Jonathan Pritchard
@jkpritch.bsky.social
My lab at Stanford studies human population genetics and complex traits.
Pinned
Jonathan Pritchard
@jkpritch.bsky.social
· Sep 23
Two new chapters from my free online book in human genetics out this weekend!
These complete Part 3 of the book, on human population structure and history:
3.3: Human prehistory [separate thread]
3.4: Ancient DNA: a genetic time capsule [this thread]
web.stanford.edu/group/pritch...
These complete Part 3 of the book, on human population structure and history:
3.3: Human prehistory [separate thread]
3.4: Ancient DNA: a genetic time capsule [this thread]
web.stanford.edu/group/pritch...
Reposted by Jonathan Pritchard
Delighted to have our work on 🧬 resilience to 🩸cancer led by @g-agarwal.bsky.social & amazing collaborators, including @kharaslab.bsky.social, published in @science.org: www.science.org/doi/10.1126/... 🧵
January 2, 2026 at 2:01 PM
Delighted to have our work on 🧬 resilience to 🩸cancer led by @g-agarwal.bsky.social & amazing collaborators, including @kharaslab.bsky.social, published in @science.org: www.science.org/doi/10.1126/... 🧵
Sunset on 2025. Wishing my Bluesky friends all the very best in the new year.
January 1, 2026 at 2:33 AM
Sunset on 2025. Wishing my Bluesky friends all the very best in the new year.
Reposted by Jonathan Pritchard
One of the most pleasant surprises of the past 20 years was the transformation of Wikipedia into arguably the most reliable general information source freely accessible to the public. It’s not perfect — I’ve certainly seen errors — but it’s kind of shockingly good.
One might consider a donation.
One might consider a donation.
December 23, 2025 at 1:55 PM
One of the most pleasant surprises of the past 20 years was the transformation of Wikipedia into arguably the most reliable general information source freely accessible to the public. It’s not perfect — I’ve certainly seen errors — but it’s kind of shockingly good.
One might consider a donation.
One might consider a donation.
I love this plot illustrating the famous generation-time effect on mutation rates with modern data!
In fact, they appear to be eerily similar. The per generation mutation rate seems to lay between 10-9 and 10-8 per bp in all animal taxa surveyed to date–despite vast differences in environments, life histories, and three orders of magnitude variation in the generation time: 4/n
December 22, 2025 at 4:18 PM
I love this plot illustrating the famous generation-time effect on mutation rates with modern data!
Reposted by Jonathan Pritchard
Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social,
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
What sets the mutation rate of a cell type in an animal species?
Germline mutation rates per generation are strikingly similar across animals, despite vast differences in life histories. Analogously, in at least one somatic cell type, mutation rates at the end of l...
www.biorxiv.org
December 22, 2025 at 3:09 PM
Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social,
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
Reposted by Jonathan Pritchard
www.cell.com/cell/fulltex...
On how ~neutrally evolving CAG repeats over the lifespan eventually exerts neurodegenerative phenotype in Huntington’s disease.
On how ~neutrally evolving CAG repeats over the lifespan eventually exerts neurodegenerative phenotype in Huntington’s disease.
December 21, 2025 at 10:05 PM
www.cell.com/cell/fulltex...
On how ~neutrally evolving CAG repeats over the lifespan eventually exerts neurodegenerative phenotype in Huntington’s disease.
On how ~neutrally evolving CAG repeats over the lifespan eventually exerts neurodegenerative phenotype in Huntington’s disease.
Reposted by Jonathan Pritchard
All right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.
December 21, 2025 at 3:10 AM
All right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.
Reposted by Jonathan Pritchard
I guess the preprint came out in 2024 but it was published this year so I'll say this paper from @jeffspence.github.io and @hakha.bsky.social which is probably the paper that pleiotropy-pilled me the most. Really got me to think about what GWAS means www.nature.com/articles/s41...
