David Enard
@denard.bsky.social
Evolutionary Biologist. Ancient epidemics. Genomic adaptation.
Reposted by David Enard
📖Latest from the lab:
Evo. characterization #antiviral #SAMD9/9L across #kingdoms🚶♀️🦍🦠🧫🖥️: ancient #convergence + #adaptations @natecoevo.nature.com
Led by amazing Alexandre Legrand +major contributions by Rémi Demeure & Amandine Chantharath @ciri-lyon.bsky.social 1/n
www.nature.com/articles/s41...
Evo. characterization #antiviral #SAMD9/9L across #kingdoms🚶♀️🦍🦠🧫🖥️: ancient #convergence + #adaptations @natecoevo.nature.com
Led by amazing Alexandre Legrand +major contributions by Rémi Demeure & Amandine Chantharath @ciri-lyon.bsky.social 1/n
www.nature.com/articles/s41...
Evolutionary characterization of antiviral SAMD9/9L across kingdoms supports ancient convergence and lineage-specific adaptations - Nature Ecology & Evolution
A search for analogues of the human SAMD9/9L antiviral genes identifies convergent evolution of this gene family in the bacterial and animal kingdoms, with species-specific and recent genomic signatur...
www.nature.com
November 12, 2025 at 5:55 PM
📖Latest from the lab:
Evo. characterization #antiviral #SAMD9/9L across #kingdoms🚶♀️🦍🦠🧫🖥️: ancient #convergence + #adaptations @natecoevo.nature.com
Led by amazing Alexandre Legrand +major contributions by Rémi Demeure & Amandine Chantharath @ciri-lyon.bsky.social 1/n
www.nature.com/articles/s41...
Evo. characterization #antiviral #SAMD9/9L across #kingdoms🚶♀️🦍🦠🧫🖥️: ancient #convergence + #adaptations @natecoevo.nature.com
Led by amazing Alexandre Legrand +major contributions by Rémi Demeure & Amandine Chantharath @ciri-lyon.bsky.social 1/n
www.nature.com/articles/s41...
Resending this, please RT!
Come join us in beautiful Britanny, France in May 2026 for a workshop that I am organizing with @lucievirevolte.bsky.social and @psudmant.bsky.social on Rapid host adaptations to infections:
sites.google.com/berkeley.edu...
sites.google.com/berkeley.edu...
November 12, 2025 at 6:29 PM
Resending this, please RT!
Reposted by David Enard
Excited to share our new preprint on BioRxiv!
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons
Background. Paramecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual gene...
www.biorxiv.org
November 10, 2025 at 9:21 AM
Excited to share our new preprint on BioRxiv!
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
Reposted by David Enard
Community competitions help benchmark approaches in computational biology. Struck et al. now present GHIST 2024 - The First Genomic History Inference Strategies Tournament, for the inference of evolutionary history from genome data.
🔗 doi.org/10.1093/molbev/msaf257
#evobio #molbio #compbio #popgen
🔗 doi.org/10.1093/molbev/msaf257
#evobio #molbio #compbio #popgen
November 6, 2025 at 3:20 PM
Community competitions help benchmark approaches in computational biology. Struck et al. now present GHIST 2024 - The First Genomic History Inference Strategies Tournament, for the inference of evolutionary history from genome data.
🔗 doi.org/10.1093/molbev/msaf257
#evobio #molbio #compbio #popgen
🔗 doi.org/10.1093/molbev/msaf257
#evobio #molbio #compbio #popgen
Reposted by David Enard
If you're looking for a faculty position at the intersection of ecology and computing (both broadly defined), please apply to this joint search between the CEE Department and the College of Computing at MIT: cee.mit.edu/people/share...
Faculty Position in the Department of Civil and Environmental Engineering and the Schwarzman College of Computing - cee.mit.edu
The Department of Civil and Environmental Engineering (CEE), together with the Schwarzman College of Computing (SCC) at the Massachusetts Institute of Technology (MIT) in Cambridge MA, seeks candidate...
cee.mit.edu
November 5, 2025 at 7:27 PM
If you're looking for a faculty position at the intersection of ecology and computing (both broadly defined), please apply to this joint search between the CEE Department and the College of Computing at MIT: cee.mit.edu/people/share...
