Figure 1.
Examples of recombination events that create an outgroup clade.
Each panel shows an example of a local genealogical tree (solid lines) for the currently sampled yeast populations (green), with samples from the wine/European (W/E), North American (N.A.), sake (S), West African (W.A.), and Malaysian (M) populations. In each panel, a dot indicates a recombination event. The dashed line indicates the recombinant lineage, which determines a new local tree on the other side of the breakpoint in which the three Malaysian strains are now at the outgroup position. In the absence of gene flow from an unsampled donor, two possible causes are A, the recombination occurred in a lineage ancestral to the Malaysian samples; and B, the recombination occurred in a lineage not ancestral to the Malaysian samples. C, Gene flow into the Malaysian population from an unsampled source (orange) will manifest as an inference of the former type of recombination.
Figure 2.
An example ancestral recombination graph for variation at the yeast gene encoding SAW1 (YAL027W) and flanking sequence.
The upper table shows allelic variation across the seven distinct haplotypes in this region; dots represent sites identical to S. paradoxus. Vertical lines mark boundaries of the region and also two inferred recombination events in an inferred ARG, shown in the bottom panel. In the latter, nodes represent inferred coalescent and recombination events, and edges represent passage through evolutionary time. Labels on each edge represent the coordinates of sites that underwent inferred mutations along the respective branch. Extant S. cerevisiae genomes are at the leaves of the graph. Recombination vertices are indicated by the coordinate of the breakpoint and are shown as ellipses. At recombination vertices, edges labeled P indicate sites upstream of and including the breakpoint inherited from the “prefix” lineage, and edges labeled S represent downstream sites inherited from the “suffix” lineage. Annuli indicate vertices which are the most recent common ancestor of the whole sample at some site. Genomic coordinates for this region encompassed the open reading frame (ORF) and 200 bp upstream. The image is adapted from the output of kwarg, using Graphviz [37].
Figure 3.
Inferred recombination by the outgroup clade at recombination block boundaries, in ancestral recombination graphs inferred from yeast sequence.
Each panel represents results from regions of yeast genes in which the population indicated at the top occupied an outgroup position in the inferred genealogy. For each such region, the -axis reports the identity of the population with the strongest evidence for disrupting recombination at the boundaries of the region, using the recombination score described in Materials & Methods. The
-axis indicates the number of regions with inferred recombinations involving the respective population from the
-axis label. Populations are wine/European (W/E), North American (N.A.), sake (S), West African (W.A.), and Malaysian (M).
Figure 4.
strains in which a set of
strains form an outgroup clade. A recombination occurs (marked by a dot), and the recombinant lineage (dashed line) recoalesces into the tree so that the clade is no longer an outgroup (satisfying
). Notation is defined in the main text.
Table 1.
Recombination by the outgroup clade at block boundaries, in theoretical predictions from a simple coalescent model of a single panmictic population.
Table 2.
Fractions of disrupting recombination events that occur in lineages ancestral to members of the outgroup clade in yeast ARGs, from simple coalescent simulations.
Table 3.
Observed fractions of disrupting recombination events that occur in lineages ancestral to members of the outgroup clade in yeast ARGs.
Table 4.
Evaluating observed fractions of disrupting recombination events that occur in lineages ancestral to members of the outgroup clade in yeast ARGs.
Table 5.
Fractions of disrupting recombination events that occur in lineages ancestral to members of the outgroup clade in ARGs, from complex coalescent simulations.
Table 6.
Evaluating observed fractions of disrupting recombination events that occur in lineages ancestral to members of the outgroup clade in ARGs from complex coalescent simulations.