Lightnews — Scholar-powered news

Reposted by Alexei Drummond

Molecular Biology and Evolution @molbioevol.bsky.social · Jun 17

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

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

doi.org

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Andrew Rambaut @arambaut.bsky.social · Jul 2

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

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Clare I. M. Adams @clare-edna.bsky.social · Jul 9

@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.

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Alexei Drummond @alexeidrummond.bsky.social · Apr 23

Taming the BEAST Beijing!

July 14th-18th 2025

Register now :) Application deadline 25th April.

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

Taming the BEAST Beijing

taming-the-beast.org

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Alexei Drummond @alexeidrummond.bsky.social · Feb 14

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...

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...

journals.plos.org

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David Pollock @genomesevolve.bsky.social · Jan 10

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

Michelle Wille @duckswabber.bsky.social · Jan 9

cattle B3.13 genotype H5N1 viruses rapidly accumulated adaptations in polymerase genes = better replication in bovine cells, + other mammalian species including humans and pigs: PB2 M631L, PA K497R and PB2 D740N
👉 www.biorxiv.org/content/10.1...

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Peter Gleick @petergleick.bsky.social · Dec 25

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...

Elon Musk takes aim at Wikipedia

The billionaire has become one of the most prominent supporters of President-elect Donald Trump.

www.newsweek.com

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Alex Mackintosh @thymelicus.bsky.social · Dec 12

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

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

tinyurl.com

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Dec 10

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

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Ben Moore @bentm.bsky.social · Dec 5

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.

Rod Emmerson @rodemmerson.bsky.social · Dec 5

www.nzherald.co.nz/nz/rod-emmer... Rod Emmerson’s cartoons: Week of December 2 - 8

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Ni-cola Ga-stan @nicgaston.bsky.social · Dec 5

My slightly more considered take on the Marsden fund changes is now here. This govt is focused on the impacts of funding — I don’t mind that — but they don’t seem to have thought for a second about the impact of the lack of it.

On people; on society; on academic freedom.

Funding research for economic return sounds good – but that’s not how science really works

The Marsden Fund was set up to support pure research. Diverting half of it to fund applied research undermines New Zealand’s potential to generate ideas that underpin commercial success.

theconversation.com

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Simon Dellicour @sdellicour.bsky.social · Dec 4

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)

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Paul Gardner @ppgardne.bsky.social · Dec 5

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???

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Harald Ringbauer @hringbauer.bsky.social · Dec 3

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/...

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Altmetric @altmetric.com · Dec 3

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

@altmetric.com on Bluesky

We’re no experts but this sounds like it might be suboptimal for disseminating research. [contains quote post or other embedded content]

bsky.app

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Diego Ortega-Del Vecchyo @delvecchyo.bsky.social · Dec 2

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

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.

meetings.cshl.edu

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Stephane Guindon @stephaneguindon.bsky.social · Dec 2

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

www.pnas.org

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Altmetric @altmetric.com · Dec 3

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.

‘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

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Alexei Drummond @alexeidrummond.bsky.social · Nov 26

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).

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Rob Lanfear @roblanfear.bsky.social · Nov 26

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.

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Jonathan Pritchard @jkpritch.bsky.social · Nov 22

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?

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Alexei Drummond @alexeidrummond.bsky.social · Nov 19

This paper suggests some other directions:

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

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...

pubmed.ncbi.nlm.nih.gov

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Alexei Drummond @alexeidrummond.bsky.social · Nov 16

My son claims 399 and his logic seems sound.

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Deon de Jager @ddj-sa.bsky.social · Nov 15

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

DNA sequences from the quagga, an extinct member of the horse family - Nature

Nature - DNA sequences from the quagga, an extinct member of the horse family

www.nature.com

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Alexei Drummond @alexeidrummond.bsky.social · Nov 16

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.

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