Sign in

Professor Mary J O'Connell

@evol-molly.bsky.social
407 followers 372 following 18 posts

Evolutionary Biologist, Mammals, Phylogenies, Comparative Genomics, Art and Running

PostsRepliesMedia
Reposted by Professor Mary J O'Connell
Jonathan Fenn @jfennbio.bsky.social · 06/08/2026
I was honoured to make a small contribution to this paper published today in Cell, detailing the first T2T genome assembly of the zebra finch, a crucial model species for neurobiology: tinyurl.com/tguttata
tinyurl.com
The complete genome of a songbird
Bird genomes are the smallest among amniotes; however, they remain challenging to assemble due to their structural complexity. This study presents a f…
12617
Reposted by Professor Mary J O'Connell
Vertebrate Genomes Project @vertebrategenomes.bsky.social · 06/08/2026
We are excited to officially share the first fully phased telomere-to-telomere (T2T) reference genome for a songbird! 🐦 www.cell.com/cell/fulltex...
manuscript alert

The Complete Genome of a Songbirda major milestone in bird genomics

This new genome closes nearly all previous gaps, including complex heterochromatic regions, microchromosomes, and sex chromosomes. Built using a combination of PacBio HiFi long reads, ONT ultra-long reads, Arima Genomics Hi-C reads for chromosome scaffolding, and Illumina parental short reads for haplotype phasing, this T2T assembly provides an unprecented view of the zebra finch genome and advances research of vocal learning and evolution.featured in a special issue in Cell

Images:
- Article title and authors
- QR code for manuscript
- Cell T2T issue cover
14116
Reposted by Professor Mary J O'Connell
anais @anaislughe.bsky.social · 27/07/2026
this is how I look when I zone out
static.klipy.com
Smiling Puffer Fish in the Ocean
Alt: Smiling Puffer Fish in the Ocean
1663892
Reposted by Professor Mary J O'Connell
Joanna Masel @joannamasel.bsky.social · 27/07/2026
Our 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
academic.oup.com
Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models
Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig
07839
Reposted by Professor Mary J O'Connell
Journal of Experimental Biology @jexpbiol.bsky.social · 27/07/2026
Sperm whales rest in an unusual position, sleeping vertically underwater. In their recent paper, Freymond & co show that the whales blow bubbles in their sleep to keep themselves from shooting to the surface, letting them sleep soundly beneath the waves doi.org/10.1242/jeb....
Two resting sperm whales blowing bubbles. Photo credit: Stéphane Granzotto www.stephanegranzotto.com
1185
Reposted by Professor Mary J O'Connell
Rob Waterhouse @rmwaterhouse.bsky.social · 27/07/2026
Hot off the press @official-smbe.bsky.social MBE - a phylum-wide assessment to systematically evaluate, refine, and revise current understanding of the evolutionary dynamics of the #arthropod moulting genetic toolkit! academic.oup.com/mbe/advance-...
academic.oup.com
Evolutionary dynamics of the arthropod moulting machinery
Abstract. Exoskeletons define arthropods, providing support for segmented bodies and appendages while protecting against environmental stress and predation
13616
Reposted by Professor Mary J O'Connell
Steven Salzberg @stevensalzberg.bsky.social · 07/07/2026
Our new genome annotation method relies almost entirely on transcriptome and alignment evidence, and as a result outperforms pretty much all other de novo pipelines. Check out the just-published paper led by Aleksey Zimin: rdcu.be/frSOg
rdcu.be
Efficient evidence-based genome annotation with EviAnn
Nature Methods - EviAnn surpasses existing genome annotation methods by leveraging gene expression and protein sequence homology evidence to achieve higher accuracy and efficiency.
04420
Reposted by Professor Mary J O'Connell
Marcela Uliano-Silva @marcelauliano.bsky.social · 01/07/2026
Evolution of genomes drives me. So does social justice. Had a blast speaking on LINE1s creating novelty in sloths genomes and Justice, Equity, Diversity and Inclusion Challenges to sequence all life on Earth with and for the benefit of all at #SMBE2026 Paper at: link.springer.com/article/10.1...
