Andy Foote
@andrewfoote.bsky.social
Evolutionary biologist using ancient and modern DNA to study evolution through time and space.
Three new evolutionary ecology PhD positions are open in Switzerland (Eawag, and Uni. Bern) to work on Greenland lake ecosystems. We are interested in how stickleback and copepods evolve, and how their evolution affects the trajectories of lake ecosystem development. apply.refline.ch/673277/1403/...
3 PhD positions in the fields of Evolutionary Ecology, Evolutionary Genomics, and Ecosystem Science
The Department of Fish Ecology & Evolution (FishEc) has vacancies for
apply.refline.ch
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...
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 ...
biorxiv.org
Part of my PhD work is now published in @genomebiolevol.bsky.social academic.oup.com/gbe/article/...
Genomic Signatures of Selection Are Enriched in Differentially Expressed Genes in Sticklebacks Adapting to Contrasting Environments
Abstract. Whole genome scans have identified numerous adaptive alleles in many species; however, linking these alleles to specific phenotypes remains a maj
academic.oup.com
Now out in Genetics: academic.oup.com/genetics/adv...
Mean fitness is maximized in small populations under stabilizing selection on highly polygenic traits
Abstract. Stabilizing selection commonly acts on complex traits that affect individual fitness. Here, we relate mean fitness under stabilizing selection to
academic.oup.com
Aaron Ragsdale@apragsdale.bsky.social · 11mo agoIn an earlier project simulating quantitative traits/stabilizing selection in a human-Neanderthal model, I became a bit curious about some observed fitness dynamics that I wasn’t expecting. I’m not sure if this is all that interesting or relevant, but at least it’s short.
How local is local adaptation? Researchers transplanted more than 700 lab-raised stickleback fish among lake and stream environments, finding that adaptation to specific sites can outweigh adaptation to broader habitat differences. In PNAS: https://ow.ly/yTOk50ZP97o
@fanny-pouyet.bsky.social et al. benchmarked three tree sequence reconstruction methods software by comparing the imbalance of reconstructed trees by these methods with that of the true simulated trees. 🔗 academic.oup.com/gbe/article/... #societyjournal #compbio
Comparing ARG Inference Methods Under Transmission of Reproductive Success: Tree Imbalance Matters
Abstract. Inferring coalescent trees from genomic data has become a major subject in population genetics, particularly with the recent advances in tree seq
academic.oup.com
Recombination helps evolution—but it can also cause mutations. New theory shows that even small increases in mutation near crossovers can oppose the evolution of higher recombination rates. By @sarperotto.bsky.social and Bret Payseur academic.oup.com/evlett/advan...
Elevated mutation near crossovers inhibits the evolution of recombination
Abstract. Recombination diversifies offspring genomes and helps ensure chromosome segregation during meiosis. Mutation rates are elevated near crossovers d
academic.oup.com
New paper! Costs and benefits of group size for sperm whales of the open ocean royalsocietypublishing.org/rsbl/article... w/ Hal Whitehead, Sam Walmslsey and @anaeg.bsky.social 🐋🦑 @seamammalresearch.bsky.social
Costs and benefits of group size for sperm whales of the open ocean
Abstract. Individual feeding success can change with the size of a social group through competition, cooperation, recruitment and other processes. Female s
royalsocietypublishing.org
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
🚨 Paper alert: if you are working on #metagenomics, particularly from #ancientDNA, and want to get into de novo #assembly, check out our latest work: 📄 De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag (journals.plos.org/ploscompbiol...) (1/4)
De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag
Author summary Advancements in genomic sequencing analyses are increasingly allowing researchers to reconstruct the genomes of microbial ‘dark matter’—those microbial species that are difficult to iso...
journals.plos.org
Must-know numbers in human genetics -- As many of you know, I'm writing a free online textbook in human genetics. In this blog post I cover a key skill for genome scientists from that book: how to use mental math to figure out key genome properties. jkpritchard.substack.com/p/on-fermi-p...
On Fermi Problems in Human Genetics
and some very useful numbers about human genomes to get you started!
jkpritchard.substack.com
Happy to share my work with my advisor Zachary Szpiech! Why are associations between ROH & complex traits inconsistent across studies? We use realistic simulations to show how demographic history and genetic architecture interact to shape the phenotypic impact of ROH. www.biorxiv.org/content/10.6...
The Influence of Demographic History and Genetic Architecture on Complex Traits via Runs of Homozygosity
Runs of homozygosity (ROH) are contiguous genomic regions where all sites are homozygous, inherited from identical haplotypes due to shared ancestry. The number and length of ROH in individuals varies...
biorxiv.org
Fantastic dental calculus and where to find it! Now published (not quite with this title) @ecol-evol.bsky.social doi.org/10.1002/ece3... @johnlrichards.bsky.social uncovers general rules for the formation of preserved oral microbiomes in mammals. With @markella-morait.bsky.social and many others
Dental Calculus Formation Is Linked to Diet and Phylogeny in Mammals
In a survey of > 1600 specimens across all mammalian orders, we found that most species present dental calculus. We found calculus production to be strongly associated with herbivory, and we provide ...
doi.org
Katerina Guschanski@kguschan.bsky.social · last yr.Fantastic dental calculus and where to find it Johnny Richards and team (@markella-morait.bsky.social + curators from 5 museums) survey >140 mammalian species with >1,600 specimens to understand what factors determine dental calculus formation. #aDNA #museomics www.biorxiv.org/content/10.1...
