MEPGT
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mepgt.bsky.social
MEPGT
@mepgt.bsky.social
PhD student in Uppsala University and Zhejiang University
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🙌Very important method! I have tested in many plants species and got robust values under kind help of Bastiaan (he is a very nice guy!). Now pulished in Genome Biology
doi.org/10.1186/s130...

ParaMask: identify multicopy genomic regions, corrects major biases in WGS data

github.com/Fulgione-gro...
Reposted by MEPGT
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
www.science.org
January 30, 2026 at 6:11 AM
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A phylogeny of 4'854 #insects --- with structural #genomics shedding light on protein functions & remote homologs www.nature.com/articles/s41... #biodiversity
Structural genomics sheds light on protein functions and remote homologs across the insect tree of life - Cell Research
Cell Research - Structural genomics sheds light on protein functions and remote homologs across the insect tree of life
www.nature.com
January 28, 2026 at 1:19 PM
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Discover eco-evolutionary assembly processes within Oceanic island systems in this perspective, published as part of our #SpecialIssue "Evolution on Islands"! 👇🧪🌍
Eco-evolutionary assembly processes within oceanic island systems
Abstract. Oceanic islands provide classic model systems for the study of biotic assembly and for the role of evolutionary radiations within this process. H
doi.org
January 22, 2026 at 5:31 PM
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📢 Three new #bioRxiv preprints from our team on holocentric chromosomes.

Together, they connect centromere repeat evolution, karyotype dynamics, and meiotic recombination outcomes, revealing how holocentric genomes evolve and function. 🧬👇
January 21, 2026 at 2:45 PM
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We have compiled a special issue for @evolappjournal.bsky.social on Effective population size in Conservation and Biodiversity Monitoring, dedicated to the late Michael W. Bruford.
This SI is a must read for everyone who struggles with what "effective population size" means.
#consgen
The Importance of Effective Population Size in Conservation and Biodiversity Monitoring
Effective population size (Ne) is a key concept in biology and conservation. Stripped to its bare essentials, it reflects how much genetic drift a population experiences, expressed as a number of ind...
onlinelibrary.wiley.com
January 17, 2026 at 8:22 PM
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Interested in genetic diversity-area relationships as a potential proxy for genetic diversity? Check out Chloé Schmidt's latest 😀
@chloology.bsky.social 🧪🌎🧬🌐
#consgen #popgen #evobio
with Sean Hoban, @debbiemleigh.bsky.social, & Walter Jetz
onlinelibrary.wiley.com/doi/full/10....
January 9, 2026 at 5:38 PM
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PhD on Begonia speciation at RBGE/Glasgow! Looking at the genomics of reproductive isolation and how fast it evolves - is it the reason this is one of the largest genera of flowering plants?
www.findaphd.com/phds/project...
January 8, 2026 at 7:16 AM
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In a new GBE Review, @david-peede.bsky.social et al. overview the SMC model and extensions, discuss examples of discoveries made with the help of SMC-based inference, and comment on the assumptions, benefits, and drawbacks of various methods.

🔗 doi.org/10.1093/gbe/...

#genome #evolution #compbio
Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies
Abstract. Genomes contain the mutational footprint of an organism’s evolutionary history, shaped by diverse forces including ecological factors, selective
doi.org
January 8, 2026 at 8:02 AM
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Interestingly @pnas.org charge an open access publication fee for commentaries they themselves have invited. This becomes apparent after the article is written & accepted. Those choosing not to pay are published later and behind a paywall. Writing a p*ssed-off email resolved the issue in this case.
January 8, 2026 at 7:28 AM
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I'm excited to share that our preprint is now available on bioRxiv! Our study challenges the widespread use of molecular genetic diversity as a predictor adaptive potential, with important implications for how genetic data is used to inform conservation decisions.

www.biorxiv.org/content/10.6...
Nucleotide diversity is a poor predictor of short-term adaptive potential
A capacity to adapt is essential for a population to avoid extinction in a changing world and is recognised as a global conservation priority. Adaptation requires additive (heritable) genetic variatio...
www.biorxiv.org
January 6, 2026 at 8:26 AM
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A must read for conservation geneticists on the utility (or not??) of using molecular diversity to predict adaptive potential 👇🏻
I'm excited to share that our preprint is now available on bioRxiv! Our study challenges the widespread use of molecular genetic diversity as a predictor adaptive potential, with important implications for how genetic data is used to inform conservation decisions.

www.biorxiv.org/content/10.6...
Nucleotide diversity is a poor predictor of short-term adaptive potential
A capacity to adapt is essential for a population to avoid extinction in a changing world and is recognised as a global conservation priority. Adaptation requires additive (heritable) genetic variatio...
www.biorxiv.org
January 6, 2026 at 9:14 AM
Reposted by MEPGT
Tree evolution is surprisingly quirky! 🌳 Trees are likely ancestral in many plant groups, often re-evolve on islands, and Arabidopsis can be made tree-like by tweaking a few genes. We revisited what genes really make a tree a tree using comparative genomics. @trhvidsten.bsky.social #trees #evolution
October 24, 2025 at 7:09 AM
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i am offering a post-doc position in my brand-new project TreeGD that will investigate genomic diversity of trees species in switzerland, with a special focus on gene conservation units, rare species (but not only), and seeds stands.

