Andy Foote

Complex patterns of hitchhiking mutation load among stickleback populations Positive selection causes beneficial alleles to rapidly rise to high frequency in a population. This can cause linked genetic variation to "hitchhike", and thereby also rise in frequency. This linked ...

working link: www.biorxiv.org/content/10.1...

Complex patterns of hitchhiking mutation load among stickleback populations https://www.biorxiv.org/content/10.1101/2025.07.24.666323v1

New lab preprint led by Jana Nickel (not on BS): doi.org/10.1101/2025...
Investigating hitchhiking mutation load in threespine sticklebacks. I'll be presenting this work in a few hours at #Stickleback2025 here in beautiful Bamfield

#PopGen New preprint of the team on the discovery of a very high rate of polymorphic duplication in a marine bivalve.

Imagine looking at the distribution of the allelic coverage fraction at heterozygous calls in an indivdual and getting this distribution 👇 😱😱😱

My talk from this year's probgen is finally out.

Where do linear mixed models and random effects come from?

They emerge from *mutations* on Ancestral Recombination Graphs.

Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context Ongoing advances in population genomic methodologies have recently enabled the study of millions of loci across hundreds of genomes at a relatively low cost, by leveraging a combination of low-covera....

If you go for WGS this study offers some useful insights on when imputation and when pseudohaploid approaches work best and give closest result to truth onlinelibrary.wiley.com/doi/10.1111/...

Innovative DNA assembly process produces high-quality reference genomes for endangered dolphins Creating genomes from DNA is hugely important for managing threatened species—understanding their past and how they have adapted to their environment helps conservationists protect them.

🧪 Great work on Hector’s & Māui genomes with @laninsky.bsky.social @emma-carroll.bsky.social

phys.org/news/2025-07...

Thank you so much, @biogeneurope.bsky.social and big kudos to our 🇬🇷 and 🇵🇱 colleagues for all their efforts. For little Bulgaria, this is an important event.
Many thanks to @pensoft.net and @iboleurope.bsky.social too, for their unwavering support.

Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context Ongoing advances in population genomic methodologies have recently enabled the study of millions of loci across hundreds of genomes at a relatively low cost, by leveraging a combination of low-covera...

Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context onlinelibrary.wiley.com/doi/10.1111/...

Continuous mitochondrial diversity of Danube sturgeon species over millennia: insights from ancient DNA | Philosophical Transactions of the Royal Society B: Biological Sciences Sturgeons, an iconic group of large fishes inhabiting marine and freshwater ecosystems, have historically had significant economic and cultural value, particularly prized for their meat and roe (cavia...

Our latest work is out! Ancient DNA from Danube sturgeon fossils dating back 10,000 years reveals that, despite centuries of decline, some populations have preserved high genetic diversity and ancient lineages. doi.org/10.1098/rstb...
@royalsociety.org @lukeeholman.bsky.social

Frontiers | Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life Reference genomes from representative species across families provide the critical infrastructure for research and conservation. The Cetacean Genomes Project...

The Cetacean Genomes Project is happy to share a milestone publication, presenting the first 18 reference-quality, chromosome-resolved genomes of whales, dolphins and porpoises across the cetacean tree of life. www.frontiersin.org/journals/mar...

Very pleased to see this officially out - Genome Architecture and Speciation in Plants and Animals. With @siluwang.bsky.social, @dortizba.bsky.social and Loren Rieseberg. onlinelibrary.wiley.com/doi/10.1111/...

So well deserved! Congratulations @mhssinding.bsky.social

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

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

Cell Press: STAR Protocols STAR Protocols is an open access, peer-reviewed journal from Cell Press. We offer structured, transparent, accessible, and repeatable step-by-step experimental and computational protocols from all are...

Interested in measuring genetic load? We have a new paper out providing a modified version of GERP which is more user friendly in wildlife species and with scripts to automate making input files and pulling out derived alleles in your species #consgen #popgen star-protocols.cell.com/protocols/4202

A great opportunity!

Whales, Greenland, and some really old mud. My first PhD chapter now published in @natcomms.nature.com reveals 12,000 years of marine mammal history around Northern Greenland through DNA hidden in marine mud. Check it out: rdcu.be/emdYS
#sedaDNA #Greenland #Arctic #whales #seals

Postdoc job alert! I'm hiring a 3-yr postdoc to work on our Social Modifiers of Primate Lifespans grant. Job info and how to apply below. Deadline June 1. Pls share! jobs.exeter.ac.uk/hrpr_webrecr...

