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PubMed1999

Population structure and genetic variation of european wild rabbits (Oryctolagus cuniculus) in east anglia

The European wild rabbit (Oryctolagus cuniculus) is an introduced species in Britain, and populations have been profoundly influenced by both man and disease. In stable environmental conditions, distinct social behaviour is observed, and this social structure leads to significant genetic structuring at the intrapopulation level. In this study, European wild rabbits were sampled from 17 sites across the East Anglian region of Britain and genotyped with nine microsatellite loci. Genotypical proportions deviated significantly from Hardy-Weinberg equilibrium, reflecting a degree of population subdivision and non-random mating. Several estimates of measures of population genetic structure revealed that populations are genetically distinct and have small effective population sizes. These distinctive properties are seen to be the combined effects of the social structure and random drift acting on bottlenecked populations after myxomatosis. It is concluded that the genetic structure seen in rabbit populations today is unlikely to reflect historical structuring present before myxomatosis, but that it results from recent events.

Journal Article↗
PubMed2005

Logistic regression protects against population structure in genetic association studies.

We conduct an extensive simulation study to compare the merits of several methods for using null (unlinked) markers to protect against false positives due to cryptic substructure in population-based genetic association studies. The more sophisticated "structured association" methods perform well but are computationally demanding and rely on estimating the correct number of subpopulations. The simple and fast "genomic control" approach can lose power in certain scenarios. We find that procedures based on logistic regression that are flexible, computationally fast, and easy to implement also provide good protection against the effects of cryptic substructure, even though they do not explicitly model the population structure.

Animals↗
PubMed2003

Clonal population structure of Pseudomonas avellanae strains of different origin based on multilocus enzyme electrophoresis.

To assess the genetic diversity and genetic relationships of Pseudomonas avellanae, the causative agent of hazelnut decline, a total of 102 strains, obtained from central Italy (provinces of Viterbo and Rome) and northern Greece, were studied using multilocus enzyme electrophoresis (MLEE). Their allelic variation in 10 loci was determined. All loci were polymorphic and 53 electrophoretic types (ETs) were identified from the total sample. The mean genetic diversity (H) was 0.65 and this value ranged from 0.37 for the least polymorphic to 0.82 for the most polymorphic locus. The dendrogram originated from MLEE data indicated two main groups of ETs, A and B. The groups do not appear to be correlated to the geographic origin of the strains, although all the ETs from northern Greece clustered into subgroup B1. Pseudomonas syringae pv. actinidiae and P. syringae pv. theae, included in the analysis as outgroups, clustered apart. The index of association (I(A)) for P. avellanae was 0.90. The I(A) values were always significantly different from zero for the population subsets studied and no epidemic structure was found. These results would indicate that the population structure of P. avellanae is clonal either in northern Greece or in central Italy. The recent outbreaks of the bacterium in new areas of hazelnut cultivation would explain the current clonal structure that is persisting over decades.

Alleles↗
PubMed2001

Genetic variation and population structure of the mixed-mating cactus, Melocactus curvispinus (Cactaceae).

Genetic diversity was measured in the mixed-mating cactus, Melocactus curvispinus, in Venezuela. Allozyme diversity was surveyed in 19 putative loci over 18 populations. Compared to other plant taxa, this cactus is rich in polymorphic loci (Ps=89.5%), with high numbers of alleles per polymorphic locus (APs=3.82), but moderate levels of heterozygosity (Hes=0.145). Substantial levels of inbreeding were detected across loci and populations at macrogeographic (FIS=0.348) and regional levels (FIS=0.194-0.402). Moderate levels of genetic differentiation among populations were detected at macrogeographical (FST=0.193) and regional (FST=0.084-0.187) scales, suggesting that gene flow is relatively restricted, but increases within regions without topographic barriers. The population genetic structure observed for this cactus was attributed to, at least, three factors: short-distance pollination and seed dispersal, the mixed-mating condition of the species, and genetic drift. High genetic identities between populations (I=0.942) supported the conspecific nature of all populations surveyed. The levels and patterns of genetic structure observed for M. curvispinus were consistent with its mating system and gene dispersal mechanisms.

Cactaceae↗
PubMed2000

Higher impact of female than male migration on population structure in large mammals.

We simulated large mammal populations using an individual-based stochastic model under various sex-specific migration schemes and life history parameters from the blue whale and the Asian elephant. Our model predicts that genetic structure at nuclear loci is significantly more influenced by female than by male migration. We identified requisite comigration of mother and offspring during gravidity and lactation as the primary cause of this phenomenon. In addition, our model predicts that the common assumption that geographical patterns of mitochondrial DNA (mtDNA) could be translated into female migration rates (Nmf) will cause biased estimates of maternal gene flow when extensive male migration occurs and male mtDNA haplotypes are included in the analysis.

Animals↗
PubMed2002

The contribution of haploids, diploids and clones to fine-scale population structure in the seaweed Cladophoropsis membranacea (Chlorophyta).

Local populations of Cladophoropsis membranacea exist as mats of coalesced thalli composed of free-living haploid and diploid plants including clonally reproduced plants of either phase. None of the phases are morphologically distinguishable. We used eight microsatellite loci to explore clonality and fine-scale patch structure in C. membranacea at six sites on the Canary Islands. Mats were always composites of many individuals; not single, large clones. Haploids outnumbered diploids at all sites (from 2:1 to 10:1). In both haploid and diploid plants, genetic diversity was high and there was no significant difference in allele frequencies. Significant heterozygote deficiencies were found in the diploid plants at five out of six sites and linkage disequilibrium was associated with the haploid phase at all sites. Short dispersal distances of gametes/spores and small effective population sizes associated with clonality probably contribute to inbreeding. Spatial autocorrelation analysis revealed that most clones were found within a radius of approximately 60 cm and rarely further than 5 m. Dominance of the haploid phase may reflect seasonal shifts in the relative frequencies of haploids and diploids, but may alternatively reflect superiority of locally adapted and competitively dominant, haploid clones; a strategy that is theoretically favoured in disturbed environments. Although sexual reproduction may be infrequent in C. membranacea, it is sufficient to maintain both life history phases and supports theoretical modelling studies that show that haploid-diploid life histories are an evolutionarily stable strategy.

Chlorophyta↗
PubMed1991

[Immunochemical characteristics of the population structure of antibody-producing cells in experimental influenza].

The authors presented the results of population study of specific IgG-antibody-forming cells (AFC) in the pool of mice splenocytes performed in the time-course of simulated influenza with the help of experimental mathematical approach which permitted making a detailed observation of the functional structure of the population and analysing the changes in the spectrum of the AFC subpopulations in the time-course of viral disease. Mathematical simulation of the main stage of immunopointed identification of AFC on +nitrocellulose filters (NCF) permitted the verification of the ratio between the characteristic features of the spots on the NCF and the number and affinity of cell-secreting IgG antibodies. New data are obtained on the formation of the population of +virus-specific IgG-AFC which are featured by discreteness of the AFC +affinity ++ spectrum, cyclic changes in their activity and shifts in the stages of the AFC subpopulation activity. The authors substantiated the necessity to revise the existing theoretical models of the formation of humoral immune response to viral infections.

Animals↗
PubMed2005

Population structure of Y chromosome SNP haplogroups in the United States and forensic implications for constructing Y chromosome STR databases.

A set of 61 Y chromosome single-nucleotide-polymorphisms (Y-SNPs) is typed in a sample of 2517 individuals from 38 populations to infer the geographic origins of Y chromosomes in the United States and to test for paternal admixture among African-, European-, Hispanic-, Asian-, and Native-Americans. All of the samples were previously typed with the 11 core U.S. Y chromosome short tandem repeats (Y-STRs) recommended by SWGDAM, which revealed high levels of among ethnic group variation and low levels of among-population-within-ethnic-group variation. Admixture estimates vary greatly among populations and ethnic groups. The frequencies of non-European (3.4%) and non-Asian (4.5%) Y chromosomes are generally low in European-American and Asian-American populations, respectively. The frequencies of European Y chromosomes in Native-American populations range widely (i.e., 7-89%) and follow a West to East gradient, whereas they are relatively consistent in African-American populations (26.4+/-8.9%) from different locations. The European (77.8+/-9.3%) and Native-American (13.7+/-7.4%) components of the Hispanic paternal gene pool are also relatively constant among geographic regions; however, the African contribution is much higher in the Northeast (10.5+/-6.4%) than in the Southwest (1.5+/-0.9%) or Midwest (0%). To test for the effects of inter-ethnic admixture on the structure of Y-STR diversity in the U.S., we perform subtraction analyses in which Y chromosomes inferred to be admixed by Y-SNP analysis are removed from the database and pairwise population differentiation tests are implemented on the remaining Y-STR haplotypes. Results show that low levels of heterogeneity previously observed between pairs of Hispanic-American populations disappear when African-derived chromosomes are removed from the analysis. This is not the case for an unusual sample of European-Americans from New York City when its African-derived chromosomes are removed, or for Native-American populations when European-derived chromosomes are removed. We infer that both inter-ethnic admixture and population structure in ancestral source populations may contribute to fine scale Y-STR heterogeneity within U.S. ethnic groups.

