New paper out in eLife! 🌱🧬 We built a k-mer method to profile genome content directly from sequencing reads and applied it to 1,000+ wild *Arabidopsis thaliana* genomes. I started this project 9 years ago during my PhD. I'm beyond thrilled to see it out. 1/7 elifesciences.org/articles/108...
Chris Fiscus
Chris Fiscus
@fiscuscj.bsky.social
evolutionary geneticist, former postdoc @UCIrvine. Views my own. https://allmylinks.com/fiscuscj
152 followers147 following74 posts
Finally, the GWAS hits were enriched for rare alleles, suggesting purifying selection constraining repeat expansion and contraction. We look forward to seeing if our results are unique to Athal or reflect plant genome evolution more generally. 6/7 elifesciences.org/articles/108...
Lastly, I want to highlight that this paper was published with eLife's new pub model and we had a great experience. I really appreciate the flexibility as it's hard to finish projects after 5PM (yay industry!). Highly recommend trying it out for your next paper 7/7 elifesciences.org/articles/108...
New paper out in eLife! 🌱🧬 We built a k-mer method to profile genome content directly from sequencing reads and applied it to 1,000+ wild *Arabidopsis thaliana* genomes. I started this project 9 years ago during my PhD. I'm beyond thrilled to see it out. 1/7 elifesciences.org/articles/108...
We treated repeat CN like a phenotype and did GWAS. Most repeat CNV mapped in-cis to pericentromeres, where repeats are clustered in the Athal genome. However, we also found several common hits potentially regulating repeat CNV in trans. 4/7 elifesciences.org/articles/108...
The potential trans-regulators of repeat CNV were enriched for genes involved in DNA replication, repair, and methylation. This suggests natural variation in mutational machinery likely regulates repeat dynamics (and thus genome evolution)! 5/7 elifesciences.org/articles/108...
New paper out in eLife! 🌱🧬 We built a k-mer method to profile genome content directly from sequencing reads and applied it to 1,000+ wild *Arabidopsis thaliana* genomes. I started this project 9 years ago during my PhD. I'm beyond thrilled to see it out. 1/7 elifesciences.org/articles/108...
The k-mer method is ref. free, but can be used to est. copy number of a given sequence, e.g. a canonical repeat. Although not as good as a full assembly, this could be a cost effective way to measure CN in many samples with low coverage or reanalyze NCBI SRA 2/7 elifesciences.org/articles/108...
The vast majority of repeats had CNV in the pop. By our estimate, repeat expansions were much more common than repeat contractions. Perhaps unsurprising to the Athal community, accessions from Sweden & Africa were the most diverged compared to everything else. 3/7 elifesciences.org/articles/108...
Chris Fiscus reposted
Chris Fiscus reposted
Been working on my NSF PRFB proposal for what seems like weeks now. Thankful for the examples provided in @jrossibarra.bsky.social 's github page (github.com/RILAB/statem...). The current call is AI in biology, and fortunately thats a lot of what I do, so I'm giving it a shot!
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We're hiring an ecologist at UC Berkeley! The Dept. of Integrative Biology is hiring a tenure-track Assistant Professor in Ecology. Plants/algae, invertebrates, microbes, or marine systems a priority. Come join us!! Apply by Oct 5, 2026. aprecruit.berkeley.edu/JPF05489 PS: Please share!
New paper out in PNAS! 🍇🧬 Vitis phylogenomics is a tangled vine. Highlights: • ~14% of the average grape genome comes from introgression • Two classic “hybrid species” are better described as hybrid swarms • Repeated adaptation is fueled by introgression and standing genetic variation
Chris Fiscus reposted
Find myself and the rest of the Specht lab at Botany 2026!! #PlantPeopleFTW #Botany2026 @botanyballer.bsky.social @brythebotanist.bsky.social @arayabelle.bsky.social @jlandisbotany.bsky.social @spechtlab.bsky.social
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uchicago.wd5.myworkdayjobs.com/External/job... The Kreiner and Carley Lab groups are hiring a shared Research Analyst to help lead wet lab protocol development and management. We're a fun group and would love to hear from you :) Get in touch with questions!
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Just posted: a group paper describing major updates to my software pixy, for population genetic summary statistics. www.biorxiv.org/content/10.6... New since 2021: arbitrary ploidy, multiallelic sites, missingness-aware Watterson's θ and Tajima's D, Hudson's FST, multicore execution!
Chris Fiscus reposted
Chris Fiscus reposted
Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...
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Did you know that the flowers of avocado trees change sex every day? Scientists have noticed this nearly 100 years ago but only now do we how it works. Life is amazing.
Chris Fiscus reposted
Folks! @gcbias.bsky.social and I have two slots left in our popgen workshop. Aug 10-21, 9-11am (Pacific) via zoom. We’re raising money for research grants for grad students. $500 a seat. Spots available to first folks to respond. DM me if interested.
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Job opening: I'm looking for a lab tech primarily supporting ongoing projects and running computational analyses for the lab. Apply here and reach out with questions! utah.peopleadmin.com/postings/205...
Chris Fiscus reposted
PhD Position at Uppsala University. Sophie Karrenberg’s Lab. the project is about sex chromosome evolution in plants. Come join us! Deadline 22 July. www.uu.se/en/about-uu/...
