Fig. 7

The state space of AD-LIBS hidden Markov model. The three round states (AA, AB, and BB) are ancestry states that can emit scores. AA represents regions where both homologous chromosomes derive ancestry from ancestral population A, AB represents regions of heterozygous ancestry, and BB represents regions homozygous for population B ancestry. The three square states (sAA, sAB, and sBB) are skip states, each associated with one of the three ancestry states. Skip states can only emit scores representing windows of the genome in which data are too sparse to infer ancestry. Each skip state is more likely to transition back to its associated ancestry state than to one of the others. Arrow colors represent different types of transition probabilities. Green arrows are starting probabilities and are related to the pre-estimated percent ancestry derived from each ancestral population (A and B). Blue arrows represent recombination events; their probability is related to the probability of a recombination event having happened at a given site in the time since admixture, as well as the probability of sampling a base from population A or B. Black arrows are related to the probability of skipping a given window, computed from the number of “N” bases encountered. Red arrows are transitions to the end state, with probabilities related to the number of windows on the chromosome or scaffold being scanned. Gold arrows represent probabilities that are computed after other probabilities, by subtracting from 1 the sum of all other transition probabilities out of a given state