or eclampsia. Finally, birth weight, rate of the presence of proteinuria, and total protein excretion on 24-hour urine were similar in the subgroups of AA, AC, and CC genotypes in the study group. Our study demonstrated no association between PAPP-A gene rs7020782 polymorphism and PE/IUGR.

Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse

Przewalski's horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still endangered, with just 2,109 individuals, one-quarter of which are in Chinese and Mongolian reintroduction reserves [1]. These horses descend from a founding population of 12 wild-caught PHs and possibly up to four domesticated individuals [2-4]. With a stocky build, an erect mane, and stripped and short legs, they are phenotypically and behaviorally distinct from domesticated horses (DHs, Equus caballus). Here, we sequenced the complete genomes of 11 PHs, representing all founding lineages, and five historical specimens dated to 1878-1929 CE, including the Holotype. These were compared to the hitherto-most-extensive genome dataset characterized for horses, comprising 21 new genomes. We found that loci showing the most genetic differentiation with DHs were enriched in genes involved in metabolism, cardiac disorders, muscle contraction, reproduction, behavior, and signaling pathways. We also show that DH and PH populations split ∼45,000 years ago and have remained connected by gene-flow thereafter. Finally, we monitor the genomic impact of ∼110 years of captivity, revealing reduced heterozygosity, increased inbreeding, and variable introgression of domestic alleles, ranging from non-detectable to as much as 31.1%. This, together with the identification of ancestry informative markers and corrections to the International Studbook, establishes a framework for evaluating the persistence of genetic variation in future reintroduced populations.

Comparative genomic analyses of freshly isolated Giardia intestinalis assemblage A isolates.

BackgroundThe diarrhea-causing protozoan Giardia intestinalis makes up a species complex of eight different assemblages (A-H), where assemblage A and B infect humans. Comparative whole-genome analyses of three of these assemblages have shown that there is significant divergence at the inter-assemblage level, however little is currently known regarding variation at the intra-assemblage level. We have performed whole genome sequencing of two sub-assemblage AII isolates, recently axenized from symptomatic human patients, to study the biological and genetic diversity within assemblage A isolates.ResultsSeveral biological differences between the new and earlier characterized assemblage A isolates were identified, including a difference in growth medium preference. The two AII isolates were of different sub-assemblage types (AII-1 [AS175] and AII-2 [AS98]) and showed size differences in the smallest chromosomes. The amount of genetic diversity was characterized in relation to the genome of the Giardia reference isolate WB, an assemblage AI isolate. Our analyses indicate that the divergence between AI and AII is approximately 1 %, represented by ~100,000 single nucleotide polymorphisms (SNP) distributed over the chromosomes with enrichment in variable genomic regions containing surface antigens. The level of allelic sequence heterozygosity (ASH) in the two AII isolates was found to be 0.25–0.35 %, which is 25–30 fold higher than in the WB isolate and 10 fold higher than the assemblage AII isolate DH (0.037 %). 35 protein-encoding genes, not found in the WB genome, were identified in the two AII genomes. The large gene families of variant-specific surface proteins (VSPs) and high cysteine membrane proteins (HCMPs) showed isolate-specific divergences of the gene repertoires. Certain genes, often in small gene families with 2 to 8 members, localize to the variable regions of the genomes and show high sequence diversity between the assemblage A isolates. One of the families, Bactericidal/Permeability Increasing-like protein (BPIL), with eight members was characterized further and the proteins were shown to localize to the ER in trophozoites.ConclusionsGiardia genomes are modular with highly conserved core regions mixed up by variable regions containing high levels of ASH, SNPs and variable surface antigens. There are significant genomic variations in assemblage A isolates, in terms of chromosome size, gene content, surface protein repertoire and gene polymorphisms and these differences mainly localize to the variable regions of the genomes. The large genetic differences within one assemblage of G. intestinalis strengthen the argument that the assemblages represent different Giardia species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1893-6) contains supplementary material, which is available to authorized users.

