Jun Ishigohoka
@junishigohoka.bsky.social
📤 186
📥 238
📝 42
Evolutionary biologist Tübingen < Plön < Kiel < Sapporo < Tokyo
https://junishigohoka.github.io/
pinned post!
Happy to share our new paper OA in Genetics. We show that population genomic methods based on ARGs (ancestral recombination graphs i.e. genetic ancestry along chromosomes) for demography inference can be biased when applied to genomes with wide high-recombining regions.
doi.org/10.1093/gene...
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High-recombining genomic regions affect demography inference based on ancestral recombination graphs
Abstract. Multiple methods of demography inference are based on the ancestral recombination graph. This powerful approach uses observed mutations to model
https://doi.org/10.1093/genetics/iyaf004
10 months ago
1
30
19
reposted by
Jun Ishigohoka
Yun Deng
3 days ago
Work from my amazing undergrad
@leyan-wang.bsky.social
is just preprinted! TL;DR: If you worry that ARG methods might fail on unphased data due to phasing errors, you may not need to. Check it out & consider reposting to support a great young scientist!
add a skeleton here at some point
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www.jneurosci.org/content/45/4...
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The Hidden Benefits of Noise: Low-Frequency tRNS and Dynamic Visual Noise Enhance Visual Processing
Sensory and perceptual processing are inherently shaped by both internal and external noise sources. While noise is typically seen as disruptive, it can, under certain conditions, enhance the detectio...
https://www.jneurosci.org/content/45/48/e0853252025
3 days ago
0
0
0
reposted by
Jun Ishigohoka
Dirk Metzler
3 days ago
PhD position available for theoretical and statistical modeling in my joint
@gevol.bsky.social
project with
@luisapallares.bsky.social
on the evolution of transcriptional variability and its role in adaptation and evolutionary innovation. See
job-portal.lmu.de/jobposting/6...
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PhD candidate in biology — theoretical and statistical modeling (m/f/x)
https://job-portal.lmu.de/jobposting/6a8b9208b560e8b1abe95e8a6fa3e4a1bebb35840
0
5
12
www.nature.com/articles/s41...
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Progressive coevolution of the yeast centromere and kinetochore - Nature
Thousands of centromeres were identified and tracked across two major fungal clades, showing that new centromeres spread progressively and that the kinetochore acts as a filter to determine which new ...
https://www.nature.com/articles/s41586-025-09779-1
3 days ago
0
0
1
www.biorxiv.org/content/10.1...
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Mean fitness is maximized in small populations under stabilizing selection on highly polygenic traits
Stabilizing selection commonly acts on complex traits that affect individual fitness. Here, we relate mean fitness under stabilizing selection to population size and trait architecture, using a simple...
https://www.biorxiv.org/content/10.1101/2025.11.17.688329v1
10 days ago
0
1
0
reposted by
Jun Ishigohoka
bioRxiv Evolutionary Biology
11 days ago
Parallel and non-parallel features of adaptive radiation in Yucatan pupfishes
https://www.biorxiv.org/content/10.1101/2025.11.17.688971v1
0
2
2
reposted by
Jun Ishigohoka
Jesper Boman
11 days ago
Changing Views on Speciation
onlinelibrary.wiley.com/doi/10.1111/...
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Changing Views on Speciation
Our understanding of speciation processes is constantly changing. Two important concepts that have influenced thinking over the long term are the isolation and the genic views of speciation. However,...
https://onlinelibrary.wiley.com/doi/10.1111/mec.70175
0
3
2
reposted by
Jun Ishigohoka
MPI for Evolutionary Biology
15 days ago
Big cheers from MPI for Evolutionary Biology! 🎉 Our alumna Dr. Christin Nyhoegen wins the KlarText Prize 2025 for her piece “Penicillin and a Small Dose of Mathematics.” She shows how math helps improve antibiotic treatments and prevent resistance. 👏
#KlarTextPreis
#MPIEvolBio
#ScienceCommunication
0
18
5
reposted by
Jun Ishigohoka
EvolDir
18 days ago
Postdoc position available at Max Planck Institute, Germany, focusing on the genetic basis of polygenic traits in Drosophila. Applications due by Dec 22, 2025. More info:
[email protected]
.
