Fig 1.
Possible discrepancy between one- and two-sided (species) screenings.
Screening for phylogenetic markers based on all possible tree topologies for three species A, B, C when only one reference genome A (a-c) or B (d-f) is available. The red lineage indicates the branches where markers can be detected. Screening from A reveals three markers. The two light red markers are artifacts from ancient incomplete lineage sorting (ILS) and the dark red marker is a phylogenetically informative marker. Screening from B reveals 11 markers with 8 markers supporting B plus C and one marker supporting A plus (B plus C). The two light red markers in (d) are the same detected from species A in (a). The correct topology is shown in tree (f). This correct tree would not be detectible by screening only from the genome of species A.
Fig 2.
Schematic representation of various species trees.
In all trees, lineage A is the red branch, lineage B is the green branch, and lineage C is the blue branch. (a) C-tree. First split: the ancestral population at time point t0 segregates into two branches, later one of them forms lineage C. At time point t1 the other branch diverges into the two lineages A and B. (b) A-tree. First split: the ancestral population at time point t0 segregates into two branches, later one of them forms lineage A. At time point t1 the other branch diverges into the two lineages B and C. (c) B-tree. First split: the ancestral population at time point t0 segregates into two branches, later one of them forms lineage B. At time point t1 the other branch diverges into the two lineages A and C. (d) ABC-tree. At the time point t0 the ancestral population segregates into three branches, later forming the three lineages A, B, and C (trifurcation). (e) Schematic representation of ancestral hybridization. B-fusion. First split: the ancestral population segregates at time point t0 into two branches. Subsequently, one of the branches (blue) splits after t1 generations, and the other branch (red) splits after t2 generations. The remaining parts of the blue and red lineages form lineages C and A, respectively. The derivates from the two joining populations form lineage B. The proportions of the parental populations forming lineage B are indicated by the coefficients γ1 and γ2, respectively.
Fig 3.
Schematic representation of all possible phylogenetic patterns.
For the markers n1—(AB)C, n2—(AC)B, and n3—(BC)A, their sum n is fixed (n = n1+n2+n3). The triangle reflects all possible combinations of n1, n2, and n3, whereby the values at the corners are (n1:0:0), (0:n2:0), and (0:0:n3) (counterclockwise from the upper corner). The respective trees indicate supported tree configurations (C-tree, A-tree, and B-tree), red balls consolidate insertion support for the given branches. The grey scale arrowheads within the triangle indicate the statistically significant combinations of supporting tree configurations shown at the corners of the triangle; the darker the arrow the more significant support for the corresponding tree, the lighter the arrow the less support and the more the branching resembles a polytomy. The circular area at the center of the triangle denotes the polytomy zone (ABC-tree, where n1 = n2 = n3). The trees on the outside edges of the central triangle indicate hybridization zones (B-fusion, C-fusion, and A-fusion, denoted as A(B)C hybridization (where n1≥n2, and n2>n3), A(C)B hybridization (where n1≥n3, and n2<n3), and B(A)C hybridization (where n2≥n3, and n1<n2), respectively).