Genetic structuring of Salminus hilarii Valenciennes, 1850 (Teleostei: Characiformes) in the rio Paraná basin as revealed by microsatellite and mitochondrial DNA markers

Genetic variation of Salminus hilarii was assessed by screening microsatellite loci and mitochondrial D-loop DNA across four sampling in the upper rio Paraná basin of Brazil. Genetic diversity - measured as mean expected heterozygosity (0.904) and mean number of alleles across populations (13.7) - was reasonably high. Differentiation of microsatellite allele frequencies among populations was shown to be low but significant by AMOVA Φ ST (0.0192), and high by D EST (0.185). D-loop variation was high, with haplotypic diversity of 0.950 and nucleotide diversity of 0.011. Mitochondrial DNA-based estimates for population differentiation were high, with an overall Φ ST of 0.173. The results of tests of nuclear and mitochondrial variation yielded no unequivocal inference of historical demographic bottleneck or expansion. Genetic differentiation observed among S. hilarii populations in the rio Grande may be caused by a combination of historical differentiation and recent gene-flow disruption caused by the dams followed by reproduction of isolated spawning assemblages in mid-sized tributaries of the respective reservoirs. We present spatially more intensive sampling of S. hilarii populations across the rio Paraná basin in order to more effectively distinguish between historical and contemporary differentiation.

Phenotypic and Genotypic Diversity for Drought Tolerance among and within Perennial Ryegrass Accessions

Perennial ryegrass (Lolium perenne L.) is a popular cool-season forage and turfgrass in temperate regions. Due to its self-incompatible and out-crossing nature, perennial ryegrass may show a high degree of heterozygosity. Perennial ryegrass generally is susceptible to drought stress, but variations of drought response of individual genotypes within a particular accession or cultivar are not well understood. The objective of this study was to characterize phenotypic diversity of drought tolerance within and among accessions in relation to genetic diversity in perennial ryegrass. Five individual genotypes from each of six accessions varying in origin and growth habits were subjected to drought stress in a greenhouse. Leaf wilting, plant height, chlorophyll fluorescence (Fv/Fm) and leaf water content (LWC) differed significantly among accessions as well as among genotypes within each accession under well-watered control and drought stress conditions. Fv/Fm was highly correlated with LWC under drought stress. Genetic diversity among and within accessions were identified by using previously characterized 23 simple sequence repeat markers. Across accessions, the mean major allele frequency, gene diversity, and heterozygosity values were 0.66, 0.43, and 0.66, respectively. Accessions with closer genetic distance generally had similar drought responses, while accessions with greater genetic distance showed distinct drought tolerance. Significant differences in drought tolerance among and within accessions, especially for individual genotypes within one accession, indicated that variations of drought response could be used for enhancing breeding programs and studying molecular mechanisms of stress tolerance in perennial ryegrass.

The role of climate and out-of-Africa migration in the frequencies of risk alleles for 21 human diseases.

BackgroundDemography and environmental adaptation can affect the global distribution of genetic variants and possibly the distribution of disease. Population heterozygosity of single nucleotide polymorphisms has been shown to decrease strongly with distance from Africa and this has been attributed to the effect of serial founding events during the migration of humans out of Africa. Additionally, population allele frequencies have been shown to change due to environmental adaptation. Here, we investigate the relationship of Out-of-Africa migration and climatic variables to the distribution of risk alleles for 21 diseases.ResultsFor each disease, we computed the regression of average heterozygosity and average allele frequency of the risk alleles with distance from Africa and 9 environmental variables. We compared these regressions to a null distribution created by regressing statistics for SNPs not associated with disease on distance from Africa and these environmental variables. Additionally, we used Bayenv 2.0 to assess the signal of environmental adaptation associated with individual risk SNPs. For those SNPs in HGDP and HapMap that are risk alleles for type 2 diabetes, we cannot reject that their distribution is as expected from Out-of-Africa migration. However, the allelic statistics for many other diseases correlate more closely with environmental variables than would be expected from the serial founder effect and show signals of environmental adaptation. We report strong environmental interactions with several autoimmune diseases, and note a particularly strong interaction between asthma and summer humidity. Additionally, we identified several risk genes with strong environmental associations.ConclusionsFor most diseases, migration does not explain the distribution of risk alleles and the worldwide pattern of allele frequencies for some diseases may be better explained by environmental associations, which suggests that some selection has acted on these diseases.