#postdoc
0
1
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Next year Ig Nobel Electrostatics facilitate midair host attachment in parasitic jumping nematodes | PNAS
www.pnas.org/doi/10.1073/...
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Electrostatics facilitate midair host attachment in parasitic jumping nematodes | PNAS
Jumping can be hazardous for entomopathogenic nematodes (EPNs) as those that fail to attach to an insect host face death by predation or starvation...
https://www.pnas.org/doi/10.1073/pnas.2503555122#sec-2
about 1 month ago
0
4
1
elifesciences.org/articles/105...
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The general version of Hamilton’s rule
The flexibility of the general version of Hamilton's rule allows the rule to match the complexity of the model of social behaviour, or the complexity implied by the data.
https://elifesciences.org/articles/105065?utm_source=bluesky&utm_medium=social&utm_campaign=organic_assessment
about 1 month ago
0
1
1
A mosaic of modular variation at a single gene underpins convergent plumage coloration | Science
www.science.org/doi/10.1126/...
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A mosaic of modular variation at a single gene underpins convergent plumage coloration
The reshuffling of genomic variation from multiple origins is an important contributor to phenotypic diversification, yet insights into the evolutionary trajectories of this combinatorial process and ...
https://www.science.org/doi/10.1126/science.ado8005
about 1 month ago
0
1
0
reposted by
Jun Ishigohoka
PLOS Biology
about 1 month ago
Winter-active
#herbivores
struggle to get
#nitrogen
in winter, when dietary
#protein
is scarce. This study shows that winter protein restriction drives gut
#microbiome
remodeling in the
#pika
, increasing microbiome N recycling & helping maintain protein balance
@plosbiology.org
🧪
plos.io/4nZ86I6
0
10
3
reposted by
Jun Ishigohoka
MPI for Biological Intelligence
about 1 month ago
What is the genetic basis of bird migration? Find out in our next keynote lecture by Miriam Liedvogel
@genmig.bsky.social
, Professor of Ornithology at the Uni Oldenburg and Director of the Institute of Avian Research! 📍October 21 at 11am in House 4 in Seewiesen Art by
@somedonkey.bsky.social
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13
4
www.biorxiv.org/content/10.1...
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The demographic history, genomic variation, and transcontinental genotype-phenotype-environment map of mungbean
The breeding of mungbean, a crucial Asian legume, has been hampered by the lack of genomic resources. The International Mungbean Improvement Network (IMIN) aims to ensure global access to diverse germ...
https://www.biorxiv.org/content/10.1101/2025.10.16.682767v1
about 1 month ago
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0
0
journals.plos.org/plosbiology/...
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A large-scale study across the avian clade identifies ecological drivers of neophobia
Neophobia (the aversive response to novelty) varies considerably across species and individuals, and can impact adaptability and survival. This study assesses neophobia in 1400 subjects from 136 bird ...
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003394
about 2 months ago
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1
1
reposted by
Jun Ishigohoka
Luisa F. Pallares
about 2 months ago
We have put together a comprehensive eQTL map for D. melanogaster using thousands of genetically diverse flies 🪰🪰🪰🪰🪰 We hope this helps -as similar resources have done in yeast and humans- to understand how genetic variation 🧬 regulates complex traits variation 🪰 via transcriptional regulation ⬆️⬇️
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Saturating the eQTL map in Drosophila: Genome-wide patterns of cis and trans regulation of transcriptional variation in outbred populations
Pallares et al. collect over a thousand RNA-seq and DNA samples from Drosophila melanogaster flies to investigate the genetic basis of gene expression variation. They find eQTLs for 98% of the genes a...
https://www.cell.com/cell-genomics/fulltext/S2666-979X(25)00289-7
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www.nature.com/articles/s41...
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Learned use of an innate sound-meaning association in birds - Nature Ecology & Evolution
Over 20 species of geographically and phylogenetically diverse bird species produce convergent whining vocalizations towards their respective brood parasites. Model presentation and playback experimen...
https://www.nature.com/articles/s41559-025-02855-9
about 2 months ago
0
1
1
reposted by
Jun Ishigohoka
PLOS Biology
about 2 months ago
Genetic architectures of
#ComplexTraits
vary widely.
