ajmongue.bsky.social
Assistant Professor of Molecular Ecology at University of Florida's Department of Entomology and Nematology. Comparative genomics and evolutionary genetics of weird reproductive systems.
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Love a good soft scale!
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Love this! My hot take is that pokemon reproduction isn't bad (=unrealistic), just that pokemon generally are sexually reproducing with leaky paternal genome elimination haha
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You can divide a hot minute by 60 and it has the same value, baffling
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I don't know about hoppers specifically, but you'll see similar variation in katydids: ui.charlotte.edu/story/unique...
If it's a conserved pigment pathway, similar mutants have probably evolved in your hoppers as well?
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Grinding in liquid nitrogen should work. Another option is the Powermasher, basically a mini drill pestle with textured tubes. We have one and use it regularly. It WILL break up tissue...the issue is going too far and shearing DNA afterward. It's a reasonable option with a light touch.
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So the omniprep protocol has a chloroform phase separation step that takes care of most lipids for us (and with all the wax scale insects make it can be A Lot)
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We have tried a bit with bead based kits but ultimately we use a modified omniprep extraction most of the time (happy to pass it along). The other important consideration is tissue smooshing upstream of extraction. If don't have one, I recommend a dounce homogenizer. It's been great for us!
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We have had good success with pacbio from ethanol preserved samples. Of course we prefer fresh from life or snap frozen tissue, but failing that the higher the ethanol percentage the better (100%). What's your extraction protocol?
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Ironically I've had the best luck finding them on magnolias haha
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Go for it! They're pretty quick and easy all things considered!
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Thank you! I'm excited to start getting some momentum going!
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I see students using AI to assist them with bash scripting in a cluster environment. These tools often "work" (give you correct syntax) but can make you a jerk, like requesting 30 nodes from the scheduler for a command that does not include parallelization. Still can't beat human proofreading imo.
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Haha my apologies, I guess I scrolled too quickly. Does @thymelicus.bsky.social still work on Leps? He was doing great pop gen when we with both in Edinburgh!
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I've wondered if the last few years is just a very long stress dream and I'm going to wake up and it'll be the morning of my PhD qualifying exams actually 😅
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😂 well played! What are the odds?
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Would love to get on this list @hanliconius.bsky.social, I work a lot with lep sex chromosomes and just started a big project on bagworm moths!
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We do but it's not as flexible/convenient as bigger sequencing companies. One thing I liked about Novogene was being able to request a final target amount of sequencing in Gb per sample rather than having to do flow cell juggling math.
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What's your input for the contact map, HiC reads?
We use Arima's pipeline for mapping, then vizualize in Juicebox. Happy to share some notes if that's what you're looking for
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I'd love to be included!
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Okay wrapping up: this odd genetic system creates contrasting evolutionary dynamics for the sexes. How do these patterns extend to longer evolutionary time? More soon, stay tuned to the Mongue lab as we continue exploring paternal genome elimination and other weird repro!
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If we look at the amount of adaption involved (let's save the pop gen methods for a future thread?), the pattern reverses: female-biased genes evolve less adaptively than those expressed in males! Why? Because haploid selection slows evolution but also removes more weakly deletetious variants.
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So different dynamics for the sexes and lots of sex-specific gene expression? This creates differing evolutionary trajectories for genes. First, genes expressed partly or entirely in males more slowly than female-biased genes. Evolution is faster on the female side in mealybugs! But..
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As you've maybe noticed, males and females are highly sexually dimorphic! Males are small, winged, and don't eat as adults. Females are large, sessile, and long-lived. This dimorphism extends to gene expression as well. Most genes are expressed in one sex or the other, but not both.
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This dynamic has two consequences: (1) males express genes in a haploid state, which should create more efficient selection than in diploids (2) fathers cannot pass on genes directly to their sons. They have to pass through a daughter to end up in a grandson.
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Mealybugs are sexually reproducing but have no sex chromosomes. Sex is determined by whether an embryo expreses 1 or 2 copies of the genome, so haplodiploidy BUT unlike other haplodiploids, eggs that develop male are fertilized too. They just eliminate their paternally inherited chromosomes!
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