JX Chen
@gobiologycn.com
Phylogenomics | Systematics | Natural History | Biodiversity
http://www.gobiologycn.com/ABOUT_ME/aboutme.html
http://www.gobiologycn.com/ABOUT_ME/aboutme.html
Reposted by JX Chen
LoL-align: sensitive and fast probabilistic protein structure alignment https://www.biorxiv.org/content/10.1101/2025.11.24.690091v1
November 26, 2025 at 2:46 AM
LoL-align: sensitive and fast probabilistic protein structure alignment https://www.biorxiv.org/content/10.1101/2025.11.24.690091v1
Reposted by JX Chen
An archaeal genetic code with all TAG codons as pyrrolysine www.science.org/doi/abs/10.1... #jcampubs
An archaeal genetic code with all TAG codons as pyrrolysine
Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...
www.science.org
November 21, 2025 at 4:20 PM
An archaeal genetic code with all TAG codons as pyrrolysine www.science.org/doi/abs/10.1... #jcampubs
Reposted by JX Chen
Nature research paper: Convergent genome evolution shaped the emergence of terrestrial animals
go.nature.com/4i0i61w
go.nature.com/4i0i61w
Convergent genome evolution shaped the emergence of terrestrial animals - Nature
Comparisons of 154 genomes from 21 animal phyla and outgroups have been used to reconstruct ancestral adaptation to life on land across 11 distinct terrestrialization events, revealing strong evidence for convergent genomic evolution across the animal kingdom and recurring periods of terrestrial colonization.
go.nature.com
November 13, 2025 at 9:18 AM
Nature research paper: Convergent genome evolution shaped the emergence of terrestrial animals
go.nature.com/4i0i61w
go.nature.com/4i0i61w
Reposted by JX Chen
Reposted by JX Chen
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A
Insertion of an invading retrovirus regulates a novel color trait in swordtail fish
For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable wi...
shorturl.at
November 12, 2025 at 8:34 PM
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A
Reposted by JX Chen
My book 'The Tree of Life' is published in the USA and Canada today.
Available as book, on kindle and as audio.
I would be really grateful for reposts.
www.amazon.com/Tree-Life-So...
www.amazon.ca/Tree-Life-So...
Available as book, on kindle and as audio.
I would be really grateful for reposts.
www.amazon.com/Tree-Life-So...
www.amazon.ca/Tree-Life-So...
November 11, 2025 at 12:01 PM
My book 'The Tree of Life' is published in the USA and Canada today.
Available as book, on kindle and as audio.
I would be really grateful for reposts.
www.amazon.com/Tree-Life-So...
www.amazon.ca/Tree-Life-So...
Available as book, on kindle and as audio.
I would be really grateful for reposts.
www.amazon.com/Tree-Life-So...
www.amazon.ca/Tree-Life-So...
Reposted by JX Chen
Efficient inference of large phylogenetic trees as applied to birds: academic.oup.com/sysbio/advan... 🧪🪶 (📷Zhao et al.)
November 9, 2025 at 4:47 PM
Efficient inference of large phylogenetic trees as applied to birds: academic.oup.com/sysbio/advan... 🧪🪶 (📷Zhao et al.)
Reposted by JX Chen
New Nature paper!
Vaga et al. (2025) reconstruct a time-calibrated phylogeny of stony (scleractinian) corals, which suggests that some could be resilient to climate change.
Congrats @claudiavaga.bsky.social
Link to paper: doi.org/10.1038/s415...
Vaga et al. (2025) reconstruct a time-calibrated phylogeny of stony (scleractinian) corals, which suggests that some could be resilient to climate change.
Congrats @claudiavaga.bsky.social
Link to paper: doi.org/10.1038/s415...
A global coral phylogeny reveals resilience and vulnerability through deep time - Nature
The most recent common ancestor of the stony coral Scleractinia dates to about 460 million years ago and was probably a solitary, heterotrophic and free-living organism.
doi.org
October 23, 2025 at 4:46 PM
New Nature paper!
Vaga et al. (2025) reconstruct a time-calibrated phylogeny of stony (scleractinian) corals, which suggests that some could be resilient to climate change.
Congrats @claudiavaga.bsky.social
Link to paper: doi.org/10.1038/s415...
Vaga et al. (2025) reconstruct a time-calibrated phylogeny of stony (scleractinian) corals, which suggests that some could be resilient to climate change.
Congrats @claudiavaga.bsky.social
Link to paper: doi.org/10.1038/s415...