@yuvalsim.bsky.social
@jkpritch.bsky.social
@gs2747.bsky.social
&co show these diffs arise from mutational target size & heritability per site; when controlled for, all tested traits have similar architectures
@plosbiology.org
🧪
plos.io/47mZXqT
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9
3
reposted by
Jun Ishigohoka
bioRxiv Evolutionary Biology
about 2 months ago
An empirical long-term competition among natural yeast isolates reveals that short-term fitness largely but not entirely predicts long-term outcomes
https://www.biorxiv.org/content/10.1101/2025.10.09.681448v1
0
1
2
reposted by
Jun Ishigohoka
Kaiser Lab
2 months ago
How can larval
#competition
for space, adult
#reproductive
#timing
and the
#tides
interact to produce different timing strains, aka
#chronotypes
, of the marine insect
#Clunio
? See our latest preprint with Alec Jacobsen &
@gokhalecs.bsky.social
#evolution
#ecology
#chronobiology
#circalunar
#clock
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How competition can drive allochronic divergence: a case study in the marine midge, Clunio marinus
Synchronizing mating to extrinsic environmental cycles can increase the chance of successful reproduction. However, the resulting temporally-assorted mating may precipitate speciation if coupled with ...
https://www.biorxiv.org/content/10.1101/2025.09.16.676472v1
1
8
2
reposted by
Jun Ishigohoka
bioRxiv Genomics
about 2 months ago
Read mismapping from segmental duplications drives spurious trans associations
https://www.biorxiv.org/content/10.1101/2025.10.08.681258v1
0
2
1
reposted by
Jun Ishigohoka
Kaiser Lab
about 2 months ago
WE ARE HIRING! Please spread widely!
#Postdoc
in
#Evolutionary
#Genomics
->
www.mpg.de/25524526/
#Postdoc
in
#Molecular
#Biology
&
#Cell
#Signalling
->
www.mpg.de/25524509/
@mpi-evolbio.bsky.social
@maxplanck.de
#ScienceJobs
#EvoBio
#MolBio
#Ecology
#Chronobiology
#Marine
#EntoSky
#Biodiversity
0
12
14
reposted by
Jun Ishigohoka
Nature
about 2 months ago
This year’s Nobel Prize in Physiology or Medicine has been awarded to three scientists for discovering a class of immune cells that help to prevent the body from attacking its own tissues
go.nature.com/48QDdAJ
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Medicine Nobel goes to scientists who revealed secrets of immune system ‘regulation’
Mary Brunkow, Fred Ramsdell and Shimon Sakaguchi discovered cells that protect the body from autoimmune diseases.
https://go.nature.com/48QDdAJ
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www.biorxiv.org/content/10.1...
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Predator induced phenotypes are inherited over four generations in genetically identical Daphnia lumholtzi
Environmental variation can induce phenotypic changes through adaptation of populations and acclimation of individuals. Whereas adaptation can lead to persistent changes within a population via allele...
https://www.biorxiv.org/content/10.1101/2025.09.28.679097v1
about 2 months ago
0
0
2
reposted by
Jun Ishigohoka
PLOS Biology
2 months ago
How are
#circadian
rhythms established during development? This study shows that maternal metabolic signals oscillate in the fetal
#SCN
before the endogenous
#clock
becomes functional, offering a plausible mechanism for maternal entrainment of the developing clock
@plosbiology.org
🧪
plos.io/3VD45fZ
0
11
5
reposted by
Jun Ishigohoka
Oikos
2 months ago
📜Forum: A trait-based framework for adaptive phenotypic plasticity under global change
vist.ly/48kss
#BehavioralPlasticity
#ClimateChange
#ExtremeEvents
#GeneByEnvironmentInteractions
#IntraspecificVariation
#MorphologicalPlasticity
#PhysiologicalPlasticity
#Stochasticity
#Variability
1
8
4
reposted by
Jun Ishigohoka
bioRxiv Evolutionary Biology
2 months ago
Evolution of the rate, spectrum, and fitness effects of mutation under minimal selection in Caenorhabditis elegans
https://www.biorxiv.org/content/10.1101/2025.09.24.678306v1
0
1
1
Categorical and semantic perception of the meaning of call types in zebra finches | Science
www.science.org/doi/10.1126/...
