iiinova — where your digital self keeps evolving

Darrin T. Schultz @dts.bsky.social · 19/08/2026

I would like to note that 39% of the genomes were from labs or institutions that submitted 20 or fewer! Individual contributions are still critical, even in the age with large sequencing consortia. Contact me if you'd like me to connect you to resources to start your own genome assembly project!

The full list of genomes used in this study, as well as the percent
of genomes contributed by submitter, is in table S1. We recognize
the substantial investments made by genome sequencing consortia
and individual laboratories in producing the chromosome- scale ge-
nomes analyzed in this study. Below, we briefly note the contributors
of 0.75% or more of the total genomes to our dataset based on NCBI
“Assembly Submitter”: The Wellcome Sanger Institute (previously
known as “The Sanger Centre” and “Wellcome Trust Sanger Insti-
tute”; 2655 genomes or 45.62% of genomes in the dataset), Geno-
scope CEA (117, 2.0%), the Vertebrate Genomes Project (108, 1.86%),
Northwest A&F University (83 genomes, 1.43%), the DNA Zoo (52
genomes, 0.89%), and the US Department of Agriculture (45, 0.77%).
Additional institutions contributing more than 20 genomes include
Zhejiang University; China Agricultural University; Centro Nacio-
nal de Análisis Genómico; Institute of Oceanology, Chinese Acade-
my of Sciences; Institut de Biologia Evolutiva Consell Superior
d’Investigacions Científiques- Universitat Pompeu Fabra (CSIC- UPF);
University of Cambridge; Nanjing Agricultural University; European
Molecular Biology Laboratory’s European Bioinformatics Insti-
tute (EMBL- EBI), Wellcome Trust Genome Campus, Cambridge;
Chinese Academy of Agricultural Sciences; The Max Planck Institute
of Molecular Cell Biology and Genetics; Bat1K Project; Southwest
University; GenoFish; Ocean University of China; Princeton Uni-
versity; Rothamsted Research; and Huazhong Agricultural University.
The remaining 39.23% of genomes in the dataset were submitted to
NCBI by contributors with 20 or fewer chromosome- scale genome
uploads after filtering.

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

4. The smaller pieces, each standalone. odp draws chromosome-scale dot plots between any two species. chromsim simulates fusion-with-mixing. breakpointer2 infers inversion breakpoints from whole-genome alignments. Check the supplement for links to the software! github.com/conchoecia/odp

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

3.5 The second clickable is the And the orthology graph database, written by Fatih Sarıgöl at the University of Vienna, queryable in your browser: metazoa.csb.univie.ac.at/neo4j

Graph representation of orthology and genome context across species. This figure
depicts the graph database encoding the relationships between the 4,454 species with
chromosome-scale genomes in our dataset. (A) Data model used in the Neo4j database. Nodes
represent biological entities: chromosome (CHR), gene (GENE), orthogroup (OG), and ancestral
linkage group (ALG). Solid “location” edges (relationships) connect a feature (node) to the
chromosome on which it resides within a genome. “Orthology” edges connect genes to
orthogroups (OGs). Example node properties stored in the database (e.g., taxid, assembly,
species, lineage, genomic coordinates) are indicated in dashed boxes. ( B ) This subgraph shows
the genomic relationship between the ALG A1a and the genomes of the jellyfish Rhopilema
esculentum (red) and the scallop Pecten maximus (blue). For each species, there are genes
connected to (orthologous to) the BCnS ALG A1a OGs. These displayed genes are connected to
the chromosome on which they exist for both species. The Pecten and Rhopilema chromosomes
have been highly conserved since the myriazoan ancestor, and retain single chromosomes for the BCnS A1a ALG. Node size encodes entity type, as in panel A, and as shown in the legend: large
nodes are chromosomes (CHR), medium gray nodes are orthogroups (OG), small nodes are
genes (GENE). ( C ) Pecten maximus and the Hawaiian bobtail squid Euprymna scolopes : There
are multiple chromosomes in the squid genome that contain genes from ALG A1a, reflecting the
complex rearrangements of BCnS ALGs in the evolutionary history of cephalopods since the
common ancestor of all mollusks. ( Together
these networks show how the graph captures both orthology and genomic context, enabling
qualitative assessment of one-to-one versus split linkage relationships across species.