0306
Reposted by Professor Mary J O'Connell
Tahir Ali @tahirali-biomics.bsky.social · 02/07/2026
#SMBE2026 — A wake‑up call Moisés Expósito‑Alonso showed the hard truth: genetic diversity is collapsing, and global policy is still treating it as optional. Species have already lost >10% of their genetic variation — the very engine of adaptation and survival.
098
Reposted by Professor Mary J O'Connell
Jonathan Fenn @jfennbio.bsky.social · 26/06/2026
Here's the full schedule for the @evol-molly.bsky.social lab group at SMBE next week:
O’Connell Group at SMBE 2026

Jonathan Fenn – Wednesday 1st July 14:35-14:50
S22 Evolution of gene regulation: insights from novel molecular and statistical approaches
Coevolution of microRNAs and their gene targets leads to novel traits – insights from across the vertebrate tree of life.

Christopher Taylor – Wednesday 1st July 14:35-14:40
Open 8: Molecular and genome evolution 3
Convergent molecular evolution of thermal tolerance in mammals.

Alan Beavan – Poster Group A (Monday 29th June 18:00-20:00)
Board Number 313	Paper Number 1142	2nd floor: Arkaden 6
Constructive neutral evolution explains the emergence of specialised ribosomes in diverse eukaryotes.
011
Professor Mary J O'Connell @evol-molly.bsky.social · 25/06/2026
We hope you enjoy the latest paper from Dr Alan Beavan and the @ribocode.bsky.social team, with many thanks to the @ukri.org for BBSRC sLoLa funding: www.biorxiv.org/content/10.6...
biorxiv.org
Constructive neutral evolution explains the emergence of specialised ribosomes in diverse eukaryotes.
Throughout eukaryotic evolution, the structure of the ribosome has been highly conserved, featuring 80 common protein gene families. However, in many eukaryotes, paralogs of these proteins are present...
083
Reposted by Professor Mary J O'Connell
Monica Morrill @mmorrillart.bsky.social · 15/04/2026
This is a small painting I made several years ago after visiting Algonquin Provincial Park in Ontario Algonquin Sunset 12x12 acrylic on canvas
562711219
Professor Mary J O'Connell @evol-molly.bsky.social · 24/03/2026
At the university of Melbourne with my @leverhulme.ac.uk personal fellowship award. I will be giving a research seminar here on Thursday at noon if you are about and/or want to hear more!:)
070
Reposted by Professor Mary J O'Connell
MU-Peter Shimon 🀄 @mu-peter.bsky.social · 23/03/2026
Female birds more likely to sing when extended family help Territoriality modulates the coevolution of cooperative breeding and female song in songbirds🧪 www.nature.com/articles/s41... Cooperative breeding shapes the evolution of vocal communication differently based on territorial context and sex
Phylogeny showing the classifications of cooperative breeding (outer circle) and female song (inner circle) for 1,041 Oscine species.
22710
Professor Mary J O'Connell @evol-molly.bsky.social · 19/03/2026
We are recruiting ! ... the second PhD position available with us at University of Manchester: www.findaphd.com/phds/project...
findaphd.com
MicroRNA evolution and the genetic basis of placental phenotypic diversity across mammals at The University of Manchester on FindAPhD.com
PhD Project - MicroRNA evolution and the genetic basis of placental phenotypic diversity across mammals at The University of Manchester, listed on FindAPhD.com
065
Professor Mary J O'Connell @evol-molly.bsky.social · 19/03/2026
Come join us for a PhD at the University of Manchester :
findaphd.com
Defining the landscape of stop codon readthrough across vertebrate genomes at The University of Manchester on FindAPhD.com
PhD Project - Defining the landscape of stop codon readthrough across vertebrate genomes at The University of Manchester, listed on FindAPhD.com
065
Reposted by Professor Mary J O'Connell
Fiona J Whelan @whelanfj.bsky.social · 14/03/2026
Application deadline this Monday!
