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Nikhil Sharma

@nikhil-sharma.bsky.social

49 Followers  |  107 Following  |  3 Posts  |  Joined: 01.04.2025  |  2.0187

Latest posts by nikhil-sharma.bsky.social on Bluesky

Just outπŸ“’ 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

14.10.2025 15:10 β€” πŸ‘ 17    πŸ” 8    πŸ’¬ 1    πŸ“Œ 0
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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...

We have put together a comprehensive eQTL map for D. melanogaster using thousands of genetically diverse flies πŸͺ°πŸͺ°πŸͺ°πŸͺ°πŸͺ° We hope this helps -as similar resources have done in yeast and humans- to understand how genetic variation 🧬 regulates complex traits variation πŸͺ° via transcriptional regulation ⬆️⬇️

14.10.2025 12:55 β€” πŸ‘ 19    πŸ” 10    πŸ’¬ 0    πŸ“Œ 0
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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 ...

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

17.09.2025 08:11 β€” πŸ‘ 7    πŸ” 2    πŸ’¬ 1    πŸ“Œ 0
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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

09.10.2025 06:56 β€” πŸ‘ 9    πŸ” 12    πŸ’¬ 1    πŸ“Œ 1

Adaptive Dynamics of Quantitative Traits in a SteadilyChanging Environment https://www.biorxiv.org/content/10.1101/2025.09.28.679017v1

29.09.2025 23:32 β€” πŸ‘ 6    πŸ” 1    πŸ’¬ 0    πŸ“Œ 0
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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...

Rafting against the evolutionary waterfall! πŸš£β€β™‚οΈπŸ’¨ - see our new paper on the challenge of artificial selection of microbial collectives elifesciences.org/articles/97461

18.09.2025 03:06 β€” πŸ‘ 2    πŸ” 2    πŸ’¬ 0    πŸ“Œ 1
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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

27.09.2025 17:32 β€” πŸ‘ 38    πŸ” 6    πŸ’¬ 3    πŸ“Œ 1

"Editor"

22.09.2025 17:24 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0
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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...

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

16.09.2025 17:33 β€” πŸ‘ 37    πŸ” 21    πŸ’¬ 1    πŸ“Œ 1
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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/...

11.09.2025 15:52 β€” πŸ‘ 18    πŸ” 7    πŸ’¬ 1    πŸ“Œ 2

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!

11.09.2025 02:21 β€” πŸ‘ 26    πŸ” 5    πŸ’¬ 1    πŸ“Œ 0
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W 3 professorship in Molecular and Evolutionary Zoology - Kiel, Schleswig-Holstein (DE) job with Christian-Albrechts-UniversitΓ€t 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...

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...

08.09.2025 14:32 β€” πŸ‘ 23    πŸ” 46    πŸ’¬ 0    πŸ“Œ 0
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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...

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...

08.09.2025 14:41 β€” πŸ‘ 30    πŸ” 17    πŸ’¬ 0    πŸ“Œ 0

All the best!

02.09.2025 09:54 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
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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 ...

New paper from Burcu - working towards describing 'immune education' journals.plos.org/plosbiology/...

17.08.2025 11:57 β€” πŸ‘ 26    πŸ” 6    πŸ’¬ 1    πŸ“Œ 0
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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...

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...

11.08.2025 14:59 β€” πŸ‘ 12    πŸ” 6    πŸ’¬ 1    πŸ“Œ 0

Congratulations Gaurav!

25.07.2025 12:55 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
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.

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.

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🧡:

23.07.2025 14:21 β€” πŸ‘ 67    πŸ” 27    πŸ’¬ 5    πŸ“Œ 3

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.

19.07.2025 14:25 β€” πŸ‘ 19    πŸ” 6    πŸ’¬ 1    πŸ“Œ 0
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=w0βˆ’cp+bq+Ο΅, 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 Ο΅ 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+Ο΅ (orange line) results in a β€œbenefit” b that sheds little light on the nature of the cooperative trait. (B) Fitting a quadratic model w=w0+b0,1q+b0,2q2+Ο΅ (orange curve), as van Veelen’s framework allows for, yields a more informative characterization of cooperation in this scenario.

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=w0βˆ’cp+bq+Ο΅, 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 Ο΅ 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+Ο΅ (orange line) results in a β€œbenefit” b that sheds little light on the nature of the cooperative trait. (B) Fitting a quadratic model w=w0+b0,1q+b0,2q2+Ο΅ (orange curve), as van Veelen’s framework allows for, yields a more informative characterization of cooperation in this scenario.

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.

15.07.2025 13:57 β€” πŸ‘ 17    πŸ” 3    πŸ’¬ 4    πŸ“Œ 0
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.

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.

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 πŸ§ͺ plos.io/46LjCRt

15.07.2025 14:11 β€” πŸ‘ 3    πŸ” 3    πŸ’¬ 0    πŸ“Œ 0

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