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PubMed1997

Genetic selection strategies--population genetics.

This paper provides an overview of the association between population genetics and selection strategies in poultry. Relationships between artificial and natural selection and among causes contributing to limits to artificial selection are discussed. Homeostasis and resource allocations at the individual and at the population level are reviewed. Examples from poultry demonstrate where human intervention has circumvented biological limits. Lastly, this paper considers the role of population genetics in future breeding strategies for poultry.

Animal Husbandry↗
PubMed2006

RAPD analysis of genetic diversity and population genetic structure of Stipa krylovii Reshov. in Inner Mongolia steppe.

Random amplified polymorphic DNA (RAPD) analysis was used to characterize the genetic diversity and population genetic structure of Stipa krylovii populations in Inner Mongolia steppe of North China. Thirteen 10 bp oligonucleotide primers, which generated 237 RAPD bands, were used to analyze 90 plants of five populations from three regions, meadow steppe, typical steppe and desert steppe, from the east to the west. The genetic diversity of Stipa krylovii that was revealed by observed number of alleles (na), expected number of alleles (ne), Nei's diversity index (h), Shannon's diversity index (H), amplificated loci, polymorphic loci and the percentage of polymorphic loci (PPB) increased from the east to the west. The Pearson's correlation analysis between genetic diversity parameters and ecological parameters indicated that the genetic diversity of Stipa krylovii was associated with precipitation and cumulative temperature variations along the longitude (humidity were calculated by precipitation and cumulative temperature). Dendrogram based on Jaccard's genetic distance showed that the individuals from the same population formed a single sub-group. Although most variation (56.85%) was within populations, there was high genetic differentiation among populations of Stipa krylovii, high differentiation within and between regions by AMOVA analysis. Either Nei's unbiased genetic distance (G(ST)) or gene flow (Nm) among pairwise populations was not correlated with geographical distance by Mantel's test (P > 0.05), suggesting that there was no consistency with the isolation by distance model in these populations. Natural selection may have played a role in affecting the genetic diversity and population structure, but habitat destruction and degradation in northern grassland in China may be the main factor responsible for high genetic differentiation among populations, within and among regions.

China↗
PubMed1979

Human pancreatic amylase polymorphism: formal genetics and population genetics.

The genetically determined polymorphism of human pancreatic amylase (E.C. 3.2.1.1), AMY2, is demonstrated in serum specimens by agarose gel electrophoresis. We investigated 325 mother-child pairs and 2594 unrelated individuals from southwestern Germany. This study confirms the formal hypothesis of two common alleles AMY1/2, AMY2/2 and possibly two rare alleles AMY3/2, AMY4/2 at an autosomal locus AMY2. The frequency of the AMY1/2 allele was calculated as 0.951; AMY3/2 and AMY4/2 seem to have a frequency of 0.001 in this sample.

Alleles↗
PubMed2003

Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China.

Genetic diversity and population genetic structure of natural Oryza rufipogon populations in China were studied based on ten microsatellite loci. For a total of 237 individuals of 12 populations collected from four regions, a moderate to high level of genetic diversity was observed at population levels with the number of alleles per locus ( A) ranging from 2 to 18 (average 10.6), and polymorphic loci ( P) from 40.0% to 100% (average 83.3%). The observed heterozygosity ( H(O)) varied from 0.163 to 0.550 with the mean of 0.332, and the expected heterozygosity ( H(E)) from 0.164 to 0.648 with the mean of 0.413. The level of genetic diversity for Guangxi was the highest. These results are in good agreement with previous allozyme and RAPD studies. However, it was unexpected that high genetic differentiation among populations was found ( R(ST) = 0.5199, theta = 0.491), suggesting that about one-half of the genetic variation existed between the populations. Differentiation (pairwise theta) was positively correlated with geographical distance ( r = 0.464), as expected under the isolation by distance model. The habitat destruction and degradation throughout the geographic range of O. rufipogon may be the main factor attributed to high genetic differentiation among populations of O. rufipogon in China.

China↗
PubMed1998

Molecular population genetics of the red kangaroo (Macropus rufus): mtDNA variation.

