Please share! My lab is recruiting a postdoctoral scholar in evolutionary development. For more details feel free to email me.

@nahuja.bsky.social also sequenced 20 additional Nanomia from around the world. Population genomics supports three previously described species plus at least one additional undescribed species, with some species occurring in overlapping geographic regions.

Key developmental gene families, including homeobox and Wnt genes, have not undergone major expansions. And genes expressed in the same zooids are generally not clustered together in the genome

Does that unusual genome organization explain the extraordinary division of labor among zooids? We looked for some obvious possibilities and there is no smoking gun.

The Nanomia septata genome is ~1.7 Gb on just 8 chromosomes. Closely related non-siphonophore hydrozoans have 15 chromosomes, indicating extensive fusion, translocation, and genome reorganization during siphonophore evolution.

Siphonophores are colonial animals- Like a coral, they have many genetically identical bodies that grow from same embryo. But siphonophore bodies are specialized for different tasks and precisely organized. Many open questions about how this unique colony-level organization evolved and develops.

Totally- can ask it to show all evidence. Just references, or references with text that contains relevant evidence

Let us know how you use it, and please provide feedback on the github issue tracker.

There is no strict criterion for what a relevant pdf is, you could put anything you want in (eg a giant folder of mollusc development papers), but most of our optimization has been around handling the challenges that arise when analyzing systematic/ morphology/ taxonomy papers.

Processing is roughly O(n), we have used it with less than a hundred pdfs, results improve the more you have. Developed it against libraries that are ~2,000 pdfs and ~20,000 pdfs

Heavy processing (language detection, OCR, text extraction, figure segmentation, caption binding, chunking, vector embedding, etc) happens once. pdf processing is idempotent - add new pdfs to library, hit run, and only new files are processed.

All scanned pdfs are re-OCRed. It handles pdfs spanning centuries of typesetting conventions (the oldest pdfs we have used it on are for documents from the 16th century). Original language is preserved, LLM handles translation, supporting of multilingual document sets.

There are multiple optional constrained ontologies that improve performance, including a recommended bibliography file with reference data for the pdfs and DwC-A files with taxonomic data.

"I am new to the study of Hydrozoa. Write a summary about the diversity of the group, the history of its study, and major open questions about their biology. Make it accessible to someone with no expertise in Hydrozoa"

"Create a character matrix for all the most commonly scored traits of siphonophores and generate a tsv table of data I can map onto a phylogeny". It will identify which traits are scored most consistently across species, extract the relevant data from across papers, and generate the table.

"Make a single figure that shows bracts and nectophores for all species of Lensia" It will then search for mentions of Lensia in figure captions, grab relevant figure regions across multiple papers, and organize them all in one plot.

"I am collecting siphonophores in the surface waters of Saint Helena. What species can I expect to see? How can I tell them apart?" It will then search for species expected in the area, identify diagnostic traits, and streamline to those relevant at your location.