Zach B. Hancock

Predicting the contribution of single trait evolution to rescuing a plant population from demographic impacts of climate change Abstract. Evolutionary adaptation can allow a population to persist in the face of a new environmental challenge. With many populations now threatened by e

Really interesting quantitative genetic data/modeling work in @evolletters.bsky.social: Predicting the contribution of single trait evolution to rescuing a plant population from demographic impacts of climate change

doi.org/10.1093/evle...

The most important paper in evolutionary biology I'd never heard of:

1/

www.sciencedirect.com/science/arti...

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)

...and if you missed it, here are 60 phylogenetically diverse brown algae genomes
www.cell.com/cell/fulltex...

NSF unexpectedly changed (at the last minute) who is eligible to apply for the Grad Research Fellowship, dropping 2nd year students. We started a petition to reverse this unfair change, Sign here:
laurenkuehne.github.io/grfpChanges/
and please spread the word!!!!

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome Summary · Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biod...

New — with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social, and many more — we created seven new high-quality genomes and explored pangenomic variation in the emerging oilseed crop pennycress (Thlaspi arvense). 1/

Visualizing Human Genetic Diversity A key insight from human genetics is that, as a species, we are all very genetically similar to one another and share much of our genetic variation. Our genome can be depicted as a string of letters (...

Another year using @kitchensjn.bsky.social + @gcbias.bsky.social's intuitive circle plots to discuss human genetic variation in my undergrad genetics class james-kitchens.com/blog/visuali...

Genomic divergence across the tree of life | PNAS Nucleotide sequence data are being harnessed to identify species, even in cases in which organisms themselves are neither in hand nor witnessed. Bu...

Genomic divergence across the tree of life 🧪🌐https://www.pnas.org/doi/10.1073/pnas.2319389122

k-mer-based diversity scales with population size proxies more than nucleotide diversity in a meta-analysis of 98 plant species Abstract. A key prediction of neutral theory is that the level of genetic diversity in a population should scale with population size. However, as was note

k-mer-based diversity scales with population size proxies more than nucleotide diversity in a meta-analysis of 98 plant species.

academic.oup.com/evlett/artic...

Map of the US titled: “How big is the teaching penalty in your state?” Map shows the relative teacher pay penalty for each state, ranging from 38.5% to 10%

The US has been leaving school teachers behind for nearly 30 years.

In 20 states, teachers made 25% less than their peers.

What’s the teacher pay gap in your state?

Find out here: www.epi.org/publication/...

Genetic assimilation and accommodation shape adaptation to heat stress in a splash pool copepod https://www.biorxiv.org/content/10.1101/2025.09.09.675189v1

Very excited to see this work in press! I think there is a reason to believe that this is a common means of stabilizing large-effect polymorphisms in general and might be an important reason for why diploidy is so common. news.stanford.edu/stories/2025...

Hybridization and introgression are major evolutionary processes. Since the 1940s, the prevailing view has been that they shape plants far more than animals. In our new study (www.science.org/doi/10.1126/...
), we find the opposite: animals exchange genes more, and for longer, than plants

Graph showing a positive correlation between "bias in adaptive outcome" on the vertical axis and "mutation bias" on the horizontal axis, with 14 data points representing 14 respective species, with a line of best fit equal to a slope of 0.82 on the log-scale axes. Each data point contains horizontal and vertical error bars to illustrate the uncertainty in both the mutational and adaptive data. The 95% confidence interval of the slope is shown in parentheses (0.44 to 1.24), based on 10,000 simulated data sets, where the simulated data sets are based on statistical resampling of the empirical data (i.e. "bootstrap" data sets). Regression lines based on these bootstrap data sets are shown as light gray lines. The type of bias reported here refers to the ratio of transitions versus transversions, where transitions are a DNA mutation that preserves the basic structure of the DNA base (i.e. a purine-to-purine or pyrimidine-to-pyrimidine mutation), and transversions are mutations that alter the structure of the DNA base at a particular site (i.e. replacing a purine with a pyrimidine or vice versa). In other words, this graph shows that transitions contribute more toward adaptive evolution in species where transitions arise at a higher rate.

NEW PAPER! Some kinds of genetic mutations are more likely to arise than others. Such "biases" in mutation vary between species.

Analyzing data from 14 species, we show that this variation explains species differences in the genetics of adaptation!

(1/3)

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

Sorting of ancestral polymorphism and its impact on morphological phylogenetics and macroevolution Abstract. Intraspecific phenotypic variation provides the basic substrate upon which the evolutionary processes that give rise to morphological innovation,

Excited to share a new paper! "Sorting of ancestral polymorphism and its impact on morphological phylogenetics and macroevolution". Part of some work I've been doing on modelling the evolution of polymorphic traits in fossil echinoderms.

