Puneeth Deraje

PhD advert

I recently moved my lab to Purdue University and am looking for graduate students. We are working at the interface of population genomics, quantitative genetics and functional genomics to understand how plants adapt to extreme environments. Reach out if you would like to discuss potential projects.

Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes Lactase persistence (LP), the ability to digest lactose from milk into adulthood, is a classic example of natural selection in humans. Multiple mutations upstream of the LCT gene are associated with L...

Exciting new study led by @ekerdoncuff.bsky.social and @meaghanmarohn.bsky.social on the evolution of Lactase Persistence in South Asia.
www.biorxiv.org/content/10.1...

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

Proud of the latest edition of my free intro biostats book.

gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/

Not complete but at a good point to take a break, and I think its quite usable

dm me with comments , ideas etc

456: Kaleda Denton | Following the Majority - How Conformity Shapes Culture and AI In this episode of the Armen Show, Armen Shirvanian interviews Dr. Kaleda Denton, a post-doctoral fellow at the Santa Fe Institute. They discuss the interdisciplinary nature of the Institute, the concept of niche construction in biology, and the dynamics of decision-making, particularly the differences between following the mean versus the majority. The conversation also explores the limitations of game theory, the role of cultural evolution in cooperation, and the impact of AI on accessibility and learning. They delve into the importance of reducing polarization while maintaining diversity in viewpoints, emphasizing the need for mixing and collaboration across different fields and perspectives. In this engaging conversation, Dr. Kaleda Denton and Armen Shirvanian explore a variety of topics including the distinction between majority and mean opinions, the challenges of reading in the digital age, and the implications of large language models (LLMs) on culture. They discuss the importance of communication in society, the influence of close circles versus wider communities in learning, and the role of influential figures in personal development. The conversation also delves into the concept of memes and cultural transmission, the impact of role models on cumulative culture, and the question of human uniqueness in the context of cultural evolution. Check out Kaleda's website at https://www.kaledadenton.com/ 00:00 Introduction to the Podcast and Guest 03:01 The Santa Fe Institute: A Unique Interdisciplinary Environment 05:56 Niche Construction and Extended Evolutionary Synthesis 08:56 Mean vs. Majority: Insights from Research 12:08 Game Theory and Its Limitations 15:03 Cultural Evolution and Cooperation 17:59 The Role of AI in Learning and Accessibility 20:54 Conformity Across Species and LLMs 23:59 The Importance of Current Information 27:03 Final Thoughts on AI and Human Interaction 36:57 The Quirks of AI Hallucinations 38:53 The Evolution of Language Models 39:35 Agency and Individuality in AI Interactions 41:41 The Flattening of Ideas and Language 43:42 Cognitive Offloading and Its Consequences 45:04 Reducing Polarization Through Interaction 48:39 The Importance of Mixing Perspectives 50:02 The Dangers of Majority Influence 53:51 Understanding Mean vs. Majority Opinions 01:04:32 Risks and Opportunities in Cultural Evolution 01:10:02 The Impact of Headlines on News Consumption 01:11:46 The Need for Positive News 01:15:04 Learning from Close Circles vs. Wider Communities 01:17:23 Influential Figures in Personal Development 01:18:44 The Evolution of Human Uniqueness 01:22:38 Understanding Memes and Cultural Transmission 01:23:10 The Multiplicative Costs of Altruism 01:36:09 The Role of Role Models in Cumulative Culture

Honoured to have done my first ever podcast on The Armen Show! Besides science, math, & academia, we talked about:

-LLMs hyping up bad ideas
-My 5 foster cats, but whether I'm secretly a dog person
-How it would be nice to "skip" & "mute" people in real life 😛

Check it out! 😄

tinyurl.com/yc4hjz2x

Distinct haplotypes and reversed dominance at a single-gene balanced polymorphism controlling heterodichogamy in two genera of wingnuts In the angiosperm mating system of heterodichogamy, two hermaphroditic morphs temporally alternate between male and female flowering phases, promoting…

Congratulations to @jeffgroh.bsky.social on the publication of his paper on an ancient balanced polymorphisms controlling heterodichogamy in two genera of wingnuts. The paper shows the putative turnover & reversal of dominance of a mating type polymorphism
www.sciencedirect.com/science/arti...

We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT

Human-mediated land-use and climate change occur simultaneously, but how do they interact to shape adaptive dynamics? Super excited to share the first paper from the Kreiner lab, led by postdoc extraordinaire @rpineau.bsky.social

Posterior distributions of estimated rates of brain and body mass coevolution.

A very interesting and clever study which explores how change is distributed between anagenesis and cladogenesis (gradual vs punctuational change) in the light of brain-body size allometry in modern primates.
🧪 ⚒️ #Paleobio #EvoBio #Macroecology
academic.oup.com/evolut/artic...

I wrote a commentary about the recent paper by @deepaagashe.bsky.social and @vrindarvkm.bsky.social

Also go have a look at the original paper if you haven't !

The timeframe of prediction for eco-evolutionary dynamics | PNAS www.pnas.org/doi/10.1073/...

Inference of complex demographic history using composite likelihood based on whole-genome genealogies Accurate parametric inference on complex demographic models is a continuing challenge in population genetics. Ancestral recombination graphs (ARGs) provide richer information than simple population ge...

