Nikhil Sharma
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Nikhil Sharma
@nikhil-sharma.bsky.social
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Reposted by Nikhil Sharma
nikoletaglyn.bsky.social
🗞️📣 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)
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...
journals.plos.org
November 3, 2025 at 10:54 AM
Reposted by Nikhil Sharma
cbank.bsky.social
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
October 28, 2025 at 4:22 PM
Reposted by Nikhil Sharma
paulbrainey.bsky.social
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...
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 ...
doi.org
October 30, 2025 at 10:18 PM
Reposted by Nikhil Sharma
yuvalsim.bsky.social
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/...
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...
journals.plos.org
October 24, 2025 at 1:51 AM
Reposted by Nikhil Sharma
kanekiyom.bsky.social
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
October 14, 2025 at 3:10 PM
Reposted by Nikhil Sharma
luisapallares.bsky.social
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 ⬆️⬇️
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...
www.cell.com
October 14, 2025 at 12:55 PM
Reposted by Nikhil Sharma
clocksevolution.bsky.social
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
September 17, 2025 at 8:12 AM
Reposted by Nikhil Sharma
clocksevolution.bsky.social
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
October 9, 2025 at 6:56 AM
Reposted by Nikhil Sharma
biorxiv-evobio.bsky.social
Adaptive Dynamics of Quantitative Traits in a SteadilyChanging Environment https://www.biorxiv.org/content/10.1101/2025.09.28.679017v1
September 29, 2025 at 11:32 PM
Reposted by Nikhil Sharma
hyejinpark.bsky.social
Rafting against the evolutionary waterfall! 🚣‍♂️💨 - see our new paper on the challenge of artificial selection of microbial collectives elifesciences.org/articles/97461
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...
elifesciences.org
September 18, 2025 at 3:06 AM
Reposted by Nikhil Sharma
kylejcard.bsky.social
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
September 27, 2025 at 5:32 PM
Reposted by Nikhil Sharma
joannamasel.bsky.social
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
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...
doi.org
September 16, 2025 at 5:33 PM
Reposted by Nikhil Sharma
mkhochb.bsky.social
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/...
September 11, 2025 at 3:52 PM
Reposted by Nikhil Sharma
deepaagashe.bsky.social
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!
vrindarvkm.bsky.social Vrinda Ravi Kumar @vrindarvkm.bsky.social · Sep 10
Our work on evolutionary rescue is finally out in this week's issue of PNAS! Check out the NCBS communications team piece on our work quoted below.
ncbsbangalore.bsky.social National Centre for Biological Sciences, Bengaluru @ncbsbangalore.bsky.social · Sep 10
#LatestPublication
Vrinda & team from Dr Deepa Agashe's lab tracked beetle populations for 5+ years in harsh environments. Findings show how traits of founders influenced the long-term survival of their descendants.

🔗 bit.ly/42hsviC

@deepaagashe.bsky.social

🧵Check out the thread to know more!👇
September 11, 2025 at 2:21 AM
Reposted by Nikhil Sharma
schulenburglab.bsky.social
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...
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...
www.nature.com
September 8, 2025 at 2:32 PM
Reposted by Nikhil Sharma
schulenburglab.bsky.social
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...
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...
www.nature.com
September 8, 2025 at 2:41 PM
Reposted by Nikhil Sharma
jessmetcalf.bsky.social
New paper from Burcu - working towards describing 'immune education' journals.plos.org/plosbiology/...
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 ...
journals.plos.org
August 17, 2025 at 11:57 AM
Reposted by Nikhil Sharma
kaumudi.bsky.social
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...
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...
www.biorxiv.org
August 11, 2025 at 2:59 PM
Reposted by Nikhil Sharma
gauravathreya.bsky.social
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.
July 23, 2025 at 2:21 PM
Reposted by Nikhil Sharma
deepaagashe.bsky.social
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.
roliroberts.bsky.social Roli Roberts @roliroberts.bsky.social · Jul 16
Elegant empirical validation of a theoretical expectation that changing your mutation bias allows you to access more beneficial mutations. From @deepaagashe.bsky.social & colleagues in @plosbiology.org
plosbiology.org PLOS Biology @plosbiology.org · Jul 15
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
July 19, 2025 at 2:25 PM
Reposted by Nikhil Sharma
evodynamics.bsky.social
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.
July 15, 2025 at 1:57 PM
Reposted by Nikhil Sharma
plosbiology.org
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.
July 15, 2025 at 2:11 PM