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Nikhil Sharma

@nikhil-sharma.bsky.social
74 followers 135 following 6 posts

Postdoctoral researcher at MPI for Evolutionary Biology. Mathematical biology, evolutionary dynamics, evolutionary graph theory.

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Reposted by Nikhil Sharma
Michael Manhart @michaelmanhart.bsky.social · 25/09/2026
Two interesting Ph.D. student opportunities in microbial ecology, evolution, and systems biology, in labs I think very highly of: Tobias Bollenbach, U. Cologne (bpsb.uni-koeln.de/open-positions) Andrew Letten, U. Queensland (evoldir.net/brian/evoldi...)
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Kaiser Lab @clocksevolution.bsky.social · 17/09/2026
We have a new #preprint on #lunar #reproductive #timing as a #magictrait in #speciation www.biorxiv.org/content/10.6... with former PhD students Alexander Jacobsen 🧪💻 Runa Ekrem 🦟🌊 🙏 Big thanks to both for the great work! #EvoBio #barriers #Chronobiology #circadian #MarineEcology
Full moon and new moon strains from Roscoff differ in lunar reproductive timing (A). Genotyping of 11 divergent loci (B) in 797 field-caught individuals shows that thetwo timing strains are distinct genetic entities (C).
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SMB - Society for Mathematical Biology @smbmathbiology.bsky.social · 03/09/2026
Here's a new #BullMathBio paper by @yuxuanzhao.bsky.social, Kaisheng Zhu, Yefei Zhang, and @danielcooney1.bsky.social on Pattern Formation in a Spatial Public Goods Dilemma due to Diffusive or Directed Motion. 🧪 link.springer.com/article/10.1...
link.springer.com
Pattern Formation in a Spatial Public Goods Dilemma due to Diffusive or Directed Motion - Bulletin of Mathematical Biology
The costly provision of public goods serves as a model problem for the evolution of cooperative behavior, presenting a social dilemma between the collective benefits of shared resources and the indivi...
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Daniel Cooney @danielcooney1.bsky.social · 26/08/2026
I am really happy to share this new preprint with Olivia Clifton and Stephanie Dodson on Kernel-Dependent Pattern Formation in a Population Model with Nonlocal Facilitation and Competition. 🧪 arxiv.org/abs/2608.23964
arxiv.org
Kernel-Dependent Pattern Formation in a Population Model with Nonlocal Facilitation and Competition
Spatial patterns, such as those in dryland vegetation models, have historically been studied in systems of reaction-diffusion systems with pattern onset via a Turing bifurcation from a spatially uni...
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Joshua B. Plotkin @jplotkin.bsky.social · 10/08/2026
Happy to share a new paper led by the terrific Anzhi Sheng. We find that allocation policies that promote cooperation tend to concentrate benefits among the well-connected. And so structured societies must weigh collective success against the inequality it generates. www.nature.com/articles/s41...
Cooperation conflicts with equality when allocating public goods

Anzhi Sheng, Qi Su, Alex McAvoy, Long Wang & Joshua B. Plotkin 
Nature  655, 1217-1225 (2026)

Cooperation is typically seen as the ideal outcome in a social dilemma. Because cooperators are vulnerable to exploitation, much of the literature has focused on mechanisms, such as spatial structure, that support prosocial behaviour and the production of public goods1,2,3,4,5,6,7,8,9,10,11. Yet the rules for distributing these goods also shape behaviour and long-term prosperity. Here we study policies for allocating public goods, comparing equitable allocation, in which returns are proportional to potential contributions, with uniform allocation, in which all individuals receive equal shares. For most social networks, we find that uniform allocation facilitates the spread of cooperation compared with equitable allocation. But this success comes with a cost. Uniform allocation concentrates resources in a small number of highly connected individuals12, whereas peripheral individuals receive fewer benefits and may even be worse off than in a non-cooperative society. We develop a theoretical analysis of the tension between cooperation and equality, and we identify this conflict across diverse empirical social networks. Our results show that inequality may be an unavoidable consequence of allocation policies designed to foster cooperation in spatially heterogeneous populations. The question of how to promote cooperation is therefore incomplete: because policies that facilitate cooperation can also generate social stratification, we must weigh the benefits of cooperation against the inequality that accompanies it.