Reposted by David Enard
Join us on Nov 18 at 2:30 PM MST to learn about CAMBIUM grad fellowships in biodiversity informatics & climate change @uarizona.bsky.social. For incoming Fall 2026 students interested in big data, ecology, evolution, climate adaptation & more. Register: events.trellis.arizona.edu/en/f44lNu67/... 🌵🧬🌐
November 3, 2025 at 11:50 PM
Join us on Nov 18 at 2:30 PM MST to learn about CAMBIUM grad fellowships in biodiversity informatics & climate change @uarizona.bsky.social. For incoming Fall 2026 students interested in big data, ecology, evolution, climate adaptation & more. Register: events.trellis.arizona.edu/en/f44lNu67/... 🌵🧬🌐
Also addresses the problem of studying positive selection in the presence of constraint. Many observed differences in + sel. are in fact just differences in selective constraint and the space it leaves for + sel., thus masking the true correspondence between + sel. and selective pressures.
This preprint shows that the huge recent progress of non-coding effect predictions is likely going to help tremendously in this area. A must read.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 31, 2025 at 6:33 PM
Also addresses the problem of studying positive selection in the presence of constraint. Many observed differences in + sel. are in fact just differences in selective constraint and the space it leaves for + sel., thus masking the true correspondence between + sel. and selective pressures.
Reposted by David Enard
just in time for #batweek --Phylogenetic and ML analyses show that viral epidemic potential is not uniform among bats: virulence, transmissibility, and death burden cluster within distinct clades.🦇@carolinecummings.bsky.social @colincarlson.bsky.social @viralemergence.org go.sn.pub/acnbg1
October 30, 2025 at 2:54 PM
just in time for #batweek --Phylogenetic and ML analyses show that viral epidemic potential is not uniform among bats: virulence, transmissibility, and death burden cluster within distinct clades.🦇@carolinecummings.bsky.social @colincarlson.bsky.social @viralemergence.org go.sn.pub/acnbg1
This preprint shows that the huge recent progress of non-coding effect predictions is likely going to help tremendously in this area. A must read.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 29, 2025 at 1:18 PM
This preprint shows that the huge recent progress of non-coding effect predictions is likely going to help tremendously in this area. A must read.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by David Enard
The Johri Lab has an open postdoc position. Please send me an email, if interested. Start date is flexible. Please do share! Thank you in advance.
October 28, 2025 at 9:31 PM
The Johri Lab has an open postdoc position. Please send me an email, if interested. Start date is flexible. Please do share! Thank you in advance.
Reposted by David Enard
I'm recruiting PhD students for the Barker Lab @uofa-eeb.bsky.social We study plant evolutionary genomics - polyploidy, hybridization & machine learning for genome evolution. Work with Selaginella, Xanthisma, Brassica & more. Funding available via CAMBIUM Fellowships. Reach out if interested! 🧬🌵🤖
October 24, 2025 at 5:01 AM
I'm recruiting PhD students for the Barker Lab @uofa-eeb.bsky.social We study plant evolutionary genomics - polyploidy, hybridization & machine learning for genome evolution. Work with Selaginella, Xanthisma, Brassica & more. Funding available via CAMBIUM Fellowships. Reach out if interested! 🧬🌵🤖
Reposted by David Enard
The CAMBIUM NSF NRT is recruiting PhD students @uarizona.bsky.social! Fellowships for interdisciplinary training in biodiversity big data to adapt to & mitigate climate change impacts. Great fit for evolutionary genomics, bioinformatics, plant adaptation, ecology & more. cambium.arizona.edu 🧬🌐🌎
October 24, 2025 at 5:19 AM
The CAMBIUM NSF NRT is recruiting PhD students @uarizona.bsky.social! Fellowships for interdisciplinary training in biodiversity big data to adapt to & mitigate climate change impacts. Great fit for evolutionary genomics, bioinformatics, plant adaptation, ecology & more. cambium.arizona.edu 🧬🌐🌎
Reposted by David Enard
Just left Roscoff this morning after an excellent week long meeting on speciation. I cannot recommend the location
highly enough!
highly enough!
October 24, 2025 at 8:49 AM
Just left Roscoff this morning after an excellent week long meeting on speciation. I cannot recommend the location
highly enough!
highly enough!
Come join us in beautiful Britanny, France in May 2026 for a workshop that I am organizing with @lucievirevolte.bsky.social and @psudmant.bsky.social on Rapid host adaptations to infections:
sites.google.com/berkeley.edu...
sites.google.com/berkeley.edu...
