Fig. 2
From: Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca
Inferences of admixture proportion and time and demographic history. a Estimated introgression proportions from llama to alpaca by using Local Ancestry Inference (LAI) (left). The X-axis indicates the guanaco-ancestry proportions in each sequenced alpaca individuals (Y-axis; N = 8). The right panel showed the introgression proportions by using ABBA-BABA (fd) method. The arrow showed the introgression direction from llama to alpaca. b Estimated introgression proportions from alpaca to llama by using LAI (left). The X-axis indicates the vicuna-ancestry proportions in each sequenced llama individuals (Y-axis; N = 8). The right panel showed the introgression proportions by using ABBA-BABA (fd) method. The arrow showed the introgression direction from alpaca to llama. c Inference of admixture time in alpaca by analyzing the LAI tract length. Dotted line indicates the median value of admixture time. d Change in linkage disequilibrium estimated Ne using SNeP over approximately the last 200 generations (AlpGua: alpaca genome that removed guanaco ancestry sites; AlpVic: alpaca genome that only remain vicuña ancestry sites). e Inference of admixture time in llama by analyzing the LAI tract length. Dotted line indicates the median value of admixture time. f Variation in estimated Ne compared to the overall decline slope, with changes below the 0 value on the Y-axis indicating a steeper decline and above the line indicating a shallower decline. The steeper decline event at 110 generations BP (black arrow) coincides with the date of admixture identified by LAI tract analysis