Big thanks to @grrlscientist.bsky.social for featuring our work in Forbes magazine!
tinyurl.com/h8yj5cdf
The piece covers our recent study on time-lagged genetic diversity loss in the critically endangered regent honeyeater, published last week in @royalsocietypublishing.org
tinyurl.com/44m3b522

In a new #GENETICS research, @dandanpeng.bsky.social, Mulder, and @docedge.bsky.social evaluate the performance of several ancestral recombination graph (ARG) estimation methods used for determining the historical time course of a population-mean polygenic score.

Read more: buff.ly/ztrRU83

Genomic regions of current low hybridisation mark long-term barriers to gene flow in scarce swallowtail butterflies Author summary Efforts to understand how new species evolve typically approach the problem through either: 1) investigating patterns of genetic exchange across ‘hybrid zones’ — where closely related s...

Speciation genomics in scarce swallowtails Iphiclides podalirius and I . feisthamelii : dx.plos.org/10.1371/jour...

Junior faculty job alert in Germany - Marine Evolutionary Genomics @geomarkiel.bsky.social / University of Kiel www.geomar.de/en/karriere/... Marine study system of your choice (no microbes, sorry…), excellent infrastructure and ship access, moderate teaching requirements, closing date 6 June

Post-Doctoral Researcher – Haplotype-Resolved Assembly and Structural Variation of Polyploid Genomes in Transmissible Cancers of the Blue Mussel (M/F) - work environment: Host-Pathogen-Environment Interactions Laboratory (UMR5244 IHPE), Montpellier - main mission:

#PostDoc in #Montpellier on mussel transmissible cancers #TransCan These weird cancers have undergone genome doublings and aneuploidisation You will play with PacBio and Nanopore data Join the #HyperCan team in a joyfull environment. #MarEvol #PopGen #MusselsAreCool euraxess.ec.europa.eu/jobs/333894

Interactions Between Killer Whales (Orcinus orca) and Neonate Long‐Finned Pilot Whales (Globicephala melas) off South Iceland This study documents two encounters off south Iceland where neonate pilot whales were observed in the company of killer whale groups, with no other pilot whales in the vicinity. The interactions invo...

New paper about unusual encounters in Icelandic waters…

In June 2022 and 2023, neonate pilot whales were observed swimming alone among groups of killer whales off south Iceland - with no other pilot whales in sight.
🧶⬇️

onlinelibrary.wiley.com/doi/10.1002/...

Join us for ARGEvol, a conference on ancestral recombination graphs in Vila do Conde, Portugal from Nov 12-14, 2025. Complete the interest survey: https://framaforms.org/argevol-conferenceworkshop-interest-survey-1742308127. #conference

Associate Professor in evolutionary genomics of vertebrates (279638) | NTNU - Norwegian University of Science and Technology Job title: Associate Professor in evolutionary genomics of vertebrates (279638), Employer: NTNU - Norwegian University of Science and Technology, Deadline: Sunday, May 25, 2025

The Department of Natural History at the museum in Trondheim is seeking an associate professor in vertebrate evolutionary genomics using ancient DNA approaches.
Working alongside great colleagues including @museumevogen.bsky.social

Deadline May 25

www.jobbnorge.no/en/available...

Ancient stickleback genomes reveal the chronology of parallel adaptation https://www.biorxiv.org/content/10.1101/2025.04.14.648705v1

Lovely 3 days with high-school kids and their biology teacher learning about the biodiverse but fragile Burgaski lakes #wetlands in #Bulgaria. We collected #biodiversitydata, we sampled #eDNA, and we enjoyed sharing sense of wonder for nature together.

#ProBleu #OceanLiteracy #CitizenScience

Predicting kinship dynamics during pre- and post reproductive life stages https://www.biorxiv.org/content/10.1101/2025.04.11.648073v1

🦒🧬 New preprint🦒🧬
We investigated the degree of admixture, genetic diversity and inbreeding in ex situ giraffes using WGS data from the famous Marius, 12 zoo giraffes, and a data set from 71 wild giraffes.
#ConsGen #PopGen #Genomics #Giraffes #Marius
www.biorxiv.org/content/10.1...