SGID Silkworm Genome Informatics Database
Parameters Description
Basics D is domesticated silkworm, bombyx mori. W is wild silkworm, bombyx mandarina. CSRT is the capital letter abbreviation of coalcsent simulation rank test.
Pi Pi, nucleotide diversity, is a concept in molecular genetics which is used to measure the degree of polymorphism within a population.

Cited from Wiki

Theta Theta, watterson estimator is a method for describing the genetic diversity in a population. It was developed by Margaret Wu and G. A. Watterson in the 1970s. It is estimated by counting the number of polymorphic sites. It is a measure of the "population mutation rate" (the product of the effective population size and the neutral mutation rate) from the observed nucleotide diversity of a population.

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Tajima's D Tajima's D is a population genetic test statistic created by and named after the Japanese researcher Fumio Tajima. Tajima's D is computed as the difference between two measures of genetic diversity: the mean number of pairwise differences and the number of segregating sites, each scaled so that they are expected to be the same in a neutrally evolving population of constant size.
A negative Tajima's D signifies an excess of low frequency polymorphisms relative to expectation, indicating population size expansion (e.g., after a bottleneck or a selective sweep) and/or purifying selection. A positive Tajima's D signifies low levels of both low and high frequency polymorphisms, indicating a decrease in population size and/or balancing selection.

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CLR CLR, composite likelihood ratio, is a estimator to detect directional selection from DNA sequence data. The higher the value, the higher possibility of positive selection at the test region.

Cited from Zu and Bustamante, 2005

Genetic bottleneck A population bottleneck or genetic bottleneck is a sharp reduction in the size of a population due to environmental events (such as famines, earthquakes, floods, fires, disease, or droughts) or human activities (such as genocide). Such events can reduce the variation in the gene pool of a population; thereafter, a smaller population, with a smaller genetic diversity, remains to pass on genes to future generations of offspring through sexual reproduction. Genetic diversity remains lower, increasing only when gene flow from another population occurs or very slowly increasing with time as random mutations occur.

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The model of silkworm domestication is basing on Yang et al. 2014
Positive selection Positive selection, or directional selection is a mode of natural selection in which an extreme phenotype is favored over other phenotypes, causing the allele frequency to shift over time in the direction of that phenotype. Under directional selection, the advantageous allele increases as a consequence of differences in survival and reproduction among different phenotypes. The increases are independent of the dominance of the allele, and even if the allele is recessive, it will eventually become fixed.

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Balancing selection Balancing selection refers to a number of selective processes by which multiple alleles (different versions of a gene) are actively maintained in the gene pool of a population at frequencies larger than expected from genetic drift alone. This can happen by various mechanisms, in particular, when the heterozygotes for the alleles under consideration have a higher fitness than the homozygote. In this way genetic polymorphism is conserved.

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