MEPGT
@mepgt.bsky.social
PhD student in Uppsala University and Zhejiang University
Pinned
MEPGT
@mepgt.bsky.social
· Oct 24
🙌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...
doi.org/10.1186/s130...
ParaMask: identify multicopy genomic regions, corrects major biases in WGS data
github.com/Fulgione-gro...
Reposted by MEPGT
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...
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
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...
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...
Reposted by MEPGT
An efficient, accessible solution for #genome annotation in both research and applied settings www.nature.com/articles/s41...
Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods
By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...
www.nature.com
November 26, 2025 at 6:56 AM
An efficient, accessible solution for #genome annotation in both research and applied settings www.nature.com/articles/s41...
Reposted by MEPGT
The last work of my PhD is finally out: www.pnas.org/doi/10.1073/...! This work is about accurately estimating branch length in the Ancestral Recombination Graph (ARG), which is achieved by a really simple framework with minimal assumptions. (1/n)
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
November 25, 2025 at 8:27 PM
The last work of my PhD is finally out: www.pnas.org/doi/10.1073/...! This work is about accurately estimating branch length in the Ancestral Recombination Graph (ARG), which is achieved by a really simple framework with minimal assumptions. (1/n)
Reposted by MEPGT
Just out in Systematic Biology, we explore the role of gene flow in island phylogeography of the Solomons Black-and-white Monarch complex. doi.org/10.1093/sysb...
Up first, strong genetic structure between islands groups and weak (but present!) structure between Pleistocene-connected islands (🧵)
Up first, strong genetic structure between islands groups and weak (but present!) structure between Pleistocene-connected islands (🧵)
November 21, 2025 at 6:29 PM
Just out in Systematic Biology, we explore the role of gene flow in island phylogeography of the Solomons Black-and-white Monarch complex. doi.org/10.1093/sysb...
Up first, strong genetic structure between islands groups and weak (but present!) structure between Pleistocene-connected islands (🧵)
Up first, strong genetic structure between islands groups and weak (but present!) structure between Pleistocene-connected islands (🧵)
Reposted by MEPGT
And another paper from the admixlab: SAI - statistics for adaptive introgression!
doi.org/10.1093/molb...
doi.org/10.1093/molb...
SAI: A Python Package for Statistics for Adaptive Introgression
Abstract. Adaptive introgression is an important evolutionary process, which can be identified with widely used summary statistics, such as the number of u
doi.org
November 20, 2025 at 12:51 PM
And another paper from the admixlab: SAI - statistics for adaptive introgression!
doi.org/10.1093/molb...
doi.org/10.1093/molb...
Reposted by MEPGT
This just out from @mortonarboretum.bsky.social Rebekah Mohn: reference genome and read mapping method both affect phylogenetic inference & heterozygosity estimates across species.
Punchline? Use a closely related but not conspecific reference.
Open-access!
onlinelibrary.wiley.com/doi/10.1111/...
Punchline? Use a closely related but not conspecific reference.
Open-access!
onlinelibrary.wiley.com/doi/10.1111/...
Variant Calling in the Goldilocks Zone: How Reference Genome Choice and Read Mapping Stringency Impact Heterozygosity Estimates and Phylogenetic Analyses
The increasing numbers of published reference genomes and affordability of whole genome resequencing have enabled multispecies population genomic and phylogenomic studies on non-model organisms, but ...
onlinelibrary.wiley.com
November 20, 2025 at 1:32 PM
This just out from @mortonarboretum.bsky.social Rebekah Mohn: reference genome and read mapping method both affect phylogenetic inference & heterozygosity estimates across species.
Punchline? Use a closely related but not conspecific reference.
Open-access!
onlinelibrary.wiley.com/doi/10.1111/...
Punchline? Use a closely related but not conspecific reference.
Open-access!
onlinelibrary.wiley.com/doi/10.1111/...
These weasels have locally adapted their winter coats to varying snow cover thanks to a million-year-old mutation 🌿
buff.ly/TnOfYWt
buff.ly/TnOfYWt
November 19, 2025 at 2:30 PM
Nearly one year visiting in EBC, Uppsala university. Nice community and coffee, fresh air and comfortable workplace. I'll be back next year (hope so)🎄🌻.
November 17, 2025 at 8:51 PM
Nearly one year visiting in EBC, Uppsala university. Nice community and coffee, fresh air and comfortable workplace. I'll be back next year (hope so)🎄🌻.