073
Reposted by Professor Mary J O'Connell
Jeni Sage Sidwell @jsidwell.bsky.social · 05/03/2026
Offering a few free commissions to improve my sci comm skills & portfolio. I can do hand-painted illustrations for figures, design infographics, and even sound design and music for research promotion or podcasts. jenisidwell.com #sciencecommunication #marinemammals #lifesciences #datavisualization
052
Professor Mary J O'Connell @evol-molly.bsky.social · 27/02/2026
If you are looking for activities to do for the #BritishScienceWeek, take a look at our “How are proteins made?” from RiboCode sLoLa project. Designed for schools in the UK and Ireland, ages 7-11 (~KS2/Second to Fifth Class/P4-7). Download the free resources and enjoy:) ribocode.org/resources/
041
Reposted by Professor Mary J O'Connell
Molecular Biology and Evolution @molbioevol.bsky.social · 17/02/2026
Emerling, @freddelsuc.bsky.social et al. investigated candidate genes related to dentition, gustation, and mastication in nine convergent myrmecophagous mammalian lineages, finding that convergent evolution of myrmecophagy was a protracted process. 🔗 doi.org/10.1093/molbev/msag009 #evobio #molbio
doi.org
Pseudogenes document protracted parallel regression of oral anatomy in myrmecophagous mammals
Abstract. Adaptation to ant and/or termite consumption (myrmecophagy) in mammals constitutes a textbook example of convergent evolution, being independentl
01612
Professor Mary J O'Connell @evol-molly.bsky.social · 11/02/2026
Reflecting on what has been a thought provoking and enjoyable experience at my first SBS research away day today at UoManchester. First up was a fantastic talk from @whelanfj.bsky.social and the day just kept on giving! Feeling hugely excited for what is to come in my new academic home :)
040
Reposted by Professor Mary J O'Connell
EvolDir @evoldir.bsky.social · 09/02/2026
Join the online course "A Hands-on Course in Bayesian Modelling and Evolutionary Analysis using RevBayes" from April 21-24. More details at www.physalia-courses.org/courses-wo…. #course
physalia-courses.org
A hands-on course in Bayesian modelling and evolutionary analysis using RevBayes
21-24 April 2026
083
Reposted by Professor Mary J O'Connell
Leverhulme Trust @leverhulme.ac.uk · 05/02/2026
Leverhulme Early Career Fellow, Dr Katherine Davey, conducts new research @manmetuni.bsky.social offering the first national picture of how inequalities emerge for academically successful working-class women. media.leverhulme.ac.uk/feature/kdavey
media.leverhulme.ac.uk
Degrees of opportunity? Working-class women’s lives beyond the elite university
Employing innovatively creative methods, Katherine Davey’s research interrogates the nuanced relationship between social class and gender, offering the first national picture of how inequalities emerg...
064
Professor Mary J O'Connell @evol-molly.bsky.social · 03/02/2026
Congratulations to Eilidh Ward (first author and PhD student co-supervised by co-authors Julie Aspden, David Westhead and yours truly) on this lovely contribution - a method to visually inspect reads from novel open reading frames: doi.org/10.1093/bioa...
doi.org
InspectorORF: a tool for visualising Ribo-Seq and additional genomic or transcriptomic data
AbstractMotivation. The advent of ribosome profiling (an adaptation of RNA sequencing) to determine the translatome, has led to a huge improvement in our u
062
Reposted by Professor Mary J O'Connell
Mario Vallejo-Marin @nicrodemo.bsky.social · 28/01/2026
Join us at the Evolutionary Biology Centre at Uppsala University. We’re searching for an Assistant Professor in Biology. www.uu.se/en/about-uu/...