Genomic and Genotyping Characterization of Haplotype-Based Polymorphic Microsatellites in Prunus

Efficient utilization of microsatellites in genetic studies remains impeded largely due to the unknown status of their primer reliability, chromosomal location, and allele polymorphism. Discovery and characterization of microsatellite polymorphisms in a taxon will disclose the unknowns and gain new insights into the polymorphic alleles. In this study, we revealed the polymorphism status, primer categorization, chromosomal distribution, gene function, and genotyping performance of 319 haplotype-based polymorphic microsatellites (HPM) in expressed sequence tags (EST) of Prunus species, including peach, apricot, almond, plums, and cherries. Of the HPM, 262 are between two EST haplotypes and 57 are among three and more EST. In terms of species, 127 microsatellite polymorphisms are from different EST of peach, 108 from different EST between peach and other species, and 84fromdifferent EST between non-peach species. Based on the primer sequence alignments on the peach genome, there was one HPM per 678 kb and the 319 HPM were grouped into seven categories. The primers from the “deletion” category tended to yield higher allele numbers and polymorphism information content (PIC) values. Statistical analysis revealed the mean allele number, heterozygosity, PIC, and gene diversity value were all significantly higher in the HPM than in the haplotype-based non-polymorphic microsatellites (HNM), suggesting utilization of HPM markers could substantially increase the likelihood of allele polymorphism. Of the 234 unigenes annotated, 99 (42.3%) were categorized into binding function and 84 (35.9%) into catalytic activity, implying that these polymorphic alleles might have evolved primarily to play regulatory roles or catalyze enzymatic reactions.

Population Structure of Vitis rupestris, an Important Resource for Viticulture

The wild North American grapevine Vitis rupestris Scheele is an important genetic resource for viticulture, but its natural populations have been severely depleted. We collected samples from seven V. rupestris populations from the Ozark Plateau in Missouri and the Ouachita Mountains in Oklahoma and genotyped them with 14 microsatellite markers to assess allelic diversity, heterozygosity, and genetic differentiation at various levels of population structure. We found that genetic diversity in V. rupestris was similar to that measured in many V. vinifera L. ssp. sylvestris populations and in other outcrossing angiosperms. We detected significant genetic differentiation among populations (ΦPT = 0.105); there was no significant deviation from Hardy–Weinberg equilibrium in some populations, and there was moderate inbreeding in others. Pronounced differentiation between Missouri and Oklahoma populations was supported by a Bayesian clustering approach and principle coordinate analyses and was apparently a function of geographic distance. Genetic differentiation among Missouri populations was modest. We posit that population differentiation and genetic drift may be inherent characteristics of V. rupestris.

Metallothionein 2A core promoter region genetic polymorphism and its impact on the risk, tumor behavior, and recurrences of sinonasal inverted papilloma (Schneiderian papilloma).

