Hey genomics colleagues: are they any software programs you wish still worked on your modern OS? I’m trying to get a list of dead software that lost support and fell out of fashion, not due to method but due to software support. #genomics #evosky #evolbio #popgen #Evolution
An old quip: "All stories you read in the newspaper are completely true except those for which you have first-hand information." This has many corollaries, e.g. "All clades are purely diverging, without introgression, except for those for which you have the pertinent data." 🧪 #evolbio
Julia Margaret Cameron (c. 1868) / Wikimedia Commons.
Today is Darwin’s Day 🧬 — a reminder that evolution isn’t just history but a living process. At the MPI for Evolutionary Biology we explore evolutionary change — how life adapts, diversifies, and evolves — using theory, experiments, and data from nature.
#DarwinsDay #Evolution #EvolBio
Screenshot of Mesquite's log window, saying: "ZoL: The Great Phylogenetic Adventure! Level 1 You are standing in an open field. In front of you, to your surprise, is an organism. You recognize that it is a Kelp (Ochrophyta). There is a small mailbox here."
Does Mesquite's phylogenetic adventure game look familiar to anyone? 🧪 #evolbio
Mesquite's two icons, one against a black background, and one against a sun on a sky blue background.
Mesquite 4.02 update released! It fixes a few bugs and adds Codon Alignment and various other improvements. Also, much faster with genomics files with 1000s of loci. www.mesquiteproject.org 🧪 #evolbio
@bembidion.bsky.social
Nodes with the largest HOG + pathway component gains were the ancestors of:
- All Eukaryotes
- Flowering plants 🌻
- Slime molds (!)
- Metazoans 🦐
- Vertebrates 🚶♂️
#EvoBio #evolbio
3/10
1/3🧵Kicking off on #bugsky today & introducing Wood Wide Ants, aka WWA! We're researchers studying the #evolbio of the #ant Formica paralugubris and its kin, through #genomics, #SciComm & #CitizenScience📚🐜🧪🧬🖥️ #insects #mirmecology @sib.swiss @biogeneurope.bsky.social @ergabiodiv.bsky.social
Biennial Meeting of the Spanish Society of Evolutionary Biology
21-23 January 2026, Valencia, @sesbe-org.bsky.social
sesbe2026.es
🧪 #ecoevo #evosky #evolbio
@uv.es @ucciuv.bsky.social @ibe-barcelona.bsky.social @ibmcp.bsky.social @dicv.csic.es @sibecol.bsky.social @raciencias.bsky.social
“We must therefore try to establish a new standpoint which … takes account of organic wholeness, but … treats it in a manner which admits of scientific investigation.”
🐋🌱🦫🦋 #HistSTM #PhilSci #evolbio #STS 🧪
Cover of General System Theory.
Ludwig von Bertalanffy—the architect of “General System Theory”—was born OTD in 1901.
Mechanism “provides us with no grasp of … organic 'wholeness,’ … of organic 'teleology,’ or of the historical character of organisms.…”
🌱🐋🦫🦋 #HistSTM #PhilSci #evolbio #STS 🧪
Manuscript title page of On the Origin of Species, in Charles Darwin’s hand.
OTD in 1854, Charles Darwin began sorting his notes in preparation for writing a treatise with the working title “Natural Selection.”
He would never publish the book, instead publishing a short “abstract”—titled “On the Origin of Species”—in 1859.
🐋🌱 #HistSTM #evolbio 🧪
The goal "is to identify each animal's perceptual cues among all the stimuli in its environment and to build up the animal's specific world with them.”
🌱🐋🦫🦋 #HistSTM #evolbio #philsci #psychsky 🧪
von Uexküll's diagram of the functional cycle that creates an animal's inner perceptual world, from his Theoretical Biology (1926), 155.
Jakob von Uexküll was born OTD in 1864.
Each animal inhabits its own individual "umwelt," comprising only those aspects of the world that are relevant to its survival and flourishing.
🌱🐋🦫🦋 #HistSTM #evolbio #philsci #psychsky 🧪
CEB seminar late post: PhD candidate Andrea Piccinini shared the first observation of post-copulatory mate guarding behaviour in a WA wishbone spider (Aname sp.)—a rare insight into mygalomorph mating behaviour.👏
#EvolBio #SpiderBehaviour #SexualSelection #UWA #Mygalomorphs
🐸 Last week at CEB, Shengyao discussed the population genomics of the Howard River toadlet (Uperoleia daviesae), a short-range endemic frog threatened by urbanisation near Darwin.