Reposted by JX Chen
Quest for Orthologs 8 meeting report/review: where AI, protein structure, isoforms & domains meet orthology. We review recent developments in the field, with applications from environmental genomics to agriculture. Many authors, led by @irenejulca.bsky.social. Open access: doi.org/10.1007/s002...
Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration - Journal of Molecular Evolution
The rapid advancement of DNA sequencing technologies and computational algorithms has led to an unprecedented surge in genomic data, driven by several large-scale sequencing projects worldwide. Orthol...
doi.org
October 23, 2025 at 6:22 AM
Quest for Orthologs 8 meeting report/review: where AI, protein structure, isoforms & domains meet orthology. We review recent developments in the field, with applications from environmental genomics to agriculture. Many authors, led by @irenejulca.bsky.social. Open access: doi.org/10.1007/s002...
Reposted by JX Chen
Gene annotations matter for downstream analyses: different structural gene-annotation pipelines yield markedly different orthology calls. We compare four strategies across species and argue for standards & QC before inference. Work led by @silviaprietob.bsky.social. Paper: doi.org/10.1093/bioi...
October 23, 2025 at 6:20 AM
Gene annotations matter for downstream analyses: different structural gene-annotation pipelines yield markedly different orthology calls. We compare four strategies across species and argue for standards & QC before inference. Work led by @silviaprietob.bsky.social. Paper: doi.org/10.1093/bioi...
Reposted by JX Chen
Even more exciting is we find evidence for functional convergence over a macroevolutionary scale spanning 50 million years!! In mini species, growth inhibitor genes (ING2 and CDKN1B) are expressed at higher levels, while in large-bodied species the growth-factor gene TGFB3 is expressed more.
October 22, 2025 at 9:39 PM
Even more exciting is we find evidence for functional convergence over a macroevolutionary scale spanning 50 million years!! In mini species, growth inhibitor genes (ING2 and CDKN1B) are expressed at higher levels, while in large-bodied species the growth-factor gene TGFB3 is expressed more.
Reposted by JX Chen
@notothentoma.bsky.social @arcolon14.bsky.social & @jpostlethwait.bsky.social show how Antarctic white-blooded icefishes, the only vertebrates without hemoglobin, independently lost hemoglobin cluster genes, driven by TEs and repeats.
🔗 doi.org/10.1093/gbe/evaf184
#genome #evolution #TEsky
🔗 doi.org/10.1093/gbe/evaf184
#genome #evolution #TEsky
October 20, 2025 at 10:43 AM
@notothentoma.bsky.social @arcolon14.bsky.social & @jpostlethwait.bsky.social show how Antarctic white-blooded icefishes, the only vertebrates without hemoglobin, independently lost hemoglobin cluster genes, driven by TEs and repeats.
🔗 doi.org/10.1093/gbe/evaf184
#genome #evolution #TEsky
🔗 doi.org/10.1093/gbe/evaf184
#genome #evolution #TEsky
Reposted by JX Chen
New preprint up with collaborators Jianguo Lu, @mpodobnik.bsky.social, Uwe Irion, Braedan McCluskey, John Postlethwait and others. New Danio genomes, evolution and pigment pattern variation. Long time in the making www.biorxiv.org/content/10.1...
October 19, 2025 at 10:28 PM
New preprint up with collaborators Jianguo Lu, @mpodobnik.bsky.social, Uwe Irion, Braedan McCluskey, John Postlethwait and others. New Danio genomes, evolution and pigment pattern variation. Long time in the making www.biorxiv.org/content/10.1...
Reposted by JX Chen
Have been a bit silent recently as I've been working on this new version of our preprint! In this study, we present a generalizable evo-devo model to explore principles of evolutionary innovations. A thread 🧵 ahead about this, and what's new... 1/11
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
A simple model reveals why complex evolutionary innovations follow predictable paths
Determining the principles underlying the origin of novel characters has been a fundamental goal of evolutionary biology. Yet, key mechanisms remain poorly understood, hindered by the lack of a genera...
