Theoretical biologist and advisor to data scientists at the University of Arizona. Mostly theoretical population genetics and molecular evolution, but I've also published in biochemistry, infectious disease, aging, economics, education. Opinions are my own
We derive a working hypothesis for how the genetic code evolved, by assuming LUCA-depleted amino acids came early, using codons we infer via the 2-1-3 rule. We validate with independent data and a control ordering ecoevorxiv.org/repository/v... @seekingluca.bsky.social @hanonmcshea.bsky.social 1/13
The series of genetic codes that preceded our ownecoevorxiv.orgOur paper on how better amino acid substitution matrices trained on cleaned alignments improve gene tree inference, and on best practice for cleaning MSAs more broadly, is now out academic.oup.com/mbe/advance-.... New options in both IQTree and Muscle5. @phylowheeler.bsky.social
Improved gene tree inference from removing alignment errors both from focal genes and when training substitution modelsAbstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely aligacademic.oup.comJoanna MaselSequence alignments are notoriously prone to error. Our latest preprint offers a new tool for filtering errors out, assesses it and other filtering tools, and recommends new best practice. www.biorxiv.org/content/10.6... @phylowheeler.bsky.social 1/10
Our new paper doi.org/10.1098/rspb... on long-term genetic threats to small populations finds that "mutational meltdown" (bad mutations fixing) is less of a problem than "mutational drought" (too few good new mutations) @wmawass.bsky.social @uliseshmc.bsky.social @jeremyjberg.bsky.social 1/5
Extinction vortices are driven more by a shortage of beneficial mutations than by deleterious mutation accumulationAbstract. Habitat loss contributes to extinction risk in multiple ways. Genetically, small populations can face an ‘extinction vortex’—a positive feedbackdoi.orgOur paper unpacking "fitness" is out doi.org/10.1093/gene.... How to define fitness depends on what question you ask. Selection acts on organismal vital rates, longer-term outcomes make sense for genetic lineages, models link them. "Invasion fitness" = speed, but sometimes probability matters more.
Why there are so many definitions of fitness in modelsAbstract. Evolutionary “fitness” is operationalized in many different ways in models. Its role is to quantify that which is favored by natural selection. Gdoi.orgJoanna MaselOur latest preprint doi.org/10.32942/X2V... explains why fitness can be defined in so many ways, and which version(s) you should use when. Fitness quantifies what natural selection favors. 1/
We are failing the hantavirus drill. But even this great @dwallacewells.bsky.social article doesn't discuss frequent PCR tests for those quarantining at home. High viral load would trigger strict isolation before most transmission. Testing beats quarantining in a facility. Yes, it can be done.
Opinion | Hantavirus Isn’t Just a Threat. It’s a Test.www.nytimes.comWe (with @dornhaus.bsky.social) finally wrote up our class on how to teach modeling to biologists, which ends up being a non-trivial exercise in understanding the roles that theory plays in the scientific method. We hope others will use our class, or simply enjoy the manuscript!
Anna DornhausPreprint: What good is modeling? Introducing biology students to theory - arxiv.org/abs/2604.13344 - how to teach and think about what modeling contributes to science. How does it fit into the scientific method? This is often misunderstood.