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Gene family phylogenies reflect both speciation and duplication events, and these events can be distinguished by reconciled tree analyses if the gene and species trees are known.
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By definition, each PoGO represents a group of genes that diverged from an ancestral gene through speciation and duplication.
Novel CPs emerge from speciation and duplication events occurring after the split of fish from A1.
It is getting more complicated as speciation and duplication events can occur alternately.
In summary, extant teleost fishes inherited OR genes from their common ancestors during speciation and duplication.
The SDI unrooted algorithm [ 41] was first used to predict speciation and duplication events.
We dated sequence divergence and speciation and duplication events using the rate of synonymous (Ks) substitutions.
Notung version 2.6 [ 24] was used to infer the relative timing of speciation and duplication events.
Since local synteny is able to differentiate some speciation and duplication events, a phylogenetic tree (or duplication-speciation history) of ambiguous many-to-many orthologs may be determined using local synteny information.
A speciation and duplication inference (SDI) algorithm, based on the reconciliation of the gene tree with a trusted species tree [ 36], was used to infer orthology, paralogy, speciation nodes and gene duplication events.
Trees were rooted on time, and speciation and duplication inference algorithm (SDI), based on the reconciliation of the gene tree with a trusted species tree [ 66], was used to infer orthology, paralogy, speciation nodes and gene duplication events.
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