In understanding the relationship between phylogenetic diversity and trait/functional diversity, I often wonder if this is also related to the genes that make up the phylogenetic tree. If they do not code for the traits in question, isn't it natural if it is not related to the traits?
Hi Sabhrina,
usually when constructing a phylogenetic tree for such analyses it is normal not to have the specific genes that code for the traits in the functional diversity analyses. This is because of several reasons, but I will only name a few.
(1) functional traits under investigation rarely have a single gene that codes for this trait. Rather the expression of several genes will influence the way certain phenotypes develop (also note that phenotypes are in addition influenced by the environment)
(2) unless you isolate, and sequence the genes of the individuals you want yourself, it is rare to find exactly the gene you are looking for for each species in your analysis to build the phylogeny using that gene. (Generally phylogenetic diversity or trait diversity analyses are done at such a scale, that it is simpler, faster and more cost-effective to source the sequences from repositories such as GenBank)
(3) In phylogenetic analyses of trait diversity or trait evolution it is typical to construct a phylogenetic tree from a combination genes with a known substitution rate in order to properly calibrate the phylogeny. For this ND2 and cytochrome b are popular and reliable choices.
Hi Anna,
Thank you for your answer. Indeed there are limitations with the genes involved in terms of calibration...
I am still curious though: hypothetically speaking, if only we made the phylogenetic tree with all the genes that code for the functional traits, will phylogenetic diversity definitely correlate with functional diversity? Does it make sense to ask this?
If we assume that phylogenetic diversity generally correlates with functional diversity (of course there are exceptions, especially in extremely morphologically clades) it would indeed be interesting to see if this relationship is still observed with genes under strong selection (as genes coding for functional traits would be). I think the relationship you would observe will depend strongly on the trait.
- Badges
- Science topic
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics