DormanResearch : StatisticalGenetics

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• Ewens1972?: The famous sampling theorem.
• Weir1984?: Defines $^ θ w$, the weighted average $F$-statistic over loci (see Michalakis1996?).
• Slatkin1991?: Shows $F S T = f 0 - f 1 1 - f 1 = t ¯ 0 - t ¯ 1 t ¯ 1$, where $f 0$ is probability of IBD for two alleles draw from the same population, $f 1$ is the probability of IBD for two alleles drawn from different populations, $t ¯ 0$ is the mean time to coalescent for two alleles drawn from the same population, and $t ¯ 1$ is the mean time for two alleles drawn from different populations.
• Excoffier1992: Introduces AMOVA, an extension of Cockerham1969? and Cockerham1973? (also see Weir1984?, Long1986?) for the ANOVA of gene frequencies, to the case of molecular data.  It works by reducing the molecular data to pairwise distance estimates, ideally trying to estimate the number of mutations separating every pair of haplotypes.l
• Michalakis1996?: Proofs Weir1984?'s $^ θ w$ is identical to fixation index $F S T$.
• IBD
• Thompson2008?: IBD process along four chromsomes
• Browning2011?: fastIBD is an approximate fast version of Thompson2008?
• Brown2012?: extends Thompson2008? to >4 chromosomes
• Thompson2013a?: IBD review
• Heritability
• Yang2010c?: heritability estimation based on IBS sharing from population samples instead of family-based methods; better because shared environment events and dominance and epistatis effects are minimized
• Price2011?: heritability by IBD segment-sharing instead of IBS sharing
• Browning2013b?: IBD-based heritability picks up effects of rare variants (Zaitlen2013?), but misses deep coinheritance, and thus loses some precision.
• Mapping
• Purcell2007?: pairwise IBD mapping; cases have higher rates of IBD at a locus than controls
• See DetectingSelection for a bibliography of papers focusing on the detection of selection.

0STAT 536 - Population Genetics
MathematicalPopulationGenetics?
QuantitativeGeneticsChaps15?
MathStatMethodsforGeneticAnalysis?
Stat536Prep

0STAT 537 - Molecular Genetics
StatisticalGenomics?
transposonMaside03.pdf: population genetics of $S$-element in D. melanogaster uses various population genetics methods to discern the timing and growth of a transposon element family.  The statistics are fairly standard, appearing Watterson's diversity, Tajima's D, Fu's F test, etc.