December 21, 2025 at 6:07 AM
I guess the preprint came out in 2024 but it was published this year so I'll say this paper from @jeffspence.github.io and @hakha.bsky.social which is probably the paper that pleiotropy-pilled me the most. Really got me to think about what GWAS means www.nature.com/articles/s41...
Reposted by Jonathan Pritchard
Reposted by Jonathan Pritchard
As a (to me very enjoyable) part of this paper, we worked out what mutation-selection balance looks like in finite populations with varying degrees of inbreeding.
Our latest preprint revisits the classic model of mutation-selection balance.
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes
The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model predicts a simple relationship between the total frequency ...
www.biorxiv.org
December 13, 2025 at 10:43 PM
As a (to me very enjoyable) part of this paper, we worked out what mutation-selection balance looks like in finite populations with varying degrees of inbreeding.
Reposted by Jonathan Pritchard
Now TWO great new papers on why frequencies of disease genes rarely match expectations
Here was the first: www.nature.com/articles/s41...
Here was the first: www.nature.com/articles/s41...
December 13, 2025 at 5:44 PM
Now TWO great new papers on why frequencies of disease genes rarely match expectations
Here was the first: www.nature.com/articles/s41...
Here was the first: www.nature.com/articles/s41...
Our latest preprint revisits the classic model of mutation-selection balance.
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes
The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model predicts a simple relationship between the total frequency ...
www.biorxiv.org
December 13, 2025 at 4:45 PM
Our latest preprint revisits the classic model of mutation-selection balance.
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Do human recessive genes fit Haldane's 100-year old model?
This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io
www.biorxiv.org/content/10.6...
Reposted by Jonathan Pritchard
“Brilliance wrapped in modesty, decency, and good humor.” So true. 😭 May his memory be a blessing.
We learned today that Paul Rathouz of UT-Austin (previously Chicago and UW-Madison) died on Dec. 10.
Few people I've known have enwrapped their brilliance with such modesty, decency, and good humor.
A mensch's mensch. RIP.
Few people I've known have enwrapped their brilliance with such modesty, decency, and good humor.
A mensch's mensch. RIP.
December 12, 2025 at 12:10 AM
“Brilliance wrapped in modesty, decency, and good humor.” So true. 😭 May his memory be a blessing.
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Causal modelling of gene effects from regulators to programs to traits - Nature
Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.
www.nature.com
December 11, 2025 at 5:54 PM
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Reposted by Jonathan Pritchard
After time in the Bay Area, I’ve started a new role as Lecturer in the Department of Allergy and Rheumatology at the University of Tokyo. We’re the group of clinicians who see patients with autoimmune diseases, while researching new treatments and patient stratification. (continued)
December 11, 2025 at 3:15 AM
After time in the Bay Area, I’ve started a new role as Lecturer in the Department of Allergy and Rheumatology at the University of Tokyo. We’re the group of clinicians who see patients with autoimmune diseases, while researching new treatments and patient stratification. (continued)
Reposted by Jonathan Pritchard
Our latest collaboration with @jkpritch.bsky.social – led by joint post-doc Mineto Ota – is in @nature.com today: www.nature.com/articles/s41...
December 10, 2025 at 10:57 PM
Our latest collaboration with @jkpritch.bsky.social – led by joint post-doc Mineto Ota – is in @nature.com today: www.nature.com/articles/s41...
Reposted by Jonathan Pritchard
Our new ancient DNA paper has just been published!
We present 28 new genomes from southern Africa - several of them high-coverage whole genomes.
Exciting to be moving towards population-level representation of ancient southern African genetic diversity!
www.nature.com/articles/s41...
We present 28 new genomes from southern Africa - several of them high-coverage whole genomes.
Exciting to be moving towards population-level representation of ancient southern African genetic diversity!
www.nature.com/articles/s41...
Homo sapiens-specific evolution unveiled by ancient southern African genomes - Nature
The genomes of 28 ancient southern African individuals dated to between 10,200 and 150 years before present offer insights into the evolution of Homo sapiens.
www.nature.com
December 3, 2025 at 4:42 PM
Our new ancient DNA paper has just been published!