October 23, 2025 at 1:20 PM
Come join us in beautiful Britanny, France in May 2026 for a workshop that I am organizing with @lucievirevolte.bsky.social and @psudmant.bsky.social on Rapid host adaptations to infections:
sites.google.com/berkeley.edu...
sites.google.com/berkeley.edu...
This is going to be invaluable as an otugroup to study modern human genomic adaptation.
A high-coverage genome from a 200,000-year-old Denisovan 💀 www.biorxiv.org/content/10.1... 🧬🖥️🧪
A high-coverage genome from a 200,000-year-old Denisovan
Denisovans, an extinct sister group of Neandertals who lived in Eastern Eurasia during the Middle and Late Pleistocene, are known only from a handful of skeletal remains and limited genetic data,…
www.biorxiv.org
October 21, 2025 at 6:21 PM
This is going to be invaluable as an otugroup to study modern human genomic adaptation.
Reposted by David Enard
A high-coverage genome from a 200,000-year-old Denisovan 💀 www.biorxiv.org/content/10.1... 🧬🖥️🧪
A high-coverage genome from a 200,000-year-old Denisovan
Denisovans, an extinct sister group of Neandertals who lived in Eastern Eurasia during the Middle and Late Pleistocene, are known only from a handful of skeletal remains and limited genetic data,…
www.biorxiv.org
October 21, 2025 at 3:55 PM
A high-coverage genome from a 200,000-year-old Denisovan 💀 www.biorxiv.org/content/10.1... 🧬🖥️🧪
The new Flex-sweep v2 is ready! We welcome feedback from users to further improve user experience and address compatibility issues that often occur given the many moving parts. Flex-sweep v2 now implements DANN from the Siepel lab. journals.plos.org/plosgenetics...
Postdoc J. M. Moreno is very close to release Flex-sweep v2 to make users' life easier. v2 is entirely recoded, faster and uses much less RAM. Robustness is up thanks to adding Siepel's lab domain adaptive step.
Available soon at pypi.org/project/flex...
flexsweep.readthedocs.io/en/latest/
Available soon at pypi.org/project/flex...
flexsweep.readthedocs.io/en/latest/
October 21, 2025 at 3:38 PM
The new Flex-sweep v2 is ready! We welcome feedback from users to further improve user experience and address compatibility issues that often occur given the many moving parts. Flex-sweep v2 now implements DANN from the Siepel lab. journals.plos.org/plosgenetics...
An example: properly aligning homologous coding sequences to run dN/dS tests of positive selection is a deceptively difficult task. I have been doing it for ~20 years and still finding ways to improve the process. It is not a flashy task, and won't get CNS papers, but it is still absolutely vital.
1/2) With hindsight, many previous publications on genomic adaptation and claims made were 10 to 20 years premature. Data (sequencing, alignment, annotation, etc.) quality was simply not there, and will likely only fully happen with long read, individual level assemblies.
October 21, 2025 at 3:05 PM
An example: properly aligning homologous coding sequences to run dN/dS tests of positive selection is a deceptively difficult task. I have been doing it for ~20 years and still finding ways to improve the process. It is not a flashy task, and won't get CNS papers, but it is still absolutely vital.
1/2) With hindsight, many previous publications on genomic adaptation and claims made were 10 to 20 years premature. Data (sequencing, alignment, annotation, etc.) quality was simply not there, and will likely only fully happen with long read, individual level assemblies.
October 21, 2025 at 2:55 PM
1/2) With hindsight, many previous publications on genomic adaptation and claims made were 10 to 20 years premature. Data (sequencing, alignment, annotation, etc.) quality was simply not there, and will likely only fully happen with long read, individual level assemblies.
Reposted by David Enard
In a new paper led by Jiaqi Yang we trace the distribution of Denisovan introgressed DNA in ancient modern human genomes over time.
www.cell.com/current-biol...
www.cell.com/current-biol...
An early East Asian lineage with unexpectedly low Denisovan ancestry
Yang et al. study Denisovan ancestry in ancient and present-day humans. In contrast
to other East Asians, genomic comparisons suggest that the Jomon derived most of their
ancestry from a deep lineage ...
www.cell.com
October 20, 2025 at 7:39 PM
In a new paper led by Jiaqi Yang we trace the distribution of Denisovan introgressed DNA in ancient modern human genomes over time.
www.cell.com/current-biol...
www.cell.com/current-biol...
