University:
Boston University
Course:
CAS BI 108 | Biology 2
Academic year:

2024
Views:

111

Pages:

14
Author:

Annabel Combs

Signatures in the frequency spectrum Signatures in the frequency spectrum • Tajima’s D test (Tajima 1989) is a common statistical test for the frequency spectrum ‣ Perhaps the most widely used test (Dietrich, pers. comm.) ‣ Used extensively on human DNA (Carlson et al 2005; Nielsen et al 2005; Oleksyk et al 2010) Signatures in the frequency spectrum • • Tajima’s D test (Tajima 1989) is a common statistical test for the frequency spectrum ‣ Perhaps the most widely used test (Dietrich, pers. comm.) ‣ Used extensively on human DNA (Carlson et al 2005; Nielsen et al 2005; Oleksyk et al 2010) Compares two different estimates of the neutral parameter where each estimate is sensitive to different features of the frequency spectrum ‣ Number of segregating sites vs average number of pairwise nucleotide differences Signatures in the frequency spectrum • Tajima’s D statistic compares the difference between the two estimates (normalized) • Expectations: N eutrality D=0 P urif ying selection P ositive selection D<0 D>0 Taking a closer look Taking a closer look • Tajima’s D test (as do all molecular tests) presupposes a sequence evolution model Taking a closer look • Tajima’s D test (as do all molecular tests) presupposes a sequence evolution model • The sequence evolution model is essential to determine the precise patterns in the frequency spectrum indicative of different evolutionary forces Taking a closer look • Tajima’s D test (as do all molecular tests) presupposes a sequence evolution model • The sequence evolution model is essential to determine the precise patterns in the frequency spectrum indicative of different evolutionary forces • Sequence evolution models make significant idealizations about the evolutionary process (rates, rate heterogeneity, demographics) Taking a closer look Taking a closer look • The test detects patterns in the spectra: departures from the neutral spectrum or those indicative of different regimes of selection Taking a closer look • The test detects patterns in the spectra: departures from the neutral spectrum or those indicative of different regimes of selection • This is done using a sequence evolution model that incorporates randomly occurring adaptive mutations: the PRF model (Sawyer and Hartl 1992) Taking a closer look Taking a closer look • We can stipulate the model and parameter values using background theory or information ‣ Involves problematic idealizations about the nature and rate of evolutionary processes Taking a closer look • We can stipulate the model and parameter values using background theory or information ‣ • Involves problematic idealizations about the nature and rate of evolutionary processes Or, we can select the model and parameter values based on molecular data ‣ Relies on model selection statistics (now the standard strategy)