Homology, Phylogenomics,HGT and its consequences

713/813 Lecture 3

Richard Owen (1804-1892)

• Owen defined homology as "the same organ in different animals under every variety of form and function." – 1843

• Postulated a common structural plan (“archetype”) exists for all vertebrates.

Identifying Orthologs: Symmetrical Best Hits

Phylogenomics

How does HGT happen?

How does HGT alter phylogenetic inference?

Lerat et al 2003 overview2003:• 13 gamma-proteobacterial genomes• 14,158 gene families• 7,655 contain only one gene• One family contains 544 members (ABC transport)• 275 genes found in all 13 genomes, 205 present only

in single copy• With these 205 “good orthologs,” constructed

phylogenies using various methods; produced 6 possible tree topologies, one was best supported

• Evaluated gene trees against the consensus tree; only two genes rejected this consensus

Method for identifying homologs and building gene families

This acquiescence [between the individual gene trees and the consensus tree] could be taken as confirmation of the concatenate tree or some similar topology, but it could also mean that there is very little phylogenetic signal at all in these gene datasets. Failure to reject is not the same as support. Therefore, it is essential to show that the 203 genes do have some phylogenetic signal by demonstrating that they will reject some reasonably large fraction of a representative sample of the many possible alternative13-taxon topologies…

…There is no evidence (with either the AU or SH tests) to indicate that the individual true topologies of most genes are those of the concatenate, or even that they are the same as each other. And just as the AU test more strongly differentiates among topologies, it also more strongly identifies sizeable subsets of genes that do reject the first tree and its close alternatives.

What are the functional/ecological constraints on HGT?