Analysis of Variance↗
PubMed2006

PSMIX: an R package for population structure inference via maximum likelihood method.

BACKGROUND: Inference of population stratification and individual admixture from genetic markers is an integrative part of a study in diverse situations, such as association mapping and evolutionary studies. Bayesian methods have been proposed for population stratification and admixture inference using multilocus genotypes and widely used in practice. However, these Bayesian methods demand intensive computation resources and may run into convergence problem in Markov Chain Monte Carlo based posterior samplings. RESULTS: We have developed PSMIX, an R package based on maximum likelihood method using expectation-maximization algorithm, for inference of population stratification and individual admixture. CONCLUSION: Compared with software based on Bayesian methods (e.g., STRUCTURE), PSMIX has similar accuracy, but more efficient computations.PSMIX and its supplemental documents are freely available at http://bioinformatics.med.yale.edu/PSMIX.

Algorithms↗
PubMed2003

Assessing population structure and gene flow in Montana wolverines (Gulo gulo) using assignment-based approaches.

In North America, wolverines once occupied a continuous range from Alaska southward to New Mexico. In the lower 48 states, small remnant populations remain only in the northwestern United States. Among these remnant populations, the Montana population has the highest probability of long-term persistence given its size and proximity to healthy populations in Canada. In this study, we evaluate population genetic structure and gene flow among Montana wolverines using 10 polymorphic microsatellite loci. Bayesian and frequency-based assignment tests revealed significant population substructure and provide support for at least three subpopulations in Montana. FST values between subpopulations ranged from 0.08 to 0.10 and provide evidence for male-biased dispersal. The high degree of population substructure and low levels of gene flow contrast results from wolverine population genetic studies in less fragmented landscapes of Alaska and Canada. This study provides additional support for the hypothesis that large carnivore populations of Montana are becoming increasingly fragmented due to human development and disturbance.

Animals↗
PubMed1990

Population structure analysis using polygenic traits: estimation of migration matrices.

Many studies of subdivided populations have attempted to determine the underlying migration rates that generate observed patterns of genetic differentiation. Most previous analyses have yielded only qualitative inferences about migration. In this paper I present a new method for estimating the full migration matrix from information on polygenic trait variation. The method employs multivariate quantitative genetic theory to provide a matrix formulation of the expected covariance structure in multigenerational subdivided populations for which information is available at different points in the life cycle. I develop a restricted maximum likelihood technique (REML) to take account of this additional life-cycle information and to estimate both the migration matrix and the ratio of effective population size to census size. To make the problem computationally tractable, the migration matrix is modeled as a log-linear function of a few covariates, such as subdivision size and geographic distance. I apply the technique to data on dermatoglyphic ridge counts for 1015 individuals of the Jirel population of east Nepal, considering two different age cohorts. In the adult cohort (individuals over 21 years of age) I examine data by both birthplace and residence and for the subadult cohort (under 21 years of age), by birthplace. Results from the REML technique reveal that the best-fitting migration model is a finite island model with an estimated endemicity of 0.730 +/- 0.105 and an estimated ratio of effective size to census size of 0.287 +/- 0.095. Both estimates are reasonable given known demographic data. In addition, Fst values predicted by the migration model are concordant with REML estimates obtained directly from the dermatoglyphic variation.

Adolescent↗
PubMed1996

Molecular characterization of clonal population structure and biogeography of arctic apomictic Daphnia from Greenland and Iceland.