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Categorical and semantic perception of the meaning of call types in zebra finches
Vocal communication in social animals involves the production and perception of various calls that ethologists categorize into call types based on their acoustical structure and behavioral context. Wh...
https://www.science.org/doi/10.1126/science.ads8482?utm_campaign=ScienceMagazine&utm_medium=ownedSocial&utm_source=twitter
2 months ago
0
0
1
reposted by
Jun Ishigohoka
Luisa F. Pallares
2 months ago
Jun
@junishigohoka.bsky.social
is the first postdoc of the lab. Today, during
#postdocappreciationweek
, I just want to let you all know that Jun is t h e b e s t! 🤓 I'm very happy he decided to join us here at
@mpi-bio-fml.bsky.social
. Looking forward to our papers together, Jun! 💻🧬🪰🔢
0
26
2
reposted by
Jun Ishigohoka
PLOS Biology
2 months ago
How do your
#linguistic
,
#economic
&
#gender
backgrounds impact your
#scientific
productivity?
@tatsuya-amano.bsky.social
& co reveal that being a woman, a non-native English speaker, and from a low-income country is associated with a 70% reduction in productivity
@plosbiology.org
🧪
plos.io/4n3RLRQ
1
15
10
academic.oup.com/jeb/article/...
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Distribution theories for genetic line of least resistance and evolvability measures
Abstract. Quantitative genetic theory on multivariate character evolution predicts that a population’s response to directional selection is biased towards
https://academic.oup.com/jeb/article/37/12/1576/7657502
2 months ago
0
1
0
www.biorxiv.org/content/10.1...
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A model-free method for genealogical inference without phasing and its application for topology weighting
Recent advances in methods to infer and analyse ancestral recombination graphs (ARGs) are providing powerful new insights in evolutionary biology and beyond. Existing inference approaches tend to be d...
https://www.biorxiv.org/content/10.1101/2025.07.22.666161v2
2 months ago
0
0
0
reposted by
Jun Ishigohoka
Graham Coop
3 months ago
Celebrating my 18 year anniversary of thinking I'll learn ggplot2 next month.
add a skeleton here at some point
4
85
6
reposted by
Jun Ishigohoka
Yun S. Song
3 months ago
SINGER, our ARG inference method, is finally published and freely available online:
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
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Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes - Nature Genetics
SINGER is a method for creating ancestral recombination graphs to understand the genealogical history of genomes. The method has increased speed, and thus scalability, without sacrificing accuracy.
https://doi.org/10.1038/s41588-025-02317-9
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www.cell.com/current-biol...
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Learned precision tool use in carrion crows
Moll et al. show that carrion crows—which do not habitually use tools in the wild—can be trained to use a stick tool as an extension of their body. Trained crows flexibly adjust tool orientation and d...
https://www.cell.com/current-biology/fulltext/S0960-9822(25)01100-5
3 months ago
0
0
1
"A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact"
academic.oup.com/genetics/art...
add a skeleton here at some point
3 months ago
0
3
2
reposted by
Jun Ishigohoka
3 months ago
Gene expression changes aren’t just about mean shifts — variability shifts matter too, especially for aging. We're thrilled to introduce QRscore, a flexible non-parametric framework for detecting shifts in mean and variance across conditions.
doi.org/10.1016/j.cr...
1
12
4
reposted by
Jun Ishigohoka
Adam Blake
5 months ago
Our new paper is now out in
@jexpbiol.bsky.social
!!! We had all sorts of fun generating LED stimuli for mosquitos to investigate their visual preferences in the presence of different odors. The paper is open access and available here:
journals.biologists.com/jeb/article/...
2
37
15
reposted by
Jun Ishigohoka
Molecular Biology and Evolution
3 months ago
@anaignatieva.bsky.social
et al. model the impact of recombination on the correlation structure between genealogical local trees, and develop a statistical test to identify clades spanning unexpectedly long genomic regions. 🔗
doi.org/10.1093/molbev/msaf190
#evobio
#molbio
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The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies
Abstract. Recent breakthroughs have enabled the accurate inference of large-scale genealogies. Through modelling the impact of recombination on the correla
https://doi.org/10.1093/molbev/msaf190
0
3
1
reposted by
Jun Ishigohoka
Daniel Bolnick
3 months ago
In the earliest stages of adaptive introgression, beneficial immigration can drive genome-wide changes. In a new preprint
www.biorxiv.org/content/10.1...
colleagues & I document exceptionally rapid genomic introgression in a lake population of stickleback.
