Fig. 11.

A gene tree $(T,t,\lambda ,\sigma )$ reconciled with a species tree S. Here, we have two transfer edges uv and $v{b}^{\prime }$ with $t(u)=t(v)=▵$. For the two children w and v of u it holds $\sigma (L(T(w)))\cap \sigma (L(T(v)))\ne \mathrm{\varnothing }$, a property that is shared with duplication vertices. For the two children $b^{\prime }$ and $c^{\prime }$ of v it holds $\sigma (L(T(b^{\prime })))\cap \sigma (L(T(c^{\prime })))=\mathrm{\varnothing }$, a property that is shared with speciation vertices. In this example, c and $c^{\prime }$ are xeno-orthologs and the pairs $(c,c^{\prime }),(c^{\prime },c)$ will be excluded from the resulting orthology relation (color figure online)