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Calculation of Q<sub>ST</sub> is subject to several assumptions: populations must be in [[Hardy–Weinberg principle|Hardy-Weinberg Equilibrium]], observed variation is assumed to be due to [[additive genetic effects]] only, selection and [[linkage disequilibrium]] are not present,<ref name="Cubry_2017">{{cite journal | vauthors = Cubry P, Scotti I, Oddou-Muratorio S, Lefèvre F | title = Generalization of the Q<sub>ST</sub> framework in hierarchically structured populations: Impacts of inbreeding and dominance | journal = Molecular Ecology Resources | volume = 17 | issue = 6 | pages = e76–e83 | date = November 2017 | pmid = 28681534 | doi = 10.1111/1755-0998.12693 | s2cid = 206947951 | url = https://hal.archives-ouvertes.fr/hal-01576329/file/Cubry_etal_MainText_FinalDraft_2.pdf }}</ref> and the subpopulations exist within an island model.<ref name="de_Villemereuil_2022">{{Cite journal | vauthors = de Villemereuil P, Gaggiotti OE, Goudet J |date=2022 |title=Common garden experiments to study local adaptation need to account for population structure |journal=Journal of Ecology |volume=110 |issue=5 |pages=1005–1009 |doi=10.1111/1365-2745.13528 |s2cid=225136876 |issn=0022-0477|url=https://serval.unil.ch/notice/serval:BIB_07E8157C6B8F }}</ref>
Calculation of Q<sub>ST</sub> is subject to several assumptions: populations must be in [[Hardy–Weinberg principle|Hardy-Weinberg Equilibrium]], observed variation is assumed to be due to [[additive genetic effects]] only, selection and [[linkage disequilibrium]] are not present,<ref name="Cubry_2017">{{cite journal | vauthors = Cubry P, Scotti I, Oddou-Muratorio S, Lefèvre F | title = Generalization of the Q<sub>ST</sub> framework in hierarchically structured populations: Impacts of inbreeding and dominance | journal = Molecular Ecology Resources | volume = 17 | issue = 6 | pages = e76–e83 | date = November 2017 | pmid = 28681534 | doi = 10.1111/1755-0998.12693 | s2cid = 206947951 | url = https://hal.archives-ouvertes.fr/hal-01576329/file/Cubry_etal_MainText_FinalDraft_2.pdf }}</ref> and the subpopulations exist within an island model.<ref name="de_Villemereuil_2022">{{Cite journal | vauthors = de Villemereuil P, Gaggiotti OE, Goudet J |date=2022 |title=Common garden experiments to study local adaptation need to account for population structure |journal=Journal of Ecology |volume=110 |issue=5 |pages=1005–1009 |doi=10.1111/1365-2745.13528 |s2cid=225136876 |issn=0022-0477|url=https://serval.unil.ch/notice/serval:BIB_07E8157C6B8F }}</ref>


== Q<sub>ST</sub>-F<sub>ST</sub> Comparisons ==
== Q<sub>ST</sub>-F<sub>ST</sub> comparisons ==
Q<sub>ST</sub>–F<sub>ST</sub> analyses often involve culturing organisms in consistent environmental conditions, known as [[Transplant experiment|common garden experiments]],<ref name="Leinonen_2013">{{cite journal | vauthors = Leinonen T, McCairns RJ, O'Hara RB, Merilä J | title = Q(ST)-F(ST) comparisons: evolutionary and ecological insights from genomic heterogeneity | journal = Nature Reviews. Genetics | volume = 14 | issue = 3 | pages = 179–190 | date = March 2013 | pmid = 23381120 | doi = 10.1038/nrg3395 | s2cid = 6312222 }}</ref> and comparing the [[Phenotype|phenotypic]] variance to genetic variance. If Q<sub>ST</sub> is found to exceed F<sub>ST</sub>, this is interpreted as evidence of divergent selection, because it indicates more differentiation in the trait than could be produced solely by [[genetic drift]]. If Q<sub>ST</sub> is less than F<sub>ST</sub>, [[balancing selection]] is expected to be present. If the values of Q<sub>ST</sub> and F<sub>ST</sub>are equivalent, the observed trait differentiation could be due to genetic drift.<ref name="de_Villemereuil_2022" />
Q<sub>ST</sub>–F<sub>ST</sub> analyses often involve culturing organisms in consistent environmental conditions, known as [[Transplant experiment|common garden experiments]],<ref name="Leinonen_2013">{{cite journal | vauthors = Leinonen T, McCairns RJ, O'Hara RB, Merilä J | title = Q(ST)-F(ST) comparisons: evolutionary and ecological insights from genomic heterogeneity | journal = Nature Reviews. Genetics | volume = 14 | issue = 3 | pages = 179–190 | date = March 2013 | pmid = 23381120 | doi = 10.1038/nrg3395 | s2cid = 6312222 }}</ref> and comparing the [[Phenotype|phenotypic]] variance to genetic variance. If Q<sub>ST</sub> is found to exceed F<sub>ST</sub>, this is interpreted as evidence of divergent selection, because it indicates more differentiation in the trait than could be produced solely by [[genetic drift]]. If Q<sub>ST</sub> is less than F<sub>ST</sub>, [[balancing selection]] is expected to be present. If the values of Q<sub>ST</sub> and F<sub>ST</sub>are equivalent, the observed trait differentiation could be due to genetic drift.<ref name="de_Villemereuil_2022" />


Revision as of 14:36, 15 March 2023

In quantitative genetics, QST is a statistic intended to measure the degree of genetic differentiation among populations with regard to a quantitative trait. It was developed by Ken Spitze in 1993.[1] Its name reflects that QST was intended to be analogous to the fixation index for a single genetic locus (FST).[2][3] QST is often compared with FST of neutral loci to test if variation in a quantitative trait is a result of divergent selection or genetic drift, an analysis known as QST–FST comparisons.

