Fig 1.
Phylogenomic view of trait evolution in the presence of incomplete lineage sorting (ILS) and introgression.
Left: The three possible genealogies of three taxa A, B, and C. Right: Phylogenetic network that models an underlying species tree (A,(B,C)) along with a reticulation from A to B, and whose associate inheritance probability is γ. The embedded solid gene tree involves ILS but no introgression, whereas the dashed gene tree involves introgression but not ILS. The states Sa, Sb, and Sc of an incongruent binary character are shown at the leaves of the phylogenetic network.
Fig 2.
The interaction of evolutionary parameters affects the need for introgression to explain trait patterns.
G-XRF is shown as a function of internal branch length T2 − T1 and inheritance probability γ when reticulation time Tr = 0.1 coalescent units and population mutation rate θ = 0.01 (top row), and as a function of θ and Tr when T2 − T1 = 10 and γ = 0.5 (bottom row).
Fig 3.
The interaction of evolutionary parameters affects the need for introgression to explain observed state counts.
The x- and y-axis in each panel correspond to the frequency of character state 1 in taxon B and the reticulation time Tr. Columns correspond to three different relative forward/backward character substitution rates and rows correspond to three different population mutation rates. In all panels T2 − T1 = 10 coalescent units and γ = 0.5.
Fig 4.
G-XRF values in the presence of trait polymorphism.
The x- and y-axis in each panel correspond to the inheritance probability γ and reticulation time Tr, respectively. Columns correspond to three different relative forward/backward character substitution rates, and rows correspond to three different frequencies of all 1 in taxon B. In all panels T2 − T1 = 10 coalescent units and θ = 0.01.
Fig 5.
Inferred species tree (left) and network (right) of the Jaltomata data set.
The major tree inside the species network is obtained by removing the blue reticulation edge leading to I1.
Fig 6.
G-XRF values of three trait patterns (X, Y and Z) as the ratio of forward to backward substitutions is varied.
Each box plot summarizes 3,000 G-XRF values obtained from the species network and corresponding major tree sampled from the posterior distribution of Jaltomata species networks.