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Kieran Samuk

@ksamuk.bsky.social
1.1K followers 591 following 10 posts

Assistant Professor in the EEOB Department at UC Riverside. Studying evolution and recombination using genomics. 🍁🔬🖥️. samuklab.com

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Reposted by Kieran Samuk
Maria Akopyan, PhD @akopyan.bsky.social · 24/09/2026
New preprint out today! [1/5] Can higher recombination rates help populations adapt more quickly to environmental change? We used forward-time simulations to find out. www.biorxiv.org/content/10.6...
biorxiv.org
Recombination accelerates adaptation across genetic architectures and demographic histories
According to classic population genetics theory, recombination shapes the efficacy of natural selection. However, whether variation in recombination rate itself translates into meaningful differences ...
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Reposted by Kieran Samuk
Tom Booker @tombooker.bsky.social · 24/09/2026
I’m keen to share this preprint. There is growing evidence that associative overdominance leads to the maintenance heterozygosity and we wondered how this would affect variance for traits under stabilizing selection: www.biorxiv.org/content/10.6...
biorxiv.org
Maintenance of quantitative genetic variation in regions of restricted recombination via associative overdominance
Mutation-selection balance is the most plausible general mechanism for the maintenance of additive genetic variance (VA) for quantitative traits in natural populations. It is well established that the...
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Reposted by Kieran Samuk
Dr. Paige Duffin @paigeduffin.bsky.social · 14/09/2026
I’m excited to share the 🌷🪻 "meadow plot" 🌻🌷, a new pop genomics visualization tool I created to ID putative selective sweeps across the genome using windowed π & FST estimates from pixy. User-friendly tutorial here: paigeduffin.github.io/meadow_plot_... Please help spread the word by sharing! 🧬
paigeduffin.github.io
Meadow Plot Tutorial
A step-by-step tutorial for creating meadow plots and candidate peak summaries from pixy output.
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Reposted by Kieran Samuk
Henry Arenas-Castro @henryarenas.bsky.social · 03/08/2026
"How two hybridizing monkeyflowers resist phenotypic homogenization" I'm very happy to share this. We would really appreciate your feedback!
Slide with the title and authors list of a manuscript along with illustrations of the monkeyflowers Mimulus guttatus (left) and Mimulus glaucescens (right). In the background, a Manhattan plot with outlier loci and QTL locations.
Title: Maintenance of phenotypic divergence in two sympatric monkeyflowers with weak reproductive isolation
Authors: Henry Arenas-Castro, Cage Cochran, Quinn Evans, Hongfei Chen, Jenn M. Coughlan
Manuscript: bioRxiv, 10.64898/2026.07.28.741377
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Kieran Samuk @ksamuk.bsky.social · 03/08/2026
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!
Alt text: Schematic of the pixy workflow. Left, inputs: a bgzipped, tabix- or CSI-indexed VCF with callable sites supplied as an all-sites VCF or gVCF blocks, a populations file, and optional BED and sites files. Centre, core: windowing by fixed width, BED or region; statistic selection; options for Hudson's FST, multiallelic SNPs, automatic ploidy detection and multicore execution. Right, outputs: one TSV per statistic for pi, dxy, FST, Watterson's theta and Tajima's D, with raw count columns for exact aggregation. Bottom, development: GitHub fork and pull request, local checks with ruff, mypy and pytest, continuous integration across Python 3.10 to 3.14, and distribution through conda-forge. Features new since the 2021 release are badged "new".
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Nature @nature.com · 24/04/2025
Scientists must push back against the threat of rising white nationalism and the dangerous and pseudoscientific ideas of eugenics go.nature.com/4jGqiUc
go.nature.com
Eugenics is on the rise again: human geneticists must take a stand
Scientists must push back against the threat of rising white nationalism and the dangerous and pseudoscientific ideas of eugenics.
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Reposted by Kieran Samuk
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 21/04/2025
Evidence of parental care as a novel reproductive isolating mechanism www.biorxiv.org/content/10.1101/202…
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Reposted by Kieran Samuk
Maria Akopyan, PhD @akopyan.bsky.social · 18/04/2025
