Figure 1

Possible outcomes of incomplete paralogue sampling. Possible outcomes of incomplete paralogue sampling (bold lines) in relation to different relative ages of gene duplications. a) Recent gene duplications. The copies (inparalogues) are monophyletic within terminal taxa (e.g. organisms). The relationships among these remain unchanged, regardless of which copies are included in the study. b) An early gene duplication has created two ancient outparalogues. If different paralogues are sequenced for different taxa, the ingroup will not become monophyletic. c) A gene duplication has created two recent outparalogues. Organismal phylogenetic inference will give erroneous results, if some of the paralogues remain undetected. A through D represent ingroup taxa, numbers indicate sequence copies.