Puneeth Deraje

Reflections on the Human Genome Diversity Project: a conversation with Marcus W. Feldman, Henry T. Greely, and Mary-Claire King Abstract. The Human Genome Diversity Project (HGDP) began in 1991 as an initiative to study genetic variation from human populations worldwide. In 2002, th

If you research or are simply interested in human genetic variation, ancient and modern, read my and Noah Rosenberg's latest in GENETICS academic.oup.com/genetics/art... 1/2

Check out this comprehensive review of models in evolutionary rescue as well as connections with empirical work! It was fun to be a (small) part of this cool group led by Matt and Hildegard!

Talk alert!

Third talk in the series "Applications of Network Science"!

Featuring Guim Aguadé-Gorgorió, a Post-Doctoral fellow at ISEM.

Guim will be covering minimal models of co-existence in complex ecology!

🗓️ Feb 9, 2026 | ⏱️ 8:30 PM IST

Join at: northeastern.zoom.us/j/9832742702...

New paper! From Sam Snodgrass and @genomeofforrest.bsky.social, w/ @druncie.bsky.social, @gcbias.bsky.social, and a collaboration with Andres Moreno and @santiagogmm.bsky.social. Can we quantify the impact of humans on maize dispersal?

Plant yourself in a comfy chair and lend me your ear:

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Talk Alert!

Excited to kick off brand new series: Forms and Flows.

First talk by Shubham S, a PhD candidate at @ncbsbangalore.bsky.social.

He will discuss about a landscape description of the dynamics of Turing patterns.

🗓️ Feb 6, 2026 | ⏰ 20:30 (IST)

Join: northeastern.zoom.us/j/9832742702...

Please join us for a @smtpb.bsky.social panel discussion about publishing theory in biology w/ @joshuasweitz.bsky.social (Co-Chief Editor of J Theor Biol), Mark Lewis (Advising Editor for J Math Biol & Bull Math Biol), and me (Theor Pop Biol)

13 Feb 2026 9:00AM–10:00AM PST

smtpb.org/event-6520871

Join the symposium "The genetic basis of evolutionary rescue" at SMBE 2026 in Copenhagen (June 28 - July 2). Submit abstracts by Feb 3. More info: https://smbe2026.org. Organizers: Matthew Osmond & Hildegard Uecker. #conference

Consequences of Deforestation on Functional Community Structure Reverse at High Elevations | The American Naturalist: Vol 207, No 1 Abstract Functional diversity is expected to decrease following land conversion. Empirically, however, the consequences of such changes are highly variable. One possible explanation is that the magnit...

ICYMI: Lertzman-Lepofsky et al. find that elevation interacts with deforestation to shape community structure among Anolis lizards and suggest that this interaction is key to understanding community assembly in the Anthropocene.

Read now!
www.journals.uchicago.edu/doi/abs/10.1...

How Genotype-by-Environment Interactions Can Maintain Variation in Mutualisms | The American Naturalist Abstract Coevolution requires reciprocal genotype-by-genotype (G × G) interactions for fitness, which occur when the fitness of a genotype in one species depends on the genotype it interacts with in a...

Carlson et al. build a mathematical model considering how genotype-by-environment interactions can maintain variation and parametrize their model to test its applicability to real mutualisms.

Read now ahead of print!
www.journals.uchicago.edu/doi/10.1086/...

Calling all Canadian prospective grad students! Domestic PhD & MSc application deadline = Jan 9 for EEB @ U. Toronto! Great community of researchers! Guaranteed funding >$40k/y! Join us! eeb.utoronto.ca/education/gr...

Alignment across taxonomic levels in strategies rather than in traits along elevational gradients Abstract. Trait variation along environmental gradients can indicate the different strategies that organisms have evolved in response to environmental hete

A bit late, but really happy to see my first PhD paper out!
We studied trait-elevation relationships in multiple traits spanning growth, size (both above and belowground) and leaf economics to understand whether these align at within- and among-species scales.

academic.oup.com/evlett/advan...

Employment - Ecology & Evolutionary Biology

EEB Postdoctoral Fellowship @ U.Toronto app deadline Jan 15 2026. Opportunity for independent research, encourages collab across labs/disciplines. Lots of great folks to interact with, Come join us!
eeb.utoronto.ca/employment-2/

Robustness of Ancestral Recombination Graph Inference Tools to Phasing Errors Ancestral Recombination Graphs (ARGs) are fundamental population genetic structures that encode the genealogical history of a sample of haplotypes along the genome. They have recently received substan...

We are excited to share our recent work on the surprising robustness of Ancestral Recombination Graph (ARG) inference tools to computational phasing errors, now available on BioRxiv: biorxiv.org/content/10.1....
This work is co-advised by @yundeng.bsky.social and Rasmus Nielsen.
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ESEB's Global Evolutionary Biology Initiative invites project applications supporting local evolutionary research networks. Deadline: March 1, 2026. Max funding: €10,000. Apply: office@eseb.org. More … https://eseb.org/prizes-funding/global-evolutionary-biology-initiative/events-supported-by-gebi/.

Latest in #GENETICS: @petrelharp.bsky.social and the team show how non-coalescing haplotypes can be inserted into ancestral recombination graphs (ARGs), resulting in ARGs that are smaller, faster to compute with, and have additional ancestral information. buff.ly/X801LTO

Poster announcing the workshop.

Join us for an @smtpb.bsky.social workshop on Modern Coexistence Theory. We'll cover mathematical foundations, the theory of partitioning, and data-based applications. Featuring @swatipatel.bsky.social, Nick Kortessis, & Lauren Shoemaker. Zoom link here: smtpb.org/event-6426026

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

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.

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)