As part of a continuing international project to characterize the population genetic (clonal) structure of arctic members of the Daphnia pulex complex, 34 populations from western Iceland (N = 1373), and 76 populations from western Greenland (N = 2917), were surveyed for allozymic variation at six polymorphic enzyme loci. Mean clonal richness (+/- SE) was 1.91 +/- 0.19 and 1.50 +/- 0.12 for Iceland and Greenland populations, respectively. Mean clonal diversity (+/-1 SE) was 1.20 +/- 0.07 and 1.13 +/- 0.04 for Iceland and Greenland populations, respectively. Four widely distributed clones constituted 92.2% of the total animals surveyed from Iceland, while three locally abundant clones constituted 80.1% of the total animals collected primarily from Disko Island, western Greenland. Selected populations were screened for mitochondrial (mt)DNA variation using PCR-based RFLP analysis of a 2100 bp fragment containing part of the ND4 and ND5 genes. One mtDNA haplotype was very widespread in both western Greenland and western Iceland, although, a number of mutational derivatives were also detected. These data indicate the potential for long-distance dispersal of mtDNA lineages, of the order of hundreds or thousands of kilometers across the arctic. Phylogenetic analysis of the sequence of a 254 base pair (bp) fragment of the control region of the mtDNA molecule revealed two major clades one of which consisted solely of non-melanic lineages, and the other of which consisted almost exclusively of melanic lineages (i.e. one non-melanic lineage also clustered in this clade). Sequence divergence between the two clades averaged 7.3%. Both mitochondrial analyses did not reveal any distinct intraregional clustering of lineages. We discuss our results in reference to previous molecular work done on this arctic Daphnia complex, and we attempt to infer phylogeographic patterning based on geological/glaciological historical events in this region of the arctic.

Animals↗
PubMed2005

Population structure, admixture, and aging-related phenotypes in African American adults: the Cardiovascular Health Study.

U.S. populations are genetically admixed, but surprisingly little empirical data exists documenting the impact of such heterogeneity on type I and type II error in genetic-association studies of unrelated individuals. By applying several complementary analytical techniques, we characterize genetic background heterogeneity among 810 self-identified African American subjects sampled as part of a multisite cohort study of cardiovascular disease in older adults. On the basis of the typing of 24 ancestry-informative biallelic single-nucleotide-polymorphism markers, there was evidence of substantial population substructure and admixture. We used an allele-sharing-based clustering algorithm to infer evidence for four genetically distinct subpopulations. Using multivariable regression models, we demonstrate the complex interplay of genetic and socioeconomic factors on quantitative phenotypes related to cardiovascular disease and aging. Blood glucose level correlated with individual African ancestry, whereas body mass index was associated more strongly with genetic similarity. Blood pressure, HDL cholesterol level, C-reactive protein level, and carotid wall thickness were not associated with genetic background. Blood pressure and HDL cholesterol level varied by geographic site, whereas C-reactive protein level differed by occupation. Both ancestry and genetic similarity predicted the number and quality of years lived during follow-up, but socioeconomic factors largely accounted for these associations. When the 24 genetic markers were tested individually, there were an excess number of marker-trait associations, most of which were attenuated by adjustment for genetic ancestry. We conclude that the genetic demography underlying older individuals who self identify as African American is complex, and that controlling for both genetic admixture and socioeconomic characteristics will be required in assessing genetic associations with chronic-disease-related traits in African Americans. Complementary methods that identify discrete subgroups on the basis of genetic similarity may help to further characterize the complex biodemographic structure of human populations.

Black or African American↗
PubMed1998

Allele-specific population structure of Drosophila melanogaster alcohol dehydrogenase at the molecular level.

The history of the Drosophila melanogaster alcohol dehydrogenase (ADH) Fast/Slow polymorphism was studied by recording molecular variation and inversion polymorphism in 233 chromosomes from European and African populations. Silent molecular variation in the Slow allele was very different between standard chromosomes and chromosomes bearing the In(2L)t inversion. Within populations, inverted Slow haplotypes were more variable than standard Slow haplotypes. Between populations, geographical structure was almost nonexistent for inverted Slow haplotypes and highly significant for standard Slow. All Fast haplotypes occurred on standard chromosomes. They showed little variation within and between populations. They were highly significantly closer to standard Slow haplotypes from Europe. These results suggest that the current range of Fast and In(2L)t Slow haplotypes is recent and that an older genetic differentiation between populations was followed by allele-specific gene flow.

Alcohol Dehydrogenase↗
PubMed2001

Distribution of individual inbreeding coefficients, relatedness and influence of stocking on native anadromous brown trout (Salmo trutta) population structure.

