Genomics

Linkage Disequilibrium Decay

the phenomenon where LD is high for genetic markers that are physically close together, but decays (drops toward zero) as the physical distance (in kilobases or megabases) between loci increases. measured by parameters like r² over increasing genetic distance.

Tajima’s D

Tajima’s D = Nucleotide Diversity - Watterson’s Theta

a population genetic statistic that is used to test if a population is evolving neutrally or evolving under a non-random process, including directional selection or balancing selection, demographic expansion or contraction, genetic hitchhiking, or introgression.

Negative Tajima’s D

Tajima’s D = Nucleotide Diversity - Watterson’s Theta

Occurs when Watterson’s Theta is greater than nucleotide diversity (𝜃S > 𝜃π).

Excess of low frequency alleles. May suggest positive selection, recent deleterious alleles, or population expansion.

Positive Tajima’s D

Tajima’s D = Nucleotide Diversity - Watterson’s Theta

Occurs when nucleotide diversity is greater than Watterson’s theta (𝜃_π > 𝜃_S).

Excess of intermediate frequency alleles. May suggest balancing selection, partial sweep, or population bottleneck. 

Selective Sweep

a process where beneficial mutation rises in frequency until it is fixed in the population. Leads to the reduction or elimination of genetic variation among nucleotide sequences that are near the mutation (genetic hitchhiking)

Hard Sweep

when a single mutation event generates one new allele, which generates a beneficial/adaptive allele. When adaptive, the allele becomes fixed in a population and also drags along with it other alleles that are closely linked.

Soft Sweep

occurs from from standing genetic variation (an allele was already floating around in the population) or multiple independent mutations at the exact same site (same mutation pops up independently in different individuals around the same time). Retains genetic varaition around the locus.

Balancing Selection

a type of natural selection that keeps multiple versions of a gene, or alleles, active in a population. Its main mechanisms are heterozygote advantage and frequency-dependent selection.

Frequency-Dependent Selection

the fitness of a trait depends on how common or rare it is in the population.

Negative Frequency-Dependent Selection

When rare phenotypes have more fitness. Fitness will decrease as a phenotype becomes more common.

Example: Immune systems target common strains of bacteria or viruses, leaving rare microbial strains free to infect hosts and thrive

Positive Frequency-Dependent Selection

When common phenotypes have more fitness. Fitness increases as a phenotype becomes more common, while rare variants are penalized and driven out.

Example: Common stripe patterns in herd animals (like zebras) confuse predators through sheer uniformity; an individual with a bizarre or rare visual mutation stands out from the group and suffers higher rates of predation

Watterson’s Theta

quantifies the number of segregating or polymorphic sites within a cohort, scaled by a constant. The higher this statistic, the more sites are found to be polymorphic.

Since Watterson’s theta counts all segregating sites (S) equally, it is strongly influenced by rare alleles.

Nucleotide Diversity

Average proportion of nucleotides that differs between any randomly paired set of sequences. The higher this statistic, the more differences you will expect to see between any pair of randomly sampled DNA sequences.

DNA methylation

where small chemical tags called methyl groups (CH3) attach to DNA, repressing gene transcription (i.e., turning genes off) without changing the actual genetic code

Genetic Swamping

process that happens when a small group of organisms, with unique genetic traits, mixes with a much larger group of organisms of the same species through gene flow. Over time, the unique genes of the smaller group get diluted and eventually disappear because the genes of the larger group become dominant.