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An allele, or allelomorph, is a variant of the sequence of nucleotides at a particular location, or locus, on a DNA molecule.
Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure.
Allele frequency, or gene frequency, is the relative frequency of an allele at a particular locus in a population, expressed as a fraction or percentage. Specifically, it is the fraction of all chromosomes in the population that carry that allele over the total population or sample size. Microevolution is the change in allele frequencies that occurs over time within a population.
A haplotype is a group of alleles in an organism that are inherited together from a single parent.
In population genetics, linkage disequilibrium (LD) is a measure of non-random association between segments of DNA (alleles) at different positions on the chromosome (loci) in a given population based on a comparison between the frequency at which two alleles are detected together at the same loci and the frequencies at which each allele is detected at that loci overall, whether it occurs with or without the other allele of interest. Loci are said to be in linkage disequilibrium when the frequency of being detected together is higher or lower than expected if the loci were independent and associated randomly.
A DNA segment is identical by state (IBS) in two or more individuals if they have identical nucleotide sequences in this segment. An IBS segment is identical by descent (IBD) in two or more individuals if they have inherited it from a common ancestor without recombination, that is, the segment has the same ancestral origin in these individuals. DNA segments that are IBD are IBS per definition, but segments that are not IBD can still be IBS due to the same mutations in different individuals or recombinations that do not alter the segment.
Genetic association is when one or more genotypes within a population co-occur with a phenotypic trait more often than would be expected by chance occurrence.
In genetics, a locus is a specific, fixed position on a chromosome where a particular gene or genetic marker is located. Each chromosome carries many genes, with each gene occupying a different position or locus; in humans, the total number of protein-coding genes in a complete haploid set of 23 chromosomes is estimated at 19,000–20,000.
Coalescent theory is a model of how alleles sampled from a population may have originated from a common ancestor. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structure, meaning that each variant is equally likely to have been passed from one generation to the next. The model looks backward in time, merging alleles into a single ancestral copy according to a random process in coalescence events. Under this model, the expected time between successive coalescence events increases almost exponentially back in time. Variance in the model comes from both the random passing of alleles from one generation to the next, and the random occurrence of mutations in these alleles.
The term transheterozygote is used in modern genetics periodicals in two different ways. In the first, the transheterozygote has one mutant (-) and one wildtype allele (+) at each of two different genes. In the second, the transheterozygote carries two different mutated alleles of the same gene. This second definition also applies to the term "heteroallelic combination".
A tag SNP is a representative single nucleotide polymorphism (SNP) in a region of the genome with high linkage disequilibrium that represents a group of SNPs called a haplotype. It is possible to identify genetic variation and association to phenotypes without genotyping every SNP in a chromosomal region. This reduces the expense and time of mapping genome areas associated with disease, since it eliminates the need to study every individual SNP. Tag SNPs are useful in whole-genome SNP association studies in which hundreds of thousands of SNPs across the entire genome are genotyped.
In genomics, a genome-wide association study, is an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. GWA studies typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major human diseases, but can equally be applied to any other genetic variants and any other organisms.
Population structure is the presence of a systematic difference in allele frequencies between subpopulations. In a randomly mating population, allele frequencies are expected to be roughly similar between groups. However, mating tends to be non-random to some degree, causing structure to arise. For example, a barrier like a river can separate two groups of the same species and make it difficult for potential mates to cross; if a mutation occurs, over many generations it can spread and become common in one subpopulation while being completely absent in the other.
Zygosity is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism.
Microfluidic whole genome haplotyping is a technique for the physical separation of individual chromosomes from a metaphase cell followed by direct resolution of the haplotype for each allele.
Jonathan Karl Pritchard is an English-born professor of genetics at Stanford University, best known for his development of the STRUCTURE algorithm for studying population structure and his work on human genetic variation and evolution. His research interests lie in the study of human evolution, in particular in understanding the association between genetic variation among human individuals and human traits.
Quantitative trait loci mapping or QTL mapping is the process of identifying genomic regions that potentially contain genes responsible for important economic, health or environmental characters. Mapping QTLs is an important activity that plant breeders and geneticists routinely use to associate potential causal genes with phenotypes of interest. Family-based QTL mapping is a variant of QTL mapping where multiple-families are used.
In genetics, haplotype estimation refers to the process of statistical estimation of haplotypes from genotype data. The most common situation arises when genotypes are collected at a set of polymorphic sites from a group of individuals. For example in human genetics, genome-wide association studies collect genotypes in thousands of individuals at between 200,000-5,000,000 SNPs using microarrays. Haplotype estimation methods are used in the analysis of these datasets and allow genotype imputation of alleles from reference databases such as the HapMap Project and the 1000 Genomes Project.
Mega2 is a data manipulation software for applied statistical genetics. Mega is an acronym for Manipulation Environment for Genetic Analysis.
This glossary of genetics and evolutionary biology is a list of definitions of terms and concepts used in the study of genetics and evolutionary biology, as well as sub-disciplines and related fields, with an emphasis on classical genetics, quantitative genetics, population biology, phylogenetics, speciation, and systematics. Overlapping and related terms can be found in Glossary of cellular and molecular biology, Glossary of ecology, and Glossary of biology.
References
- ↑ Thompson, Elizabeth A. (2000). "Statistical Inference from Genetic Data on Pedigrees". NSF-CBMS Regional Conference Series in Probability and Statistics. 6. doi:10.1214/cbms/1462106037. ISBN 0-94-0600-49-8. JSTOR 4153187.
- ↑ Lange, Kenneth (2003). Mathematical and Statistical Methods for Genetic Analysis. New York: Springer-Verlag. p. 4. ISBN 0-387-95389-2.
- ↑ Pritchard, Jonathan K.; Stephens, Matthew; Donnelly, Peter (2000). "Inference of population structure using multilocus genotype data". Genetics. 155 (2): 945–959. doi:10.1093/genetics/155.2.945. PMC 1461096 . PMID 10835412.