We examined polymorphism at seven microsatellite loci in 4023 brown trout (Salmo trutta) collected from 32 tributaries to the Limfjord, Denmark (approximately 200 km) and from two hatcheries used for stocking. Populations differ in their estimated sizes and stocking histories. Mean individual inbreeding coefficients do not differ among locations within rivers. Relatedness varies between sites within rivers indicating varied local dynamics at a very small geographical scale. Relatedness is sometimes lower than expected among an equal number of simulated individuals with randomized genotypes, suggesting structure within locations. Five per cent of the genetic variance is distributed among rivers (F(ST) = 0.049), but in the western, less heavily stocked, area of the Limfjord a higher proportion of the genetic variance is distributed among rivers than among locations within rivers. The reverse is true of the eastern, more heavily stocked, area of the Limfjord. Here, a higher proportion of the genetic variance is distributed among locations within rivers than among rivers. Assignment tests reveal that the majority of trout (mean 77% of all fish) are more probably of local origin than hatchery origin but this proportion varies regionally, with rivers in the western area of the Limfjord showing a relatively high (mean 88%) and those in the eastern area showing a relatively low (mean 72%) proportion of locally assigned trout. These results can be interpreted as reflecting stocking impact. Also, the proportion of locally assigned trout correlates with the populations' stocking histories, with rivers presently subjected to stocking (hatchery trout) showing low (mean approximately 0.73), and rivers where stocking was discontinued showing high (mean approximately 0.84) proportions of local fish, probably reflecting lower survival of hatchery than of wild trout. There is evidence for isolation by distance at a large geographical scale when individual river populations are pooled into nine geographical regions but not at a small geographical scale when populations are considered individually. We reject the null hypothesis that stocking has had no impact on population structure but the relatively high proportion of locally assigned trout in populations where stocking with domestic fish no longer takes place suggests limited long-term success of stocking.

Animals↗
PubMed2000

[Analyses of the population structures of Mallophaga infesting urban pigeons].

A total of 70 pigeons from Cracow area was examined and the representation of bird lice (Mallophaga) infesting them estimated. Mostly the populations of two dominant species: Columbicola columbae columbae (L.) and Campanulotes bidentatus compar (Burm.) were assessed. 47% of birds inspected had less than 100 specimens of Mallophaga, although the highest infested one had 900 specimens. Sex and age of pigeons did not influence the number of bird lice present, and only weak health condition of individuals allowed higher infestation. The sex structure of ectoparasites was balanced, with a slightly higher number of females during the year of study. The highest number of bird lice was detected in autunm and the larvae definitely predominated then, as well. Similar tendency was observed in C. c. columbae populations. The course of age dynamic of C. b. compar was somewhat different, having the peak in July, and the imago stage dominated in this species. The populations of in C. c. columbae showed developmental signs, whereas the population structures of C. b. compar gave evidence of their regression.

Animals↗
PubMed2001

Evolution in a spatially structured population subject to rare epidemics.

We study a model that gives rise to spatially inhomogeneous population densities in a system of host individuals subject to rare, randomly distributed disease events. For stationary hosts that disperse offspring over short distances, evolutionary dynamics can lead to persistent populations with a variety of spatial structures. A mean-field analysis is shown to account for the behavior observed in simulations of a one-dimensional system, where the evolutionarily stable state corresponds to the solution of a straightforward optimization problem. In two dimensions, evolution drives the system to a stable critical state that is less well understood.

Animals↗
PubMed2001

Bottlenecks, drift and differentiation: the population structure and demographic history of sika deer (Cervus nippon) in the Japanese archipelago.

We assessed genetic differentiation and diversity in 14 populations of sika deer (Cervus nippon) from Japan and four populations of sika deer introduced to the UK, using nine microsatellite loci. We observed extreme levels of differentiation and significant differences in diversity between populations. Our results do not support morphological subspecies designations, but are consistent with previous mitochondrial DNA analyses which suggest the existence of two genetically distinct lineages of sika deer in Japan. The source of sika introduced to the UK was identified as Kyushu. The underlying structure of Japanese populations probably derives from drift in separate glacial refugia and male dispersal limited by distance. This structure has been perturbed by bottlenecks and habitat fragmentation, resulting from human activity from the mid-nineteenth century. Most current genetic differentiation and differences in diversity among populations probably result from recent drift. Coalescent model analysis suggests sika on each of the main Japanese islands have experienced different recent population histories. Hokkaido, which has large areas of continuous habitat, has maintained high levels of gene flow. In Honshu the population is highly fragmented and is likely to have been evolving by drift alone. In Kyushu there has been a balance between gene flow and drift but all the populations have experienced high levels of drift. Habitat fragment size was not significantly associated with genetic diversity in populations but there was a significant correlation between habitat fragment size and effective population size.

Alleles↗