Written in Rust.

It is now the first analysis we run on new data. We use it for QC (verifying species ids and testing for contamination). We then drop sPCR products into a phylogeny to see where our new samples fit in with previous data. Less than an hour after data delivery we already know a lot about our samples.

Because it uses PCR primers, the regions it assembles correspond to the best sampled gene regions in public archives. This provides a bridge between raw genomic data and decades of work sequencing specific PCR amplified genes from a broad diversity of organisms.

Here, for example, is a one-liner that downloads 1M reads from SRA accession SRR23143286 (the siphonophore Nanomia bijuga), runs sPCR with the cnidarian primer panel, and dumps the amplified products to the terminal. It took 41 seconds to run on my laptop, including data download.

You can work with local raw data, or give it an SRA or ENA accession number and it downloads (and caches) the data directly. And it only downloads the number of reads you ask it to analyze, so no long waits for giant files that fill your disk.

Depending on the gene, genome, and primers, reliable assembly can take as few as 1M reads. High copy genes, like mitochondrial genes and rRNA are often robust with a small number of reads. Single copy nuclear genes take more data and work best with specific (non-degenerate) primers.

You can specify primer sequences at command line, or in a yaml primer panel file. It comes pre-loaded with panels for a few clades. Users can develop and optimize their own primer panels, and submit for inclusion in sharkmer. Let is know what clades and genes you would like to have primer panels for

Available at github.com/caseywdunn/s... . Can also be installed from bioconda.

Sharkmer: repurposing PCR primers for targeted genome assembly using in silico PCR AbstractSummary. We introduce an in silico PCR (sPCR) method for the assembly of specific genomic regions spanned by PCR primers using raw sequence reads.

Ever wanted to assemble specific genes out of raw sequence reads? Try sharkmer, a tool for in silico PCR (sPCR) developed with @shchurch.bsky.social - academic.oup.com/bioinformati.... Feed it raw reads and primer sequences, it gives you amplicon sequences. Can work on a laptop in minutes.

eLetter coauthors include @gobiologycn.com @jacobmusser.bsky.social @stevehaddock.bsky.social @xingxingshen.bsky.social

Integrative phylogenomics positions sponges at the root of the animal tree Determining whether sponges or ctenophores root the animal tree has important implications for understanding early animal evolution. Here, we examined support for these competing hypotheses by constru...

We thank the authors for helping us understand and address these issues. Text of our eLetter is at the bottom of their article www.science.org/doi/10.1126/..., and the full letter is at github.com/caseywdunn/s...

More than half the genes they scored as supporting sponges-sister in their new dataset had no ctenophores, and therefore no information about the root. This helped reveal issues with quartet and likelihood calculations.

Our eLetter github.com/caseywdunn/s... responding to a recent Science paper was just posted. The paper found more genes with consistent support for sponge-sister than ctenophore-sister. We found several technical issues that, when corrected, reverse the conclusions and recover ctenophore-sister.

More at news.yale.edu/2025/10/22/h...

Serene Learning: Hands-on course on Horse Island YouTube video by Yale University

It has been wonderful to teach Invertebrate Zoology in the field - youtu.be/cPqdVsxsnSs?...

Interested in joining our lab (dunnlab.org) as a postdoc to work on siphonophores, processes that structure diversity in the open ocean, or natural history? If so, please reach out to discuss a nomination for the Donnelley Postdoctoral Fellowship - yibs.yale.edu/donnelley-fe...

I hope to take a PhD student in 2026 to study siphonophores. Please reach out if you are interested in applying this fall. For examples of recent lab projects see www.sciencedirect.com/science/arti... and academic.oup.com/gbe/article/...

As the Gulf Stream carries man o’ war colonies north, winds push them on shore 🏖️, causing strandings along the U.S. East Coast - from Florida in the winter to New England in the summer.

From surfacing to stranding: The origins and dispersal dynamics of a neustonic siphonophore The siphonophore Physalia physalis regularly strands along the US East Coast, yet the dynamics driving its seasonal and geographic distribution in this region remain poorly understood. Building on a n...

Check out our preprint 🧪 on the origin & dispersal dynamics of a sailing ⛵ #siphonophore! We use #iNaturalist and particle tracking simulations to show that juvenile man o' war surface in the Gulf of Mexico & Straits of FL and disperse rapidly along the Gulf Stream 🌊

www.biorxiv.org/content/10.1...

Our new paper on structure and growth of Porpita porpita - rdcu.be/etcY6 . Like Velella and Physalia, this is a colonial cnidarian that floats at the surface of the Ocean. The whole colony arises form a single embryo through clonal growth that gives rise to many specialized bodies.

Physalia megalista, a cnidiran with a gas filled float, raised sail, and long blue tentacles hanging below. Image credit: Dalila Destanović

Excited to share our study on sailing siphonophores, AKA bluebottles or man-o'-war! 🌊 we received hundreds of samples from scientists around the world, part of a huge effort to sequence genomes and test for multiple species 🧬 out today in @currentbiology.bsky.social doi.org/10.1016/j.cu... 🦑🧪📌

Applying to Biology PhD programs Each year I advise undergraduate students who are applying to grad school, help evaluate grad school applications, and talk with…

I wrote this essay a few years ago with general background and advice for anyone applying to start a PhD in Biology - medium.com/@caseywdunn/... . If that is you, now is the time to start the process (reading literature, reaching out to possible advisors, ...) ahead of fall deadlines.

I hope to take a PhD student in the coming application cycle. Please reach out if you are interested in joining our lab in EEB at Yale, especially if interested in working on the natural history/ phylogenetics/ morphology/ population biology/ development/ genomics of siphonophores. dunnlab.org

Postdoc job opportunity! We're looking for ECR in evolutionary genomics to study the relation between intra-specific gene expression variability, polymorphism, and macro-evolutionary rates. We have the data in 3 fishes & amphioxus, just waiting for your expertise and enthusiasm!
tinyurl.com/3aewk286

Our chromosome-scale genome assembly of Nanomia septata, a siphonophore - doi.org/10.1101/2025... . Much larger than many other cnidarian genomes, fewer chromosomes, and highly rearranged. No smoking gun for how they achieve complex colony-level organization. Great work Namrata Ahuja and friends!

Yale Department of Ecology and Evolutionary Biology is running an assistant professor search for a Global Change Ecologist - apply.interfolio.com/164677 . Please consider applying.

The xenacoelomorph gonopore is homologous to the bilaterian anus The bilaterian through gut with an anal opening is a key invention in animals, since it facilitates effective food processing, which allows animals to grow to a larger body size. However, because non-...

This paper provides now solid evidence that the xenacoelomorph male gonopore is homologous to the bilaterian hindgut.
www.biorxiv.org/content/10.1...

Three lightning bolts visible on a black background. The horizon is a bit offset since this was handheld from the deck of a boat.

Even on a dive boat, sometimes the most spectacular displays are above water. This was from when @caseywdunn.bsky.social and I were on a small liveaboard off Komodo, Indonesia.
I like the offset paths of the double-flash on the right.

Written in #rustlang 🦀

Why use PCR primer sequences to pull regions from NGS data? Because then you get the exact regions that are best sampled in public databases, and because primers are the result of decades of work to find the best binding sites that work well across species and flank regions of interest.