James Kitchens
@kitchensjn.bsky.social
Reposted by James Kitchens
Did you know there are 2 types of avocado varieties? A-types switch from female to male, B-types male to female, within a single day. This reciprocal sex alternation promotes cross-pollination and has a simple genetic basis. Read more in this recent preprint from the final chapter of my PhD thesis 🥑
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado
In avocado and certain wild relatives in Lauraceae, pollination occurs via a synchronized rhythm of floral sex timing between two hermaphroditic flowering types. A-type plants present female-phase flo...
www.biorxiv.org
December 29, 2025 at 7:13 PM
Did you know there are 2 types of avocado varieties? A-types switch from female to male, B-types male to female, within a single day. This reciprocal sex alternation promotes cross-pollination and has a simple genetic basis. Read more in this recent preprint from the final chapter of my PhD thesis 🥑
Reposted by James Kitchens
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
December 25, 2025 at 6:47 PM
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.
Reposted by James Kitchens
🧬 Just out in Bioinformatics Advances: “tskit arg visualizer: Interactive plotting of ancestral recombination graphs.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf302
Authors include: @kitchensjn.bsky.social, @yanwong.bsky.social
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf302
Authors include: @kitchensjn.bsky.social, @yanwong.bsky.social
December 18, 2025 at 10:02 AM
🧬 Just out in Bioinformatics Advances: “tskit arg visualizer: Interactive plotting of ancestral recombination graphs.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf302
Authors include: @kitchensjn.bsky.social, @yanwong.bsky.social
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf302
Authors include: @kitchensjn.bsky.social, @yanwong.bsky.social
Reposted by James Kitchens
The UC Davis Ecology and Evolution in Working Landscapes REU provides undergrads with research experience in ecology and evolution in natural and managed landscapes. Apply now through Feb 15 via etap.nsf.gov
Contact me or @clhom.bsky.social for questions!
Contact me or @clhom.bsky.social for questions!
Ecology, Evolution, and Working Landscapes
ecoevoreu.ucdavis.edu
December 5, 2025 at 5:12 PM
The UC Davis Ecology and Evolution in Working Landscapes REU provides undergrads with research experience in ecology and evolution in natural and managed landscapes. Apply now through Feb 15 via etap.nsf.gov
Contact me or @clhom.bsky.social for questions!
Contact me or @clhom.bsky.social for questions!
Reposted by James Kitchens
Super proud of @alyssa-phillips.bsky.social 's paper, now out on biorxiv! She resolves the origin(s) of polyploid big blue-stem, a dominant species in the midwest tall-grass prairie. Her common garden analysis also informs on environmental adaptation and hints at the impacts of polyploidy.
The origins and adaptive consequences of polyploidy in a dominant prairie grass
Polyploidy is ubiquitous across North American prairies, which provide essential ecosystem services and rich soil for agriculture. Yet the mechanism driving polyploid abundance is unclear. Multiple hy...
www.biorxiv.org
November 26, 2025 at 5:54 AM
Super proud of @alyssa-phillips.bsky.social 's paper, now out on biorxiv! She resolves the origin(s) of polyploid big blue-stem, a dominant species in the midwest tall-grass prairie. Her common garden analysis also informs on environmental adaptation and hints at the impacts of polyploidy.
Reposted by James Kitchens
The last work of my PhD is finally out: www.pnas.org/doi/10.1073/...! This work is about accurately estimating branch length in the Ancestral Recombination Graph (ARG), which is achieved by a really simple framework with minimal assumptions. (1/n)
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
November 25, 2025 at 8:27 PM
The last work of my PhD is finally out: www.pnas.org/doi/10.1073/...! This work is about accurately estimating branch length in the Ancestral Recombination Graph (ARG), which is achieved by a really simple framework with minimal assumptions. (1/n)
Reposted by James Kitchens
Super excited about our schedule for BAPG at stanford on Dec 6. bapg2025.github.io/bapg2025stan... Amazing talks, a fabulous keynote, a lively poster session. A brilliant and interactive community. What’s not to love? 1/2 @sophiejwalton.bsky.social
BAPG Fall 2025
Bay Area Population Genomics Conference @ Stanford
bapg2025.github.io
November 24, 2025 at 10:54 PM
Super excited about our schedule for BAPG at stanford on Dec 6. bapg2025.github.io/bapg2025stan... Amazing talks, a fabulous keynote, a lively poster session. A brilliant and interactive community. What’s not to love? 1/2 @sophiejwalton.bsky.social
Reposted by James Kitchens
Latest in #GENETICS: @petrelharp.bsky.social and the team show how non-coalescing haplotypes can be inserted into ancestral recombination graphs (ARGs), resulting in ARGs that are smaller, faster to compute with, and have additional ancestral information. buff.ly/X801LTO
November 21, 2025 at 7:02 PM
Latest in #GENETICS: @petrelharp.bsky.social and the team show how non-coalescing haplotypes can be inserted into ancestral recombination graphs (ARGs), resulting in ARGs that are smaller, faster to compute with, and have additional ancestral information. buff.ly/X801LTO
Reposted by James Kitchens
Wisconsin Evolution is accepting applications for our Seminar Series' Early Career Scientist Award. Come share your evolution research and visit UW-Madison's evolution community. Open to grad students and postdocs (<5 yrs post PhD) from outside UW-Madison.