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

3. Two things you can click around to explore the genome data: I built an interactive version of the genome map. Hover any of the dots, search by taxon, lasso a region, export the table. This is useful for seeing how similar one genome is to others! atlas.evogeno.me

This shows a genome 2-dimensional scatter plot. A UMAP embedding of genome similarity across species. There is a web interface to search for species.

it is available at https://atlas.evogeno.me/

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

2. egt, the analysis software Every method in the paper is a subcommand: ALG fusion and dispersal inference, the topology embeddings, clade-specific locus pairs, the rate-through-time analyses, GO enrichment. Point it at your own clade! check the repo for more info. github.com/conchoecia/egt

diagram showing a phylogenetic tree on the left, with chromosomes remaining unfused in species 1 and species 2, but fused in species 3 and species 4. The next panel shows clusters of closely associated genes in the clade of species one plus species two, and a different cluster in the fused-and-mixed chromosome in the other clade of species 3 and species 4. This information is included in a distance embedding used to show distance-conserved loci in a genome. This information can also be used to embed whole genomes and describe them by similarity.

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

One example. A translation initiation gene and a V-ATPase subunit sit head to head, under 5 kb apart, in 90.4% of the 2,113 vertebrate species we checked. In humans, a single transcription factor (TF) binds between them. Outside vertebrates they are on the same chromosome but don't share that TF!

A plot comparing the genomic distance between one pair of genes across two large animal groups. In deuterostome genomes the pair sits at a consistently narrow separation, appearing as a tight spike. In spiralian genomes the same pair varies widely, from closely linked to many megabases apart.

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

Genes thrown together by a fusion-with-mixing or regular inversion can then stay together for hundreds of millions of years. We call this entanglement (sorry, physicists): a new neighborhood becomes hard to separate, plausibly because the new neighbors begin sharing regulation (but often neutral).

A diagram of a thoroughly mixed chromosome with red and blue genes interleaved. Curved arrows connect regulatory elements to genes from the other original chromosome, forming a web of cross-connections that would be broken if the mixing were reversed.

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

Do heavily rearranged genomes eventually converge on some shared scrambled state? No. We embedded every genome by its internal architecture. Flies, nematodes, leeches, comb jellies and octopus are all thoroughly reshuffled, and each ends up somewhere different.

Twelve small copies of the same genome scatter plot, each highlighting one animal group in color against all other genomes in gray. Deuterostomes, protostomes, arthropods, molluscs, cnidarians, sponges and others each occupy their own separate region of the plot rather than overlapping.

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

One of my favorite tidbits from the paper is that species with a lot of chromosomes tend to have very few chromosomal fusions or ALG losses (see lamprey - right). How high chromosome numbers and whether fusions are selected against is a fantastic (albeit very expensive) next question!

Same alt text as the previous image, except highlighting that lamprey has many chromosomes and is shifted to the right.

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

Lineages tend to leave the ancestral karyotype in two opposite directions. Consolidation: fuse inward. True oysters have fused their way down to 10 chromosomes, and all 29 ancestral units are still intact inside them. Dissociation: break or duplicate outward. Octopus, leeches, vertebrates.

$A two-panel heatmap plotting animal genomes by their chromosome count. The upper blue panel shows the fraction of ancestral chromosome pairs that are fused; the lower red panel shows ancestral homology lost through gene dispersal. Labeled groups including nematodes, beetles, spiralians, moths, flies, teleost fish and birds occupy distinct regions.$

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

Chromosome evolution is also not a steady clock! While this topic deserves its own unique study and requires further calibration, we found differing bursts, rates, and dips of chromosome fusion and fissions (splits) across different clades in the animal tree.

Alt text: A chart of chromosome fusion rate through geologic time, running from about 700 million years ago to the present. The rate is high in the Ediacaran, peaking near 0.25 fusions per million years, then drops sharply through the Paleozoic and stays low for the rest of the record. This is likely due to branch sampling bias, however.

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

There are exactly 406 ways to pick two of those 29 ancestral units and fuse them (29 choose 2). Every single one has happened somewhere in the animal tree! At the whole-chromosome scale, evolution has sampled the entire menu.

A dense band of 406 horizontal tracks, one for each possible pair of ancestral chromosome units, plotted across the animal phylogeny. Colored marks show where each pair is found together on the same chromosome. Every track carries marks somewhere in the tree. There is an animal tree with thousands of genomes showing where ancestral linkages have fused or mixed.

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

DNA doesn't "sit still" though. Rarely, two chromosomes fuse. Internal inverted pieces gradually shuffle the two halves into each other, like shuffling two decks of cards. We call it fusion-with-mixing, and once you shuffle, you can't un-shuffle. Sometimes they don't shuffle after fusing.