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

Puente-Lelievre et al. have systematically reviewed how protein structures can be used to trace evolutionary histories. This rapidly advancing field has not yet caught up with the burgeoning databases of high quality protein structure predictions provided by AlphaFold and other tools.

In a new GBE Review, @cpuentelelievre.bsky.social @proteinmechanic.bsky.social & J. Douglas give an overview on protein structural phylogenetics, how to obtain evolutionary insights from structural data, and key applications and future directions.

🔗 doi.org/10.1093/gbe/evaf139

#genome #evolution

Last lecture of summer popgen:"Evolutionary QuantGen: why (almost) everything we learned is (kinda) wrong". how selection on traits affects alleles. Architecture, stabilizing selection, popgen on gene sets, corn example & a shiny app from @mgstetter.bsky.social mgstetter.shinyapps.io/quantgensimA...

Notes from Beethoven’s genome Wesseldijk et al. compare the genomic information collected from Ludwig van Beethoven with population-based datasets used to quantify musical achievement.

If someone you know buys into claims about "genetic optimization" of embryos using polygenic scores of cognition, just send them our 2024 paper on Beethoven & musicality. We wrote it to help communicate limits of individual-level genetic predictions & complexity of links between DNA & behaviour. 🧪👇

Estimation of demography and mutation rates from one million haploid genomes Samples of millions of genomes provide substantial information about recent demography and mutation, but standard population-genetic methods make assumptions not met in these data. We introduce DR EVI...

📣Online NOW!
📄Estimation of demography and mutation rates from one million haploid genomes
🧑‍🤝‍🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social

Our paper showing that variation in transcription factor binding sites underlies the majority of additive genetic variance for phenotypic variation in maize is finally out!

Sadly they didn't use our suggested cover image below (made by the inimitable Andi Kur).

www.nature.com/articles/s41...

SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes https://www.biorxiv.org/content/10.1101/2025.08.07.669155v1

Dynamics of Deleterious Mutations and Purifying Selection in Small Population Isolates Abstract. The genomic consequences of prolonged population decline and isolation are increasingly recognized, but quantitative assessments of mutation load

Chen et al investigate deleterious mutations and purifying selection in 17 stickleback populations, finding that inbreeding predicts realized loads of deleterious mutations, and genomic consequences of isolation in small populations are predictable.

🔗 doi.org/10.1093/molbev/msaf110

#evobio #molbio

Biologist folk (especially in evolutionary biology and/or ecology, but it don’t matter):

Can you give me your favorite examples of trade offs in biology? Organism or system don’t matter. Primary literature or reviews preferred.

Predicting the direction of phenotypic difference Nature Communications - Here authors reveal a method to predict key information on phenotypes - their direction. This is achievable even for phenotypes with incomplete genotype-to-phenotype...

Given two genomes, can you tell who’s taller or more prone to a disease? How confident can you be? A fresh take on phenotypic inference, now out:
rdcu.be/exW4f
See thread🧵👇:

Evaluating the roles of drift and selection in trait loss along an elevational gradient The evolutionary mechanisms underlying loss or retention of traits that have lost function are poorly understood. Short stamens in Arabidopsis thaliana pro

Sophie Buysse's paper on short stamen loss in Arabipsis is published in this month's Evolution issue!! academic.oup.com/evolut/artic... @journal-evo.bsky.social

A high-resolution two-step evolution experiment in yeast reveals a shift from pleiotropic to modular adaptation Evolution is expected to involve mutations that are small and modular in effect, but recent findings suggest that mutations early in an adaptive process can have strong and pleiotropic effects. This s...

Hopeful monsters? Great talk from @petrovadmitri.bsky.social at #SMBE2025 about dimensionality of adaptation. Here's one of the papers he mentioned (shift from pleiotropy to modularity) with @grantkinsler.bsky.social &co in @plosbiology.org: journals.plos.org/plosbiology/...

No new genes needed to fly - just rewire what you have! 🦇🧬

Great new paper from the labs of @fany-real.bsky.social @stemundi.bsky.social @dariloops.bsky.social

doi.org/10.1038/s415...

#EvoDevo #SingleCell #BatWings

Gene regulatory networks and essential transcription factors for de novo-originated genes Nature Ecology & Evolution - A combination of computational methods applied to single-cell RNA sequencing data and genetic experiments shows that a small number of transcription factors are...

Our latest paper is out: rdcu.be/ev6Ym — one of my favorite projects. It began about 8 years ago when Nobel laureate Torsten Wiesel asked me: what transcription factors regulate new genes? I had no idea then. Now we have some answers.

Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c...

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁
Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference - Nature Methods BEAST X advances Bayesian phylogenetic, phylogeographic and phylodynamic analysis by incorporating a broad range of complex models and leveraging advanced algorithms and techniques to boost statistica...

BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference

www.nature.com/articles/s41...