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theobioarne.bsky.social @theobioarne.bsky.social · 21/07/2026
What can we learn from disruptions of seasonal patterns of disease during the pandemic? A new paper by @michaelsieber.bsky.social in PLOS Global Public Health, journals.plos.org/globalpublic..., was featured in the German news such as @zeit.de or @spiegel.de - and may be of interest also here. 1/3
journals.plos.org
Shifts in seasonal timing of respiratory diseases and causes of death following a natural pandemic event
Seasonal respiratory infections typically surge within a limited time window, but what determines the exact timing within a given year is not well understood. Major causes of death show a similar seas...
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Nikhil Sharma @nikhil-sharma.bsky.social · 24/04/2026
Congratulations Amor! @amordamatac.bsky.social
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Chaitanya Gokhale @gokhalecs.bsky.social · 24/02/2026
Thrilled to share our new paper with the brilliant @srishtipatil.bsky.social & @sabinenoebel.bsky.social ! 🎉 Can mate copying maintain phenotypic diversity with multiple male options to choose from? find out @ doi.org/10.1073/pnas... @dkfz.bsky.social @unihalle.bsky.social @cctb-wue.bsky.social
doi.org
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...
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Nikoleta Glynatsi @nikoletaglyn.bsky.social · 03/11/2025
🗞️📣 New paper "Exact conditions for evolutionary stability in indirect reciprocity under noise" with @chilbe.bsky.social & @yohm.bsky.social How can cooperation persist in large groups of unrelated individuals? Reputation 🗣️ But which social norms make this stable, even when mistakes happen? 🧵(1/6)
journals.plos.org
Exact conditions for evolutionary stability in indirect reciprocity under noise
Author summary Understanding how cooperation can evolve and be sustained is a central question in evolutionary biology and social science. One prominent explanation is indirect reciprocity, where indi...
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Claudia Bank @cbank.bsky.social · 28/10/2025
We have an open PhD position (application deadline 9 January 2026) in "Theory of fitness landscapes" at @unibe.ch 🤓⛰️📊👩‍💻🎓: banklab.github.io/positions/ Please share widely! #QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
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Paul Rainey @paulbrainey.bsky.social · 30/10/2025
Many are painfully aware that the environment within which we function -- as scientists -- needs fixing. We've come up with a proposal for academic renewal. It's not perfect, but its a start. Input, comments, suggestions are welcome. Making a difference matters 👇 doi.org/10.5281/zeno...
doi.org
Pursuit of Knowledge: A Charter for Academic Renewal
This paper identifies systemic problems in how academic research is structured, evaluated, and supported. It argues for a realignment of incentives and institutional cultures to restore trust, enable ...
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Yuval Simons @yuvalsim.bsky.social · 24/10/2025
Why do complex traits differ in their genetic architecture? In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits. Thread: journals.plos.org/plosbiology/...
journals.plos.org
Simple scaling laws control the genetic architectures of human complex traits
Genome-wide association studies have revealed that the genetic architectures of complex traits vary widely. This study shows that differences in architectures of highly polygenic traits arise mainly f...
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Masaru Kanekiyo @kanekiyom.bsky.social · 14/10/2025
Just out📢 Our new paper published in @natmicrobiol.nature.com describes highly potent cross-neutralizing human monoclonal antibodies against H5Nx influenza viruses. Close collaboration with Sara Andrews lab and Tongqing Zhou lab at the VRC. Link to the article: rdcu.be/eKV9T 1/2
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Luisa F. Pallares @luisapallares.bsky.social · 14/10/2025
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 ⬆️⬇️
cell.com
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...