Uppsala in late autumn
1159185
Reposted by Professor Mary J O'Connell
Rob Waterhouse @rmwaterhouse.bsky.social · 27/01/2026
Pre-announcement ... keep an eye out for news of our upcoming #Biodiversity #Bioinformatics Summer School 21-26 June in Germany co-organised by @sib.swiss & @denbi.bsky.social ... sign up to the mailing list to be sure not to miss it! www.sib.swiss/training/upc...
sib.swiss
Upcoming training courses
The SIB Swiss Institute of Bioinformatics is an academic not-for-profit organization whose mission is to lead and coordinate the field of bioinformatics in Switzerland.
116656
Reposted by Professor Mary J O'Connell
Jane @localnotail.bsky.social · 25/01/2026
Mother nature is a raver.
Marram grass leaf. Light micrograph of a cross section through a closed (unravelled) leaf of Marram grass, Ammophila arenaria. The deeply grooved leaf is thrown into folds.
The folds conserve water and withstand salt, and prevent excessive evaporation. 
Round vascular bundles are visible inside each fold, serving to transport food and water through the leaf. They look like smiley faces.
The large "eyes" are the xylem, which transport water. 
The bright blue "mouths" are the phloem, which transport sugars produced during photosynthesis. 
The spiky, curved structure is a natural adaptation to drought conditions, helping the leaf to roll up and conserve water. 
Spines on the surface discourage animals from eating the leaf. Marram grass is important in coastal ecology, since it is one of the commonest grass species in Britain to stabilize sand dunes.
301698210
Reposted by Professor Mary J O'Connell
Alexis Stamatakis @stamatak.bsky.social · 26/01/2026
The abstract submission deadline (Jan 31st) for the 2026 Mathematical and Computational Evolutionary Biology Meeting on Crete mceb2026.sciencesconf.org is this Saturday!
021
Reposted by Professor Mary J O'Connell
Chris Creevey @hairyllama.bsky.social · 23/01/2026
Last chance to apply for our funded PhD opportunity. w. Prof. Fredric Coulon @ Cranfield University. This will investigate expansion of ML models for AMR phenotype detection to agriculture settings to create a sensor-ready hit list. Detail here: www.findaphd.com/phds/project...
findaphd.com
From Genomic Context to Sensor Design: Computational Identification of AMR Biomarkers in Agriculture (project at Queen's University Belfast) at University of Reading on FindAPhD.com
PhD Project - From Genomic Context to Sensor Design: Computational Identification of AMR Biomarkers in Agriculture (project at Queen's University Belfast) at University of Reading, listed on FindAPhD....
056
Reposted by Professor Mary J O'Connell
Monica Bettencourt-Dias @monicabettencourt.bsky.social · 23/01/2026
📣 Please spread: we’re hiring a Lab Manager! It is a critical position in our new lab. As our lab moves to Barcelona and joins the @crg.eu, we’re looking for a Lab Manager to help build the lab and set the lab atmosphere. 🔗 Apply here 👉 recruitment.crg.eu/content/jobs...
29194
Reposted by Professor Mary J O'Connell
Leverhulme Trust @leverhulme.ac.uk · 22/01/2026
A new study by Philip Leverhulme Prize Winner Harrison Steel, @gabriel-abrahams.bsky.social and others has proved for the first time that it is possible to deliberately engineer quantum mechanical processes occurring inside a protein, and use these to create new sensing technologies.
121
Reposted by Professor Mary J O'Connell
Alexis Stamatakis @stamatak.bsky.social · 19/01/2026
The submission deadline (Jan 31st) for the 2026 Mathematical and Computational Evolutionary Biology Meeting in Crete mceb2026.sciencesconf.org is getting closer!