Apply by Dec 15th here: shorturl.at/4a4O6
Apply by Dec 15th here: shorturl.at/4a4O6
Early Career Scientist Awards 2026
Application to the UW-Madison Evolution Seminar Series - Early Career Scientist Awards.
urldefense.com
November 19, 2025 at 8:55 PM
Wisconsin Evolution is accepting applications for our Seminar Series' Early Career Scientist Award. Come share your evolution research and visit UW-Madison's evolution community. Open to grad students and postdocs (<5 yrs post PhD) from outside UW-Madison.
Apply by Dec 15th here: shorturl.at/4a4O6
Apply by Dec 15th here: shorturl.at/4a4O6
Reposted by James Kitchens
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
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
Postdoctoral Research Fellow
The department of Biology is a large, unified department with strong undergraduate degrees, nationally-ranked graduate programs, and world-class research spanning the breadth of biological questions a...
indiana.peopleadmin.com
August 11, 2025 at 11:51 AM
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
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
Reposted by James Kitchens
Yes! And also we have an exciting announcement - we are so lucky to have the privilege of having Brenna Henn give the keynote. hennlab.ucdavis.edu
November 13, 2025 at 8:37 PM
Yes! And also we have an exciting announcement - we are so lucky to have the privilege of having Brenna Henn give the keynote. hennlab.ucdavis.edu
Reposted by James Kitchens
Donate to the UC Davis pantry give.ucdavis.edu/FASA/322731 & Yolo foodbank yolofoodbank.org?form=foodfirst if you can
November 7, 2025 at 6:53 PM
Donate to the UC Davis pantry give.ucdavis.edu/FASA/322731 & Yolo foodbank yolofoodbank.org?form=foodfirst if you can
Reposted by James Kitchens
With @aconga.bsky.social we wrote a short Dispatch to highlight two awesome companion papers in @currentbiology.bsky.social by @jeffgroh.bsky.social, @gcbias.bsky.social and by Liu et al. on how the control of heterodichogamy is going nuts in the Juglandaceae :
www.cell.com/current-biol...
www.cell.com/current-biol...
November 5, 2025 at 8:00 AM
With @aconga.bsky.social we wrote a short Dispatch to highlight two awesome companion papers in @currentbiology.bsky.social by @jeffgroh.bsky.social, @gcbias.bsky.social and by Liu et al. on how the control of heterodichogamy is going nuts in the Juglandaceae :
www.cell.com/current-biol...
www.cell.com/current-biol...
Reposted by James Kitchens
Writing a letter for a great undergrad researcher in the lab. Check out their awesome GitHub repo on the transposable element simulations they wrote in slim! github.com/vibhachand/s...
GitHub - vibhachand/slim-TE-demography-simulation-project
Contribute to vibhachand/slim-TE-demography-simulation-project development by creating an account on GitHub.
github.com
October 31, 2025 at 8:28 PM
Writing a letter for a great undergrad researcher in the lab. Check out their awesome GitHub repo on the transposable element simulations they wrote in slim! github.com/vibhachand/s...
Reposted by James Kitchens
Marine bio folks: Does anyone know of any non-toxic aquarium safe paint that could be used to tag crustaceans?
I have been supergluing sequins onto the carapace of a mantis shrimp, but it falls off after several days. Looking for something a bit longer term/
Please RT!
I have been supergluing sequins onto the carapace of a mantis shrimp, but it falls off after several days. Looking for something a bit longer term/
Please RT!
October 29, 2025 at 2:46 PM
Marine bio folks: Does anyone know of any non-toxic aquarium safe paint that could be used to tag crustaceans?
I have been supergluing sequins onto the carapace of a mantis shrimp, but it falls off after several days. Looking for something a bit longer term/
Please RT!
I have been supergluing sequins onto the carapace of a mantis shrimp, but it falls off after several days. Looking for something a bit longer term/
Please RT!
Reposted by James Kitchens
Bumping this up one last time. I'm looking to hire graduate student(s) to work on an NSF-funded project to study elevational range shifts among dragonflies here in Colorado. @cudenverclas.bsky.social 🧪🌍🐙
Applications will be considered until Nov 1. See post below for more details
Applications will be considered until Nov 1. See post below for more details
October 24, 2025 at 12:24 PM
Bumping this up one last time. I'm looking to hire graduate student(s) to work on an NSF-funded project to study elevational range shifts among dragonflies here in Colorado. @cudenverclas.bsky.social 🧪🌍🐙
Applications will be considered until Nov 1. See post below for more details
Applications will be considered until Nov 1. See post below for more details
Reposted by James Kitchens
Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...
