Josef Uyeda
@pseudacris.bsky.social
The pattern on the back of this Nepenthes pitcher plant takes me back to playing MS-DOS games in the 90s.
October 3, 2025 at 1:23 AM
The pattern on the back of this Nepenthes pitcher plant takes me back to playing MS-DOS games in the 90s.
“There’s a hyperparasitoid (Hypopteromalus tabacum) on a parasitoid (Cotesia congregata) on a Sphinx (Ceratomi catalpae) on a tree (Catalpa sp.) by the pond in the middle of VT.” Fun find this week. My mind is all children’s songs these days but the lyrics might need some work….
September 11, 2025 at 3:37 PM
“There’s a hyperparasitoid (Hypopteromalus tabacum) on a parasitoid (Cotesia congregata) on a Sphinx (Ceratomi catalpae) on a tree (Catalpa sp.) by the pond in the middle of VT.” Fun find this week. My mind is all children’s songs these days but the lyrics might need some work….
To Craig's point, I always bring up the CRAZY stat buried in Morgan et al. '22:
Babies of profs become faculty ~9.5% of the time, while the overall prob a STUDENT IN A PHD becomes faculty = ~12%. One would hope ≥20 years of work & commitment toward a goal puts you far ahead of babies, but no.
Babies of profs become faculty ~9.5% of the time, while the overall prob a STUDENT IN A PHD becomes faculty = ~12%. One would hope ≥20 years of work & commitment toward a goal puts you far ahead of babies, but no.
July 10, 2025 at 2:49 PM
To Craig's point, I always bring up the CRAZY stat buried in Morgan et al. '22:
Babies of profs become faculty ~9.5% of the time, while the overall prob a STUDENT IN A PHD becomes faculty = ~12%. One would hope ≥20 years of work & commitment toward a goal puts you far ahead of babies, but no.
Babies of profs become faculty ~9.5% of the time, while the overall prob a STUDENT IN A PHD becomes faculty = ~12%. One would hope ≥20 years of work & commitment toward a goal puts you far ahead of babies, but no.
Had a wonderful group for our 2025 EQG workshop at Mountain Lake Biological Station! Huge thanks to the instructors, participants, and station staff for helping us pull this off! If you're interested in what we talked about, materials available here:
eqgw.github.io/2025/schedul...
eqgw.github.io/2025/schedul...
June 16, 2025 at 5:18 PM
Had a wonderful group for our 2025 EQG workshop at Mountain Lake Biological Station! Huge thanks to the instructors, participants, and station staff for helping us pull this off! If you're interested in what we talked about, materials available here:
eqgw.github.io/2025/schedul...
eqgw.github.io/2025/schedul...
6. Less broadly applicable, but layeranalyzer (Reitan & Liow, 2019; 17 cits). This isn't phylogenetic but great for macroevolutionary timeseries when you want to test for correlative or causal connections between variables.
besjournals.onlinelibrary.wiley.com/doi/full/10....
besjournals.onlinelibrary.wiley.com/doi/full/10....
May 21, 2025 at 8:06 PM
6. Less broadly applicable, but layeranalyzer (Reitan & Liow, 2019; 17 cits). This isn't phylogenetic but great for macroevolutionary timeseries when you want to test for correlative or causal connections between variables.
besjournals.onlinelibrary.wiley.com/doi/full/10....
besjournals.onlinelibrary.wiley.com/doi/full/10....
5. This one isn't really undercited, but Phylogenetically aligned component analysis by Collyer & Adams (2020, 64 cits) is a beautiful method we're finding very useful in the lab. Again, something that may be more what you want than PCAs.
besjournals.onlinelibrary.wiley.com/doi/full/10....
besjournals.onlinelibrary.wiley.com/doi/full/10....
May 21, 2025 at 8:06 PM
5. This one isn't really undercited, but Phylogenetically aligned component analysis by Collyer & Adams (2020, 64 cits) is a beautiful method we're finding very useful in the lab. Again, something that may be more what you want than PCAs.
besjournals.onlinelibrary.wiley.com/doi/full/10....
besjournals.onlinelibrary.wiley.com/doi/full/10....