A diagram of two chromosomes, one red and one blue, fusing end to end and then, over successive time steps going down the page, becoming progressively interleaved by inversions until red and blue segments are thoroughly intermixed. A wedge alongside marks increasing entropy through time.

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

(Almost) Every animal alive today descends from an ancestor whose genome was built from around 29 ancestral units of linked genes. More than 600 million years later, those 29 are still detectable across all animals, and we can use them to reconstruct the history of chromosomes over time.

Two dot plots side by side, each comparing one animal's chromosomes against the 29 ancestral animal linkage groups. In both, that animal's chromosomes run along the bottom and the 29 ancestral units, labeled A1a, A1b, A2, B1 and so on, run up the side. Each colored dot is a gene, and a tight single-colored square means one whole chromosome corresponds to one ancestral unit.

Left: the lancelet Branchiostoma floridae, a small elongated fish-like animal, shown in silhouette. Its chromosomes form a clean staircase of tight colored squares up the diagonal, with almost nothing scattered off it.

Right: the jellyfish Rhopilema esculentum, also in silhouette. Its chromosomes form the same clean staircase, in the same order, with the same one-to-one correspondence.

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

Our new paper in Science Advances asks how animals' genomes have changed since their origin from a common ancestor over 600 million years ago, and what patterns in their DNA have arisen in the churn of speciation and extinction. www.science.org/doi/10.1126/...

Five-panel diagram explaining fusion-with-mixing in chromosome evolution. Red and blue represent two different ancestral chromosomes throughout.

A, Fusion-with-mixing: a red chromosome and a blue chromosome fuse into one half-red, half-blue bar. Down the page, successive rows show inversions, drawn as X-shaped crossings between rows, progressively interleaving the two colors until the bottom bar is finely striped. A widening gray wedge labeled Entropy runs alongside an arrow marked Time plus evolution, pointing down.

B, Independent regulation: two separate chromosomes, one red and one blue. In each, a regulatory element, drawn as an oval, acts by an arrow on a gene within its own chromosome only.

C, FWM and novel regulation: on a fused, mixed chromosome, a red gene and a blue gene now sit next to each other across an inversion breakpoint. Red and blue arrows show regulatory elements reaching across it to act on the other chromosome's gene.

D, Regulatory entanglement: an extensively mixed chromosome, finely striped. Below it, a row of alternating red and blue genes is linked by a dense web of crossing curved arrows, so many overlapping regulatory connections that unmixing the chromosome would break them.

E, Emergence of entangled loci: a five-species phylogeny. A red and a blue chromosome fuse at an ancestral node, and helical icons on later branches mark continued mixing. Colored boxes mark four new red-blue regulatory interactions arising after inversions. Species A keeps its two chromosomes separate. In species B through E, the two earliest interactions, cyan boxes 1 and 2, are present in every descendant lineage, while later ones, yellow 3 and magenta 4, appear in fewer.

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Darrin T. Schultz @dts.bsky.social · 19/08/2026

I'm thrilled to share that I've started as an Assistant Professor in Biological Sciences and the Oceans Research Center at Lehigh University! I'm building a group in evolutionary genomics to study the origin of animals, and to use those concepts to better understand human disease. More: evogeno.me

Darrin Schultz, a man with curly dark hair and tortoiseshell glasses, smiling at the camera in a brown blazer over a blue patterned shirt with sunglasses hooked on the collar, standing in front of a stone wall.

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Darrin T. Schultz @dts.bsky.social · 06/03/2026

One thing I'm doing since joining the Tan Lab @ Stanford is working on the computational stack of 3D genome research. I put Dip-C v1.0 out as a release! This is an archive of the original Python 2 code from the single-cell 3D genomes in Science, Nat Struct Mol Biol, and Cell (2018–2023). 🧬

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Darrin T. Schultz @dts.bsky.social · 05/03/2026

When you zoom out from individual genes to consider the context of whole chromosomes across animal diversity, animal evolution takes on a different look. Oleg Simakov and I published a review in @annualreviews.bsky.social on topological approaches in comparative genomics. 🧬 doi.org/10.1146/annu...

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Darrin T. Schultz @dts.bsky.social · 07/12/2023

Our paper on the octopus genome made the cover of G3! 🐙 Congrats to my mentee Dalila Destanović, Eve Seuntjens, and the CNAG team in Barcelona! Photo courtesy of David Stohlmann - a graduate student at the University of Vienna. academic.oup.com/g3journal/ar...

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