fishgenomes.bsky.social
Associate Professor of Biological Sciences. We study genomes (WGD, etc.), and the ecology and evolution of fishes.
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Very cool - congrats!
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Degradation makes it hard to get the concentrations right. At least for ONT, the balance between adapters/ligase and DNA, etc. is tricky if there's a ton of small fragments in the tube, even if some long fragments are present.
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Sorry, *DNA/RNA Shield
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EtOH generally gives poor results (low molec weight DNA) for long read sequencing. Freezing on dry ice is best, but if remote, RNA/DNA Shield is best option, RNAlater second best for fish DNA in our experience. Extraction approach also matters greatly.
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There are archaeological samples for Great Lakes as well, depending on what timeline you're after. We also have some genetic data on timing.
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See Paleolox here: deepblue.lib.umich.edu/handle/2027....
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We've been looking for this exact tool - thank you!
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To elaborate, are there aspects of zebrafish (or insert vertebrate model) development that are challenging to study because they happen too quickly to properly capture with approaches available, but if the clock ticked slower one might be able to examine?
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Yes, very cool system! Taxa are usually described by observable phenotypes (morphology), but much of what happens with a plant (and perhaps animals) involves invisible-to-the-eye phenotypes (secondary compounds, etc) and lots of pleiotropy etc?
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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.
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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)
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We were just trying to save words by substituting a term for a definition, but that backfired, ha!
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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.
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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.
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Amazing thank you!! 149 in 48 mo.!
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Yes, and thanks for the devo-evo earworm @devoevomed.bsky.social!
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Looks cool - congrats!
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Science can't either.
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Has Elon purchased @altmetric.com yet?
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$$$$$ keep it going
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How about getting off Twitter as a perhaps more important first step?
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But with much better underlying science, management, awareness in general (in some ways). Yes, lots still to do.