We are advertising a 3 year postdoc position for a project on ARGs and structural variation! Based at Oxford stats. Closing date noon 12 October, full details here: my.corehr.com/pls/uoxrecru...
Job Details
my.corehr.com
Leo Speidel
@leospeidel.bsky.social
Statistical and Population Genetics | RIKEN, iTHEMS (Japan) | 🇯🇵🇩🇪🇬🇧 |
I’m looking to hire an NIH funded postdoc to join our lab here at Davis (please RT). Ongoing areas of interest include: 1) polygenic signals of selection from time series, ARGs, GWAS, etc 2) The interpretation of GWAS, polygenic scores, & sources of confounding
Excited for @gabrielesgarlata.bsky.social’s new preprint on the Genome-Wide Effect of Drift and Selection over a Single Generation 1/n www.biorxiv.org/content/10.6...
The Genome-Wide Effect of Drift and Selection over a Single Generation
The relative importance of genetic drift versus selection to evolutionary change has long been debated. This debate has mainly focused over long-time-scales (e.g. hundreds of thousands of generations)...
biorxiv.org
The first manuscript from my postdoc is out (doi.org/10.64898/202...)! We introduce 𝐭𝐢𝐦𝐞-𝐬𝐭𝐫𝐚𝐭𝐢𝐟𝐢𝐞𝐝 𝐬𝐭𝐚𝐭𝐢𝐬𝐭𝐢𝐜𝐬 for studying population structure change over time, with the temporal resolution of Ancestral Recombination Graphs (ARGs). Joint with @jkpritch.bsky.social and @jeffspence.github.io. 1/n
Coalescent-Based Time-Stratified Statistics Reveal Population Structure Dynamics using the Ancestral Recombination Graph
Many questions in population genetics are concerned with reconstructing evolutionary history through time, such as inferring how population structure has changed throughout the past. Yet, many existing approaches have only an implicit temporal component, using quantities such as allele frequency or haplotype length as rough proxies for age. Recent advances in the inference of Ancestral Recombination Graphs (ARGs) have made it possible to estimate the entire sequence of local genealogies along the genome. These genealogies explicitly encode how samples are related to each other at different time points in the past, enabling the inference of how population structure has changed over time. To this end, recent work has used ARGs to define time-stratified versions of widely-used population genetics summary statistics in an attempt to capture the population structure present within a particular time window. Here, we show that naive approaches result in statistics that cannot be interpreted solely in terms of the population structure present within the time window they are targeting. To address this problem, we introduce a framework of coalescent-based time-stratified statistics, which use coalescence probabilities to partition classical summary statistics into interval-specific contributions. Using coalescent simulations, we demonstrate that these statistics accurately isolate population structure at different temporal depths and avoid spurious signals. Our results highlight the necessity of integrating coalescent theory into ARG-based temporal analyses and provide a principled and practical foundation for studying the dynamics of population structure through time. ### Competing Interest Statement The authors have declared no competing interest. National Human Genome Research Institute, https://ror.org/00baak391, R01HG014005
google.com
Very good preprint on the evolution of the canine genome through joint dog and wolf genealogies (by Jasmin Rees @mattiassherman.bsky.social @anders-bergstrom.bsky.social @leospeidel.bsky.social and colleagues) 🧪🧬🐶🐺 www.biorxiv.org/content/10.6...
Joint dog and wolf genealogies reveal the evolution of the canine genome
Dogs and their closest extant relative, the grey wolf, diverged around 30k years ago, but have since experienced complex histories of gene flow involving other canids, adaptive pressures due to close ...
biorxiv.org
New preprint! "Joint dog and wolf genealogies reveal the evolution of the canine genome" We build genealogies of dogs and wolves to find two strong mutation-rate pulses, GC-biased gene conversion, selection, and inter-species gene flow shaping the canine genome. www.biorxiv.org/content/10.6...
Joint dog and wolf genealogies reveal the evolution of the canine genome
Dogs and their closest extant relative, the grey wolf, diverged around 30k years ago, but have since experienced complex histories of gene flow involving other canids, adaptive pressures due to close ...
biorxiv.org
Postdoctoral job announcement: come to Cambridge and work on population genetic modelling with environmental and ancient DNA, jointly with @gamzeandgursoy.bsky.social and me. Details at www.jobs.cam.ac.uk/job/55580/ - applications by June 16th.
