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There are several often noted examples of convergent evolution (eyes, bat/bird wing evolution etc.) How do we rule out horizontal gene transfer in these cases?

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You know that bat wings are modified hands, while bird wings are modified arms. And human eyes and insect eyes are very different. –  swbarnes2 Jul 21 at 19:17

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Without any molecular evidence you could infer convergent evolution if the species being compared shared a common ancestor that lacked the trait in question.

With genomic and developmental data you would measure the degree of similarity shared between the relative factors in each species. Little or no similarity indicates convergent evolution.

Horizontal gene transfer is predominantly found in bacteria. Although there are examples of limited gene transfer in eukaryotes, the donor is almost always bacteria. And there are currently no known cases of multi-gene transmission of complex networks.

It is interesting to contemplate how a full network might be transmitted horizontally. Horizontal Network Transfer would first require a mechanism for segregating the relevant genes from the rest of the genome. It would also require invasive machinery that allows the large amount of foreign genetic material to bypass the host's defense systems. Furthermore, integration of a foreign network is increasingly more difficult with the more genes you transmit due to positional and regulatory effects of the host genome. And on top of that, it is highly unlikely that a full complement of genes involved in a complex developmental process would function in any way resembling eye or wing development. These networks have been coevolving within massively complex genomic environments for hundreds of millions of years. Expressing a large network in a foreign cell would likely prove toxic.

A looser definition of HGT might include bioengineering, specifically stable transgene integration.

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A small comment on the use of the term homology. Homology is an absolute state, i.e. genes (for instance) are either homologous or not homologous. Referring to degrees of homology is misusing the term. Genes can be identical to a certain degree which not necessarily means that they are homologous. –  RickardSjogren Jul 21 at 9:10
    
@RickardSjogren you're right. I've edited the answer to use the correct term. Thanks! –  yummyclaypot Jul 21 at 14:27

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