junishigohoka.bsky.social
Jun Ishigohoka
@junishigohoka.bsky.social
180 followers 220 following 33 posts
Evolutionary biologist Tübingen < Plön < Kiel < Sapporo < Tokyo https://junishigohoka.github.io/
junishigohoka.github.io
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junishigohoka.bsky.social
Jun Ishigohoka @junishigohoka.bsky.social · Jan 27
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...
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
doi.org
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Reposted by Jun Ishigohoka
nature.com
Nature @nature.com · 3d
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
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.
go.nature.com
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junishigohoka.bsky.social
Jun Ishigohoka @junishigohoka.bsky.social · 8d
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
1
Reposted by Jun Ishigohoka
plosbiology.org
PLOS Biology @plosbiology.org · 9d
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
Rhythmic metabolites in the E19 SCN peak during the day. Majority of rhythmic lipids and polar metabolites in the E19 SCN peak during the day, while there are more diverse phase clusters in the developed P28 SCN postweaning. Polar metabolites and lipids identified as rhythmic in E19 SCN (E19 clusters 1, top, and 2, bottom) were divided into subgroups based on hierarchical K-means clustering. Line plots on the left show traces of the normalized level of each rhythmic compound in each corresponding cluster. Bar plots on the right represent the lipid classes and polar metabolites in each rhythmic cluster.
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Reposted by Jun Ishigohoka
oikosjournal.bsky.social
Oikos @oikosjournal.bsky.social · 9d
📜Forum: A trait-based framework for adaptive phenotypic plasticity under global change

vist.ly/48kss

#BehavioralPlasticity #ClimateChange #ExtremeEvents #GeneByEnvironmentInteractions #IntraspecificVariation #MorphologicalPlasticity #PhysiologicalPlasticity #Stochasticity #Variability

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Reposted by Jun Ishigohoka
biorxiv-evobio.bsky.social
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 12d
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
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junishigohoka.bsky.social
Jun Ishigohoka @junishigohoka.bsky.social · 15d
Categorical and semantic perception of the meaning of call types in zebra finches | Science www.science.org/doi/10.1126/...
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...
www.science.org
Reposted by Jun Ishigohoka
luisapallares.bsky.social
Luisa F. Pallares @luisapallares.bsky.social · 20d
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! 💻🧬🪰🔢
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Reposted by Jun Ishigohoka
plosbiology.org
PLOS Biology @plosbiology.org · 19d
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
Scientific productivity gap based on English-language peer-reviewed papers. Shown are the maximum % differences in the number of peer-reviewed papers published by female native English speakers from a high-income country (-45%), female non-native English speakers from a high-income country (-60%), and female non-native English speakers from a lower-middle income country (-70%), compared to male native English speakers from a high-income country (red flag). Credit: Tatsuya Amano
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junishigohoka.bsky.social
Jun Ishigohoka @junishigohoka.bsky.social · 22d
academic.oup.com/jeb/article/...
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
academic.oup.com
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junishigohoka.bsky.social
Jun Ishigohoka @junishigohoka.bsky.social · 23d
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
Reposted by Jun Ishigohoka
gcbias.bsky.social
Graham Coop @gcbias.bsky.social · 27d
Celebrating my 18 year anniversary of thinking I'll learn ggplot2 next month.
jebyrnes.bsky.social
Jarrett Byrnes @jebyrnes.bsky.social · 27d
Me right now reading “It is also the 18th anniversary of ggplot2…”
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Reposted by Jun Ishigohoka
yun-s-song.bsky.social
Yun S. Song @yun-s-song.bsky.social · 28d
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...
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.
doi.org
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junishigohoka.bsky.social
Jun Ishigohoka @junishigohoka.bsky.social · 28d
www.cell.com/current-biol...
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...
www.cell.com
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junishigohoka.bsky.social
Jun Ishigohoka @junishigohoka.bsky.social · Sep 8
"A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact"
academic.oup.com/genetics/art...
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Reposted by Jun Ishigohoka
fandingzhou.bsky.social
fandingzhou.bsky.social @fandingzhou.bsky.social · Sep 5
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...
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Reposted by Jun Ishigohoka
ajblake05.bsky.social
Adam Blake @ajblake05.bsky.social · Jul 10
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/...
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Reposted by Jun Ishigohoka
molbioevol.bsky.social
Molecular Biology and Evolution @molbioevol.bsky.social · Sep 1
@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
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
doi.org
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Reposted by Jun Ishigohoka
danielbolnick.bsky.social
Daniel Bolnick @danielbolnick.bsky.social · Aug 29
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.
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Reposted by Jun Ishigohoka
molbioevol.bsky.social
Molecular Biology and Evolution @molbioevol.bsky.social · Aug 21
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
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
doi.org
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Reposted by Jun Ishigohoka
kitchensjn.bsky.social
James Kitchens @kitchensjn.bsky.social · Aug 19
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

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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...
arxiv.org
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Reposted by Jun Ishigohoka
molbioevol.bsky.social
Molecular Biology and Evolution @molbioevol.bsky.social · Aug 20
@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
MBE - Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource
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Reposted by Jun Ishigohoka
evolletters.bsky.social
Evolution Letters @evolletters.bsky.social · Aug 18
The evolution of reversible plasticity in stable environments
doi.org/10.1093/evle...

Now in @evolletters.bsky.social by Nicole Walasek et al.
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
doi.org
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junishigohoka.bsky.social
Jun Ishigohoka @junishigohoka.bsky.social · Aug 16
www.cell.com/current-biol...
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...
www.cell.com
junishigohoka.bsky.social
Jun Ishigohoka @junishigohoka.bsky.social · Aug 14
www.nature.com/articles/s41...
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 ...
www.nature.com
1
Reposted by Jun Ishigohoka
jrossibarra.bsky.social
Jeffrey Ross-Ibarra @jrossibarra.bsky.social · Aug 11
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...
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