Research Associate in Population Genetics Modelling and Environmental DNA (Fixed Term) - Job Opportunities - University of Cambridge
Research Associate in Population Genetics Modelling and Environmental DNA (Fixed Term) in the Department of Applied Mathematics and Theoretical Physics at the University of Cambridge.
jobs.cam.ac.uk
1/ New paper out in Nature Communications! We studied the salivary amylase gene, AMY1, in Indigenous Andean populations and found evidence that high AMY1 copy number rapidly increased in frequency, likely through recent positive selection. doi.org/10.1038/s414...
Rapid adaptive increase of amylase gene copy number in Indigenous Andeans - Nature Communications
The salivary amylase gene exhibits copy-number variation linked to dietary shifts. Here, the authors describe an adaptive expansion of the amylase gene in Indigenous Andean populations coinciding with...
doi.org
Our preprint is now out, looking at genomic history and selection in Britain, with a focus on the Roman and early medieval periods. Comments welcome! www.biorxiv.org/content/10.6... @boothicus.bsky.social @leospeidel.bsky.social @pontus-skoglund.bsky.social
biorxiv.org
🏺🧪Preprint of 1039(!) whole ancient human genomes from Britain, mainly dating to 1st Millennium CE, representing the best part of 7 years of my life. Herculean effort by @marinasdsilva.bsky.social to get this over the line. 'Migration Period' is more migrationy than we could have possibly imagined.
bioRxivpreprint@biorxivpreprint.bsky.social · 5mo agoGenomic history and selection in Roman and early medieval Britain https://www.biorxiv.org/content/10.64898/2026.04.28.721361v1
New preprint led by Hrushikesh Loya, me, and Simon Myers where we introduce GhostBuster! www.biorxiv.org/content/10.6... The idea is to find all the different ways a target individual relates to reference groups in genealogies, to "bust the ghosts" in our ancestry.
biorxiv.org
Very honoured and I owe a lot to all my mentors and colleagues, thank you!
Society for Molecular Biology and Evolution@official-smbe.bsky.social · 5mo agoThe 2026 awardees of SMBE's Faculty Award are now known. We start by presenting the SMBE Early-Career Excellence Award winner - Leo Speidel - working at RIKEN, Japan. @leospeidel.bsky.social Visit our website to learn more about the SMBE Faculty Awards 🔗 smbe.org/faculty-awards #society
New ad for an independent postdoc in mathematics/statistics/machine learning for Biology in my institute at RIKEN (not my lab), ranging from 3 to 7 years. Our institute is entirely English-run, and a good mix of expertise on maths/physics/stats/bio! www.riken.jp/en/careers/r...
Seeking a few Senior Research Scientists, Research Scientists, Postdoctoral Researchers at Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical...
riken.jp
Postdoc position in my group in Tokyo! Please get in touch if you are interested. And happy to discuss projects - these would range from developing new methods to analysis of new genomes that we are now sequencing in the lab. Job Ad: www.riken.jp/en/careers/r... Lab page: speidellab.github.io
Seeking a few Postdoctoral Researchers at Mathematical Genomics RIKEN ECL Research Unit (25-695)
riken.jp
A 4-year postdoc position in population genomics is available in my group at the University of East Anglia, to work on a project sequencing a thousand fox genomes across rural and urban environments in the UK. vacancies.uea.ac.uk/vacancies/15...
Senior Research Associate in Population Genomics (RA2327) in University of East Anglia | UEA
View details and apply for this Senior Research Associate in Population Genomics (RA2327) vacancy in University of East Anglia. Faculty of Science School of Biological Sciences Senior Research A...
vacancies.uea.ac.uk
Our review of recent Sequentially Markovian Coalescent methods is up on arXiv: arxiv.org/abs/2506.00692 (based on last year's @official-smbe.bsky.social symposium)
Not Just $N_e$ $N_e$-more: New Applications for SMC from Ecology to Phylogenies
Genomes contain the mutational footprint of an organism's evolutionary history, shaped by diverse forces including ecological factors, selective pressures, and life history traits. The sequentially Ma...
arxiv.org
I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required. Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.