2
37
17
reposted by
Jun Ishigohoka
Molecular Biology and Evolution
3 months ago
Stone, Platig,
@johnquackenbush.bsky.social
&
@maudfagny.bsky.social
analyzed heritability in 29 tissue-specific eQTL networks - network structure could amplify genotype–phenotype connections and buffer deleterious effects on other traits. 🔗
doi.org/10.1093/molbev/msaf174
#evobio
#molbio
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The Importance of Regulatory Network Structure for Complex Trait Heritability and Evolution
Abstract. Complex traits are determined by many loci—mostly regulatory elements—that, through combinatorial interactions, can affect multiple traits. Such
https://doi.org/10.1093/molbev/msaf174
0
4
1
reposted by
Jun Ishigohoka
James Kitchens
3 months ago
Excited to share our new preprint for the tskit_arg_visualizer Python package! ARGs can sometimes feel like a black box, so
@yanwong.bsky.social
and I have been developing a method to programmatically drawing these graphs. 🔗
arxiv.org/abs/2508.03958
1/6
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tskit_arg_visualizer: interactive plotting of ancestral recombination graphs
Summary: Ancestral recombination graphs (ARGs) are a complete representation of the genetic relationships between recombining lineages and are of central importance in population genetics. Recent brea...
https://arxiv.org/abs/2508.03958
2
63
37
reposted by
Jun Ishigohoka
Molecular Biology and Evolution
3 months ago
@jcbnunez.bsky.social
et al. present an expanded release of the community-generated resource Drosophila Evolution over Space and Time (DEST 2.0), and showcase it by studying the species' demographic history and signatures of adaptation. 🔗
doi.org/10.1093/molbev/msaf132
#evobio
#molbio
#drosophila
1
19
10
reposted by
Jun Ishigohoka
Evolution Letters
3 months ago
The evolution of reversible plasticity in stable environments
doi.org/10.1093/evle...
Now in
@evolletters.bsky.social
by Nicole Walasek et al.
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The evolution of reversible plasticity in stable environments
Abstract. Reversible plasticity, i.e., the ability to deconstruct phenotypic specializations based on environmental conditions, is widespread in nature. De
https://doi.org/10.1093/evlett/qraf015
0
36
14
www.cell.com/current-biol...
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dArc1 controls sugar reward valuation in Drosophila melanogaster
Bervoets et al. show that the retrotransposon-derived gene dArc1 is expressed in serotonergic neurons of the Drosophila brain. They found that loss of dArc leads to sugar reward overvaluation during l...
https://www.cell.com/current-biology/abstract/S0960-9822(25)00957-1
4 months ago
0
0
0
www.nature.com/articles/s41...
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The genomic origin of the unique chaetognath body plan - Nature
Genomic, single-cell transcriptomic and epigenetic analyses show that chaetognaths, following extensive gene loss in the gnathiferan lineage, relied on newly evolved genes and lineage-specific tandem ...
https://www.nature.com/articles/s41586-025-09403-2?WT.ec_id=NATURE-202508
4 months ago
0
1
0
reposted by
Jun Ishigohoka
Jeffrey Ross-Ibarra
4 months ago
Our paper showing that variation in transcription factor binding sites underlies the majority of additive genetic variance for phenotypic variation in maize is finally out! Sadly they didn't use our suggested cover image below (made by the inimitable Andi Kur).
www.nature.com/articles/s41...
6
252
79
reposted by
Jun Ishigohoka
Jason Shepherd
4 months ago
Congrats to Sven Bervoets and co-authors for our paper on fly Arc now out in
@currentbiology.bsky.social
!! This was an awesome collaboration with
@thecaronlab.bsky.social
’s lab
@utah.edu
authors.elsevier.com/c/1lZlk3QW8S...
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45
12
reposted by
Jun Ishigohoka
Yun S. Song
6 months ago
The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs:
probgen2026.github.io
Please help spread the news.
loading . . .
Home - ProbGen 2026
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https://probgen2026.github.io
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