4. Another Michael Grundler hit, Grundler & Rabosky 2020 (24 cits) for multivariate count data.
academic.oup.com/sysbio/artic...
academic.oup.com/sysbio/artic...
May 21, 2025 at 8:06 PM
4. Another Michael Grundler hit, Grundler & Rabosky 2020 (24 cits) for multivariate count data.
academic.oup.com/sysbio/artic...
academic.oup.com/sysbio/artic...
3. The OG unappreciated PCM: SLOUCH (Hansen et al. 2008, 403 cits) now w/FAST mvSLOUCH (Bartoszek et al. 2024, 4 cits) and a GREAT Bayesian version w/new models, "blouch" (Grabowski et al. 2024, 1 cit).
academic.oup.com/sysbio/artic...
besjournals.onlinelibrary.wiley.com/doi/full/10....
academic.oup.com/sysbio/artic...
besjournals.onlinelibrary.wiley.com/doi/full/10....
May 21, 2025 at 8:06 PM
3. The OG unappreciated PCM: SLOUCH (Hansen et al. 2008, 403 cits) now w/FAST mvSLOUCH (Bartoszek et al. 2024, 4 cits) and a GREAT Bayesian version w/new models, "blouch" (Grabowski et al. 2024, 1 cit).
academic.oup.com/sysbio/artic...
besjournals.onlinelibrary.wiley.com/doi/full/10....
academic.oup.com/sysbio/artic...
besjournals.onlinelibrary.wiley.com/doi/full/10....
2. "bm" and "mk" from Grundler, Rabosky & Zapata (2022, 1 citation!). These two software packages are BLAZING FAST methods that identify shifts in rates in BM and Mk models on a tree. They're super easy to use.
github.com/blueraleigh/bm
github.com/blueraleigh/mk
academic.oup.com/sysbio/artic...
github.com/blueraleigh/bm
github.com/blueraleigh/mk
academic.oup.com/sysbio/artic...
May 21, 2025 at 8:06 PM
2. "bm" and "mk" from Grundler, Rabosky & Zapata (2022, 1 citation!). These two software packages are BLAZING FAST methods that identify shifts in rates in BM and Mk models on a tree. They're super easy to use.
github.com/blueraleigh/bm
github.com/blueraleigh/mk
academic.oup.com/sysbio/artic...
github.com/blueraleigh/bm
github.com/blueraleigh/mk
academic.oup.com/sysbio/artic...
1. Phylogenetic factor analysis (Tolkoff et al. 2018, 39 citations; Hassler et al. 2022, 19 citations). I feel like this does way better what many people want when they do a phylo PCA. Takes discrete + cont data.
besjournals.onlinelibrary.wiley.com/doi/full/10....
academic.oup.com/sysbio/artic...
besjournals.onlinelibrary.wiley.com/doi/full/10....
academic.oup.com/sysbio/artic...
May 21, 2025 at 8:06 PM
1. Phylogenetic factor analysis (Tolkoff et al. 2018, 39 citations; Hassler et al. 2022, 19 citations). I feel like this does way better what many people want when they do a phylo PCA. Takes discrete + cont data.
besjournals.onlinelibrary.wiley.com/doi/full/10....
academic.oup.com/sysbio/artic...
besjournals.onlinelibrary.wiley.com/doi/full/10....
academic.oup.com/sysbio/artic...
Japanese Jack-in-the-pulpit (Arisaema sikokianum) looking into the morning sun from my shade garden.
April 28, 2025 at 12:05 PM
Japanese Jack-in-the-pulpit (Arisaema sikokianum) looking into the morning sun from my shade garden.
They were like "why can't these sperm swim and why are there so few of them?" and turns out it's cause they basically drop them off right on top of the ovary. I hate it.
April 24, 2025 at 5:30 PM
They were like "why can't these sperm swim and why are there so few of them?" and turns out it's cause they basically drop them off right on top of the ovary. I hate it.
Shown here. Almost all analyses best supported hypothesis is dire wolf equally related to jackals/awd/wolves (Col 1). Some analyses show equivocal support for dire wolf closer related to awd/wolves than jackals (col 2). Almost no support for dire wolves closer to jackals than wolves (3rd column).
