The computation of phylogeny used to rely on sequence comparison (i.e. alignment). For genetically similar strains or species, there is typically only a few variations detectable in the aa/nt sequences of single-copy or selected gene list. On the other hand, the selection of gene list is also difficult. A prepared set of conserved genes can be efficient but may lead to bias. As an alternative, single-copy method can include more information, but a gene cannot be selected if it has no orthologs identified in the other strains/species. In case that recombination or horizontal transfer happened and even was involved in phenotype or adaptability of a pathogen, the transferred element would therefore not be included in the reconstruction of phylogeny. A problem in tracking the spread route can thus happen.
My question is: can it be possible to include genome recombination information into the reconstruction of phylogeny, or is there available method to select a suitable gene set for sequence alignment and phylogeny computation?
The answers to your questions really depend a lot on what type of organism you are studying. Horizontal transfer between bacteria is quite a bit different than horizontal transfer between mammals, for example. Some viruses undergo recombination quite frequently, and others do not. In some mammals we can be certain that there has been no gene flow between isolated populations for x number of years, and in other mammals we are not so certain of total isolation.
Even with very clear speciation events, such as modern humans now being a completely separate species from Chimpanzees, we have evidence of incomplete lineage sorting in the distant past when the human lineage split from chimpanzees, and introgresssion in more recent splits such as Neanderthals with modern humans.
https://phys.org/news/2017-02-algorithm-gene-bacterial-species.html
HI,
As mentioned above you need to be very careful while doing a proper phylogenetic analysis. Despite molecular events happening in the genome, appropriate genes/genomic regions should be identified and used for analysis. An never rely one 1 gene for inference..as it is only a gene tree and for the reasons explained well...it may or may not turned out to be a good gene..
I'd recommend a clique tree. See:
https://link.springer.com/article/10.1007/s00239-006-0082-2
Hi,
as Brian already mentioned it depends on what kind of organism you deal with. Bacteria have a lot of LGTs and if LGT (not EGT (endosymbiotic gene transfer)) really happen in eukaryotes is still debated. An accurate way to include all information in a phylogeny is to use a network (SplitsTree for example). This gives you a good overview of how strong your tree signal is and how much incompatibility (recombination events for example) you have.
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