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Figure 4.3: Black squares with a “D” indicate (required) duplications. Losses are represented by dotted lines. (a) A marsupial species tree with a polytomy. (b) The phylogeny of a hypothetical gene family sampled from the same marsupial species. (c) Hypothesis 1: the disagreement between (a) and (b) can be explained by deep coalescence (node x), followed by gene duplication (node y). (d) Hypothesis 2: the disagreement between (a) and (b) can also be explained by duplication at x, followed by gene loss, followed by duplication at y. (e) The divergence at x is designated a conditional duplication (gray square) because it is not possible to determine whether the disagreement is due to duplication or deep coalescence. The divergence at y is a required duplication.

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