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PubMed2002

Host-associated genetic differentiation in the goldenrod elliptical-gall moth, Gnorimoschema gallaesolidaginis (Lepidoptera: Gelechiidae).

Careful study of apparently generalist phytophagous insects often reveals that they instead represent complexes of genetically differentiated host races or cryptic species. The goldenrod elliptical-gall moth, Gnorimoschema gallaesolidaginis, attacks two goldenrods in the Solidago canadensis complex: S. altissima and S. gigantea (Asteraceae). We tested for host-associated genetic differentiation in G. gallaesolidaginis via analysis of variation at 12 allozyme loci among larvae collected at six sites in Iowa, Minnesota, and Nebraska. Gnorimoschema gallaesolidaginis from each host are highly polymorphic (3.6-4.7 alleles/locus and expected heterozygosity 0.28-0.38 within site-host combinations). Although there were no fixed differences between larvae from S. altissima and S. gigantea at any site, these represent well differentiated host forms, with 11 of 12 loci showing significantly different allele frequencies between host-associated collections at one or more sites. Host plant has a larger effect on genetic structure among populations than does location (Wright's FST = 0.16 between host forms vs. F(ST) = 0.061 and 0.026 among altissima and gigantea populations, respectively). The estimated F(ST) between host forms suggests that the historical effective rate of gene flow has been low (N(e)m approximately 1.3). Consistent with this historical estimate is the absence of detectable recombinant (hybrid and introgressant between host form) individuals in contemporary populations (none of 431 genotyped individuals). Upper 95% confidence limits for the frequency of recombinant individuals range from 5% to 9%. Host association is tight, but imperfect, with only one likely example of a host mismatch (a larva galling the wrong host species). Our inferences about hybridization and host association are based on new maximum-likelihood methods for estimating frequencies of genealogical classes (in this case, two parental classes, F1 and F2 hybrids, and backcrosses) in a population and for assigning individuals to genealogical classes. We describe these new methods in the context of their application to genetic structure in G. gallaesolidaginis. Population phenograms are consistent with the origin of the host forms (at least in the midwestern United States) via a single host shift: altissima and gigantea moth populations form distinct lineages with 100% bootstrap support. Genetic structure in Gnorimoschema is of particular interest because another gallmaking insect attacking the same pair of hosts, the tephritid fly Eurosta solidaginis, includes a pair of host races with partial reproductive isolation. Gnorimoschema gallaesolidaginis and E. solidaginis therefore represent the first reported case of parallel host-associated differentiation, that is, differentiation by evolutionarily independent insect lineages across the same pair of host plants.

Animals↗
PubMed1991

[Genetic-demographic structure of the Adyg population].

The results of comparative analysis of series of genetical and demographical parameters in two ethnically distinct populations coexisting in Adyg autonomous region of the Krasnodar district are presented. The parameters of population structure in Russians and Adygs were determined, such as sex and age distribution, ethnical marital assortativity, vital statistics and selection pressure. The analysis revealed that the populations only differ in the level of ethnical marital assortment: the coefficient of assortativity H is 2.54 and 1.55 for Adygs and Russians, respectively.

Demography↗
PubMedDate not supplied

Functional, structural, and genetic mitochondrial abnormalities in myocardial diseases.

Myocardial tissue is highly dependent on energy supplied by normal mitochondrial function. Therefore defects of energy production or utilization affect the heart in both syndromic and isolated disorders. Knowledge of the peculiar structural, functional, and genetic characteristics of mitochondria provides the basis for identification and classification of mitochondrial defects as well as for establishment of a diagnostic workup useful for related cardiac disorders. This review is therefore dedicated to the characteristics of normal mitochondria and the pathologic alterations of these organelles in various cardiovascular diseases.

Cardiomyopathies↗
PubMed1995

[Genetic-demographic study of mountain populations of Daghestan and migrants from it to the lowlands. Study of genetic and marital structure].

The results of a genetic and demographic study of two "split" isolates of small native ethnic groups of Daghestan are described. Parts of these populations were resettled from habitual highland ecological conditions to radically new lowland conditions in the 1940s. These split isolates were compared with a population of native inhabitants of the Daghestan lowland. It was found that, since resettling, separated populations originating from split isolates became significantly different in both marriage and genetic structures. This is manifested in different phenotypic and allelic frequencies of a number of physiological and biochemical markers and in levels of their heterozygosity. To explain the differences revealed, a hypothesis was proposed about the relationship between levels of inbreeding, heterozygosity, and physiologic sensitivity that account for the differential adaptability of members of the isolated populations to changing environmental conditions. This is the first report of a series of papers describing the experimental testing of this hypothesis. While testing the validity of the hypothesis in this study, a positive linear correlation was found between inbreeding and homozygosity levels.

