[Taxacom] Surprise from a whole-genome study - more pepper in the soup

[Sergio Vargas]

  Hi,

 > I've received the comment that basically this is a situation of 
incongruence that may be comparable to that of biogeography where 
incongruence is usually attributed to dispersal.

yes, it is pretty much that, and some of the algorithms to find HGT use 
the same logic that some biogeographic algorithms use. In some 
implementations you could actually use the same program for both purposes.

 >In this case it is the "strange" sequences that are regarded as 
anomalous and therefore an external agency is invoked because no other 
option is regarded as tenable - I presume.

well... yes, if there is a reasonable likelihood that the species will 
be in contact during part of their life cycle, as someone already 
mentioned. But the strangeness of a sequence can be assessed by several 
means (codon usage, nucleotide frequencies, rate of evolution, etc. as I 
already mentioned)

sergio