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I understand the different ways bacteria can undergo horizontal gene transfer (transformation, transduction (phages), conjugation (plasmids)).

Is there an experimental method to tell how a specific gene got into the host (during evolution)? For example if a gene A got into host X from species Y, is it possible to know how gene A was transmitted?

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    $\begingroup$ I don't understand your question. What exactly are you trying to determine/distinguish? Would you mind re-wording your question into a clearer form? $\endgroup$
    – Cantona's Collar
    Apr 5, 2015 at 23:23
  • $\begingroup$ @Soph - I've edited your question, to avoid closing the question. You can revert my editing, if you wish. $\endgroup$
    – Nandor Poka
    Apr 6, 2015 at 0:49
  • $\begingroup$ Very interesting question. My wild-guess is maybe yes by looking at the DNA regions around the gene. You would probably get some base pairs from the vector yet I am not sure how many and if this would be sufficient to map that back to a plasmid or a phage. Will look that up. $\endgroup$
    – cagliari2005
    Apr 6, 2015 at 8:27
  • $\begingroup$ @cagliari2005 - I was thinking the same. Intehration to the host genome requires homology si most likely there are some remaining eytra sequeneces around the integrated gene. $\endgroup$
    – Nandor Poka
    Apr 6, 2015 at 8:53

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If you're looking at evolutionary timescales, then the only available source of information is the target organism's genome sequence. At least some of the methods of horizontal gene transfer you mention leave a distinctive signature in the genome. For example, retrovirus particles that have become incorporated into the human genome are easily identified by their local DNA sequence.

So in terms of an experiment, you would sequence your specific gene of interest as well as the surrounding local sequence (say, 10,000 base pairs downstream and upstream of your gene). In at least some cases you would be able to say for sure "this gene arose from retroviral incorporation", whereas in others it would be more ambiguous.

References:
Belshaw, R. et al. Long-term reinfection of the human genome by endogenous retroviruses. PNAS (2004)

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