Read the paper here: doi.org/10.1007/s105...
@reneecatullo.bsky.social #EvolBio #FrogConservation #UrbanEcology #UWA
Moreno, @lionelguy.bsky.social et al. applied experimental evolution to identify genes conferring host specificity to L. pneumophila, highlighting the importance of mutations targeting the LerC protein and the LPS synthesis cluster.
🔗 doi.org/10.1093/molbev/msaf161
#evolbio #molbio #legionella
Phylogenomics processing of locus-by-locus files with inconsistent taxon names in Mesquite 4, a short video (3 minutes). youtu.be/YdSWQMkW92k (Channel: bit.ly/4eM2SLZ) 🧪 #evolbio @bembidion.bsky.social
Reading and viewing tree files output by different programs in Mesquite 4, a short video (3 minutes). youtu.be/MVk4aira8A8 (Channel: bit.ly/4eM2SLZ) 🧪 #evolbio
@bembidion.bsky.social
A two-minute video showing how to export geographic localities and trees from Mesquite 4 into Google Earth. youtu.be/tdOVmR122ts 🧪 #evolbio
Two versions of the Mesquite icon. At left is a Mesquite tree leaf against a black background. At right is leaf against a blue sky and sun.
Update! — Mesquite 4.01 released, fixing a few small and one substantive bug (for details see response post). New: NINJA (for neighbour joining), new merge taxa options, node spots, Google Earth mapping. www.mesquiteproject.org 🧪 #evolbio
@bembidion.bsky.social
A short video showing how to infer gene trees in Mesquite 4. youtu.be/xkAHBRIJ4CU 🧪 #evolbio #phylogenomics
@bembidion.bsky.social
Naiveté: Hoping people will follow your polite recommendation when defining a standard. When we defined the NEXUS file format in 1997, we considered DATA blocks to be already archaic, and recommended strongly against them. 38 years later, prominent programs still depend on them. 🤦 🧪 #evolbio
A short Quick Tip video showing how to concatenate and deconcatenate matrices in Mesquite 4. youtu.be/1etP6D3SrdE 🧪 #evolbio
@bembidion.bsky.social
A short video with a Mesquite tip showing how to display chronograms from a BEAST divergence dating analysis. youtu.be/CvxX8GauqLo 🧪 #evolbio @waynemaddison.bsky.social
The two Mesquite logos. At left, a mesquite tree leaf is against a black background. At right, a leaf is against a blue sky and sun.
Mesquite 4.0 released! A major update — many new features, small and large (phylogenomics, visualizations, workflow management, &c). Check out the trailer video: www.mesquiteproject.org.
Come discuss in our new Google Group (groups.google.com/g/mesquite-project). @bembidion.bsky.social 🧪 #evolbio
1/2 Wonderful week at @sbroscoff.bsky.social for the meeting on the origin of metazoa @cnrsbiologie.bsky.social @biologists.bsky.social
Had a poster on my new #postdoc project in the Feuda Lab about the #evolbio of #vision and #phototransduction in #ctenophores w/ #phylogenomics #singlecell
Photo of the conference programme with tide pools on thebackground
Attending this week the #originOfMetazoa conference at @sbroscoff.bsky.social @biologists.bsky.social!
So stimulating to hear wonderful works in #evolbio #bioinformatics #phylogenomics and #singlecell 🪸🪼🦠🧬
Also can't way to explore those tide pools👀
Stay tuned for updates
New paper! We report on how host reservoirs for Sin Nombre are being impacted by taxonomic changes on both the host and virus sides. Congrats to Ally and Ahmad leading this paper as undergrads at ASU School of LIfe Sciences! @arizonastateuni.bsky.social #evolbio
Yaddehige et al. present GBRAP, a parser and database for analyzing RefSeq genomes. This publicly available tool offers over 200 metrics per genome element with flexible retrieval, visualization, and export options.
🔗 doi.org/10.1093/molbev/msaf114
#evolbio #molbio #bioinformatics
