I pitched phylostratigraphy a few times in proposals and the reviewers always say something similar to your comment. I was using it (perhaps incorrectly) as trait gains/losses at specific nodes and times (with a bit of fossil information). I wish I had avoided the term though, haha. - ThreadSky

fishgenomes.bsky.social • 206 days ago

I pitched phylostratigraphy a few times in proposals and the reviewers always say something similar to your comment. I was using it (perhaps incorrectly) as trait gains/losses at specific nodes and times (with a bit of fossil information). I wish I had avoided the term though, haha.

Comments

mtanichthys.bsky.social•206 days ago

Not sure you were using it incorrectly, genomic phylostratigraphy is kind of a weird term. I kind of feel like it might be just more straightforward to say something like what it actually is, it's basically just ancestral state reconstruction to study gene origins right?

fishgenomes.bsky.social•206 days ago

I think if people know the term they like seeing it used, but if they don't, they want a definition instead. And it opens one up for unwarranted (IMO) criticism - e.g., gene origin timing is uncontroversially important; but is phylostratigraphy a sound method? (yes, if they're the same thing)

stairwaytokevin.bsky.social•205 days ago

Yeah and people can start confusing conventions for fixed aspects of an approach (pot calling kettle here, I suppose)

stairwaytokevin.bsky.social•205 days ago

In fact the fixed taxonomic unit aspect of gene phylostratigraphic papers seemed like the novel/key feature to me. Otherwise there’s no way to systematize “key nodes”. Like most of my work depends on the wonkiness of the system I work in and my knowledge of lineages and outgroups

fishgenomes.bsky.social•205 days ago

Good point. We've been trying microsynteny phylo approaches in fish and the blocks of 'synapomorphies' correspond surprisingly well with higher level taxa. I think its the same for gene birth/death and causal (mechanistic) underpinnings are the reason for that pattern, in part.

mtanichthys.bsky.social•205 days ago

There's evidence that taxonomic names tend to correspond to clades with long stem branches. This should correspond to origins of many synapomorphies, whether morphological or associated with gene origins/losses. https://academic.oup.com/sysbio/article/72/5/1188/7185916

stairwaytokevin.bsky.social•205 days ago

Yeah some things are like that in Brassicaceae (the alpha WGD event is at the stem of the family, so great) but looking deeper, specialized metabolism is a mess and genes/gene families are coming from both before and after those kinds of nodes in, frankly, baffling ways.

stairwaytokevin.bsky.social•206 days ago

Yeah; I keep looking into it or checking out papers because it’s so adjacent to work I’m doing but there are some things to it that just strike me as odd. Like much of the developments hourglass work just seems kinda fishy to me (no pun intended)

fishgenomes.bsky.social•206 days ago

We were just trying to save words by substituting a term for a definition, but that backfired, ha!

stairwaytokevin.bsky.social•206 days ago

Many such cases. I sometimes worry I'm suffering the inverse because I think people like the sound of "PhyloGWAS" over "phylogenetic linear models methods associating gene family expansions with phenotypic diversity"

fishgenomes.bsky.social•206 days ago

Young genes vs old genes is very interesting, for example. What to call the underlying taxa/clades is a different question, which seems like your real criticism.

Comments

Posting Rules

Reply