Our @ucl.ac.uk @crick.ac.uk work, out this week in @science.org, traces a genetic time series of bacterial infections to reveal when and how Borrelia recurrentis jumped from ticks to humans—via our body lice. www.science.org/doi/10.1126/...
Ancient Borrelia genomes document the evolutionary history of louse-borne relapsing fever
Several bacterial pathogens have transitioned from tick-borne to louse-borne transmission, which often involves genome reduction and increasing virulence. However, the timing of such transitions remai...
science.org
Our new paper is out in @science.org! By exploring the rich genetic diversity of Brazil, we show how fine-scale genomic analyses reveal that this diversity, rooted in Indigenous ancestry and centuries of complex demographic history, plays a key role in population health.
Our paper on ancient human population structure is now published. We find that the ancestors of modern humans lived in multiple populations during the period when Homo sapiens evolved in Africa. www.nature.com/articles/s41...
A structured coalescent model reveals deep ancestral structure shared by all modern humans - Nature Genetics
The cobraa model extends the pairwise sequentially Markovian coalescent to identify structured population history by examination of the model transition matrix. Applied to human polymorphism data, cob...
nature.com
We are excited to announce a new faculty position here in Cambridge, for researchers in computational and/or theoretical biology, based jointly in Genetics and Mathematics. Come and join us! Happy to answer questions about research, teaching and working here. www.jobs.cam.ac.uk/job/50414/
Assistant/Associate Professor in Computational Biology - Job Opportunities - University of Cambridge
Assistant/Associate Professor in Computational Biology in the Department of Applied Mathematics and Theoretical Physics at the University of Cambridge.
jobs.cam.ac.uk
Octo-squid-nautiloid sex chromosomes! www.sciencedirect.com/science/arti...
Cephalopod sex determination and its ancient evolutionary origin
Octopuses, squids, and cuttlefishes—the coleoid cephalopods—are a remarkable branch in the tree of life whose members exhibit a repertoire of sophisti…
sciencedirect.com
Thread and open access version to come- Ancient genomics and the origin, dispersal, and development of domestic sheep | Science search.app/gtSKYHF5HqRa... #adna
Ancient genomics and the origin, dispersal, and development of domestic sheep
The origins and prehistory of domestic sheep (Ovis aries) are incompletely understood; to address this, we generated data from 118 ancient genomes spanning 12,000 years sampled from across Eurasia. Ge...
search.app
I posted a couple days ago about our new paper on building causal graphs from genetic associations + Perturb-seq. Here I want to expand on the value of using DIRECTIONAL information contained in LoF burden tests.🧵 [work led by @minetoota.bsky.social ] bsky.app/profile/jkpr...
Jonathan Pritchard@jkpritch.bsky.social · 2y agoGWAS provides a unique tool in human biology as it can establish causal links from variants to trait. But interpretation is difficult as most effects flow through (unobserved) gene regulatory networks. Can we gain insight by linking to modern Perturb-seq data? www.biorxiv.org/content/10.1...
📢📢📢 #SMBE2025 Abstract Submission EXTENDED to Saturday, February 15, 2025 We also invite you to register at www.smbe2025.org @SMBEmeetings
Excited to share our preprint "A putative ecocline in Klebsiella pneumoniae" and super-interested to get your feedback. Really want to use the hive mind to get to the bottom of this phenomenon ASAP. www.biorxiv.org/content/10.1...
A putative ecocline in Klebsiella pneumoniae
Are quantitative traits important for bacteriology? The quantitative trait models used in animal and plant genetics assume that the trait takes continuous values and is influenced by many variants cir...
biorxiv.org
My bluesky debut! One week to the submission deadline for SMBE 2025, Beijing 20-24 July smbe2025.scimeeting.cn @anaignatieva.bsky.social and I are organising a symposium on popgen through time: using ARGs, aDNA, or otherwise to understand the evolutionary processes that shape genomes through time.