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Kaiser Lab @clocksevolution.bsky.social · 17/09/2025
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
biorxiv.org
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 ...
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Kaiser Lab @clocksevolution.bsky.social · 09/10/2025
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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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 30/09/2025
Adaptive Dynamics of Quantitative Traits in a SteadilyChanging Environment www.biorxiv.org/content/10.1101/202…
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Hye Jin Park @hyejinpark.bsky.social · 18/09/2025
Rafting against the evolutionary waterfall! 🚣‍♂️💨 - see our new paper on the challenge of artificial selection of microbial collectives elifesciences.org/articles/97461
elifesciences.org
The success of artificial selection for collective composition hinges on initial and target values
Mathematical modeling uncovers how initial and target compositions limit microbial community selection, as inter-community selection clashes with intra-community selection like a rafter battling a wat...
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Kyle Card @kylejcard.bsky.social · 27/09/2025
Thrilled to share our paper that just came out in PNAS! We asked a deceptively simple question: What happens when S. aureus adapts to vancomycin, a critical first-line antibiotic? 1/5
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Joanna Masel @joannamasel.bsky.social · 16/09/2025
Our new paper @asn-amnat.bsky.social develops a Grand Unified Theory including both exploitative and interference competition doi.org/10.1086/737628. The R* rule of ecology (that 2 species cannot coexist on a single resource), is widely broken, including via a new trade-off we describe. 1/9
doi.org
A Mechanistically Integrated Model of Exploitative and Interference Competition over a Single Resource Produces Widespread Coexistence | The American Naturalist
Abstract Many ecological models treat exploitative competition in isolation from interference competition. Corresponding theory centers around the R* rule, according to which consumers that share a si...
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Michael Hochberg @mkhochb.bsky.social · 11/09/2025
What future does AI hold? With @paulbrainey.bsky.social, we hypothesize that human-AI coevolution is leading to the emergence of a new evolutionary unit of selection. Science fiction or looming fact? Read our paper and judge for yourself. www.pnas.org/doi/10.1073/...
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Deepa Agashe @deepaagashe.bsky.social · 11/09/2025
About 10 years ago, we set up lots of experimental beetle populations, censused monthly. Expecting extinction, I said the workload would drop soon. But they all rescued themselves! 😱 So Vrinda & co kept counting. Many hundreds of thousands of beetles later, we have some neat outcomes. Enjoy!
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Schulenburg Lab Kiel @schulenburglab.bsky.social · 08/09/2025
We are welcoming applications for a full professorship on Molecular and Evolutionary Zoology at Kiel Univerdity, Northern Germany, with fantastic facilities and infrastructure! @uni-kiel.de @crc1182.bsky.social @transevo.bsky.social www.nature.com/naturecareer...
nature.com
W 3 professorship in Molecular and Evolutionary Zoology - Kiel, Schleswig-Holstein (DE) job with Christian-Albrechts-Universität zu Kiel | 12844416
Kiel University aims to attract more qualified women to professorship positions. The Institute of Zoology at the Faculty of Mathematics and Natural...
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Schulenburg Lab Kiel @schulenburglab.bsky.social · 08/09/2025
I am happy to announce publication of our new perspectives paper on applying evolutionary theory to host-microbiome evolution - new tricks for old dogs! @bweek.bsky.social @uni-kiel.de @transevo.bsky.social @crc1182.bsky.social www.nature.com/articles/s41...
nature.com
Applying evolutionary theory to understand host–microbiome evolution - Nature Ecology & Evolution
This Perspective discusses how well-established theoretical models of evolution can be adapted to study and generate testable predictions about the evolutionary dynamics of host–microbiota association...