Consanguinity↗
PubMed2005

The structure of genetic and environmental risk factors for anxiety disorders in men and women.

BACKGROUND: The anxiety disorders exhibit high levels of lifetime comorbidity with one another. Understanding the underlying causes of this comorbidity can provide insight into the etiology of the disorders and inform classification and treatment. OBJECTIVE: To explain anxiety disorder comorbidity by examining the structure of the underlying genetic and environmental risk factors. DESIGN: Lifetime diagnoses for 6 anxiety disorders (generalized anxiety disorder, panic disorder, agoraphobia, social phobia, animal phobia, and situational phobia) were obtained during personal interviews from a population-based twin registry. Multivariate structural equation modeling that allowed for sex differences was performed. SETTING: General community sample. PARTICIPANTS: More than 5000 members of male-male and female-female twin pairs from the Virginia Adult Twin Study of Psychiatric and Substance Use Disorders. MAIN OUTCOME MEASURES: Parameter estimates for best-fitting model. RESULTS: The full model, which contained 2 common genetic, shared environmental, and unique environmental factors plus disorder-specific factors, could be constrained to equality across male and female study participants. In the best-fitting model, the genetic influences on anxiety were best explained by 2 additive genetic factors common across the disorders. The first loaded most strongly in generalized anxiety disorder, panic disorder, and agoraphobia, whereas the second loaded primarily in the 2 specific phobias. Social phobia was intermediate in that it was influenced by both genetic factors. A small role for shared environmental influences was observed owing to a single common factor that accounted for less than 12% of the total variance for any disorder. Unique environmental influences could be explained by a single common factor plus disorder-specific effects. CONCLUSIONS: The underlying structure of the genetic and environmental risk factors for the anxiety disorders is similar between men and women. Genes predispose to 2 broad groups of disorders dichotomized as panic-generalized-agoraphobic anxiety vs the specific phobias. The remaining associations between the disorders are largely explained by a unique environmental factor shared across the disorders and, to a lesser extent, a common shared environmental factor.

Adult↗
PubMed2004

Evidence for genetic control of adult weight plasticity in the snail Helix aspersa.

Phenotypic plasticity and canalization are important topics in quantitative genetics and evolution. Both concepts are related to environmental sensitivity. The latter can be modeled using a model with genetically structured environmental variance. This work reports the results of a genetic analysis of adult weight in the snail Helix aspersa. Several models of heterogeneous variance are fitted using a Bayesian, MCMC approach. Exploratory analyses using posterior predictive model checking and model comparisons based on the deviance information criterion favor a model postulating a genetically structured heterogeneous environmental variance. Our analysis provides a strong indication of a positive genetic correlation between additive genetic values affecting the mean and those affecting environmental variation of adult body weight. The possibility of manipulating environmental variance by selection is illustrated numerically using estimates of parameters derived from the snail data set.

Animals↗
PubMed2005

Significance of habitat type for the genetic population structure of Panonychus citri (Acari: Tetranychidae).

Restricted migration and habitat fragmentation promote genetic differentiation between populations. Because most of the hosts of Panonychus citri are woody plants, mainly citrus trees that are usually planted at intervals of several metres, this mite likely faces more risks (e.g., starvation) by dispersing between host plants, compared to other spider mite species that infest both herbaceous and woody plants, such as Tetranychus urticae. Such a limited gene flow between patches (host plants) can lead to differentiation of populations even within a small area. Therefore, we hypothesize that P. citri populations are genetically differentiated not only between distant populations but also within small areas, such as within a grove. To test this hypothesis, we investigated the divergence of P. citri populations in Japanese citrus groves according to a hierarchical arrangement of geographical distance, ranging from distant populations (10 groves distributed throughout different areas in two major Japanese islands; this level of analysis is referred to as 'geographic') to local populations (different trees in a specific grove; 'local'). Three molecular markers were used: an esterase locus, one microsatellite and a point mutation in the mitochondrial cytochrome oxidase subunit I. At a local level acaricide susceptibility tests were also performed using two acaricides: fenpyroximate (25 ppm) and etoxazole (3.33 ppm). At a broad geographic level the gene diversity decreased with decreasing area size and distance between populations. By contrast, at the local level, populations maintained a significant level of variation between trees within groves, and the divergence within groves was higher than between groves. Whereas no statistical difference of the mortalities was detected among groves for the two acaricides tested, the difference was statistically significant among trees within groves in fenpyroximate (ANOVA, p<0.025) and marginal in etoxazole (0.1<p<0.05). We concluded that P. citri populations maintain a higher level of variation between trees (or patches of trees) within groves than between groves at the local level, though the gene diversity tended to be smaller with decreasing distance between populations at the geographical level. Results are discussed in relation to the dispersal behaviour of spider mites.

