That’s why I’m having a wheat beer :)
October 11, 2025 at 11:45 AM
That’s why I’m having a wheat beer :)
Our paper shows that Spinney is much more accurate than using just one tree (usually the species tree), when you want to calculate one rate, test for multiple rates, or even get a more accurate picture of ancestral states.
Try it and tell us what you think!
3/3
Try it and tell us what you think!
3/3
October 7, 2025 at 3:12 PM
Our paper shows that Spinney is much more accurate than using just one tree (usually the species tree), when you want to calculate one rate, test for multiple rates, or even get a more accurate picture of ancestral states.
Try it and tell us what you think!
3/3
Try it and tell us what you think!
3/3
The software is called Spinney (which is a small group of trees) and it calculates likelihoods by marginalizing across a small group of gene trees!
2/
2/
October 7, 2025 at 3:11 PM
The software is called Spinney (which is a small group of trees) and it calculates likelihoods by marginalizing across a small group of gene trees!
2/
2/
Anyway, no more uncorrected quantitative statements about very large clades with lots of species!
5/5
5/5
October 6, 2025 at 2:05 PM
Anyway, no more uncorrected quantitative statements about very large clades with lots of species!
5/5
5/5
I found this original method in a nice, more recent paper by Eric Stone and Arend Sidow:
4/n
pmc.ncbi.nlm.nih.gov/articles/PMC...
4/n
pmc.ncbi.nlm.nih.gov/articles/PMC...
Constructing a meaningful evolutionary average at the phylogenetic center of mass
As a consequence of the evolutionary process, data collected from related species tend to be similar. This similarity by descent can obscure subtler signals in the data such as the evidence of constra...
pmc.ncbi.nlm.nih.gov
October 6, 2025 at 2:04 PM
I found this original method in a nice, more recent paper by Eric Stone and Arend Sidow:
4/n
pmc.ncbi.nlm.nih.gov/articles/PMC...
4/n
pmc.ncbi.nlm.nih.gov/articles/PMC...
Altschul et al. provide a weigh to take a phylogenetically weighted average, so that (for instance) the fact that there are so many small rodent species doesn't skew the answer.
I have no idea why they were working on this, but presumably it's related to their work on BLAST
3/
I have no idea why they were working on this, but presumably it's related to their work on BLAST
3/
October 6, 2025 at 2:03 PM
Altschul et al. provide a weigh to take a phylogenetically weighted average, so that (for instance) the fact that there are so many small rodent species doesn't skew the answer.
I have no idea why they were working on this, but presumably it's related to their work on BLAST
3/
I have no idea why they were working on this, but presumably it's related to their work on BLAST
3/
Have you ever wanted to answer a question like "do mammals weigh more than reptiles?" or "are male insects bigger than female insects?"
If so, you would presumably get a bunch of measurements and take their average. But biological data is correlated due to phylogeny! So it's not so simple
2/
If so, you would presumably get a bunch of measurements and take their average. But biological data is correlated due to phylogeny! So it's not so simple
2/
October 6, 2025 at 2:02 PM
Have you ever wanted to answer a question like "do mammals weigh more than reptiles?" or "are male insects bigger than female insects?"
If so, you would presumably get a bunch of measurements and take their average. But biological data is correlated due to phylogeny! So it's not so simple
2/
If so, you would presumably get a bunch of measurements and take their average. But biological data is correlated due to phylogeny! So it's not so simple
2/
Sounds like a job for hemiplasy!
a man in a suit and tie is adjusting his tie with his hands
ALT: a man in a suit and tie is adjusting his tie with his hands
media.tenor.com
October 2, 2025 at 1:25 PM
Sounds like a job for hemiplasy!
This paper started because @fabiology.bsky.social and I had found that parsimony *was* consistent under the MSC (in 2018), at least for rooted 4-taxon trees. I thought maybe this would always be the true.
But no--Daniel showed definitively this is not the case. Glad that was cleared up!
2/2
But no--Daniel showed definitively this is not the case. Glad that was cleared up!
2/2
September 30, 2025 at 2:11 PM
This paper started because @fabiology.bsky.social and I had found that parsimony *was* consistent under the MSC (in 2018), at least for rooted 4-taxon trees. I thought maybe this would always be the true.
But no--Daniel showed definitively this is not the case. Glad that was cleared up!
2/2
But no--Daniel showed definitively this is not the case. Glad that was cleared up!
2/2