Nevertheless, there is still obvious tree structure in that data set. Simple though it is.
WNT type points to a specific cell or tissue.
Wnt types are members of a homologous family that evolved by duplications. They may be expressed differentially across different cell types, but what does that have to do with anything here?
If you look at vertebrates there is very little variation.
Same is true for flatworms, or ringworms, or insects. Generally speaking, members of any particular clade can be explained by fewer gene losses, than differences between clades. Generally speaking, the more closely related, the fewer gene losses we need to invoke. That is exactly what you would expect from a tree. And I have to re-emphazise just how little data there is to work with here on that graphic, with only 13 sites considered in binary form.
I have to wonder whether any of the “absent” members are actually present in pseudogene form in any of the species shown. The article doesn’t specifically state whether the “absent” members are absent because of complete deletion of the entire gene, or just pseudogenization because of nonsense mutations that render it nonfunctional. They make it clear that they consider both options as counting as a “loss”.
Two main molecular mechanisms can lead to the loss of a gene from a given genome. First, the loss of a gene can be the consequence of an abrupt mutational event, such as an unequal crossing over during meiosis or the mobilization of a transposable or viral element that leads to the sudden physical removal of the gene from an organism’s genome. Second, the loss of a gene can be the consequence of a slow process of accumulation of mutations during the pseudogenization that follows an initial loss-of-function mutation. This initial mutation can be caused by nonsense mutations that generate truncated proteins, insertions or deletions that cause a frameshift, missense mutations that affect crucial amino acid positions, changes involving splice sites that lead to aberrant transcripts or mutations in regulatory regions that abolish gene expression. In this Review, the term ‘gene loss’ is used in a broad sense, not only referring to the absence of a gene that is identified when different species are compared, but also to any allelic variant carrying a loss-of-function (that is, non-functionalization) mutation that is found within a population.