Animals↗
PubMed1979

Influence of genetic population structure on the results of chronic toxicity studies.

The importance of the genetic makeup of animals used for toxicological testing has been recognized, although there are few data regarding this. In the study discussed here offspring from a BALB/cStCrlfC3Hf/Nctr male and C57BL/6jfC3Hf/Nctr female cross were used to produce a homogeneous (F1) strain, and brother-sister mating of the F1 population was used to produce a heterogeneous (F2) strain of mice, both having essentially the same gene pool but with different distributions. The end points of mortality and body weights were used to demonstrate relative variability about a mean resulting from genetic constitution when the mice were exposed to benzidine dihydrochloride. This life-span study demonstrated that genetic constitution in research animals should be an important consideration in toxicological research. There were significant differences in body weight and mortality between the two populations, with the F2 mice exhibiting wider body weight ranges and greater susceptibility to the test chemical.

Animals↗
PubMed1984

Physical structure and genetic organisation of the genome of maize streak virus (Kenyan isolate).

The structure of the maize streak virus genome (Kenyan isolate, MSV-K), as determined from the sequence of clones obtained from DNA isolated from virus particles, is composed of one major DNA component of about 2.6 kb. MSV virion DNA is partially double-stranded, composed of a full-length virion (V) strand and a short (70-80b) primer (P) strand. The primer strand has a fixed 5'-end capped with alkaline labile material, presumably 1-2 ribonucleotides. The MSV genome has two major coding regions oriented on opposite strands and flanked by two small intergenic regions. The coding region on the P strand is composed of two major open reading frames (ORFs), arranged in tandem and in the same reading frame. Because the predicted protein derived from a composite of these two ORFs closely corresponds to the product from a single ORF in the cassava latent virus genome, it is likely that this region encodes two proteins with common amino-termini, one a read-through product of the amber codon terminator in the first ORF. The intergenic regions contain potential transcription start and stop signals oriented in the direction of the two opposing coding regions. Considerable DNA sequence heterogeneity was observed, mostly silent or conservative third base substitutions in coding regions and base substitutions, small insertions and small, close-range transpositions in intergenic regions.

Base Sequence↗
PubMed2004

The calculative nature of microbe-mineral interactions.

Microorganisms continually redefine themselves at many levels, including the molecule, cell, and community. Although it was initially assumed that this resulted from the genesis of information within DNA alone, it has since been shown that innovation originates at multiple levels. This occurs through calculative units, each unit consisting of two proliferating structures, one nested within the other and each undergoing changes in structural geometry that affect the proliferation rate of the other. For example, the recombination of genetic structures affects the proliferation of community structures, and the recombination of community structures affects the proliferation of genetic structures. The proliferation of a nested series of structures (e.g., genes proliferating within cells, cells proliferating within communities, communities proliferating within ecosystems) results in a logic circuit that calculates the form and function of each structural element in the series. In this situation each element functions as both a habitat and an inhabitant (environment and organism), and it is this dichotomy that determines the balance of nature. Nested geological structures, such as minerals and continents, also proliferate and redefine themselves in much the same way. Microbe-mineral interactions thus link nested biological calculations to an analogous set of nested geological calculations. Examples include the microorganisms involved in the nucleation (proliferation) of ferric hydroxides, carbonates, silicates, and ice crystals.

Bacteria↗
PubMed2005

Disturbed population genetics: suspected introgressive hybridization between two Mnais damselfly species (Odonata).

Mnais costalis and M. pruinosa are damselflies (Odonata: Calopterygidae) with low dispersal abilities, both during their aquatic stream-living immature stage and their flying adult stage. A previous nuclear DNA (nDNA) sequencing and morphology study showed that these two species are very closely related, and cohabit widely in western Japan. The two species, however, segregate microhabitats along a stream: M. costalis lives in the lower reaches, and M. pruinosa in the upper reaches. In this study, our analyses were based on mitochondrial DNA (mtDNA), which usually mutates faster and is more variable among individuals than nDNA, and which is inherited maternally. We found that most COI haplotypes were shared between the two species, and that for most study sites interspecific riverine genetic structures were not clarified by mtDNA analysis. Incongruent population genetic structures based on nDNA and mtDNA suggested hybridization and introgression of mtDNA between the two species.

