I think in general, the phylogenetic approach to determining HGT aims to use phylogenetic signal and/or phylogenetic inference to assess whether a particular gene is likely to have been arisen through HGT. The basic concept is that if the gene evolved "elsewhere" and was acquired through HGT, its phylogenetic signal (i.e. genetic distance) and evolutionary pattern will deviate significantly from that of the species itself.
So, for example, a gene acquired by HGT might be expected to resemble more closely the homologous gene in the "donor" organism than in the "recipient" organism where it now resides. So if you create a phylogenetic tree for the gene it should cluster with the donor, not the recipient. By contrast, a tree built from a gene not subjected to HGT would be expected to more closely resemble the species tree.
There is a very nice review in PLOS Computational Biology by Ravenhall et al. "Inferring Horizontal Gene Transfer" that covers these concepts. I'm including it here.
Article Inferring Horizontal Gene Transfer
I think in general, the phylogenetic approach to determining HGT aims to use phylogenetic signal and/or phylogenetic inference to assess whether a particular gene is likely to have been arisen through HGT. The basic concept is that if the gene evolved "elsewhere" and was acquired through HGT, its phylogenetic signal (i.e. genetic distance) and evolutionary pattern will deviate significantly from that of the species itself.
So, for example, a gene acquired by HGT might be expected to resemble more closely the homologous gene in the "donor" organism than in the "recipient" organism where it now resides. So if you create a phylogenetic tree for the gene it should cluster with the donor, not the recipient. By contrast, a tree built from a gene not subjected to HGT would be expected to more closely resemble the species tree.
There is a very nice review in PLOS Computational Biology by Ravenhall et al. "Inferring Horizontal Gene Transfer" that covers these concepts. I'm including it here.
Article Inferring Horizontal Gene Transfer
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