No, your statement is quite wrong. It is not controversial that gene trees are not perfectly congruent, but also understood that they are highly congruent, to a degree that is immensely improbable by chance. Since this is true, and since the proposed evolutionary mechanisms for the incongruencies have been observed, and since no competing explanation for the observed pattern has ever been offered, comparative genomics continues to offer powerful evidence for common descent. More powerful all the time, in fact, as more data is collected.
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