Animals↗
PubMed2005

Effects of population structure on genetic association studies.

Population-based case-control association is a promising approach for unravelling the genetic basis of complex diseases. One potential problem of this approach is the presence of population structure in the samples. Using the Collaborative Study on the Genetics of Alcoholism (COGA) single-nucleotide polymorphism (SNP) datasets, we addressed three questions: How can the degree of population structure be quantified, and how does the population structure affect association studies? How accurate and efficient is the genomic control method in correcting for population structure? The amount of population structure in the COGA SNP data was found to inflate the p-value in association tests. Genomic control was found to be effective only when the appropriate number of markers was used in the control group in order to correctly calibrate the test. The approach presented in this paper could be used to select the appropriate number of markers for use in the genomic control method of correcting population structure.

Databases, Genetic↗
PubMed2003

The structure of genetic and environmental risk factors for common psychiatric and substance use disorders in men and women.

BACKGROUND: Patterns of comorbidity suggest that the common psychiatric and substance use syndromes may be divisible into 2 broad groups of internalizing and externalizing disorders. We do not know how genetic and environmental risk factors contribute to this pattern of comorbidity or whether the etiologic structure of these groups differ in men and women. METHODS: Lifetime diagnoses for 10 psychiatric syndromes were obtained at a personal interview in more than 5600 members of male-male and female-female twin pairs ascertained from a population-based registry. Multivariate twin modeling was performed using the program Mx. RESULTS: We first fit models to the following 7 syndromes: major depression, generalized anxiety disorder, phobia, alcohol dependence, drug abuse/dependence, adult antisocial behavior, and conduct disorder. The full model, which could be constrained to equality in male and female subjects, identified 2 genetic factors. The first had strongest loadings on alcohol dependence, drug abuse/dependence, adult antisocial behavior, and conduct disorder; the second, on major depression, generalized anxiety disorder, and phobia. Alcohol dependence and drug abuse/dependence had substantial disorder-specific genetic risk factors. Shared environmental factors were most pronounced for conduct disorder and adult antisocial behavior. No clear internalizing/externalizing structure was seen for the unique environmental common factors. We then fit models to 5 internalizing syndromes. The full model, which could also be constrained to equality in men and women, revealed one genetic factor loading most heavily on major depression and generalized anxiety disorder and another loading most strongly on animal and situational phobia. CONCLUSIONS: The underlying structure of the genetic and environmental risk factors for the common psychiatric and drug abuse disorders in men and women is very similar. Genetic risk factors predispose to 2 broad groups of internalizing and externalizing disorders. Within the internalizing disorders, 2 genetic factors are seen that predispose to disorders dominated by anxious-misery and fear. Substance use disorders have disorder-specific genetic risks. The externalizing disorders of conduct disorder and adult antisocial behavior are significantly influenced by the shared environment. The pattern of lifetime comorbidity of common psychiatric and substance use disorders results largely from the effects of genetic risk factors.

Adult↗
PubMed1994

Structure and genetics of the partially duplicated gene RP located immediately upstream of the complement C4A and the C4B genes in the HLA class III region. Molecular cloning, exon-intron structure, composite retroposon, and breakpoint of gene duplication.

The correlation of many HLA-associated autoimmune and genetic diseases with the polymorphic complement C4 genes may be attributed to the presence of disease susceptibility genes in the close proximity of C4. We have cloned and characterized a pair of partially duplicated genes, RP1 and RP2, located 611 base pairs upstream of the human C4A and C4B genes, respectively. The putative RP protein, consisting of 364 amino acid residues, is basic and highly hydrophilic. There is a bipartite nuclear localization signal at residues 114-131 and therefore RP may be a nuclear protein. Northern blot analysis suggested that RP is ubiquitously expressed. The 5' region of the RP1 gene is CpG rich, which is a characteristic of housekeeping genes. The RP1 gene contains nine exons. Located in the fourth intron is a cluster of Alu elements, and a newly defined composite retroposon SVA with a SINE, multiple copies of GC-rich VNTRs and an Alu element altogether enclosed by direct terminal repeats. Members of SVA are also present in the complement C2 gene located about 20 kilobases upstream of RP1 in the HLA and in the cytochrome CYP1A1 gene. Determination of the DNA sequences for RP2 from two different HLA haplotypes revealed identical hybrid sequences which resulted from fusion of RP with the tenascin-like Gene X and truncation of the 5' regions of both genes. Cumulative data suggest that the four tandemly arranged genes RP, complement C4, steroid 21-hydroxylase (CYP21), and Gene X altogether form a modular structure, RCCX. The number of RCCX modules varies from one to three or more in the population. Absence of the truncated genes RP2 and Gene XA have been detected in genomes with single RCCX modules. Duplication of the RCCX modules probably occurred before the speciation of great apes and humans as they contain the same breakpoint region of RP and Gene X gene duplication.