We present 28 new genomes from southern Africa - several of them high-coverage whole genomes.
Exciting to be moving towards population-level representation of ancient southern African genetic diversity!
www.nature.com/articles/s41...
We present 28 new genomes from southern Africa - several of them high-coverage whole genomes.
Exciting to be moving towards population-level representation of ancient southern African genetic diversity!
www.nature.com/articles/s41...
Reposted by Jonathan Pritchard
Congratulations to Richard Durbin on being awarded our Genetics Society Medal!
November 14, 2025 at 12:40 PM
Congratulations to Richard Durbin on being awarded our Genetics Society Medal!
Reposted by Jonathan Pritchard
It was a total pleasure to work with @roshnipatel.bsky.social on this, who really led the charge in all respects. Anyone interested in learning about the intersection of population genetics and statistical genetics should check out her new lab in Oregon!
Excited to share work from my postdoc with @docedge.bsky.social and collaborators Matt Pennell and @jgschraiber.bsky.social, newly out over the weekend: www.biorxiv.org/content/10.1... (1/6)
Observational epidemiological studies can mitigate genetic confounding with the genetic relatedness matrix
Observational studies are commonly used in psychology and epidemiology to identify risk factors correlated with health outcomes. However, these studies are vulnerable to confounding when shared geneti...
www.biorxiv.org
December 2, 2025 at 12:11 AM
It was a total pleasure to work with @roshnipatel.bsky.social on this, who really led the charge in all respects. Anyone interested in learning about the intersection of population genetics and statistical genetics should check out her new lab in Oregon!
Reposted by Jonathan Pritchard
Grateful to Isabella Alves & @cterminiphd.bsky.social for writing this fantastic N&V in @natcellbio.nature.com: www.nature.com/articles/s41...
Nicely covers our 📰 led by della Volpe & co: www.nature.com/articles/s41...
Nicely covers our 📰 led by della Volpe & co: www.nature.com/articles/s41...
December 1, 2025 at 1:10 AM
Grateful to Isabella Alves & @cterminiphd.bsky.social for writing this fantastic N&V in @natcellbio.nature.com: www.nature.com/articles/s41...
Nicely covers our 📰 led by della Volpe & co: www.nature.com/articles/s41...
Nicely covers our 📰 led by della Volpe & co: www.nature.com/articles/s41...
Reposted by Jonathan Pritchard
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 Jonathan Pritchard
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 Jonathan Pritchard
We have 115 people signed up already for BAPG! Great representation across career stages too. If you want to attend don't forget to sign up. It is free but required. @sophiejwalton.bsky.social and I are looking through the wonderful talk submissions and will announce the talks shortly. Stay tuned!
November 20, 2025 at 6:30 PM
We have 115 people signed up already for BAPG! Great representation across career stages too. If you want to attend don't forget to sign up. It is free but required. @sophiejwalton.bsky.social and I are looking through the wonderful talk submissions and will announce the talks shortly. Stay tuned!
Reposted by Jonathan Pritchard
An empirical approach to evaluating the prevalence of long-lived balancing selection in humans--and important limitations. Work by @hannahmm.bsky.social
November 11, 2025 at 7:14 PM
An empirical approach to evaluating the prevalence of long-lived balancing selection in humans--and important limitations. Work by @hannahmm.bsky.social
Reposted by Jonathan Pritchard
Excited to share some new work led by grad student Sophie Walton (w/ @petrovadmitri.bsky.social). We used in vitro gut communities to study how natural selection acts on strains of the same species as they compete within larger communities. Check out Sophie's thread below for details!
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 12, 2025 at 3:43 AM
Excited to share some new work led by grad student Sophie Walton (w/ @petrovadmitri.bsky.social). We used in vitro gut communities to study how natural selection acts on strains of the same species as they compete within larger communities. Check out Sophie's thread below for details!