The genetic population structure of a large, wide-ranging marsupial, the red kangaroo (Macropus rufus) was assessed using sequence and haplotype frequency data of mitochondrial DNA (mtDNA) from locations across the species range in Australia. Results from sequence data revealed extensive haplotype diversity within the red kangaroo (32/34 sequences were unique). Sequence diversity was distributed within rather than between geographical regions across the species range. Genetic connectivity across the range of the species has therefore been maintained over the long term. On a smaller within-region scale, significant genetic structuring was evident from heterogeneity of haplotype frequencies amongst sampling sites. The geographical scale of panmictic populations differed across the continent with more restricted genetic populations occurring in areas with greater topographic and habitat complexity. We propose that these differences in area of genetic populations are the result of population responses to limiting ecological factors during drought.

Animals↗
PubMed2001

Informed consent and other ethical issues in human population genetics.

Human population genetics has entered a new era of public interest, of controversy, and of ethical problems. Population genetics raises novel ethical problems because both the individuals and the populations being studied are, in effect, "subjects" of the research. Those populations are collectively subject to possible benefits and harms from the research and have interests, somewhat different from those of the individuals, that must be considered from both ethical and practical standpoints. The chapter first describes the new setting for research in human population genetics. It then examines the most controversial ethical issue in population genetics-whether researchers must obtain the informed consent of both the individual subjects and the group as a collectivity. Other vexing issues, including special problems caused by researchers' commercial interests, confidentiality, control over research uses and materials, and return of information to the population are also considered.

Ethics, Medical↗
PubMed2002

Postglacial colonisation of western Central Europe by Polyommatus coridon (Poda 1761) (Lepidoptera: Lycaenidae): evidence from population genetics.

The genetic population structure of Polyommatus coridon (Poda 1761) over large regions of France, Italy and Germany was studied by allozyme electrophoresis. The genetic diversity within populations was high for all parameters analysed (number of alleles 2.72; observed and expected heterozygosity 19.6% and 20.3%, respectively; percentage of polymorphic loci: total: 76.4% and, with polymorphism if the frequency of the commonest allele is below 95%: 53.1%), whereas genetic differentiation between populations was comparatively low (FST = 0.021 +/- 0.002). The mean number of alleles declined significantly from southern to northern populations (r = -0.53, P = 0.0005). Similar effects were found also for other parameters of genetic diversity. This is interpreted as a loss of genetic diversity during postglacial expansion. However, samples from France and Italy had similar patterns of genetic diversity indicating no significant loss in this region. Populations from southern Germany were genetically uniform, well differentiated from French populations and showed a significant loss of genetic diversity. Probably, this is due to a bottleneck during passing through the Burgundian Gap, which is a migration corridor from north-eastern France to southern Germany. In contrast to southern German populations, western German populations were not well differentiated from French populations. Nevertheless, they were genetically impoverished, probably as a result from local bottlenecks and post-expansion phenomena.

Alleles↗
PubMedDate not supplied

Genetic variation and population genetic structure in Trifolium pratense.

Trifolium pratense (red clover) is a short-lived herbaceous plant native to southeastern Europe and Asia Minor. Widel used in agriculture, T. pratense is cultivated as an annual, winter annual, or biennial. It blooms from mid-spring to early fall and is insect pollinated and self-incompatible. Seeds are mammal and bird dispersed. Naturalized populations of T. pratense occur along roadsides and in old fields as well as native grasslands. Allozyme diversity and population genetic structure were determined for nine populations of T. pratense. Results from 13 allozyme loci indicate that genetic diversity is higher and population divergence is lower than expected based on the life-history characteristics of the species. We conclude that the high levels of genetic diversity found within populations of T. pratense suggest that these are not newly established founder populations, and that the low levels of genetic divergence seen among populations are probably due to high rates of gene flow among populations as a result of seed and pollen movement.

Chi-Square Distribution↗
PubMed2001

Estimating the unbiased estimator theta for population genetic survey data.