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Jessica Metcalf @jessmetcalf.bsky.social · 17/08/2025
New paper from Burcu - working towards describing 'immune education' journals.plos.org/plosbiology/...
journals.plos.org
A model of early-life interactions between the gut microbiome and adaptive immunity provides insights into the ontogeny of immune tolerance
The developing immune system must learn which microbes to tolerate and which to resist, but how this process unfolds is unclear. This study develops a mechanistic mathematical model of early-life gut ...
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Kaumudi Prabhakara @kaumudi.bsky.social · 11/08/2025
A new preprint! Data from a huge experiment by @prczhaoyansong.bsky.social show that similar microbial communities diverge depending on whether the carbon source is glucose or its polymer, cellulose. Diversity is comparable, but biomass, functions and taxonomy differ: www.biorxiv.org/content/10.1...
biorxiv.org
Diverse microbial communities assemble on both recalcitrant and labile carbon sources
Microbial community assembly is shaped by the nature of available resources, with labile carbon sources such as glucose often expected to support low diversity due to rapid growth and competitive excl...
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Gaurav Athreya @gauravathreya.bsky.social · 23/07/2025
Interested in host-symbiont interdependence, eukaryogenesis, and evolutionary transitions in individuality? my first paper just came out! With @gokhalecs.bsky.social and Pete Czuppon, we study when & how individuality emerges in a host-endosymbiont collective doi.org/10.1086/737588 a short thread🧵:
figure 1 from https://doi.org/10.1086/737588 describing (a) our conceptualisation of an evolutionary transition in individuality, (b) an interpretation of the traits that we consider in our mathematical model, and (c) a graphical representation of the population dynamics in the model.
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Deepa Agashe @deepaagashe.bsky.social · 19/07/2025
So happy to see this paper finally out! Ridiculous amount of work by Mrudula Sane and Shazia Parveen, showing that reversing baseline transition bias is good, as predicted by models from Lindi Wahl and co. Big thanks to @ncbsbangalore.bsky.social and DBT/WT India Alliance for support.
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Ben Allen @evodynamics.bsky.social · 15/07/2025
I wrote an Insight piece to accompany new work by Matthijs van Veelen on incorporating nonlinearity into Hamilton's rule. elifesciences.org/articles/108... TL;DR: The future of evolutionary theory is nonlinear, and our mathematical tools should reflect that.
Figure from Allen (2025): Linear and nonlinear regression models for the benefits of helping behavior.

(A) A standard approach to quantifying the benefit b
and cost c of cooperation is to apply a linear regression model of the form w=w0−cp+bq+ϵ, where w is an individual’s offspring number, w0 is a constant term, p is the genetic propensity of the individual to cooperate, q is the genetic propensity of the individual’s partner to cooperate, and ϵ is a residual term. Benefit and cost are then determined by applying least-squares regression to population data for a single generation. Here, for simplicity, we show hypothetical data for w and q only (blue points), ignoring the effects of p. In this scenario, offspring number peaks at an intermediate level of help. Fitting a linear model w=w0+bq+ϵ (orange line) results in a “benefit” b that sheds little light on the nature of the cooperative trait. (B) Fitting a quadratic model w=w0+b0,1q+b0,2q2+ϵ (orange curve), as van Veelen’s framework allows for, yields a more informative characterization of cooperation in this scenario.
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PLOS Biology @plosbiology.org · 15/07/2025
Mutations generate variation, critical for #evolution, but #MutationBias restricts the choice of mutation type. @deepaagashe.bsky.social &co use #Ecoli strains with different mutation biases to show that changing an old bias should yield more beneficial mutations @plosbiology.org 🧪 plos.io/46LjCRt
Schematic of the key prediction tested in this work. As the transversion (Tv) mutation bias of WT E. coli is shifted away from the ancestral bias, the resulting distribution of fitness effects (DFE) is predicted to change. Specifically, it should shift left with a bias reinforcement, with a lower fraction of beneficial mutations. In contrast, reversing the ancestral bias is predicted to cause right-shifted DFEs with higher proportions of beneficial mutations.
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