Inverted papillomas are a unique group of locally aggressive benign epithelial neoplasms in the nasal cavity and paranasal sinuses arising from the Schneiderian mucosa. Metallothioneins are sulfhydryl-rich heavy metal-binding proteins required for metal toxicity protection and regulation of biological mechanisms including proliferation and invasion. The goal of this study was to identify three SNPs at loci −5 A/G (rs28366003) and −209 A/G (rs1610216) in the core promoter region and at locus +838 C/G (rs10636) in 3′UTR region of the MT2A gene with IP risk and with tumor invasiveness according to Krouse staging. Genotyping was performed using the PCR restriction fragment length polymorphism technique in 130 genetically unrelated IP individuals, and 418 randomly selected healthy volunteers. The presence of the rs28366003 SNP was significantly related to the risk of IP within the present population-based case-control study. Compared to homozygous common allele carriers, heterozygosity and homozygosity for the G variant had a significantly increased risk of IP (adjusted odds ratio [OR] = 7.71, 95 % confidence interval [CI]: 4.01–14.91, p dominant < 0.001). Moreover, risk allele carriers demonstrated higher Krouse stage (pT1 vs. pT2-4) (OR = 19.32; 95 % CI, 2.30–173.53; p < 0.0001), diffuse tumor growth (OR = 4.58; 95 % CI, 1.70–12.11; p = 0.0008), bone destruction (OR = 4.13; 95 % CI, 1.50–11.60; p = 0.003), and higher incidence of tumor recurrences (OR = 5.11; 95 % CI, 1.68–15.20; p = 0.001). The findings suggest that MT2A gene variation rs28366003 may be implicated in the etiology of sinonasal inverted papilloma in a Polish population.

Genetic Diversity Analysis in Date Palm (Phoenix dactylifera L) Germplasm using Microsatellite Markers

The Date Palm (Phoenix dactylifera L), germplasm commonly cultivated in Egypt, shows a wide range ofrepining periods and fruit quality and is an unexploited resource for breeding programs. The main purpose of this studywas to genetic diversity analysis and relationships for 45 date palm genotypes and to construct a molecular databaseincluding the cultivars commonly grown in Egypt. An analysis of thirty three microsatellite simple sequence repeat(SSR) loci out of thirty five markers was performed to define allele diversity, heterozygosity and genetic structure. Theaverage number of alleles per locus was 32.3. Heterozygosity per locus was 0.64 (Dpalm-103) to 0.96 (Dplam-100, 256,mpdCIR08 and mpdCIR078) with an average of 0.89. The highest heterozygosity (0.768) was detected in Avanda,followed by Amhat (0.758) while Khalas had lowest heterozygosity value (0.455).The genetic similarity values rangedfrom 0.041 to 0.260. The obtained dendrogram showed three main clusters and generally, a good structuring of 45genotypes and accessions. The use of 33 polymorphic microsatellite markers and the level of genetic variabilitydetected within Egyptian date palm germplasm suggested that this is reliable, efficient and effective marker system thatcan be used for diversity analysis and subsequently in crop improvement programs.

Gene dynamics of toll-like receptor 4 through a population bottleneck in an insular population of water voles (Arvicola amphibius)

Understanding the extent to which diversity at immunologically important genes is reduced by demographic perturbations such as population bottlenecks, and the resulting consequences this has on individual fitness, is of fundamental importance for the effective management of genetic resources in natural populations. Toll-like receptors are key immunological genes with well-established links to fitness. Here, levels of allelic diversity and heterozygosity at the toll-like receptor 4 locus (Tlr4) were characterised across 280 water voles (Arvicola amphibius) from an isolated, island population in north west Scotland that went through a severe population bottleneck between 2004 and 2006 that eroded neutral microsatellite variation. Two functional Tlr4 alleles were resolved prior to the population crash at frequencies close to parity and an excess of heterozygote genotypes relative to Hardy–Weinberg expectations. Through the population bottleneck both alleles were retained with genotype frequencies conforming to Hardy–Weinberg expectations. Tlr4 genotype was significantly associated with gamasid mite, flea (Megabothris walkeri) and sheep tick larva (Ixodes ricinus) burdens among individuals, suggesting a mechanism through which parasite mediated selection could affect Tlr4 diversity. The results are examined with recourse to the extent that they are consistent with the effects of genetic drift and balancing selection, and their significance is discussed in relation to identifying target genes that assay ecological and adaptively meaningful genetic variation in a conservation context.