Reposted by MEPGT
NEW pub in @science.org 🥳
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
November 13, 2025 at 8:34 PM
NEW pub in @science.org 🥳
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Reposted by MEPGT
Amazing output of our #BIEN - #bigdata on #plants - project! Big congrats & thx to @gabrielmoulatlet.bsky.social for leading! 🌿🌴🌲🌳🌐🌍🌎 #macroecology
in "General laws of biodiversity: Climatic niches predict plant range size and ecological dominance globally", we provide key insights into species’ vulnerability to environmental change and the processes that structure biodiversity at global scales.
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
General laws of biodiversity: Climatic niches predict plant range size and ecological dominance globally | PNAS
A longstanding question in ecology asks whether or not species that achieve large
geographic ranges also have large climatic niche breadths. Using ...
www.pnas.org
November 13, 2025 at 10:29 PM
Amazing output of our #BIEN - #bigdata on #plants - project! Big congrats & thx to @gabrielmoulatlet.bsky.social for leading! 🌿🌴🌲🌳🌐🌍🌎 #macroecology
Reposted by MEPGT
I'm excited to read this paper: "Genetic offset and vulnerability modeling under climate change scenarios: common misinterpretations and violations of evolutionary principles" doi.org/10.1093/evol...
Genetic offset and vulnerability modeling under climate change scenarios: common misinterpretations and violations of evolutionary principles
Abstract. Genetic offset models have become a popular component of the landscape genetics toolbox, with over 600 peer-reviewed publications applying these
doi.org
November 12, 2025 at 5:42 PM
I'm excited to read this paper: "Genetic offset and vulnerability modeling under climate change scenarios: common misinterpretations and violations of evolutionary principles" doi.org/10.1093/evol...
Reposted by MEPGT
Pleased to share our latest paper led by @tomlewin.bsky.social, now out in @currentbiology.bsky.social! We present the first chromosome-level genome of a phoronid and show that shared chromosomal fusions unite phoronids and bryozoans as sister groups.
www.cell.com/current-biol...
www.cell.com/current-biol...
November 7, 2025 at 4:21 PM
Pleased to share our latest paper led by @tomlewin.bsky.social, now out in @currentbiology.bsky.social! We present the first chromosome-level genome of a phoronid and show that shared chromosomal fusions unite phoronids and bryozoans as sister groups.
www.cell.com/current-biol...
www.cell.com/current-biol...
Reposted by MEPGT
New publication out, highlighting the link between genetic diversity (GD) and policy! 🧬📜
"Conserving genetic diversity in accordance with the Global Biodiversity Framework"
www.annualreviews.org/content/jour...
We summarize the highlights in this thread. 🧵
"Conserving genetic diversity in accordance with the Global Biodiversity Framework"
www.annualreviews.org/content/jour...
We summarize the highlights in this thread. 🧵
Conserving Genetic and Genomic Diversity in Accordance with the Global Biodiversity Framework
Adopted in December 2022, the Kunming–Montreal Global Biodiversity Framework (KMGBF) under the Convention on Biological Diversity outlines a visionary road map guiding humanity's relationship wit...
www.annualreviews.org
November 9, 2025 at 4:23 PM
New publication out, highlighting the link between genetic diversity (GD) and policy! 🧬📜
"Conserving genetic diversity in accordance with the Global Biodiversity Framework"
www.annualreviews.org/content/jour...
We summarize the highlights in this thread. 🧵
"Conserving genetic diversity in accordance with the Global Biodiversity Framework"
www.annualreviews.org/content/jour...
We summarize the highlights in this thread. 🧵
Reposted by MEPGT
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Reposted by MEPGT
. @pnas.org just published the final version of our manuscript on how generation time and effective population size interact to shape vertebrate germline mutation rates, led by Luke Zhu and Annabel Beichman: www.pnas.org/doi/10.1073/...
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
May 21, 2025 at 7:33 PM
. @pnas.org just published the final version of our manuscript on how generation time and effective population size interact to shape vertebrate germline mutation rates, led by Luke Zhu and Annabel Beichman: www.pnas.org/doi/10.1073/...
Reposted by MEPGT
📣Online NOW!
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
Estimation of demography and mutation rates from one million haploid genomes
Samples of millions of genomes provide substantial information about recent demography
and mutation, but standard population-genetic methods make assumptions not met in
these data. We introduce DR EVI...
www.cell.com
August 13, 2025 at 2:40 PM
📣Online NOW!
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
Reposted by MEPGT
Our new @science.org paper is out! Cuckoos and hosts are locked in a coevolutionary arms race over egg mimicry.
