Alexei Drummond

Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data Abstract. Phylodynamic methods provide a coherent framework for the inference of population parameters directly from genetic data. They are an important to

Vaughan & @tanjastadler.bsky.social develop a method to infer multitype population trajectories and apply it to MERS-CoV, revealing transmission patterns between camels and humans.

🔗 doi.org/10.1093/molbev/msaf130

#evobio #molbio #virus

The BEAST X logo - an octopus wrapping its noodley appendages round the letter X.

BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be...

Details and instructions for installing on the BEAST website: beast.community

@alexeidrummond.bsky.social gave a wonderful keynote at @geneticsaus.bsky.social about how Bayesian/MCMC #models can be used on #cancer cells to determine when they originated and updates on #LPhy for all those #evolutionary #biologists out there.

Taming the BEAST Beijing!

July 14th-18th 2025

Register now :) Application deadline 25th April.

taming-the-beast.org/workshops/Ta...

Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities Author summary Our research introduces novel methods to analyse a set of phylogenetic tree topologies, such as those generated by Bayesian Markov Chain Monte Carlo algorithms. We define a new model fo...

Check out our new method for summarising BEAST trees. The CCD0-MAP tree gives much more accurate results than MCC tree. It returns the tree that maximises the product of sampled clade probabilities regardless of whether that tree was sampled. Highly recommend :)

journals.plos.org/ploscompbiol...

Looks like another nice example of convergence helping to identify (not so nice for us) adaptation.

Elon Musk takes aim at Wikipedia The billionaire has become one of the most prominent supporters of President-elect Donald Trump.

If you've never donated to Wikipedia, now's the time. Elon Musk is attacking it because it's one of the only sources of honest, curated information that he can't control.
www.newsweek.com/elon-musk-ta...

Genealogical asymmetry under the isolation with migration model and a two-taxon test for gene flow Abstract. Methods for detecting gene flow between populations often rely on asymmetry in the average length of particular genealogical branches, with the A

My and Derek Setter's work on gene flow is now published in the latest issue of Genetics. We show that it is possible to detect past gene flow between two populations by summarising the asymmetry in pop-specific external branch lengths. 1/2
tinyurl.com/5ff8ch9e

HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X https://www.biorxiv.org/content/10.1101/2024.12.08.627395v1

20%, under $15m, of Marsden funding went to social sciences while just under $60m went to hard sciences.
Total govt research funding in year to March 2023 was ~$1.1b (0.29% of GDP).
Cutting the humanities out of Marsden is just spite.

How fast are viruses spreading in the wild? Check out our latest study now published in @plosbiology.bsky.social: doi.org/10.1371/jour.... A study performed with Paul Bastide, Pauline Rocu, Denis Fargette, Olivier Hardy, @msuchard.bsky.social, @stephaneguindon.bsky.social, and Philippe Lemey (1/7)

Is this the shortest term thinking government NZ has ever had? Cut hospitals, cut ferries, cut R&D, cut universities, ... Is it all ignorance + arrogance, or do they think their rapture is coming? What is going on???

Sketch of IBD segments linking Medieval genomes from the Black Death (1350 CE) to modern Europeans. Logo of ERC-funded research.

PhD opportunity in computational population genetics at @MPI_EVA_Leipzig:
Join our fully funded project to develop IBD-segment tools, connecting high-quality genomes from 500 Black Death victims to modern Europeans. 🌍💻🧬
Please spread the word! 📢🙌 #aDNA #PopGen

www.eva.mpg.de/de/karriere/...

One of the reasons Bluesky is seeing more engagement: other platforms have adopted the behaviour of de-prioritising external links (like, say, to research papers) due to Ad models.

See this: bsky.app/profile/alt...

Here links can be freely shared without being drowned out or de-emphasized

Probabilistic Modeling in Genomics Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

Don't forget to submit your abstract for "Probabilistic Modeling in Genomics 2025". Deadline: January 10th, 2025. meetings.cshl.edu/meetings.asp...

Modeling the velocity of evolving lineages and predicting dispersal patterns
www.pnas.org/doi/10.1073/...

‘A place of joy’: why scientists are joining the rush to Bluesky Researchers say the social-media platform — an alternative to X — offers more control over the content they see and the people they engage with.: https://www.nature.com/articles/d41586-024-03784-6

There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research.

A Place of Joy.

Agree. I usually get good value out of reviewers comments, especially from top specialist journals (Systematic Biology, Molecular Biology and Evolution, PLoS Comp Bio etc).

My experience (in phylogenetics, not deep learning) is almost the opposite. When I ask colleagues I know well to look at something, most are polite and encouraging but not *all that critical or useful*. But when I get peer reviews back, they are _almost_ always critical, constructive, and useful.

In a new preprint led by @TheNikhilMilind, we explored a fascinating paradox:
For many traits the number of duplications or loss-of-function (LoF) mutations is correlated with phenotype. Curiously, for most traits, the AVERAGE direction of LoFs and Dups is the SAME. Why?

Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation - PubMed Models have always been central to inferring molecular evolution and to reconstructing phylogenetic trees. Their use typically involves the development of a mechanistic framework reflecting our unders...

This paper suggests some other directions:

pubmed.ncbi.nlm.nih.gov/38916476/

My son claims 399 and his logic seems sound.

Today is the 40th anniversary of the first #ancientDNA paper, ever! "DNA sequences from the quagga, an extinct member of the horse family" www.nature.com/articles/312.... The quagga was a subspecies of plains zebra endemic to #SouthAfrica (where I'm from)! #SciSky
@aarc-community.bsky.social

Sacred Kingfisher in NZ behaves similarly :) One of my favourite birds. I was very happy to spot a Belted Kingfisher when I was visiting Colorado earlier this year.

I would say model selection (by estimating marginal likelihood) is one of the most frustrating inference tasks in real-world Bayesian phylogenetic inference. The methods are very slow and seldom accurate. Model-averaging is one solution, when implemented. AI might indeed be another :)

Have ideas about how AI/deep-learning can augment Bayesian model-based (phylogenetic) inference in scientific software like BEAST2? I would love to hear from you.

We are embarking on some exploratory work in this direction and there is a lot to learn :)

Today I was reminded that I am living in a simulation. The postdoc running things seems to be testing what happens when mendacity is turned up to maximum.

Last chance to fill in our survey! Have your say while you can :) Thanks for all those of you that already have!

BEAST 2 user and developer experience and future development survey This survey aims to gather feedback from the BEAST2 user and developer community to inform the development of future versions of BEAST. Your insights will help us prioritise features, address pain poi...

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Fill in our BEAST2 user and developer survey :)

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