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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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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

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 2d

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

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Reposted by Jun Ishigohoka

Kaiser Lab @clocksevolution.bsky.social · 25d

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

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 ...

www.biorxiv.org

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Reposted by Jun Ishigohoka

bioRxiv Genomics @biorxiv-genomic.bsky.social · 3d

Read mismapping from segmental duplications drives spurious trans associations https://www.biorxiv.org/content/10.1101/2025.10.08.681258v1

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Reposted by Jun Ishigohoka

Kaiser Lab @clocksevolution.bsky.social · 3d

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

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Reposted by Jun Ishigohoka

Nature @nature.com · 6d

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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Jun Ishigohoka @junishigohoka.bsky.social · 11d

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

Reposted by Jun Ishigohoka

PLOS Biology @plosbiology.org · 13d

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

Oikos @oikosjournal.bsky.social · 13d

📜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 Evolutionary Biology @biorxiv-evobio.bsky.social · 16d

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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Jun Ishigohoka @junishigohoka.bsky.social · 18d

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

Luisa F. Pallares @luisapallares.bsky.social · 23d

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

PLOS Biology @plosbiology.org · 23d

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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Jun Ishigohoka @junishigohoka.bsky.social · 25d

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

Jun Ishigohoka @junishigohoka.bsky.social · 27d

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

Graham Coop @gcbias.bsky.social · Sep 11

Celebrating my 18 year anniversary of thinking I'll learn ggplot2 next month.

Jarrett Byrnes @jebyrnes.bsky.social · Sep 11

Me right now reading “It is also the 18th anniversary of ggplot2…”

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Reposted by Jun Ishigohoka

Yun S. Song @yun-s-song.bsky.social · Sep 11

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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Jun Ishigohoka @junishigohoka.bsky.social · Sep 10

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

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 · 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

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

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

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

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

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

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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