Excited to preprint our latest work (w/ Drew DeHaas, Zhibai Jia, Leo Speidel) on using ARGs for demographic inference. w/ applications using data from 1000 Genomes Project. www.biorxiv.org/content/10.1...

Host constraints on viral recombination and emergence https://www.biorxiv.org/content/10.1101/2025.10.01.679867v1

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

Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)

How do mate-finding Allee effects affect evolutionary rescue? https://www.biorxiv.org/content/10.1101/2025.09.27.678992v1

Photo of Dr. Meng Yuan (center), and Aneil Agrawal, Megan Bontrager, John Stinchcombe, Judith Mank, Stephen Wright, and Asher Cutter.

Congrats to Dr. Meng Yuan, who defended her PhD on the genome-wide potential for ploidy & sexual conflict in plants! Many thanks to @judithmank.bsky.social for serving as her external examiner. A fun collaboration w/ @stepheniwright.bsky.social and also @stuartmcdaniel.bsky.social for a paper!

Our paper about how ancestral recombination graphs can be used to detect "phantom" genetic interaction signals (that arise due to the genealogy, rather than "real" epistasis) is out in Genetics! Nice thread here by @linoafferreira.bsky.social

academic.oup.com/genetics/adv...

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.

Quasi epigenetic equilibrium: the implications of plasticity and variability on evolution and extinction https://www.biorxiv.org/content/10.1101/2025.08.27.672696v1

Quantitative Genetics of Microbiome Mediated Traits Abstract. Multicellular organisms host a rich assemblage of associated microorganisms, collectively known as their “microbiomes”. Microbiomes have the capa

Our Quantitative Genetic approach to Modelling Microbiome-Mediated Host Adaptation is now published in Evolution !!!

academic.oup.com/evolut/advan...

mvif season 5 keynotes

Season 5 is going to start 🔜

Check out the program and
feel free to join the keynotes by presenting your work–abstract submission is open www.microbiome-vif.org/en-US/-/info...

@kathlemon.bsky.social ‬ @saramitri.bsky.social @simrouxvirus.bsky.social @halllab.bsky.social @deepaagashe.bsky.social

Please share broadly: I am looking for a postdoctoral fellow to work on a collaborative project on the temporal population genomics of invasive Capeweed (using contemporary and herbarium genomics), with ‪‪@shaky-dingo.bsky.social‬ and colleagues

Whether you are looking to get a better grasp on how these graphs are structured or communicating findings from your latest ARG inference project, we hope that tskit_arg_visualizer becomes a useful addition to your research toolkit!

5/6

Check out this cool visualization tool for ARGs by @kitchensjn.bsky.social!! Found it super helpful to visualize an ARG as a single graph and to look at marginal trees as part of the full graph.

Thanks, Hanna! There are quite a few Kokkonuts at #ESEB2025! On Thursday, @gauravathreya.bsky.social talks about ageing + sex, @tomospotter.bsky.social talks about guppy polymorphisms, @ccrowther.bsky.social has a poster on nesting 🐢, and Victor Ronget has a poster on ageing trends in mammals + 🐦!

hello to everyone going to #ESEB2025! want to hear about the consequences of age-dependent plasticity in reproducing via sex vs. asex? I will give a talk at 11:15am on Thursday in S15.02. come for the pretty Hydra illustrations, stay for the novel evolutionary insights on facultative sex!

Quantitative Genetics of Microbiome Mediated Traits Multicellular organisms host a rich assemblage of associated microorganisms, collectively known as their “microbiomes”. Microbiomes have the capacity to influence their hosts’ fitnesses, but the condi...

hai eseb people ! come to my talk introducing the quantitative genetics of microbiome mediated traits :) 2:30-2:45 at S07.02

btw our ppr just got accepted at evolution ! amazing and challenging reviews ::)) revised pre-print here

www.biorxiv.org/content/10.1...

An illustration with populations on the left and mathematical representations of these populations in terms of birth-death processes on the right

Stochastic differential equations for trait frequencies, mean value of a trait, and the variance of a trait in the population

Hey #ESEB2025 folk! I'll be presenting my work on describing evolution in finite populations at 11:30 am on Tuesday in S-03. Drop by to learn how taking ecology and variable population size seriously changes classic pop gen descriptions like the Price eqn, revealing novel directional eco-evo forces.

Presenting Dr. @bmsacchi.bsky.social !! Bianca successfully defended her thesis on Rumex sex chromosome degeneration and regulatory evolution today. Bravo!!

Excited to finally have the pre-print up for this work on evolutionary rescue from my PhD at UBC!

Previous theoretical work on the effects of negative density-dependent growth on evolutionary rescue has uncovered inconsistent results, leading to an incomplete understanding of its influence.

Diagram from “Eco-Evolutionary Dynamics for Finite Populations and the Noise-Induced Reversal of Selection” by Ananda Shikhara Bhat and Vishwesha Guttal (Jan 2025). © University of Chicago

How Randomness Can Flip Evolution: New Study Uncovers Surprising Role of Population Noise

Summary & Analysis by Tahirah Williams of “Eco-Evolutionary Dynamics for Finite Populations and the Noise-Induced Reversal of Selection” by Bhat et al.
www.amnat.org/an/newpapers...