Alleles↗
PubMed2001

Spatial structure of lemming populations (Dicrostonyx groenlandicus) fluctuating in density.

The pattern and scale of the genetic structure of populations provides valuable information for the understanding of the spatial ecology of populations, including the spatial aspects of density fluctuations. In the present paper, the genetic structure of periodically fluctuating lemmings (Dicrostonyx groenlandicus) in the Canadian Arctic was analysed using mitochondrial DNA (mtDNA) control region sequences and four nuclear microsatellite loci. Low genetic variability was found in mtDNA, while microsatellite loci were highly variable in all localities, including localities on isolated small islands. For both genetic markers the genetic differentiation was clear among geographical regions but weaker among localities within regions. Such a pattern implies gene flow within regions. Based on theoretical calculations and population census data from a snap-trapping survey, we argue that the observed genetic variability on small islands and the low level of differentiation among these islands cannot be explained without invoking long distance dispersal of lemmings over the sea ice. Such dispersal is unlikely to occur only during population density peaks.

Animals↗
PubMed2006

Genetic and structural analysis of the basolateral amygdala complex in BXD recombinant inbred mice.

The amygdala integrates and coordinates emotional and autonomic responses. The genetics that underlie variation in amygdala structure may be coupled to variation in levels of aggression, fear, anxiety, and affiliated behaviors. We systematically quantified the volume and cell populations of the basolateral amygdala complex (BLAc) across 35 BXD recombinant inbred (RI) lines, the parental strains--C57BL/6J (B6) and DBA/2J (D2)--and F1 hybrids (n cases=199, bilateral analysis). Neuron number and volume vary 1.7- to 2-fold among strains (e.g., neuron number ranged from 88,000 to 170,000). Glial and endothelial populations ranged more widely (5- to 8-fold), in part because of higher technical error. A quantitative trait locus (QTL) for the BLAc size is located on chromosome (Chr) 8 near the Large gene. This locus may also influence volume of other regions including hippocampus and cerebellum. Cell populations in the BLAc appear to be modulated more weakly by loci on Chrs 11 and 13. Candidate genes were selected on the basis of correlation with BLAc traits, chromosomal location, single nucleotide polymorphism (SNP) density, and expression patterns in the Allen Brain Atlas. Neurod2, a gene shown to be significant for the formation of the BLAc by knockout studies, is among the candidates genes. Other candidates include Large, and Thra. Responses to drugs of abuse and locomotor activity were the most notable behavioral correlates of the BLAc traits.

Amygdala↗
PubMed1997

Geographic structure of mitochondrial and nuclear gene polymorphisms in Australian green turtle populations and male-biased gene flow.

The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.

Alleles↗
PubMed2006

Correlates of genetic differentiation and isolation by distance in 17 congeneric Silene species.

The contemporary pattern of intraspecific genetic variation can indicate the relative role of gene flow and local differentiation in shaping the evolutionary history and future trajectory of a species. To assess the recent influence of contrasting life history and demographic characteristics on genetic structure within a group of closely related species, patterns of genetic differentiation (F(ST) and related statistics) and isolation by distance (IBD) were compared among 17 congeneric herbaceous plant species. Data came from 35 published studies of 16 species, and a previously unpublished analysis of chloroplast genetic variation in the rare endemic Silene rotundifolia. Among-population genetic variance was most strongly influenced by the type of genetic marker used; cytoplasmic markers showed larger values than allozyme and anonymous nuclear markers. Other independently significant factors were geographical range size and, for allozyme studies, reproductive system; in particular, endemism and hermaphroditism were associated with higher among-population genetic variance, whereas large native geographical range and dioecy were associated with lower among-population variance. Over equivalent spatial scales, dioecious populations also showed weaker IBD than hermaphrodites, perhaps because increased population transience and/or variance in the spatial pattern of gene flow are more closely associated with dioecy in this genus. Invasive populations had both highly variable among-population genetic variance, and no evidence for IBD, consistent with nonequilibrium conditions. Other analysed factors including predominant pollinator had no discernable influence on genetic structure or patterns of IBD. In general, this comparative approach appears to be valuable for synthesizing the complementary information provided by F-statistics and IBD, and for indicating the relative importance of particular biological factors in shaping genetic variation within different species of a closely related plant group.

DNA, Chloroplast↗