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. Author manuscript; available in PMC: 2017 Jan 9.
Published in final edited form as: Syst Biol. 2014 Jul 30;63(6):988–992. doi: 10.1093/sysbio/syu050

Figure 5.

Figure 5

Effect on orthology relationships of unsorted internal paralog evolution with ILS. a) Evolution of a gene tree (thin dark lines) inside a locus tree (medium-thick branches) embedded in a species tree (thick light tree in the background) with ILS. A, B and C identify species/populations, while A0, B1, B0 and C0 represent gene copies. Black circles represent gene tree nodes (only coalescences are numbered), where the dashed line represents an extinct/unsampled lineage. Squares signal duplication events while crosses represent losses. B) Homology relationships between the gene copies (O: orthologs, UPws: within-species unsorted paralogs). c) Most parsimonious duplication/loss reconciliation of the gene and species trees. Label colors indicate different estimated loci, while text refers to the real loci.