Puneeth Deraje
puneethderaje.bsky.social
Puneeth Deraje
@puneethderaje.bsky.social
Mathematics & Evolution!

Ph.D. at University of Toronto (EEB Dept)
Alumnus IISER Mohali. He/him
Reposted by Puneeth Deraje
Big cheers from MPI for Evolutionary Biology! 🎉
Our alumna Dr. Christin Nyhoegen wins the KlarText Prize 2025 for her piece “Penicillin and a Small Dose of Mathematics.”
She shows how math helps improve antibiotic treatments and prevent resistance. 👏
#KlarTextPreis #MPIEvolBio #ScienceCommunication
November 14, 2025 at 8:26 AM
Reposted by Puneeth Deraje
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.
November 8, 2025 at 3:42 PM
Reposted by Puneeth Deraje
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 Puneeth Deraje
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
Applied Biostatistics
ybrandvain.github.io
October 24, 2025 at 2:33 PM
Reposted by Puneeth Deraje
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
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
tinyurl.com
October 23, 2025 at 8:58 PM
Reposted by Puneeth Deraje
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...
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…
www.sciencedirect.com
October 16, 2025 at 3:42 PM
Reposted by Puneeth Deraje
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
October 15, 2025 at 3:53 PM
Reposted by Puneeth Deraje
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
October 6, 2025 at 3:13 PM
Reposted by Puneeth Deraje
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...
October 11, 2025 at 10:09 PM
Reposted by Puneeth Deraje
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/...
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...
www.pnas.org
October 9, 2025 at 7:45 PM
Reposted by Puneeth Deraje
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...
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...
www.biorxiv.org
October 8, 2025 at 2:48 PM
Reposted by Puneeth Deraje
Host constraints on viral recombination and emergence https://www.biorxiv.org/content/10.1101/2025.10.01.679867v1
October 3, 2025 at 8:32 PM
Reposted by Puneeth Deraje
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)
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
academic.oup.com
October 3, 2025 at 9:54 AM
Reposted by Puneeth Deraje
How do mate-finding Allee effects affect evolutionary rescue? https://www.biorxiv.org/content/10.1101/2025.09.27.678992v1
September 28, 2025 at 8:33 AM
Reposted by Puneeth Deraje
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!
September 16, 2025 at 2:47 AM
Reposted by Puneeth Deraje
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...
September 15, 2025 at 10:33 AM
Reposted by Puneeth Deraje
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.
#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 10, 2025 at 5:23 PM
Reposted by Puneeth Deraje
Quasi epigenetic equilibrium: the implications of plasticity and variability on evolution and extinction https://www.biorxiv.org/content/10.1101/2025.08.27.672696v1
September 1, 2025 at 7:32 PM
Reposted by Puneeth Deraje
Our Quantitative Genetic approach to Modelling Microbiome-Mediated Host Adaptation is now published in Evolution !!!

academic.oup.com/evolut/advan...
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
academic.oup.com
August 29, 2025 at 6:27 PM
Reposted by Puneeth Deraje
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
August 28, 2025 at 9:41 AM
Reposted by Puneeth Deraje
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
August 27, 2025 at 12:09 PM
Reposted by Puneeth Deraje
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
August 19, 2025 at 2:33 PM
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.
August 19, 2025 at 3:25 PM
Reposted by Puneeth Deraje
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 + 🐦!
#ESEB2025 Very concentrated looks when @shikharabhat.bsky.social educates us about pop noise! One of the last talks I could attend, sorry I had to leave early (planned, still 🫤) The lab's presence continues without me so grab them for a science chat!
August 19, 2025 at 2:36 PM