April 11, 2025 at 2:47 PM
Shown here. Almost all analyses best supported hypothesis is dire wolf equally related to jackals/awd/wolves (Col 1). Some analyses show equivocal support for dire wolf closer related to awd/wolves than jackals (col 2). Almost no support for dire wolves closer to jackals than wolves (3rd column).
RE: Dire wolves. Several articles, including the science article quoting the lead author of the study, reference a finding that dire wolves are more closely related to African Jackals than Grey wolves. Yet the paper has this figure, which doesn't support that claim at all. What am I missing?
April 10, 2025 at 4:51 PM
RE: Dire wolves. Several articles, including the science article quoting the lead author of the study, reference a finding that dire wolves are more closely related to African Jackals than Grey wolves. Yet the paper has this figure, which doesn't support that claim at all. What am I missing?
Loving the CRISPR sequel to Face/off. Yes I have amazing photoshop skills thank you.
April 8, 2025 at 3:16 AM
Loving the CRISPR sequel to Face/off. Yes I have amazing photoshop skills thank you.
Deadline tomorrow, April 4th at 5:00pm! Apply & share!
April 3, 2025 at 2:59 PM
Deadline tomorrow, April 4th at 5:00pm! Apply & share!
I don't think I understand your point, the right side of the graph shows an effect across the board for women from projecting the line from the left. But really, the effect immediately before and after 0 is the cleanest test, as other confounders can come in over time. Obviously age explains trend.
April 2, 2025 at 8:43 PM
I don't think I understand your point, the right side of the graph shows an effect across the board for women from projecting the line from the left. But really, the effect immediately before and after 0 is the cleanest test, as other confounders can come in over time. Obviously age explains trend.
One week left for applications! (just a simple questionnaire).
March 30, 2025 at 1:09 PM
One week left for applications! (just a simple questionnaire).
Yo, all I was talking about. Central limit theorem breaks down binaries.
February 11, 2025 at 9:42 PM
Yo, all I was talking about. Central limit theorem breaks down binaries.
I asked ChatGPT to rewrite @waynemaddison.bsky.social and Whitton's abstract as described here. Honestly it's pretty 🔥🔥🔥
February 11, 2025 at 6:59 PM
I asked ChatGPT to rewrite @waynemaddison.bsky.social and Whitton's abstract as described here. Honestly it's pretty 🔥🔥🔥
Sure, here's some anisogamy in an animal but it's in the opposite direction. So 3). He's wrong regardless.
January 21, 2025 at 8:38 PM
Sure, here's some anisogamy in an animal but it's in the opposite direction. So 3). He's wrong regardless.
The dominance of dicots in being carnivorous argues against this claim (monocot carnivores' leaves are boring af).
December 5, 2024 at 6:39 PM
The dominance of dicots in being carnivorous argues against this claim (monocot carnivores' leaves are boring af).
New paper lead by Diego Porto & Sergei Tarasov
w/István Mikó & myself introducing a new R package, ontophylo, for reconstructing the evolutionary dynamics of phenomes! Especially cool viz tools for anatomically dependent characters on phylogenies.
besjournals.onlinelibrary.wiley.com/doi/10.1111/...
w/István Mikó & myself introducing a new R package, ontophylo, for reconstructing the evolutionary dynamics of phenomes! Especially cool viz tools for anatomically dependent characters on phylogenies.
besjournals.onlinelibrary.wiley.com/doi/10.1111/...
January 8, 2024 at 5:11 PM
New paper lead by Diego Porto & Sergei Tarasov
w/István Mikó & myself introducing a new R package, ontophylo, for reconstructing the evolutionary dynamics of phenomes! Especially cool viz tools for anatomically dependent characters on phylogenies.
besjournals.onlinelibrary.wiley.com/doi/10.1111/...
w/István Mikó & myself introducing a new R package, ontophylo, for reconstructing the evolutionary dynamics of phenomes! Especially cool viz tools for anatomically dependent characters on phylogenies.
besjournals.onlinelibrary.wiley.com/doi/10.1111/...
One of my Australian tuberous sundews, Drosera indumenta. Haven’t had the greatest luck with this group but this one looks nice this year.
November 22, 2023 at 7:49 PM
One of my Australian tuberous sundews, Drosera indumenta. Haven’t had the greatest luck with this group but this one looks nice this year.