10.12 Computing D for all populations

We can give d() a list of populations to compute the \(D\) statistic for, where:

W: A vector of our populations of interest
X: An assumed unadmixed population (Yoruba)
Y: The introgressing population (Vindija Neanderthal)
Z: Outgroup (chimpanzee)

# create vector of populations of interest
pops <- c("French", "Sardinian", "Han", "Papuan",
          # including three African populations
          "Khomani_San", "Mbuti", "Dinka")

# calculate D
d_result <- d(data = snps,
              W = pops, X = "Yoruba", Y = "Vindija", Z = "Chimp") %>%
  # convert z score into pvalue
  mutate(p = 2 * pnorm(-abs(Zscore)))

d_result

##             W      X       Y     Z       D   stderr Zscore  BABA  ABBA  nsnps
## 1      French Yoruba Vindija Chimp  0.0313 0.006933  4.510 15802 14844 487753
## 2   Sardinian Yoruba Vindija Chimp  0.0287 0.006792  4.222 15729 14852 487646
## 3         Han Yoruba Vindija Chimp  0.0278 0.006609  4.199 15780 14928 487925
## 4      Papuan Yoruba Vindija Chimp  0.0457 0.006571  6.953 16131 14721 487694
## 5 Khomani_San Yoruba Vindija Chimp  0.0066 0.006292  1.051 16168 15955 487564
## 6       Mbuti Yoruba Vindija Chimp -0.0005 0.006345 -0.074 15751 15766 487642
## 7       Dinka Yoruba Vindija Chimp -0.0009 0.006124 -0.151 15131 15159 487667
##              p
## 1 6.482763e-06
## 2 2.421441e-05
## 3 2.680963e-05
## 4 3.575987e-12
## 5 2.932586e-01
## 6 9.410104e-01
## 7 8.799757e-01

Interpretation of \(D\) results

This is the result that was published in Green et al. 2010, revealing evidence for gene flow from Neanderthals into the ancestors of non-African populations.

We see significant evidence of Neanderthal introgression into the genomes of the non-African samples (French, Sardinian, Han, Papuan), but not the African samples (although we know from recent research that this is an oversimplification).