Chris Fiscus reposted
🚨 We're hiring computational evolutionary biologists! 🚨 Boosting this - industry evolutionary biology jobs don't come along often, so if you're excited to apply your computational evolutionary biology skills to cutting-edge problems, let's talk! 🧪🧬💻
Our team at @arcadiascience.com is hiring! We're looking to hire a computational evolutionary biologist interested in asking how and why protein sequences/structures/functions differ across the tree of life 🧬 jobs.lever.co/arcadiascien... Please share widely!
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Nice writeup of the impacts of great instructor (yes, this is a Brandon Gaut stan account) www.bio.uci.edu/students-bri...
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I am recruiting a #postdoc to work on assembling and analyzing #genomes of the amazing Furnariidae. Let’s unlock the secret behind their #evolution. The official application portal will be available soon at www.uno.edu/careers. Feel free to contact me for details at sclaramu@uno.edu
Chris Fiscus reposted
The list of Ecology/Evolution/Marine Bio Labs recruiting grad students for Fall 2027 is live! PIs enter your position info here: forms.gle/MAGd4ohyPeoY... students (and PIs not recruiting) share the composite list: docs.google.com/spreadsheets... Please share widely! 🧪
Chris Fiscus reposted
postdoc alert 🚨! NIH-funded postdoc in my lab to work on Ancestral Recombination Graphs in space. Please spread the word widely in your networks, and please reach out if you're interested! (2-3yr position, start date flexible, pay/benefits good!). details here: careers.umich.edu/job_detail/2...
Chris Fiscus reposted
So no publication fees, no conferences, no international collab, and we can terminate or reject your grant anytime for any reason. This might have some impact on how science works, folks. And maybe just maybe not a positive one.
Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule. Russell Vought is going destroy American Science. elizabethginexi.substack.com/p/summary-of...
Chris Fiscus reposted
Update! The posting for the postdoc opening in my lab is up! Apply here: unc.peopleadmin.com/postings/319...
Please circulate: I will have a postdoc opening soon, ideally with a start date sometime this summer or fall. If you're interested in empirical population genetics, computational methods development, and/or evolutionary modeling via simulation, don't hesitate to reach out. For more info on the lab:
Chris Fiscus reposted
We are hiring! We’re excited to recruit a postdoc to our lab at UC Davis to work on plant immune engineering and single-cell analyses of plant pathogen interactions. Apply by June 1. Please repost. www.coakerlab.org/postdoctoral...
Chris Fiscus reposted
Congrats to @jrossibarra.bsky.social on being elected to NAS!!! 🌽💻🧬🎉
Chris Fiscus reposted
Chris Fiscus reposted
I'm hiring a postdoc (start date flexible) and a PhD student (for Fall 2027) to work in any area of computational phylogenetics! More info here: mhibbins.github.io I will be attending both PEQG and Evolution in June, so please reach out if you want to chat at these meetings!
Chris Fiscus reposted
Thank you @adrigov.bsky.social for the nice summary in Plantae.org of our paper!
Plant Science Research Weekly -- Can plants adapt quickly enough to keep up with climate change? (Science) @mexpositoalonso.bsky.social @bossdorf.bsky.social @carlos-lara0.bsky.social (Summary by Adrian Gonzalez Ortega Bluesky: @adrigov.bsky.social) buff.ly/P2kiysF #PlantaePSRW
Excited to share our new preprint! 🍇🧬 We analyzed 639 genomes across 48 grape species to understand how hybridization drives adaptation. • ~14% of average Vitis genome is introgressed • Most parallel adaptations are shared via gene flow • Two "hybrid species" are actually hybrid swarms
Chris Fiscus reposted
Chris Fiscus reposted
Chris Fiscus reposted
Friends, please help spread the word about our microbiology REU program at Montana State University. www.montana.edu/mbi/reu/ Each student receives a stipend ($7000 for 10 wks). Travel compensation, room, and board are also provided. Details in the attached pic--Feb 14 deadline 🧫🧪🦠#microsky
Chris Fiscus reposted
Congrats @jeffgroh.bsky.social et al. Some avocado trees open female-phase flowers in the morning & then male in afternoon. Others show complementary pattern (m->f), to synchronize pollination of two types. Jeff show this to be a >45Mya polymorphism at a transcription factor across 100s of species.
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado https://www.biorxiv.org/content/10.64898/2025.12.22.695989v1
Chris Fiscus reposted
Check out our new paper! :)
Differential expression of flavonoid biosynthetic pathway genes drives the production of transgressive pigments in #Nicotiana section Repandae allotetraploids New #AJB research by @emccnicotiana.bsky.social, @jlandisbotany.bsky.social, et al. doi.org/10.1002/ajb2... #botany #polyploidy
Chris Fiscus reposted
Our plant-focused REU program, led by Prof Nagel, is open for applications, please forward to undergrads and reskeet etap.nsf.gov/award/7573/o... 🌱 🧪
Chris Fiscus reposted
Hello bluesky community! I'm hiring a postdoc to do machine learning in population genetics. Starting to build up a lab at Indiana University Bloomington where I just started a faculty position. Apply with the below link: indiana.peopleadmin.com/postings/30325
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Looking forward to my lecture on Wednesday @ucriverside.bsky.social in the Botany & Plant Sciences seminar series! I’ll present some of our recent work on forward time whole genome sims & demographic inference in the polyploid continuum. See y’all there? plantbiology.ucr.edu/seminars