Applied Biostatistics
ybrandvain.github.io
October 24, 2025 at 2:47 PM
Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...
Reposted by James Kitchens
Anyone looking for an undergrad research assistant this coming summer? I have a truly phenomenal undergrad with expertise in genetic mapping, long read sequencing & bioinformatics who wants experience in another lab before grad school. She has been in our lab for 3 years & writing her first paper!
October 23, 2025 at 11:16 PM
Anyone looking for an undergrad research assistant this coming summer? I have a truly phenomenal undergrad with expertise in genetic mapping, long read sequencing & bioinformatics who wants experience in another lab before grad school. She has been in our lab for 3 years & writing her first paper!
Reposted by James Kitchens
I'm recruiting a postdoc for my group (based in beautiful Eugene, OR). Please get in touch if you're interested, esp if you'd like to chat at #ASHG25!
We'll primarily work at the intersection of statistical and population genetics, and we also have active projects related to the ethical and social implications of human genetics (ELSI). Please get in touch if that's a combination that sounds interesting to you!
October 15, 2025 at 12:52 PM
I'm recruiting a postdoc for my group (based in beautiful Eugene, OR). Please get in touch if you're interested, esp if you'd like to chat at #ASHG25!
Reposted by James Kitchens
For population genetics and evolutionary biology folks in the Bay Area: the next BAPG will be hosted by Stanford CEHG and the Petrov lab at Stanford on 12/6.
Registration is free but required. The deadline for talk submission is Nov. 16. Hope to see you soon! Pls RT!
docs.google.com/forms/d/e/1F...
Registration is free but required. The deadline for talk submission is Nov. 16. Hope to see you soon! Pls RT!
docs.google.com/forms/d/e/1F...
docs.google.com
October 20, 2025 at 10:42 PM
For population genetics and evolutionary biology folks in the Bay Area: the next BAPG will be hosted by Stanford CEHG and the Petrov lab at Stanford on 12/6.
Registration is free but required. The deadline for talk submission is Nov. 16. Hope to see you soon! Pls RT!
docs.google.com/forms/d/e/1F...
Registration is free but required. The deadline for talk submission is Nov. 16. Hope to see you soon! Pls RT!
docs.google.com/forms/d/e/1F...
Reposted by James Kitchens
Sharing our new paper, "Distinct haplotypes and reversed dominance at a single-gene balanced polymorphism controlling heterodichogamy in two genera of wingnuts". Genomics & evolution of a mating type system involving two morphs with alternating sexes in walnut relatives www.cell.com/current-biol...
Distinct haplotypes and reversed dominance at a single-gene balanced polymorphism controlling heterodichogamy in two genera of wingnuts
In most species within the walnut family, two genetically determined morphs alternate
between male and female flowering phases in time. Groh et al. identify a distinct
locus for this dimorphism in two...
www.cell.com
October 16, 2025 at 3:43 PM
Sharing our new paper, "Distinct haplotypes and reversed dominance at a single-gene balanced polymorphism controlling heterodichogamy in two genera of wingnuts". Genomics & evolution of a mating type system involving two morphs with alternating sexes in walnut relatives www.cell.com/current-biol...
Reposted by James Kitchens
Congratulations to @jeffgroh.bsky.social on the publication of his paper on an ancient balanced polymorphisms controlling heterodichogamy in two genera of wingnuts. The paper shows the putative turnover & reversal of dominance of a mating type polymorphism
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Distinct haplotypes and reversed dominance at a single-gene balanced polymorphism controlling heterodichogamy in two genera of wingnuts
In the angiosperm mating system of heterodichogamy, two hermaphroditic morphs temporally alternate between male and female flowering phases, promoting…
www.sciencedirect.com
October 16, 2025 at 3:42 PM
Congratulations to @jeffgroh.bsky.social on the publication of his paper on an ancient balanced polymorphisms controlling heterodichogamy in two genera of wingnuts. The paper shows the putative turnover & reversal of dominance of a mating type polymorphism
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by James Kitchens
We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT
October 15, 2025 at 3:53 PM
We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT
Reposted by James Kitchens
Our paper (Brieuc Lehmann is the first author) is now online in Genetics.
academic.oup.com/genetics/adv...
academic.oup.com/genetics/adv...
On ARGs, pedigrees, and genetic relatedness matrices
Abstract. Genetic relatedness is a central concept in genetics, underpinning studies of population and quantitative genetics in human, animal, and plant se
academic.oup.com
October 9, 2025 at 1:47 AM
Our paper (Brieuc Lehmann is the first author) is now online in Genetics.
academic.oup.com/genetics/adv...
academic.oup.com/genetics/adv...