063
Reposted by Professor Mary J O'Connell
EvolDir @evoldir.bsky.social · 18/01/2026
NYU's Rocha Lab seeks a Postdoctoral Associate in Evolutionary Biology. Ideal candidates hold a PhD, with expertise in genetic diversity, bioinformatics, and mentoring. Apply by Feb 26, 2026. More info: apply.interfolio.com/180051 #postdoc
apply.interfolio.com
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
021
Professor Mary J O'Connell @evol-molly.bsky.social · 15/01/2026
Interested in pangenomics ? This paper just out from Alan Beavan (not on socials), @blackpassiflora.bsky.social and @jomcinerney.bsky.social is a must: doi.org/10.1093/bioi...
doi.org
PanForest: predicting genes in genomes using random forests
AbstractMotivation. The presence or absence of some genes in a genome can influence whether other genes are likely to be present or absent. Understanding t
0125
Reposted by Professor Mary J O'Connell
Fiona J Whelan @whelanfj.bsky.social · 12/01/2026
So excited to have @szytynska.bsky.social kicking off our Evolution & Ecology day at @manchester.ac.uk today! #UoM_EEday
Sharon introducing herself and her research.
0178
Reposted by Professor Mary J O'Connell
Philip Donoghue @phil-donoghue.bsky.social · 08/01/2026
Our latest: Independent origins of spicules reconcile paleontological and molecular evidence of sponge evolutionary history, led by @meleonora-rossi.bsky.social with help from friends @bristolpalaeo.bsky.social including @anariesgo.bsky.social @evopalaeo.bsky.social Davide Pisani and many others
science.org
Independent origins of spicules reconcile paleontological and molecular evidence of sponge evolutionary history
Sponges have a cryptic Ediacaran history because ancestral sponges were soft-bodied and had low fossilization potential.
16927
Reposted by Professor Mary J O'Connell
David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 07/01/2026
300,000 Wondrous Nature Illustrations Put Online by The Biodiversity Heritage Library | Open Culture
openculture.com
300,000 Wondrous Nature Illustrations Put Online by The Biodiversity Heritage Library
Are we truly in the midst of a human-caused sixth mass extinction, an era of “biological annihilation”?
29337
Reposted by Professor Mary J O'Connell
Molecular Biology and Evolution @molbioevol.bsky.social · 05/01/2026
Thawornwattana, Rannala & @zihengyang.bsky.social use simulation to study the false positive rate of a Bayesian test of gene flow under the MSC with multiple influencing factors. 🔗 doi.org/10.1093/molbev/msaf327 #evobio #molbio #compbio
doi.org
On the robustness of Bayesian inference of gene flow to intragenic recombination and natural selection
Abstract. The multispecies coalescent (MSC) model provides a framework for detecting gene flow using genomic data, including between sister species. Howeve
053
Reposted by Professor Mary J O'Connell
David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 17/12/2025
Arctic endured year of record heat as climate scientists warn of ‘winter being redefined’
theguardian.com
Arctic endured year of record heat as climate scientists warn of ‘winter being redefined’
Region known as ‘world’s refrigerator’ is heating up as much as four times as quickly as global average, Noaa experts say
12013
Reposted by Professor Mary J O'Connell
Manlio De Domenico @manlius.bsky.social · 16/12/2025
🚨 What if evolution is the ”law”… and networks are the machines that do the work? In this paper (just published) I try to formalize how living systems are non-equilibrium, information-processing, adaptive matter. With a great biological flavor! 🧪🌐🌍🧬🦠 👉 iopscience.iop.org/article/10.1... 🧵 1/
813244
Reposted by Professor Mary J O'Connell
Prof Niamh Forde @niamhforde.bsky.social · 16/12/2025
We have a PhD studentship available starting in October 2026. Investigating climate change heat stress impacts on maternal and child health. Get in touch if you have questions! www.findaphd.com/phds/project...
findaphd.com
Harnessing comparative biology to understand climate change induced heat stress impacts on maternal and offspring health at University of Edinburgh on FindAPhD.com
PhD Project - Harnessing comparative biology to understand climate change induced heat stress impacts on maternal and offspring health at University of Edinburgh, listed on FindAPhD.com
043
Reposted by Professor Mary J O'Connell
Philip Ball @philipcball.bsky.social · 08/12/2025
Wow, this is a very impressive embryo model. "What sets the model described in this study apart from other embryo models is its ability to continuously mimic primate development from pre-implantation through to late gastrulation." (Nice, @amartinezarias.bsky.social!) www.nature.com/articles/d41...
nature.com
Primate embryo model leaps across developmental boundaries
A stem-cell-based monkey embryo model that self-organizes into a comprehensive body plan could lead the way to more-sophisticated models of early human development.