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
Genomic architecture of egg mimicry and its consequences for speciation in parasitic cuckoos
Host-parasite arms races facilitate rapid evolution and can fuel speciation. Cuculus cuckoos are deceptive egg mimics that exhibit a broad diversity of counterfeit egg phenotypes, representing host-ad...
doi.org
October 30, 2025 at 7:15 PM
Our new @science.org paper is out! Cuckoos and hosts are locked in a coevolutionary arms race over egg mimicry.
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!
doi.org/10.1126/scie...
🧵1/6
Reposted by MEPGT
Chongyi's paper from the biodiversity exploratories (@bexplo.bsky.social) is finally out ! How do genomic traits interact with community ecology?
Antropogenic
havoc. Communities shake.
Genomes grow and break.
doi.org/10.1111/1365...
Antropogenic
havoc. Communities shake.
Genomes grow and break.
doi.org/10.1111/1365...
Context‐dependent relationships between genomic traits and plant performance in temperate grasslands
Read the free Plain Language Summary for this article on the Journal blog.
doi.org
August 6, 2025 at 7:45 AM
Chongyi's paper from the biodiversity exploratories (@bexplo.bsky.social) is finally out ! How do genomic traits interact with community ecology?
Antropogenic
havoc. Communities shake.
Genomes grow and break.
doi.org/10.1111/1365...
Antropogenic
havoc. Communities shake.
Genomes grow and break.
doi.org/10.1111/1365...
Reposted by MEPGT
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.
PNAS: When islands collide: Divergence predicts outcomes of secondary contact during the fusion of Sulawesi’s paleo-archipelago, doi.org/10.1073/pnas...
October 28, 2025 at 9:59 AM
PNAS: When islands collide: Divergence predicts outcomes of secondary contact during the fusion of Sulawesi’s paleo-archipelago, doi.org/10.1073/pnas...
Reposted by MEPGT
Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...
Applied Biostatistics
ybrandvain.github.io
October 24, 2025 at 2:47 PM
Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...
🙌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...
doi.org/10.1186/s130...
ParaMask: identify multicopy genomic regions, corrects major biases in WGS data
github.com/Fulgione-gro...
October 24, 2025 at 11:17 AM
🙌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...
doi.org/10.1186/s130...
ParaMask: identify multicopy genomic regions, corrects major biases in WGS data
github.com/Fulgione-gro...
Reposted by MEPGT
My main PhD work @monteirolab.bsky.social is now in @natecoevo.nature.com! We found a Hox gene promoter that helps butterflies🦋adjust their wing eyespots in response to seasonal temperatures🍃🍂, shedding light on the evolutionary origin of phenotypic plasticity. 1/9 www.nature.com/articles/s41...
October 24, 2025 at 10:16 AM
My main PhD work @monteirolab.bsky.social is now in @natecoevo.nature.com! We found a Hox gene promoter that helps butterflies🦋adjust their wing eyespots in response to seasonal temperatures🍃🍂, shedding light on the evolutionary origin of phenotypic plasticity. 1/9 www.nature.com/articles/s41...
Reposted by MEPGT
Results I'm sad to share but must be told - branching coral are now functionally extinct in Florida - to learn more check out the full study www.science.org/doi/10.1126/... and our personal summary theconversation.com/2-iconic-cor...
Heat-driven functional extinction of Caribbean Acropora corals from Florida’s Coral Reef
In 2023, a record-setting marine heat wave triggered the ninth mass coral bleaching event on Florida’s Coral Reef (FCR). We examined spatial patterns of heat exposure along the ~560-kilometer length o...
www.science.org
October 23, 2025 at 6:26 PM
Results I'm sad to share but must be told - branching coral are now functionally extinct in Florida - to learn more check out the full study www.science.org/doi/10.1126/... and our personal summary theconversation.com/2-iconic-cor...
Reposted by MEPGT
If you like genomics, speciation, and primates, this PhD position is for you! Unraveling the genomic architecture of speciation and gene flow in guenons, a diverse group of African monkeys. Funding through DTP. Do reach out with questions! #genomics #genome_assembly
evol.mcmaster.ca/brian/evoldi...
evol.mcmaster.ca/brian/evoldi...
October 23, 2025 at 3:11 PM
If you like genomics, speciation, and primates, this PhD position is for you! Unraveling the genomic architecture of speciation and gene flow in guenons, a diverse group of African monkeys. Funding through DTP. Do reach out with questions! #genomics #genome_assembly
evol.mcmaster.ca/brian/evoldi...
evol.mcmaster.ca/brian/evoldi...