So considering genes for specific morphological and behavioural similarities may well likely be similar
So you are using the massive assumption that these genes are 'likely' to be similar, with no apparent substantiation, to deny common ancestry? You don't think that is the sort of assertion that might merit evidence to support it? Do you mean the specific genetic basis of the novel traits? In that case the assumption is even larger.
The idea that similar phenotypic traits do not imply common ancestry is clearly established, which is why convergent morphological evolution is recognised. But what evidence is there that there is an indistinguishable genetic basis? I can readily believed that the same genes or pathways may be involved but I doubt that the same mutations are.
It seems eminently possible that selection for tameness could be effectively select for a reduced level of something like testosterone which could affect behaviour, fertility and hair development. But there are many possible mutations that could produce such a reduction either in the many proteins involve in the testosterone biosynthesis pathway, the androgen receptor molecule which mediates testosterone signalling or proteins interacting with the androgen receptor. Would similar effects from disrupting the same developmental pathway, albeit as a side effect of selecting for a behavioural trait, not be the result of common ancestry? labeit at a deeper level, i.e. not the inheritance of the trait from the common ancestor but of the gene regulatory network which leads to the expression of a cluster of similar traits when it is disrupted in a similar way.
Fodor seems to be arguing against a strawman ultra-adaptationist form of Darwinian theory, in which every trait must be adaptive, that you would be hard pressed to find anyone subscribing to.
TTFN,
WK