#zoonomia
LightNews LightNews
edhagen.net
14. Consistent with much of the human genome comprising inactive and neutrally evolving TEs, studies typically find that less than 15% of the human genome is constrained by purifying selection (i.e., is functional), for example 10.7% in this recent study: www.science.org/doi/full/10....
Evolutionary constraint and innovation across hundreds of placental mammals
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter di...
www.science.org
August 15, 2026 at 8:18 PM
bivouacchillin.bsky.social
They sequenced Balto's DNA. I live for this shit
Comparative genomic of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs. By Katherine L Moon, Heather J Huson, Kathleen Morrill, Ming-Shan Wang, Xue Li, Krishnamoorthy Srikanth, Zoonomia Consortium, Kerstin Lindblad-Toh, Gavin J Svenson, Liner K Karlsson, Beth Shapiro
July 21, 2026 at 12:15 PM
tekcrispy.bsky.social
La zoonomia nos une: esto es lo que compartimos los humanos con los animales

Hay muchos patrones y genes que compartimos humanos y animales por igual. Aquí te mostramos qué nos une como seres vivos.
La zoonomia nos une: esto es lo que compartimos los humanos con los animales
Hay muchos patrones y genes que compartimos humanos y animales por igual. Aquí te mostramos qué nos une como seres vivos.
tekcrispy.net
June 7, 2026 at 11:48 PM
johntweedie.bsky.social
The library also has a first edition of Darwin’s Origin of Species. But while this wasn’t on display they did have a copy of his grandfather Erasmus Darwin’s Zoonomia on display.

It was great to see John Stevens Henslow get a mention too. He was influential in Charles Darwin’s career.
A copy of Erasmus Darwin’s Zoonomia. A painting of John Stevens Henslow as well as a painting of Henslow’s Bunting which was named after Henslow by Audubon.
June 1, 2026 at 3:56 PM
ajpoots-phd.bsky.social
#nearthisday 14 May 1794
Coloured shadows? www.jstor.org/stable/106893

Erasmus Darwin published Zoonomia, a medical work that touches upon proto-evolutionary concepts, his grandson Charles will draw on this.

John Dalton published paper on colour blindness

Glasgow Royal Infirmary first opens
An Account of Some Experiments upon Coloured Shadows. By Lieutenant-General Sir Benjamin Thompson, Count of Rumford, F. R. S. In a Letter to Sir Joseph Banks, Bart. P. R. S. on JSTOR
Benjamin Thompson, An Account of Some Experiments upon Coloured Shadows. By Lieutenant-General Sir Benjamin Thompson, Count of Rumford, F. R. S. In a Letter to Sir Joseph Banks, Bart. P. R. S., Philos...
www.jstor.org
May 14, 2026 at 9:27 PM
langurlover.bsky.social
2023: Findings from the Zoonomia Project are published, in which the genomes of 240 mammals are collected and compared; they reveal that 10.7% of the human genome is identical across almost all species
April 27, 2026 at 2:37 PM
jshendure.bsky.social
Latest from Shendure & Qiu labs (@cxqiu.bsky.social)
)! We combined a new 4M cell mouse whole embryo scATAC-seq atlas (E10-P0), millions of 'evolutionarily coherent' orthologs from 241 mammalian genomes (Zoonomia), and the CREsted CNN framework (@steinaerts.bsky.social).
April 10, 2026 at 12:40 AM
cxqiu.bsky.social
Huge team effort led by CX Qiu, Riza Daza, and Ian Welsh. Jay Shendure supervised the project. Key contributions from Rupali Patwardhan, @niklaskemp.bsky.social & @steinaerts.bsky.social (CREsted), built on our mouse timelapse with @coletrapnell.bsky.social. Grateful to the whole team and Zoonomia.
April 9, 2026 at 9:02 PM
cxqiu.bsky.social
We applied STEAM to all 241 Zoonomia genomes: 32 × 241 = 7,712 genome-wide enhancer tracks. HumMus for human + mouse. BabaGanoush for the full spread!
April 9, 2026 at 9:02 PM
cxqiu.bsky.social
Enter STEAM: we augment training with syntenic enhancer orthologs from up to 241 Zoonomia genomes — a ~200× expansion in sequence diversity, preserving cell-class labels. Orthologous enhancers are nature's data augmentation: divergent sequences, shared function.
April 9, 2026 at 9:02 PM
acstone.bsky.social
Honey badger is one of the species sequenced as part of the Zoonomia project, in an effort to better understand evolutionary constraint, and novel evolutionary genetics. www.science.org/doi/10.1126/... #2026MMM
Comparing genomes from 240 species to explore the evolution of placental mammals. The new phylogeny (black lines) has alternating gray and white shading, which distinguishes mammalian orders (labeled around the perimeter). Rings around the phylogeny annotate species phenotypes. Seven species with diverse traits are illustrated, with black lines marking their branch in the phylogeny. Sequence conservation across species is described at the top left. IMAGE CREDIT: K. MORRILL
March 27, 2026 at 12:07 AM
johnthejack.bsky.social
We owe a great deal to this lesser known Darwin
www.thetimes.com/comment/regi...
Text: Despite a famous family name, one of Britain’s greatest scientists remains largely unknown, but he described how clouds form and invented a new type of anemometer, a steam-powered vehicle and much more. Erasmus Darwin, grandfather of Charles Darwin, wrote many books, including Zoonomia, published between 1794 and 1796, which catalogued all animal life known at the time, including humans, as well as their diseases and treatments. The book also gave a detailed description of the evolution of life, including the idea that humans were descended from lower forms of life. That theory got him into trouble with the church, as happened with his grandson, and Erasmus’s reputation went into decline. Today, the theory of evolution is best remembered as Charles Darwin’s landmark achievement. Erasmus was also fascinated by meteorology. He realised that when air was lifted up, say, by passing over a mountain, its pressure decreased, expanded, and the air cooled. Thus its moisture condensed and turned into clouds and eventually rain. Text: Erasmus measured the weather and had a weather vane installed in his house, with a spindle that came through the ceiling of his study, where it operated a pointer, so that he could observe any sudden changes in wind direction from the comfort of his armchair. From these observations, he described sequences of weather, with temperature change and wind direction, which we now know as cold and warm weather fronts. He suggested that the Earth’s atmosphere was divided into three layers: the lowest layer was where clouds and lightning occurred, the middle layer was almost cloudless with a very thin atmosphere, and the top layer was where fireballs (meteors) and auroras happened. In fact, when he observed a great fireball on August 18, 1783, he calculated that its altitude was 58 miles. Erasmus also had an interest in weather lore, and wrote a rhyme on the imminent signs of rain, such as the appearance of the clouds, barometer measurements and animal behaviour. The rhyme began: “The hollow wind begins to blow/ The clouds look black, the glass is low/ The soot falls down, the spaniels sleep/ And spiders from their cobwebs creep.”
February 19, 2026 at 11:45 AM
jumibana.bsky.social
CONVERSIÓN ECOLÓGICA (2) Sobre el darwinismo