Calculation of QST

Equations

QST represents the proportion of variance among subpopulations, and is it’s calculation is synonymous to FST developed by Sewall Wright.[4] However, instead of using genetic differentiation, QST is calculated by finding the variance of a quantitative trait within and among subpopulations, and for the total population.[1] Variance of a quantitative trait among populations (σ2GB) is described as:

And the variance of a quantitative trait within populations (σ2GW) is described as:

Where σ2T is the total genetic variance in all populations. Therefore, QST can be calculated with the following equation:

Assumptions

Calculation of QST is subject to several assumptions: populations must be in Hardy-Weinberg Equilibrium, observed variation is assumed to be due to additive genetic effects only, selection and linkage disequilibrium are not present,[5] and the subpopulations exist within an island model.[6]

QST-FST comparisons

QST–FST analyses often involve culturing organisms in consistent environmental conditions, known as common garden experiments,[7] and comparing the phenotypic variance to genetic variance. If QST is found to exceed FST, this is interpreted as evidence of divergent selection, because it indicates more differentiation in the trait than could be produced solely by genetic drift. If QST is less than FST, balancing selection is expected to be present. If the values of QST and FSTare equivalent, the observed trait differentiation could be due to genetic drift.[6]

Suitable comparison of QST and FST is subject to multiple ecological and evolutionary assumptions,[8][9][10] and since the development of QST, multiple studies have examined the limitations and constrictions of QST-FST analyses. Leinonen et al. notes FST must be calculated with neutral loci, however over filtering of non-neutral loci can artificially reduce FSTvalues.[7] Cubry et al. found QST is reduced in the presence of dominance, resulting in conservative estimates of divergent selection when QST is high, and inconclusive results of balancing selection when QST is low.[5] Additionally, population structure can significantly impact QST-FST ratios. Stepping stone models, which can generate more evolutionary noise than island models, are more likely to experience type 1 errors.[6] If a subset of populations act as sources, such as during invasion, weighting the genetic contributions of each population can increase detection of adaptation.[11] In order to improve precision of QST analyses, more populations (>20) should be included in analyses.[12]

See also

References

  1. ^ a b Spitze K (October 1993). "Population structure in Daphnia obtusa: quantitative genetic and allozymic variation". Genetics. 135 (2): 367–374. doi:10.1093/genetics/135.2.367. PMC 1205642. PMID 8244001.
  2. ^ Whitlock MC (April 2008). "Evolutionary inference from QST". Molecular Ecology. 17 (8): 1885–1896. doi:10.1111/j.1365-294X.2008.03712.x. PMID 18363667.
  3. ^ McKay JK, Latta RG (June 2002). "Adaptive population divergence: markers, QTL and traits". Trends in Ecology & Evolution. 17 (6): 285–291. doi:10.1016/S0169-5347(02)02478-3.
  4. ^ Wright S (1949). "The Genetic Structure of Populations". Annals of Eugenics. 15 (4): 323–354. doi:10.1111/j.1469-1809.1949.tb02451.x. PMID 24540312.
  5. ^ a b Cubry P, Scotti I, Oddou-Muratorio S, Lefèvre F (November 2017). "Generalization of the QST framework in hierarchically structured populations: Impacts of inbreeding and dominance" (PDF). Molecular Ecology Resources. 17 (6): e76–e83. doi:10.1111/1755-0998.12693. PMID 28681534. S2CID 206947951.
  6. ^ a b c de Villemereuil P, Gaggiotti OE, Goudet J (2022). "Common garden experiments to study local adaptation need to account for population structure". Journal of Ecology. 110 (5): 1005–1009. doi:10.1111/1365-2745.13528. ISSN 0022-0477. S2CID 225136876.
  7. ^ a b Leinonen T, McCairns RJ, O'Hara RB, Merilä J (March 2013). "Q(ST)-F(ST) comparisons: evolutionary and ecological insights from genomic heterogeneity". Nature Reviews. Genetics. 14 (3): 179–190. doi:10.1038/nrg3395. PMID 23381120. S2CID 6312222.
  8. ^ Pujol B, Wilson AJ, Ross RI, Pannell JR (November 2008). "Are Q(ST)-F(ST) comparisons for natural populations meaningful?". Molecular Ecology. 17 (22): 4782–4785. doi:10.1111/j.1365-294X.2008.03958.x. PMID 19140971. S2CID 11707577.
  9. ^ Leinonen T, O'Hara RB, Cano JM, Merilä J (January 2008). "Comparative studies of quantitative trait and neutral marker divergence: a meta-analysis". Journal of Evolutionary Biology. 21 (1): 1–17. doi:10.1111/j.1420-9101.2007.01445.x. PMID 18028355. S2CID 1037769.
  10. ^ Miller JR, Wood BP, Hamilton MB (October 2008). "F(ST) and Q(ST) under neutrality". Genetics. 180 (2): 1023–1037. doi:10.1534/genetics.108.092031. PMC 2567353. PMID 18780742.
  11. ^ Marchini GL, Arredondo TM, Cruzan MB (November 2018). "Selective differentiation during the colonization and establishment of a newly invasive species". Journal of Evolutionary Biology. 31 (11): 1689–1703. doi:10.1111/jeb.13369. PMID 30120791. S2CID 52031406.
  12. ^ O'Hara RB, Merilä J (November 2005). "Bias and precision in QST estimates: problems and some solutions". Genetics. 171 (3): 1331–1339. doi:10.1534/genetics.105.044545. PMC 1456852. PMID 16085700.
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