To be conservative with interpreting significant node-specific results from AOT module, in this paper we focus on nodes that were significant for both tip and ancestral averaging.
Populations 7A-E, 19A-E, and 50A-E, descended from MA7, MA19, and MA50, respectively, had modest increases in productivity, ranging from 25 33 % of ancestral levels (average productivity of 120, 153, and 115, respectively).
We have found that the number of such events is negligible (1 such event in an ancestral node on average and 7 on average in the species, occurring mainly in chicken and lizard).
First, since the average ancestral segment length among classical inbred strains has been estimated to be 1.0 1.5 megabases (Mb) in size, the resolution is relatively good in comparison to traditional QTL mapping methods.
The red outline overlay shows the average ancestral distribution.
For a given admixture generation γ, we compute the average ancestral track length λ = 100/ γ and then t = 1000 λ (a region of 1 Mb contains ∼1000 HapMap SNPs).
These methods can be either local (focusing on origin of chromosomal segments), such as Lanc-CSV [ 7], LAMP-LD [ 8], and MULTIMIX [ 9], global (average ancestral proportions across the genome), such as ADMIXTURE [ 10], STRUCTURE [ 11, 12], or both, such as HAPMIX [ 13], LAMP [ 8, 14].
These regions were identified by searching for regions that have more ancestral alleles than the average plus 1 standard deviation.
We measured adaptation as the difference in a trait between the ancestral value and the average value in this trait among all the derived populations.
Similarly, three divisions on the left arm of the second chromosome (i.e. 22, 23 and 34) also harbor more ancestral alleles than the average plus one standard deviation for this arm.