We consider a method of approximating Weir and Cockerham's theta, an unbiased estimator of genetic population structure, using values readily available from published studies using biased estimators (Wright's F(ST) or Nei's G(ST)). The estimation algorithm is shown to be useful for both model populations and real-world avian populations. However, the correlation between Wright's F(ST) and Weir and Cockerham's theta is strong when compared among 39 empirical avian datasets. Thus, the advantage of approximating an unbiased estimator is unclear considering the small actual effect of theta's bias-removing power on empirical datasets.

Animals↗
PubMed2005

Testing population genetic structure using parametric bootstrapping and MIGRATE-N.

We present a method for investigating genetic population structure using sequence data. Our hypothesis states that the parameters most responsible for the formation of genetic structure among different populations are the relative rates of mutation (micro) and migration (M). The evolution of genetic structure among different populations requires rates of M << p because this allows population-specific mutation to accumulate. Rates of micro << M will result in populations that are effectively panmictic because genetic differentiation will not develop among demes. Our test is implemented by using a parametric bootstrap to create the null distribution of the likelihood of the data having been produced under an appropriate model of sequence evolution and a migration rate sufficient to approximate panmixia. We describe this test, then apply it to mtDNA data from 243 plethodontid salamanders. We are able to reject the null hypothesis of no population structure on all but smallest geographic scales, a result consistent with the apparent lack of migration in Plethodon idahoensis. This approach represents a new method of investigating population structure with haploid DNA, and as such may be particularly useful for preliminary investigation of non-model organisms in which multi-locus nuclear data are not available.

Animals↗
PubMed2003

Population genetic structure of Taenia solium from Madagascar and Mexico: implications for clinical profile diversity and immunological technology.

Taenia solium is a cestode parasitic of humans and pigs that strongly impacts on public health in developing countries. Its larvae (cysticercus) lodge in the brain, causing neurocysticercosis, and in other tissues, like skeletal muscle and subcutaneous space, causing extraneuronal cysticercosis. Prevalences of these two clinical manifestations vary greatly among continents. Also, neurocysticercosis may be clinically heterogeneous, ranging from asymptomatic forms to severely incapacitating and even fatal presentation. Further, vaccine design and diagnosis technology have met with difficulties in sensitivity, specificity and reproducibility. Parasite diversity underlying clinical heterogeneity and technological difficulties is little explored. Here, T. solium genetic population structure and diversity was studied by way of random amplified polymorphic DNA in individual cysticerci collected from pigs in Madagascar and two regions in Mexico. The amplification profiles of T. solium were also compared with those of the murine cysticercus Taenia crassiceps (ORF strain). We show significant genetic differentiation between Madagascar and Mexico and between regions in Mexico, but less so between cysticerci from different localities in Mexico and none between cysticerci from different tissues from the same pig. We also found restricted genetic variability within populations and gene flow was estimated to be low between populations. Thus, genetic differentiation of T. solium suggests that different evolutionary paths have been taken and provides support for its involvement in the differential tissue distribution of cysticerci and varying degrees of severity of the disease. It may also explain difficulties in the development of vaccines and tools for immunodiagnosis.

Animals↗
PubMed2002

Molecular population genetics.

Molecular population genetics is entering a new era dominated by studies of genomic polymorphism. Some of the theory that will be needed to analyze data generated by such studies is already available, but much more work is needed. Furthermore, population genetics is becoming increasingly relevant to other fields of biology, for example to genetic epidemiology, because of disease gene mapping in general populations.

Evolution, Molecular↗
PubMed2004

Neighbour joining trees, dominant markers and population genetic structure.