apply.refline.ch/273855/1782/...
Postdoktorand/-in in ökologischer Genomik 80% (w/m/d)
Die Forschungseinheit Biodiversität und Naturschutzbiologie untersucht die Vielfalt des Lebens, von der genetischen Diversität bis zur Arten- und Lebensraumvielfalt sowie ihre Interaktionen. Das für m...
apply.refline.ch
November 6, 2025 at 12:09 PM
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🌳 PhD Position in Forest Genetics @uni-freiburg.de
Join the BeGenDiv project to study genetic diversity of ~30 tree & shrub species across Germany’s Biodiversity Exploratories.
🧬 Fieldwork, lab work, bioinformatics & interdisciplinary collaboration
More info & apply: uni-freiburg.de/stellenangeb...
Universität Freiburg
uni-freiburg.de
December 19, 2025 at 3:21 PM
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Out now in @nature.com! Our comprehensive meta-analysis of global terrestrial and marine genetic diversity demonstrates rapid loss of genetic diversity and identifies conservation interventions that could mitigate this process
www.nature.com/articles/s41...
🧪🌍🦤🧬
#consgen #PopGen
Global meta-analysis shows action is needed to halt genetic diversity loss - Nature
A comprehensive meta-analysis of global terrestrial and marine genetic diversity covering more than three decades of research demonstrates rapid loss of genetic diversity and identifies conservation i...
www.nature.com
January 29, 2025 at 4:15 PM
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🌊 🐟🦭🐋🐧 I have a PhD position available (4 years, start Mid-2026) at NRM Stockholm to work on the macrogenomics of sea warming.

Apply here:

recruit.visma.com/spa/public/a...

#PhD #MarineGenomics #ClimateChange #EvolutionaryBiology #PopGen #Bioinformatics #conservationgenomics
December 19, 2025 at 5:12 PM
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I'm excited to present this new model to detect positive selection on regulatory sequences, which has been 3 years in the making!
Thanks to Alexandre Laverré and @Phylogenetrips for their amazing work on this project. 😃
https://doi.org/10.1101/2025.11.26.690685 #bioinformatics #MolecularEvolution
December 3, 2025 at 2:09 PM
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New paper out. If you like colorful birds, hybridization, and phylogenetics, read on! 🧵https://doi.org/10.1371/journal.pbio.3003501
A colorful legacy of hybridization in wood-warblers includes frequent sharing of carotenoid genes among species and genera
Introgression between species can shape evolutionary trajectories in important ways. This study of the entire family of the colorful wood-warblers (Parulidae) uses whole-genome sequencing to reveal fr...
doi.org
December 12, 2025 at 3:55 PM
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It's in print! My opinionated dive into the definition of "coevolution" is officially out in the December issue of @journal-evo.bsky.social

doi.org/10.1093/evol...
Don't ask “when is it coevolution?”—ask “how?”
Abstract. Coevolution has come to be widely understood as specific, simultaneous, reciprocal adaptation by pairs of interacting species. This strict-sense
doi.org
December 9, 2025 at 6:30 PM
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Excited to share our final accepted version of the CiFi method out today: www.nature.com/articles/s41...
December 8, 2025 at 5:54 PM
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Sequence alignments are notoriously prone to error. Our latest preprint offers a new tool for filtering errors out, assesses it and other filtering tools, and recommends new best practice. www.biorxiv.org/content/10.6... @phylowheeler.bsky.social 1/10
Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models
Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis, and is prone to error. Unfortunately, algorithms that remove likely alignment errors from MSAs sometimes also remove informati...
www.biorxiv.org
December 4, 2025 at 11:42 PM
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Excited to share our latest preprint!
@mheuertz.bsky.social & I just completed a review covering methods and empirical studies on adaptive introgression in a climate context.
We likely missed a few refs & ideas, so your feedback is highly welcome (ideally by email)!
Preprint➡️ doi.org/10.32942/X2B...
November 28, 2025 at 5:14 AM
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I'm very excited that our paper on Project Psyche is now published! 🦋🧬

Over the last two years we've built an incredible community & already made huge progress. Read about this & how @projectpsyche.bsky.social will drive exciting and collaborative science here:

www.cell.com/trends/ecolo...
Project Psyche: reference genomes for all Lepidoptera in Europe
Project Psyche is a transnational initiative to generate and study chromosome-level reference genomes of all ~11 000 species of Lepidoptera (butterflies and moths) found in Europe. Here, we describe t...
www.cell.com
November 27, 2025 at 11:14 AM
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