Using reciprocally retained gene families to detect whole-genome multiplications in plants

Although none of the reciprocally retained gene families is a perfect WGM marker on its own, we show that using an extended set of such families as input for birth-death and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mi>K</mml:mi><mml:mtext>S</mml:mtext></mml:msub></mml:math> distribution modeling approaches leads to better WGM detection performance than using entire genomes. A pipeline to use reciprocally retained gene families for <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mi>K</mml:mi><mml:mtext>S</mml:mtext></mml:msub></mml:math> distribution-based WGM inference in angiosperms has been implemented in ksrates v2.0.