Tmp. máx. lect.: 13 min. La introducción del concepto de "evolución" Erasmus Darwin (1731-1802) El abuelo de Darwin. Médico, naturalista, teósofo, filósofo y excéntrico. Escribe una botánica en verso. Llega a concebir un evolucionismo generalizado en su…
CONVERSIÓN ECOLÓGICA (2) Sobre el darwinismo
Tmp. máx. lect.: 13 min. La introducción del concepto de "evolución" Erasmus Darwin (1731-1802) El abuelo de Darwin. Médico, naturalista, teósofo, filósofo y excéntrico. Escribe una botánica en verso. Llega a concebir un evolucionismo generalizado en su Zoonomía (1794-94)  (Templado, 29). "Una sola y misma especie de filamentos vivientes es y ha sido la causa de toda la vida orgánica"((SEQUEIROS, L.
batalloso.com
January 22, 2026 at 10:05 AM
sinamajidian.bsky.social
Third day of Genome Informatics #GI2025 began with an exciting session on “AI, ML and Integrative Genomics” chaired by Irene Kaplow & Thomas Pierrot.
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
OCR Ortholog Open Chromatin Status Prediction Framework Overview. a We trained a convolutional neural network (CNN) for predicting brain open chromatin using sequences underlying brain open chromatin region (OCR) orthologs in a small number of species and used the CNN to predict brain OCR ortholog open chromatin status across the species in the Zoonomia Consortium. Specifically, we used the sequences underlying the orthologs for which we have brain open chromatin data to train a CNN for predicting open chromatin. Then, we used the CNN to predict the probability of brain open chromatin for all brain OCR orthologs; predictions are illustrated on the right. Animals for which we do not have open chromatin data are in dark gray instead of black to indicate that their brain open chromatin is imputed. While we cannot evaluate the accuracy of most of our predictions, obtaining open chromatin data from most tissues in most species is infeasible, so predictions might be the best OCR annotations that we can obtain. b To demonstrate that our models can accurately predict whether sequence differences between species are associated with open chromatin differences, in addition to the evaluations described in previous work [57], we evaluated our performance on species-specific open chromatin for a species not used in model training and clade-specific open and closed chromatin for clades not used in model training. Since such regions often comprise a minority of OCR orthologs, models could obtain good overall performance while obtaining poor performance on such regions. We also evaluated our performance on tissue-specific open and closed chromatin for a tissue not used in model training, where we expect models to predict 0 if model learns sequence signatures related to the tissue used in training. c Full mouse test set and lineage-specific OCR accuracy evaluations for mouse sequence-only brain model, illustrating that, even for the best of these models,
November 7, 2025 at 2:28 PM
jimdewilde.bsky.social
GLOBAL VC CAN PALEOGENOMICS STIMULATE INNOVATION? COLOSSAL BIOSCIENCES and SPINOFFS tinyurl.com/yvszkfkm breaking.com broadinstitute.org/bios/elinor-karlsson tinyurl.com/58wkfva3 elinork.bsky.social thexavierlab.bsky.social
Elinor Karlsson (@elinork.bsky.social)
Scientist & artist. Prof at UMass Chan Med School & Broad Institute. Rice U alum. Founder of Zoonomia & DarwinsArk.org. Wants your dog’s DNA. And your cat’s! 🇸🇪🇳🇿🇺🇸
elinork.bsky.social
September 23, 2025 at 4:09 PM
joshweinstock.bsky.social
In our annotation curation, we included lots of scATAC, cCREs from ENCODE, conservation from Zoonomia, pathogenicity from AlphaMissense, among others. Generally - PRSFNN "learns" that low-frequency SNPs in accessible chromatin are likely to have larger effect sizes (maybe not that surprising).
July 22, 2025 at 9:25 PM
edhagen.net
"heavily conditioning on the outcome of survival" and reproduction, aka natural selection 🙂

