Genomic phylostratigraphy

Genomic phylostratigraphy is a novel genetic statistical method developed in order to date the origin of specific genes by looking at its homologs across species.

This could help us better understand many evolutionary processes such as patterns of gene birth throughout evolution, or the relationship between the age of a transcriptome throughout embryonic development.

Modern implementations replace BLAST for DIAMOND since it is orders of magnitude faster [4] and have refined this process to account for sequence contamination, horizontal gene transfer and event for homology detection failure.

By studying the frequencies of expression of genes in those different phylostrata, they were able to hypothetically pinpoint the possible original formation of those germ layers to specific periods and ancestral organisms in evolutionary history.

[2] Since its invention, genomic phylostratigraphy has been regularly used by this research team[5] as well as others,[6] notably in an attempt to determine the origin of cancer genes, seemingly showing a strong link between a peak in the formation of cancer genes and the transition to multicellular organisms, a connection which had been previously hypothesised and is hence further supported by phylostratigraphy.

Using genomic phylostratigraphy, to this day scientists have found a significant phylogeny-ontogeny correlation in animals,[7] plants,[8] fungi,[9][10] and even bacterial biofilms.

However, rather than demanding to simply abandon the method, critics have been trying to work at refining it from its original state, by introducing other potential mathematical formulas or sequence searching tools,[14] although the Ruđer Bošković Institute has replied to such criticism claiming their original approach was valid and did not need to be extensively revised.

[15] This debate is also included as part of the wider discussion on the importance of de novo gene births in creating genetic diversity, in which genomic phylostratigraphy supports that they do hold a strong effect.

An example of a phylogenetic tree with its different phylostrata. Considering the large grey bars as the phylogeny of the taxa and the thin coloured lines as the various gene lineages within them, we can deduce the presence of two founder genes 1 and 2 present in their respective phylostrata 1 and 2. The phylostrata will then be usually given the name of the smallest determinable clade including all taxa present. [ 1 ]