Reposted by David Enard
Many antiphage systems use NAD+, in many ways.
@hugovaysset.bsky.social reviewed them all!
Read to know more about all their molecular mechanisms, how phages counteract them, their distribution in bacteria and their conservation in eukaryotic immunity!
www.cell.com/molecular-ce...
@hugovaysset.bsky.social reviewed them all!
Read to know more about all their molecular mechanisms, how phages counteract them, their distribution in bacteria and their conservation in eukaryotic immunity!
www.cell.com/molecular-ce...
The multifaceted roles of NAD+ in bacterial immunity
In this review, Vaysset and Bernheim examine how nicotinamide adenine dinucleotide
(NAD+) is a key player in diverse and widespread bacterial antiphage defense systems
and phage counterdefense. The au...
www.cell.com
October 17, 2025 at 5:55 PM
Many antiphage systems use NAD+, in many ways.
@hugovaysset.bsky.social reviewed them all!
Read to know more about all their molecular mechanisms, how phages counteract them, their distribution in bacteria and their conservation in eukaryotic immunity!
www.cell.com/molecular-ce...
@hugovaysset.bsky.social reviewed them all!
Read to know more about all their molecular mechanisms, how phages counteract them, their distribution in bacteria and their conservation in eukaryotic immunity!
www.cell.com/molecular-ce...
Reposted by David Enard
I'll be reviewing applications for this in a few days, so there's still time to get touch if you're interested.
I'm looking to recruit a PhD student to study patterns of local adaptation and introgression across the spruce hybrid zone in the Rockies near Calgary. Projects can include field work, bioinformatics, pop gen theory, or comparison to plant/ conifer species
yeamanlab.weebly.com/uploads/5/7/...
yeamanlab.weebly.com/uploads/5/7/...
October 16, 2025 at 6:59 PM
I'll be reviewing applications for this in a few days, so there's still time to get touch if you're interested.
PSA that if you are not aligning large numbers of coding sequences with MACSE, you are doing it wrong. Frameshift awareness is absolutely crucial to avoid alignment errors even between closely related sequences.
pubmed.ncbi.nlm.nih.gov/30165589/
pubmed.ncbi.nlm.nih.gov/30165589/
October 16, 2025 at 3:13 PM
PSA that if you are not aligning large numbers of coding sequences with MACSE, you are doing it wrong. Frameshift awareness is absolutely crucial to avoid alignment errors even between closely related sequences.
pubmed.ncbi.nlm.nih.gov/30165589/
pubmed.ncbi.nlm.nih.gov/30165589/
Reposted by David Enard
OUT TODAY: SimHumanity, a SLiM 5 model of the human genome, replete with demography, autosomes, X/Y & mtDNA.
A shared starting point for reproducible evolutionary simulations.
Huge thanks to coauthors Ben Haller, @mufernando.bsky.social & Philipp Messer.
🔗 www.pivotscipub.com/hpgg/5/4/0006
A shared starting point for reproducible evolutionary simulations.
Huge thanks to coauthors Ben Haller, @mufernando.bsky.social & Philipp Messer.
🔗 www.pivotscipub.com/hpgg/5/4/0006
October 16, 2025 at 12:10 PM
OUT TODAY: SimHumanity, a SLiM 5 model of the human genome, replete with demography, autosomes, X/Y & mtDNA.
A shared starting point for reproducible evolutionary simulations.
Huge thanks to coauthors Ben Haller, @mufernando.bsky.social & Philipp Messer.
🔗 www.pivotscipub.com/hpgg/5/4/0006
A shared starting point for reproducible evolutionary simulations.
Huge thanks to coauthors Ben Haller, @mufernando.bsky.social & Philipp Messer.
🔗 www.pivotscipub.com/hpgg/5/4/0006
Reposted by David Enard
We've made a related but different claim in bacteria:
elifesciences.org/articles/93146
elifesciences.org/articles/93146
Reversions mask the contribution of adaptive evolution in microbiomes
The timescale dependence of dN/dS in bacteria is better explained by adaptive than purifying dynamics, suggesting comparative genomics can underestimate past adaptation.
elifesciences.org
October 7, 2025 at 8:28 PM
We've made a related but different claim in bacteria:
elifesciences.org/articles/93146
elifesciences.org/articles/93146