www.biorxiv.org
October 16, 2025 at 3:03 PM
Have been a bit silent recently as I've been working on this new version of our preprint! In this study, we present a generalizable evo-devo model to explore principles of evolutionary innovations. A thread 🧵 ahead about this, and what's new... 1/11
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by JX Chen
Phylogenetic discordance and genic innovation at the emergence of modern cephalochordates https://www.biorxiv.org/content/10.1101/2025.10.14.682400v1
October 17, 2025 at 12:39 AM
Phylogenetic discordance and genic innovation at the emergence of modern cephalochordates https://www.biorxiv.org/content/10.1101/2025.10.14.682400v1
Reposted by JX Chen
Scientists electrically culled invasive fish in a 20-year battle—but the fish fought back with rapid evolution
Evolution Shocks Scientists in an Electric Battle against Invasive Bass
Scientists electrically culled invasive fish in a 20-year battle—but the fish fought back with rapid evolution
www.scientificamerican.com
September 26, 2025 at 11:33 AM
Scientists electrically culled invasive fish in a 20-year battle—but the fish fought back with rapid evolution
Reposted by JX Chen
Bumping to the Fishes! and Science feeds🐟🧪
October 13, 2025 at 5:36 PM
Bumping to the Fishes! and Science feeds🐟🧪
Reposted by JX Chen
Large citizen science datasets are powerful tools for biodiversity science, but they may have biases. Nice new paper from @louisbackstrom.bsky.social et al. showing that for eBird and Birdtrack lists there is a tendency for rare species to be over-represented
onlinelibrary.wiley.com/doi/epdf/10....
onlinelibrary.wiley.com/doi/epdf/10....
October 13, 2025 at 10:54 PM
Large citizen science datasets are powerful tools for biodiversity science, but they may have biases. Nice new paper from @louisbackstrom.bsky.social et al. showing that for eBird and Birdtrack lists there is a tendency for rare species to be over-represented
onlinelibrary.wiley.com/doi/epdf/10....
onlinelibrary.wiley.com/doi/epdf/10....
Reposted by JX Chen
ICYMI: New online: Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses
Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses
Nature Structural & Molecular Biology, Published online: 10 October 2025; doi:10.1038/s41594-025-01649-8Using a new method called FoldTree, the authors compare proteins on the basis of their shape to construct more accurate family trees over long evolutionary timescales and capture distant relationships where sequence information becomes less reliable.
go.nature.com
October 11, 2025 at 10:18 AM
ICYMI: New online: Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses
Reposted by JX Chen
Phylogenomics redefines the evolutionary history of mosquitoes https://pubmed.ncbi.nlm.nih.gov/41052354/
October 7, 2025 at 5:40 AM
Phylogenomics redefines the evolutionary history of mosquitoes https://pubmed.ncbi.nlm.nih.gov/41052354/
Reposted by JX Chen
A novel data filtering method resolves the controversy in the phylogeny of the Chondrichthyes https://www.biorxiv.org/content/10.1101/2025.08.19.671162v1
August 23, 2025 at 2:32 PM
A novel data filtering method resolves the controversy in the phylogeny of the Chondrichthyes https://www.biorxiv.org/content/10.1101/2025.08.19.671162v1
Reposted by JX Chen
🌍🦋 Across 6 continents, 21 sites & 15,000 paper moths, we joined a worldwide experiment led by @wlallen.bsky.social & Iliana Medina, showing how ecological context shapes the evolution of animal colouration.
Proud to be part of this global team effort: doi.org/10.1126/scie...
Proud to be part of this global team effort: doi.org/10.1126/scie...
September 25, 2025 at 6:39 PM
🌍🦋 Across 6 continents, 21 sites & 15,000 paper moths, we joined a worldwide experiment led by @wlallen.bsky.social & Iliana Medina, showing how ecological context shapes the evolution of animal colouration.
Proud to be part of this global team effort: doi.org/10.1126/scie...
Proud to be part of this global team effort: doi.org/10.1126/scie...
Reposted by JX Chen
I am extremely happy to see that our review on fossil tip-dating is out in early view in Systematic Biology! A huge thanks to all the authors of this massive project (@heckeberg.bsky.social, @basantakhakurel.bsky.social, Gustavo Darlim, and @hoehna.bsky.social)! academic.oup.com/sysbio/advan...
September 25, 2025 at 12:40 PM
I am extremely happy to see that our review on fossil tip-dating is out in early view in Systematic Biology! A huge thanks to all the authors of this massive project (@heckeberg.bsky.social, @basantakhakurel.bsky.social, Gustavo Darlim, and @hoehna.bsky.social)! academic.oup.com/sysbio/advan...
Reposted by JX Chen
Although chromosome-level macrosynteny is broadly conserved among cypriniforms, we demonstrate that microsynteny can resolve deep phylogenetic nodes. Both sequence-based and microsynteny-based analyses find that Gyrinocheilidae is the sister lineage to all other cypriniforms
September 21, 2025 at 6:42 PM
Although chromosome-level macrosynteny is broadly conserved among cypriniforms, we demonstrate that microsynteny can resolve deep phylogenetic nodes. Both sequence-based and microsynteny-based analyses find that Gyrinocheilidae is the sister lineage to all other cypriniforms