1186
Reposted by Professor Mary J O'Connell
James McInerney @jomcinerney.bsky.social · 05/12/2025
Latest preprint with @hairyllama.bsky.social and @evol-molly.bsky.social This is a program that helps calculate several phylogenetic support measures.
01510
Reposted by Professor Mary J O'Connell
Judith Mank @judithmank.bsky.social · 05/12/2025
Please help! We are looking for tissue-specific RNA-seq datasets or pubs with both male and female individual gene expression data, not pooled, from animal species. If you know of any relevant resources, please drop a link in the comments or send me a DM. Also, please help spread the word - thanks!
72629
Professor Mary J O'Connell @evol-molly.bsky.social · 04/12/2025
Paper out by the sensational @haideetinning.bsky.social and @niamhforde.bsky.social and co-authors. A conceptus-derived and highly conserved protein “PDI” alters function of endometrium to facilitate early preg events in mammals with different early preg phenotypes. academic.oup.com/biolreprod/a...
academic.oup.com
The embryo-derived protein PDI is highly conserved among placental mammals and alters the endometrial transcriptome and secretome in vitro across species with differing implantation strategies
SIGNIFICANCE STATEMENT We provide evidence that a highly conserved protein (PDI) alters the endometrial transcriptome in a species- and cell-specific manne
000
Reposted by Professor Mary J O'Connell
Philip Donoghue @phil-donoghue.bsky.social · 03/12/2025
Our latest, led by the inimitable Chris Kay "Dated gene duplications elucidate the evolutionary assembly of eukaryotes" in which we used gene duplications to test hypotheses of eukaryogenesis. TLDR? They're all wrong. With @tweethinking.bsky.social @anya1.bsky.social @ssolo.bsky.social Davide Pisani
nature.com
Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature
Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex ar...
13114
Reposted by Professor Mary J O'Connell
Eva Heinz @evaheinz7.bsky.social · 03/12/2025
New editor's spotlights to highlight some of the exciting work we see at #MGen, getting kicked off by @bjesseshapiro.bsky.social diving into the latest work from @sylvainbrisse.bsky.social et al 🔍 vaccine impacts on non-target species! #MicroSky #MicrobiomeSky #IDSky #MedSky #evobio #clinmicro 💻🧬 🧪
0102
Reposted by Professor Mary J O'Connell
Molecular Biology and Evolution @molbioevol.bsky.social · 02/12/2025
Sharma & Kumar present the Net Bootstrap Support (NBS) approach that accounts for phylogenetic variation in the estimates of bootstrap confidence. 🔗 doi.org/10.1093/molbev/msaf296 #evobio #molbio #phylogenetics
doi.org
Robust and Efficient Confidence Limits for Phylogenomic Inference of Organismal Relationships
Abstract. Phylogenomic data are indispensable for establishing reliable relationships needed to build a robust Tree of Life. The superalignment approach co
0115
Reposted by Professor Mary J O'Connell
Mia Levine @levine-lab.bsky.social · 28/11/2025
How to keep in step when your (protein) partner speeds up… Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection. Congrats to whole team! www.science.org/doi/10.1126/...
science.org
Rapid compensatory evolution within a multiprotein complex preserves telomere integrity
Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such comp...
612064
Reposted by Professor Mary J O'Connell
Charles Johnson @charles.littlegreenfootballs.com · 25/11/2025
i’m not crying you’re crying xkcd: Fifteen Years
xkcd.com
Fifteen Years
7750141338