🌟🌟 Postdoc position in Disease Ecology & Nature-Based Solutions 🌟🌟 We are looking for a creative and highly motivated Postdoctoral Researcher to join the UKRI @netpositivecentre.bsky.social and the @uniexecec.bsky.social in beautiful Cornwall, UK. careers.exeter.ac.uk/vacancies/11... 🦠🌳🏙️🌍🗺️🐝 🦌🕷️
Postdoctoral Research Associate / Fellow in Cornwall | University of Exeter
View details and apply for this Postdoctoral Research Associate / Fellow vacancy in Cornwall. Postdoctoral Research Associate / Fellow This UKRI funded full-time post is available from 01/1...
careers.exeter.ac.uk
Another new paper out this week: A culturally transmitted foraging technique in Indo-Pacific bottlenose dolphins can be predicted by DNA-methylation levels royalsocietypublishing.org/rstb/article...
A culturally transmitted foraging technique in Indo-Pacific bottlenose dolphins can be predicted by DNA-methylation levels
Abstract. Cultural repertoires can influence access to resources and fitness across species, impacting individuals' environmental niches and social network
royalsocietypublishing.org
1/ The world's songbirds sing in just 8 basic sounds. And where a bird lives decides which ones it uses. My first PhD paper is out now in @science.org (www.science.org/doi/10.1126/science.aee6239) Here is what we found:
📢Thinking about a postgraduate research degree or know of some good undergraduate students? Exciting opportunities to come!!
Alex Georgiev@alexvgeorgiev.bsky.social · 3mo agoSome big news to share! @rhythmsoflife.bsky.social www.bangor.ac.uk/news/2026-07...
This was a great conference! If your interests span evolution and ecology then look out for ExE2027
Sarah Jose (JoseSci)@sarahjose.bsky.social · 3mo agoMy #ExE2026 conference post is now live! It was great chatting with attendees about their research and learning more about the field. Thanks again to the organisers @erikpostma.bsky.social, @btschirren.bsky.social, @blongdon.bsky.social, @ali--wilson.bsky.social, and @hansonmark.bsky.social!
Habitat discontinuity and fidelity to migratory routes shape narwhal genetic structure and diversity https://www.biorxiv.org/content/10.64898/2026.07.12.737983v1
I've signed and sent a letter - from authors, broadcasters, journalists, artists, scholars and performers - to express our deep concern at @exeter.ac.uk’s troubling plans to make mass redundancies within the Humanities Dept @uniofexeterhass.bsky.social. I would love it if you read and shared widely.
A new chromosome-level genome for Atlantic threespine stickleback (Gasterosteus aculeatus) was recently accepted! This high-quality assembly captures key regions like Pitx1/PeLa (underpinning repeated loss of the pelvic girdle and spines), enhancing studies on adaptation and ancient DNA. 1/2
The University of Exeter have announced a programme of academic staff cuts, including all of www.exeter.ac.uk/research/gro... Sign the open letter of support at docs.google.com/forms/d/e/1F... @crab-exeter.bsky.social
Centre for Research in Animal Behaviour (CRAB) | Research Groups | University of Exeter
exeter.ac.uk
If you're @palaeogenomics.bsky.social #ICP2026 in Stockholm go see Theda's poster. Using metagenomic data from Laine et al. doi.org/10.1016/j.cu... initially generated to track adaption in threespine stickleback, Theda applies a rigourous damage-based assessment to track the microbial community.
Redirecting
doi.org
Theda Bartolomaeus@theda.bsky.social · 4mo agoAt #ICP2026 Come see my poster! Nr.165 I am looking at sediment cores where plants & animals have been investigated, BUT microbes got thrown out as contamination. I kept them, and asked: as an Arctic lake turned from marine to freshwater 13,000 years ago, did its microbial community follow? (1/2)
At #ICP2026 Come see my poster! Nr.165 I am looking at sediment cores where plants & animals have been investigated, BUT microbes got thrown out as contamination. I kept them, and asked: as an Arctic lake turned from marine to freshwater 13,000 years ago, did its microbial community follow? (1/2)
Kicking off @10klepgenomes.bsky.social field workshop in Vlahi 🇧🇬 Butterfly & moth afficinados from all over Europe start deploying their beautiful light traps to capture undersampled #biodiversityhotspots for #referencegenome sequencing. Stay tuned for more! @projectpsyche.bsky.social
I’m looking to hire one or two postdocs - possible projects include pop gen theory, methods development, and human evolutionary inference. Please share, and email if you are interested. More info: evoldir.net/brian/evoldi...
evoldir.net
New approaches to detecting and characterizing introgression in large species trees https://www.biorxiv.org/content/10.64898/2026.05.30.728990v1
🎉🐬 Very excited to share the publication of my second PhD chapter in Molecular Ecology: Check it out here: onlinelibrary.wiley.com/doi/10.1111/... (& hit me up if you wanna talk seascape genomics!) Very briefly:
Whole‐Genome‐Sequencing Reveals Demographic History and Patterns of Parallel Adaptive Evolution in Indo‐Pacific Bottlenose Dolphins (Tursiops aduncus) Across Coastal Australian Seascapes
Understanding how demographic dynamics interact with environmental heterogeneity is central to explaining patterns of genomic variation in the marine realm. Indo-Pacific bottlenose dolphins (Tursiops...
onlinelibrary.wiley.com