Protein coding sequences are highly conserved across species (and many non-coding sequences are too), e.g. www.science.org/doi/10.1126/...
Evolutionary constraint and innovation across hundreds of placental mammals
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter di...
www.science.org
June 29, 2025 at 4:11 PM
lapinpresse.bsky.social
www.radiofrance.fr/francecultur...
Zoonomia : faire sauter la banque génomique !
Le projet Zoonomia a séquencé plus de 200 espèces de mammifères. En quoi l’étude de l’ADN des mammifères peut-elle nous renseigner sur le fonctionnement de notre génome ? Quelles en sont les applicati...
www.radiofrance.fr
June 17, 2025 at 4:36 AM
ebpgenome.bsky.social
(1/3) 🌍 EBP’s Zoonomia Project (zoonomiaproject.org) is transforming how we understand both biodiversity and human health!
#Zoonomia #Science Article 2023:
www.science.org/doi/10.1126/...
www.sciencenews.org/article/find...

#ComparativeGenomics #ZoonomiaProject #Evolution #Conservation
June 12, 2025 at 5:58 PM
keun-hong.bsky.social
Huge thanks to the teams whose work inspired Gencube:
🔹 GenArk team (e.g., @genomebrowser.bsky.social )
🔹 Ensembl Beta ( @ensembl.bsky.social )
🔹 Zoonomia Consortium ( @elinork.bsky.social & @KltLab)
Your contributions to scalable infrastructure and comparative genomics were truly foundational. 🙏
April 30, 2025 at 5:12 PM
keun-hong.bsky.social
To address these challenges, we developed Gencube, a command-line tool that allows easy retrieval and integration of genome and omics data from major databases like UCSC GenArk, Ensembl Beta, Zoonomia TOGA, and more.
April 30, 2025 at 5:12 PM
drbatmo.bsky.social
If anyone is interested, I've updated our take on a cellular basis of the mammalian nocturnal-diurnal switch @biorxivpreprint.bsky.social

We've refined the paper (for the better, hopefully!) - my fave updates are the results from a collab with Zoonomia (Fig 3)

www.biorxiv.org/content/10.1...
A cellular basis for the mammalian nocturnal-diurnal switch
Early mammals were nocturnal until the Cretaceous-Paleogene extinction enabled diurnal niche expansion. Diurnality evolved multiple times independently, but the mechanisms driving this shift remain un...
www.biorxiv.org
April 24, 2025 at 10:29 AM
palaeoblog.bsky.social
Died This Day: Erasmus Darwin (Dec 12, 1731 – April 18, 1802). Grandfather of Charles Darwin, he was a philosopher/naturalist who formulated one of the first theories of evolution in his ‘Zoonomia’ (1794-1796). In it he discussed how life evolved from a single common ancestor
April 18, 2025 at 1:54 PM
kaessmannlab.bsky.social
Leveraging the conserved enhancer code and the large number of available mammalian genomes (Zoonomia consortium, doi.org/10.1038/s41586-020-2876-6), we inferred CRE accessibility across 240 mammals and reconstructed the evolutionary histories of human CREs.
March 16, 2025 at 10:31 AM
metalcat.bsky.social
www.science.org/doi/10.1126/...
Evolutionary constraint and innovation across hundreds of placental mammals
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter di...
www.science.org
December 30, 2024 at 7:32 PM