Patterns of genetic variation across the distribution range of the cockle Cerastoderma edule inferred from microsatellites and mitochondrial DNA

The edible cockle Cerastoderma edule is an ecologically and economically important species found along the northeastern Atlantic coast. In this study, microsatellite and mitochondrial cytochrome b (cyt b) gene variation was examined in 19 localities across the species’ distribution range to test whether the patterns of genetic diversity, population structure and demographic inferences deduced from the cytochrome oxidase I gene in a previous study were supported by these molecular makers. High levels of genetic diversity were detected, with allelic richness, heterozygosity and haplotype diversity, showing different geographic patterns. Through Bayesian clustering analysis, Fst estimates and AMOVA, microsatellites indicated the existence of a southern group of populations that expands up to France, a northern one composed of localities from Denmark to Russia plus one from Scotland, and a third central group comprising localities from Ireland, Great Britain and southern North Sea. Regarding the cyt b gene, Fst data supported the pattern inferred from microsatellites, but haplotype distribution and AMOVA revealed a different three-group scenario where the central group includes only the southern North Sea localities. Both marine currents and historical processes, such as a recent population expansion of the southern group, the existence of northern cryptic refugia during Pleistocene glaciations and secondary contact between the southern and northern groups of populations, may explain the genetic composition of C. edule populations. Overall, the available data suggest that in C. edule nuclear markers and even different mitochondrial genes reacted differently to the same population history.

Multilocus heterozygosity and coronary heart disease: nested case-control studies in men and women.

BackgroundGeneralized allelic heterozygosity has been proposed to improve reproductive fitness and has been associated with higher blood pressure, but its association with chronic disease is not well characterized.MethodsUsing the Affymetrix Genome-Wide Human 6.0 array, we performed whole genome scans in parallel case-control studies of coronary heart disease (CHD) nested in the Health Professionals Follow-up Study and Nurses’ Health Study. We examined ~700,000 single nucleotide polymorphisms (SNPs) in 435 men with incident CHD and 878 matched controls and 435 women with incident CHD with 931 matched controls. We examined the relationship of genome-wide heterozygosity with risk of incident of CHD and with baseline levels of cardiovascular risk factors.ResultsIn both cohorts, approximately 227650 (SD 2000) SNPs were heterozygous. The number of heterozygous SNPs was not related to risk of CHD in either men or women (adjusted odds ratios per 2000 heterozygous SNPs 1.01 [95% confidence interval, 0.91-1.13] in women and 0.94 [0.84-1.06] in men). We also found no consistent associations of genome-wide heterozygosity with levels of lipids, inflammatory markers, adhesion molecules, homocysteine, adiponectin, or body-mass index.ConclusionsIn these parallel nested case-control studies, we found no relationship of multilocus heterozygosity with risk of CHD or its major risk factors. Studies in other populations are needed to rule out associations with lower levels of heterozygosity.

Urbanisation versus agriculture: a comparison of local genetic diversity and gene flow between wood mouse Apodemus sylvaticus populations in human‐modified landscapes

Urbanisation and agriculture dramatically modify the landscapes available for use by wildlife, affecting key aspects of their ecology such as survival, foraging, predation, competition and reproductive success. Relatively little is known about the effects of urbanisation and agriculture on the genetic structure, gene flow and genetic diversity of wild species. Here, landscape genetic techniques were applied to compare local genetic diversity and gene flow between wood mouse populations in urban and arable landscapes. Using nine microsatellite markers, individuals were genotyped from six arable and seven urban sample sites. Inter‐population genetic differentiation was significantly greater in urban than arable habitat, while allele richness, private allele richness and heterozygosity were higher for arable sample sites, with varying degrees of significance. These suggest that urban habitat was sufficiently fragmented to limit gene flow. To test the effect of landscape features on gene flow, several cost‐distance measures were generated. Overland distance and Euclidean distance correlated best with inter‐population genetic differentiation in arable habitat, whereas distances that accommodated differences in habitat quality better explained differentiation in urban habitat. There was no evidence that margins adjacent to roads, rivers or railways facilitated gene flow. Together, the results indicate that urban landscapes expose wood mice to greater fragmentation in habitat quality than arable areas, leading to greater population isolation that is not mitigated by the presence of dispersal corridors.