Cover photo of the World Wildlife Fund’s Migratory Fishes report.
Photo of a European Eel underwater.
NEW: Global Assessment of Migratory Freshwater Fishes @worldwildlife.org
www.worldwildlife.org/publications...
“Vital freshwater fish migrations are collapsing; hundreds of species need urgent, coordinated cross-border action”
Please share!
I wrote a short Nature Methods News & Views piece on deep learning based gene finders such as ANNEVO. www.nature.com/articles/s41...
These are just some highlights🔆, so please check out the paper and repost🔁!! 🙂
Thanks so much @dgkontopoulos.ecoevo.social.ap.brid.gy @hillermich.bsky.social @ebpgenome.bsky.social @sgn.one and many more 🙏
Additionally, genes under positive selection suggest a mechanism by which turtle cancer resistance mainly operates through a “prevent and repair” strategy. 🩹❤️🩹
Finally, we explore turtle cancer resistance under oxidative stress. (Early)turtles faced increased oxidative stress due to their fossorial and/or aquatic lifestyle 🌊. Loss of NMRAL1 🧬decoupled increased oxidative stress exposure from stress-induced error-prone DNA repair.
This gene loss is linked to a turtle-specific deletion in a rearrangement breakpoint that inverted in chicken. These findings link breakpoints to gene loss 🧬🚫associated body plan changes 🐢and highlighting gene losses as an under-appreciated driver of evolutionary innovation.
Gene losses 🧬🚫 contributed to turtle innovations!!
Amazingly, two out of 12 typically conserved genes lost in turtles cause disproportionate dwarfism with broad compact body shapes in mammals, matching the remodeled skeletal morphology that first evolved in stem-turtles🦴🐢.
So then, what is it?
We explore the role of repeats for fissions, by using the still "intact" sister lineage to disentangle what came first, repeat increases or chromosome fissions.
Our results indicate that genome wide repeat content increases promote fissions at already repeat rich fragile sites.✅
With this insight, we test the prior hypothesis that chromosome number and sex determination coevolve in turtles.
Ancestral reconstructions reveal punctuated chromosome 🧬evolution: slow fission&fusion 🐌 rates, interrupted by dramatic accelerations📈. However, sex determination does NOT drive these❌!
Next, we identify sex chromosomes in the chelidae, which have diverse sex chromosomes (micro & macro). Combining chromosome capture, m&f resequencing data, analyses of Y linked GATA repeats and ancestral genome reconstruction, we show that genetic sex determination evolved only once on a micro-chr.
Inferred declines in the last 140k years are likely mainly driven by population structure (see www.nature.com/articles/hdy... for the theory), which calls into question common interpretations attributing similar declines to climate change.
Linking demographic inference (#PSMC) to historical climate, biome reconstructions & sex determination modes, showed ancient climate change likely drove population sizes. However, consistent recent population declines are best explained by time alone... but why?
We now fill this gap & provide seven new reference genomes 🥳🐢 #VGP
However, to study these amazing turtle traits 🐢 from a genomic perspective, one thing was lacking: Reference quality genomes 🧬 for one of the two extant turtle clades: The side-necked turtles (they actually fold their neck sideways - see below).
Turtles are just amazing🐢! These "hopeful monsters" originated during one of the biggest climate crises, remodeled the vertebrate skeleton🦴, exhibit extreme longevity 🏆 with remarkable cancer resistance and repeatedly evolved genetic sex determination🧬 from temperature dependent sex determination 🌡️.
Chelodina longicollis, Eastern Long-necked Turtle. Melbourne Museum. Photographer: David Paul, Source: Museums Victoria
I hear you want novelty🦎->🐢,
chromosome evolution 🧬,
sex determination🩷,
link population history📈 & climate🌏🌡️?
Or you share my love for wonderfully weird animals?
Side-necked turtle genomes reveal chromosomal dynamics, skeletal innovation and cancer resistance
www.biorxiv.org/content/10.6...
A 🧵
Happy to share that our work with Ekaterina Osipova, @maggiemcko.bsky.social, Tim Sackton, Maude Baldwin & fantastic collaborators on convergent and lineage-specific genomic adaptations in sugar-feeding birds is published in Science www.science.org/doi/10.1126/.... While high sugar intake ...
"Medaka: A novel model for analyzing genome-environment interactions"
by Kiyoshi Naruse & colleagues
"Endemic to habitats spanning from 4 to 40°C and varying salinities, [medaka] combines broad ecological adaptability with experimental tractability."
Read more:
authors.elsevier.com/sd/article/S...
From Permits 📜 to Samples🧪🧬
Addressing Key Challenges for High-Quality Reference Genome Generation in Europe🧬🇪🇺
Now published in Mol Ecol Res!
onlinelibrary.wiley.com/doi/10.1111/...
Thanks to the @ergabiodiv.bsky.social team!!!🙂
Want to study the genomics of repeated adaptation with data from hundreds of species? New funding for non-Canadians @ grad or postdoc level. Internal competition at UCalgary with very short deadline so please get in touch ASAP!!
sshrc-crsh.canada.ca/en/funding/o...
Integrative PhD position available in my lab on the mechanisms (gene expression, metabolism, microbiome and hormones) of intestinal remodelling in lampreys. Come work in a great and fun research environment with @nealdawson.bsky.social & Adam Dobson (not here). Apply: www.gla.ac.uk/colleges/mvl...
Happy to present TOGA2, developed by Yury Malovichko @ymalovichko.bsky.social, the faster, memory-efficient & more accurate TOGA1 successor (github.com/hillerlab/TO...). And annotations, orthologs & gene loss/dup data generated with 4 references for 883 placental mammal and with 5 refs for 676 ...
Come join us in Heidelberg for the first German fish meeting 👩🔬👨🔬🧬🔬🐟🐠
Faces of different guenon species to show their morphological differences
If you like genomics, speciation, and primates, this PhD position is for you! Unraveling the genomic architecture of speciation and gene flow in guenons, a diverse group of African monkeys. Funding through DTP. Do reach out with questions! #genomics #genome_assembly
evol.mcmaster.ca/brian/evoldi...
One week to apply for our fully funded PhD position in Norway! This is a really exciting project in collab. with University of Helsinki and Benchmark Genetics.
Samples are ready - you do (read: learn) everything - functional genomics, bioinformatics, genotype-phenotype associations 🤩
Please RT!
Exciting news!
The next #PopGroup meeting will take place in Lille 🍟, France, 7–9 January 2026 – just 1 hour by train from London, Brussels, and Paris.
This year, PopGroup will also host ALPHY, the annual meeting of Evolutionary Genomics.
More info: populationgeneticsgroup.org.uk
See you there !
This is just the first effort of our foray into cichlid behaviour and genetics! If you are interested in working on the evolution, genomics, and neurobiology of sleep and chronobiology @uoftcellsysbiol.bsky.social in beautiful Toronto, please reach out! shafer-lab.netlify.app
Please share broadly: I am looking for a postdoctoral fellow to work on a collaborative project on the temporal population genomics of invasive Capeweed (using contemporary and herbarium genomics), with @shaky-dingo.bsky.social and colleagues
I will present my freshly published paper on bat diet reconstruction and phyllostomid ancestral omnivory at ESEB @eseb2025.bsky.social, on Tuesday August 19th, poster session 2 P02.375. Looking forward to it!🦇
🧬 Explore the latest from Bioinformatics Advances: “Exonize: a tool for finding and classifying exon duplications in annotated genomes”
Full article available: https://doi.org/10.1093/bioadv/vbaf177
Authors include: @chriswheat.bsky.social