Supplemental figures S14–S17
Figure S14:
An example of the set of consistent histories (as coalescent distributions )
used to find upper and lower bounds
in figures S12 and 5.
The example shown is Poland–Germany;
“MLE” is the maximum likelihood history;
“smooth” is the smoothest consistent history;
and the remaining plots show the histories giving lower and upper bounds
for the referenced time intervals (in numbers of generations).
In each case, the segment of time on which we are looking for a bound is shaded.
Figure S15:
For those who are used to thinking in effective population sizes,
the equivalent figure to figure 4,
except with coalescent rate on the vertical axis,
rather than numbers of most recent genetic common ancestors.
Figure S16:
The maximum likelihood history (grey) and smoothest consistent history (red)
for all pairs of population groupings of figure S12
(including those of figure 5).
Each panel is analogous to a panel of figure 4;
time scale is given by vertical grey lines every 500 years.
For these plots on a larger scale see supplemental figure S17.
http://www.eve.ucdavis.edu/~plralph/ibd/boxplotted-inversions.pdf
Figure S17:
All inversions shown in S16, one per page (225 pages total).
There is one page per pair of comparisons used in figure 5.
On each page, there is one large plot, showing 10 distinct consistent histories (numbers of genetic ancestors back through time),
and below are 10 histograms of IBD block length, one for each consistent history,
showing both the observed distribution
and the partitioning of blocks into age categories predicted by that history.
The names of the two groupings are shown in the upper right:
“pointy” is the unconstrained maximum likelihood solution;
“smooth” is the smoothest consistent history;
“– lower” is the history used to find the lower bound for the time period – generations ago in figure 5;
and “– upper” is the history used to find the corresponding upper bound.
Each of these are described in more detail in the Methods.
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