Population genetic theory for 'traditional' codominant loci showing low levels of allelic diversity (eg allozymes) has been well characterised and evaluated. In contrast, appropriate methods for the analysis of data from more recently developed marker systems are still being refined. For multilocus dominant markers such as amplified fragment length polymorphisms (AFLPs) and randomly amplified polymorphic DNA (RAPDs), the methods of data analysis can be split into two main categories. In population-based approaches, population allele frequencies are compared to obtain some measure of the partitioning of genetic diversity into within- and between-population components. In contrast, individual-based approaches use individual multilocus genotypes as the unit of analysis. Inferences on population processes such as gene flow are based on inter-relationships among individual samples as visualised on phenetic diagrams such as neighbour joining trees. Using a simulation approach coupled with neighbour joining analyses, we show that while the underlying population genetic structure is an important determinant of tree shape in the analysis of dominant data, the number of loci examined also affects the topology. At low levels of population differentiation (eg FST=0.07), mutually exclusive clustering of individuals into their respective populations can occur when sufficiently large numbers of loci are scored (eg 250 loci, typical of many AFLP studies). In contrast, unresolved star-shaped topologies can be recovered at higher levels of population differentiation (FST= >0.15) when lower numbers of loci are employed (eg 50 loci, typical of many RAPD studies). Thus, the relationship between tree topology and the extent of genetic structuring of populations is contingent upon the number of dominant loci scored. The consequences of these findings for the biological interpretation of individual-based analysis of dominant data sets are discussed.

Alleles↗
PubMed2026

plinkQC: an integrated tool for ancestry inference, sample selection, and quality control in population genetics.

MOTIVATION: Population genetic analyses rely on high quality datasets that pass rigorous controls for sample and marker quality. Many analyses also require additional processing including identification of ancestry and sample relatedness. A software package that addresses all these common, yet crucial tasks is missing. RESULTS: We have developed plinkQC, an R/CRAN package that combines these functionalities into a single software package with detailed vignettes for example applications. plinkQC determines the ancestry of study samples via a pre-trained random forest classifier that reaches 98% performance accuracy with just 5% of marker overlap between reference and user data. To obtain the maximal set of unrelated study samples, we developed a graph-based pruning method, taking both relationship estimates and sample quality into account. We demonstrate optimal sample selection on the 1000 Genomes project, where we retain an additional 71 samples compared to publicly available exclusion lists. Finally, plinkQC bundles these results together with per-individual and per-marker quality control checks into three simple functions and returns both the quality controlled dataset and quality control report about each step of the analysis. AVAILABILITY AND IMPLEMENTATION: plinkQC is available as an R/CRAN package. The documentation and code are available on github: https://meyer-lab-cshl.github.io/plinkQC/ and https://github.com/meyer-lab-cshl/plinkQC_manuscript.

Software↗
PubMed2003

An RAPD (random amplified polymorphic DNA) analysis of genetic population structure of Balea biplicata (Gastropoda: Clausiliidae) in fragmented floodplain forests of the Elster/Saale riparian system.

Eight German populations of the land snail Balea biplicata (Mollusca: Clausiliidae) were studied using the randomly amplified polymorphic DNA-polymerase chain reaction and morphometrics (principal component and discriminant analysis) to examine population structure and gene flow patterns in a fragmented landscape mosaic along the Elster/Saale riparian system, Germany. A variety of population genetic analyses targeting either more on the geographic scale of gene flow (genetic distances, F statistics, Mantel test) or on local genotypic structure (heterozygosity, linkage disequilibrium, bottleneck probability) showed that (1) the population system in total is governed by high gene flow independent of geographic distance, (2) genetic structure on the narrower sampling scale is mainly determined by stochastic processes due to genetic drift in small isolated and frequently recolonized populations, and (3) the morphometrical variation of the populations was related neither to habitat nor to genetic heterogeneity. The potentials for active and passive dispersal capacity of the snails and possible environmental impacts on their population structure are discussed.

Animals↗
PubMed1999

The population genetic structure of a large temperate pollinator species, Bombus pascuorum (Scopoli) (Hymenoptera: Apidae)

The genetic population structure of the bumble bee Bombus pascuorum was studied using six microsatellite loci and a partial sequence of the mitochondrial gene cytochrome b. Eighteen populations from central and northern Europe were included in the analysis. Observed levels of genetic variability and heterozygosity were high. Estimates of population differentiation based on F- and phi-statistics revealed significant genetic differentiation among B. pascuorum populations and suggest that two partially isolated gene pools, separated by the Alps, do exist. The distribution of mtDNA haplo-types supports this view and presents direct evidence for gene flow across the Alps. Estimates of the number of migrants exchanged among populations north of the Alps suggest that historical events may have left a strong imprint on population structure.

Journal Article↗