Darrin T. Schultz

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/...

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!

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/...

Lastly, the paper! open access: science.org/doi/10.1126/sciadv.adz5561 With Arno Blümel, Dalila Destanović, Fatih Sarigol and Oleg Simakov @ @univie.ac.at

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/...

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

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/...

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

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/...

I also want to write a bit more about the technical side of the paper. This is a tree-of-life-scale dataset, so I needed to write special tools to work with the complete set of animal genomes available to us during the writing and revision process! There are 4 main resources you'll want:

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/...

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!

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/...

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.

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/...

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.

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/...

If you zoom in to what is happening in single chromosomes, there is a big spectrum of how much mixing within chromosomes (inversions) has happened. Some of the fastest are covered in other papers, like clitellate annelids. In this paper we discuss cephalopods (fast) and other mollusks (slow).

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/...

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.

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/...

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

This fall I'm teaching Marine Biology to undergraduate and graduate students! Next semester is likely a genomics lab or seminar. This really is a dream job, in a department and at a university that have been remarkably generous, supportive, and professional to me and all other brand-new PIs.

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

I'm looking for students and postdocs with burning questions about fundamental biology -- people who want to generate their own data at the bench or in the field, and use our lab's computational foundation to answer them.

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). 🧬

I'm actively developing a Python 3 rewrite that will be installable via PyPI and conda. The goal is to make Dip-C even easier to use!

A little late, but there is a fun new chapter in my life! I joined Longzhi Tan's lab at Stanford Neurobiology in November, and am now working on single-cell 3D architecture, neurodegeneration, and aging. Excited to bring a comparative genomics perspective to these topics. 🧬 Tan lab: 3dgeno.me

I feel a lot of gratitude for Oleg Simakov, my labmates, and the Dept. of Neuroscience and Developmental Biology at @univie.ac.at the University of Vienna. We worked on understanding chromosome evolution across the history of animal evolution, and I grew a lot in that time.