Phylogenetic conservatism of functional traits in microorganisms


A central question in biology is how biodiversity influences ecosystem functioning. Underlying this is the relationship between organismal phylogeny and presence of specific functional traits. The relationship is complicated by gene loss and convergent evolution, resulting in the polyphyletic distribution of many traits. In microorganisms, lateral gene transfer can further distort the linkage between phylogeny and the presence of specific functional traits. To identify the phylogenetic conservation of specific traits in microorganisms, we have developed an new index to determine the cluster size where all (or nearly all) organisms share a trait - consenTRAIT.

The approach is decribed in Martiny et al., 2013 ISME J.

We have also two additional studies that in part relied on this conceptual framework and the consenTRAIT algorithm. Here, we looked at the phylogenetic distribution of different enzyme families:

Amy Zimmerman et al.: Fine-scale phylogenetic clustering of resource-acquiring enzyme genes among sequenced prokaryotic genomes. doi:10.1038/ismej.2012.176. ISME J. 2013.

Renaud Berlemont and Adam C. Martiny. Phylogenetic distribution of potential cellulases in bacteria. Appl. Environ. Microbiol. 79:5:1545-54. 2013.



The R script for consenTRAIT can be found here.

The script requires two input files as arguments: a Newick Tree and tab delimited text file with names of each taxon in the first column and then 0 or 1 values for each trait in the following columns (and no headers).

consenTRAIT4.16 KB