Excited to share our new paper on genetic differentiation in Atlantic silversides! We investigated how genome structure influences adaptation under varying levels of gene flow using a species-specific reference genome and multiple recombination maps. Read on for insights! doi.org/10.1093/molb... 1/7
doi.org
Genetic differentiation is constrained to chromosomal inversions and putative centromeres in locally adapted populations with higher gene flow
Abstract. The impact of genome structure on adaptation is a growing focus in evolutionary biology, revealing an important role for structural variation and
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Reposted by Kieran Samuk
Scott Delaney @scott-delaney.bsky.social · 04/04/2025
An important point getting overlooked: When NIH cancels "diversity" grants (e.g., diversity supplements, Fs, Ks, etc), they aren't canceling the grants based on *what* the grant studies. They're cancelling them based on *who* is doing the research. And that disallowed "who" is anyone not white.
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Kieran Samuk @ksamuk.bsky.social · 04/02/2025
A new tool, vcfsim, developed by Paimon Goulart, a stellar undergraduate researcher in my lab! vcfsim allows for the quick and easy simulation (via parameterized msprime simulations) of "all-sites" vcfs, with arbitrary ploidy and amounts of missing data. www.biorxiv.org/content/10.1...
biorxiv.org
vcfsim: flexible simulation of all-sites VCFs with missing data
VCFs are the most widely used data format for encoding genetic variation. By design, standard VCFs do not include data from sites where all individuals are homozygous for the reference allele ("invari...
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Reposted by Kieran Samuk
Journal of Evolutionary Biology @jevbio.bsky.social · 31/01/2025
Genetics of recombination rate variation within and between species Bret Payseur academic.oup.com/jeb/advance-...
academic.oup.com
Genetics of recombination rate variation within and between species
Abstract. Recombination diversifies the genomes of offspring, influences the evolutionary dynamics of populations, and ensures that chromosomes segregate p
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Reposted by Kieran Samuk
Gavin Woodruff @weirdworms.bsky.social · 20/01/2025
! Selection Can Favor a Recombination Landscape That Limits Polygenic Adaptation academic.oup.com/mbe/article/...
academic.oup.com
Selection Can Favor a Recombination Landscape That Limits Polygenic Adaptation
Abstract. Modifiers of recombination rates have been described but the selective pressures acting on them and their effect on adaptation to novel environme
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Kieran Samuk @ksamuk.bsky.social · 26/03/2024
Pleased to announce that @susanjohnston.bsky.social and I will be hosting a symposium at @evolmtg.bsky.social #evol2024: "Recombination Rate Variation: Causes, Consequences, and Evolution". All are free to apply, see evolutionmeetings.org for details! Please share/RT.
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Reposted by Kieran Samuk
Noah Reid @noahreid.bsky.social · 07/02/2024
@ksamuk.bsky.social pointed this out on the other site, but I don't see much discussion here. GATK will now encode missing genotypes as "0/0", or homozygous ref, instead of "./." in VCF files. To identify sites with missing data, you'll have to check the DP field.
gatk.broadinstitute.org
GenotypeGVCFs and the death of the dot
If you have been keeping up with our GATK release notes, then you know that we have been rolling out a number of backend changes, tools, and features to GATK that we are hoping will improve the eff...
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Reposted by Kieran Samuk
Marko Spasojevic @m-j-spasojevic.bsky.social · 27/11/2023
Come join us at @UCRiverside! My department (EEOB) is hiring a tenure track Assistant Professor of Disease Ecology. Application review begins Jan 22nd. Details can be found here: aprecruit.ucr.edu/JPF01846 I am happy to answer questions (I'm on the search committee, but not chair)
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Reposted by Kieran Samuk
Andy Foote @andrewfoote.bsky.social · 21/11/2023
Postdoc position using genomics to study evolutionary constraint in threespine stickleback in Diana Rennison's lab. A great opportunity:
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Reposted by Kieran Samuk
Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 14/11/2023
As jobs are coming out and folks are applying, here's your regular reminder of lots of examples of successful job apps (mostly research academia but also industry, PUI, gov). And if you've gotten a job recently, please consider contributing! github.com/RILAB/statem...
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