Wrote a fun little thing on gene tree discordance:

authors.elsevier.com/a/1mzPI3QW8S...

These fuckin chuds

Naming your biology LLM after Rosalind Franklin is… hell is not hot enough

My latest Digest for Evolution is now available online. One of my favorite pieces to write. 😉

Digest: Chance and necessity shape introgression patterns across three replicate avian hybrid zones
academic.oup.com/evolut/advan...

#ornithology

A species tree and a cloudogram, both showing how much gene tree discordance there is in rockfishes

New paper led by Yu Mo, with @psudmant.bsky.social

Ever wonder how extreme genealogical discordance can help you to find the genetic basis for trait variation? Wonder no more!

www.biorxiv.org/content/10.6...

SMBE Graduate Student Excellence Award - Anjali Gupta

👏 This year's winners of our Graduate Student Excellence Award have been selected - stay with us for the next few days to learn about their research.

First is Anjali Gupta (@anjaligupta.bsky.social), PhD student at U. Kansas, researching genetic conflict.

More on Anjali ⬇️

#society

An affirmative vote for a collective bargaining agreement for United Academics of KU

I am SO grateful to my hardworking colleagues for creating this agreement. I know what it took. Proud to be a #Jayhawk, proud to be #UnionStrong. Ad astra!

Demographic reconstruction of Baiji populations over time show that their populations had declined up to 10,000 years ago, at the beginning of the Holocene, and then had began to recover until human activity drove them extinct.

Using coalescent demographic reconstructions, Zhou et al found that the extinct Baiji had undergone a bottleneck at the beginning of the Holocene but populations were recovering in the last 10,000 years until recent extinction from human activities doi.org/10.1038/ncom... #2026MMM #RIP

Our paper is on the cover of @currentbiology.bsky.social : a strawberry poison frog with the most common color morph, living up to its common name 🍓. In this issue, we uncover the genetic basis of color variation in frogs from Bocas del Toro, where blue, green, yellow, orange, and red morphs occur

Introgression and parental conflict shape repeated occurrences of postzygotic isolation in Mimulus Postzygotic reproductive isolation is often thought to accumulate as a byproduct of neutral divergence. Yet it frequently evolves rapidly, in line wit…

I am SO THRILLED to share our first fully-lab lab paper!!!!!! Led by @hybridzones.bsky.social & @hagarsoliman.bsky.social, w/ a major assist from @pfschwarz.bsky.social!!!!!!!!!!!!! Read more below, if you're curious (you should be- it's AWESOME!!!!!!!)

link: www.sciencedirect.com/science/arti...

I've slowly been reformatting notes from my population and conservation genetics course at Montana State University into a web book—a rough draft is now live here: elinck.org/popgen_conge...

Rapid divergence with gene flow creates intractable nodes in the tree of life: An empirical demonstration in the Buzzing Flowerpecker (Dicaeum hypoleucum) Abstract. The avian tree of life contains a series of famously intractable nodes and controversial relationships whose resolution varies between studies de

And now an empirical example: @devonderaad.bsky.social, @lhdecicco.bsky.social, @peterhosner.bsky.social and colleagues show how rapid divergence, gene-flow and stepping-stone island colonisation obscure phylogenetic relationships of buzzing flowerpeckers.

(8/n)

doi.org/10.1093/evol...

Special Issue: CONSERVATION GENOMICS ‐ MAKING A DIFFERENCE: Molecular Ecology: Vol 34, No 23 Molecular Ecology is an international journal for research using molecular genetic techniques to address questions in ecology, evolution, behavior and conservation.

New special issue in Molecular Ecology on Conservation Genomics #popGen #evolution 🧪🧬🖥️ onlinelibrary.wiley.com/toc/1365294x...

A colorful legacy of hybridization in wood-warblers includes frequent sharing of carotenoid genes among species and genera Introgression between species can shape evolutionary trajectories in important ways. This study of the entire family of the colorful wood-warblers (Parulidae) uses whole-genome sequencing to reveal fr...

New paper out. If you like colorful birds, hybridization, and phylogenetics, read on! 🧵https://doi.org/10.1371/journal.pbio.3003501

Warblers borrow color-related genes from evolutionary neighbors, study finds | Penn State University A new study has uncovered several instances of wood warblers — some of the most colorful birds in North America — passing color-related genes to other wood warbler species, including those that are no...

BIG day for warbler genomes, with work led by @kevinfpbennett.bsky.social! Whole genomes nearly *every species* of warbler.

Warblers the most "Pokémon" of the bird world? Well, they're also trading their coloration genes like valuable collectors cards ...

www.psu.edu/news/eberly-...
🦉🧪

I have a new preprint demonstrating a genome-architecture-aware approach to inferring species trees and introgression landscapes from a small number of genomes. If you are interested in phylogenomics, birds, or hybridization, this is for you! www.biorxiv.org/content/10.1...

A complete reference genome assembly and annotation of the Black Redstart (Phoenicurus ochruros) - Scientific Data Scientific Data - A complete reference genome assembly and annotation of the Black Redstart (Phoenicurus ochruros)

What makes a mountaineer bird?

We have published the first complete genome assembly for Redstarts (Genus: Phoenicurus), found across Asia, Europe, and Africa.

Black redstarts genome has 30% repeats, second highest known in passerines.

#genomics #ornithology

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

We can observe the complex biogeographic histories that give rise to phylogenomic discordance in real time, by studying groups of closely related organisms in early stages of the diversification process. Studying these "tips of the tree" can reveal the processes shaping global phylogenetic patterns.

Although we will never be able to reconstruct the geography of divergence at difficult nodes deep in the tree of life (at least without a time machine)...

Overall, this implies that the presence of unresolvable nodes in the tree of life may be largely attributable to real biological messiness, like cases of rapid colonization with gene flow across an island archipelago, not just a lack of sequence data or appropriate models.

Ultimately, the best demographic model was a polytomy, yet a model of rapid divergence with gene flow provided a nearly identical fit to the empirical data. Even though we think true "hard polytomies" are rare in nature, rapid divergence with gene flow is becoming recognized as relatively common.

The main conclusion is in the title "Rapid divergence with gene flow creates intractable nodes in the tree of life". One favorite result was that random downsampling of the tips resulted in conflicting species trees, at times with high support! Concerning implications for higher-level phylogenetics!

My 2nd dissertation chapter, entitled "Rapid divergence with gene flow creates intractable nodes in the tree of life: An empirical demonstration in the Buzzing Flowerpecker" will be in the forthcoming special issue of EJLS focused on phylogenomic discordance. Link: academic.oup.com/evolinnean/a...

Figure with a photo of a member of then Solomons Monarch complex, a map of the Solomon Islands (divided into four island groups, Makira being the most isolated), and a principal component analysis highlighting the distinct between-island-group structure, with moderate structure within the New Georgia Group and weaker structure within the Bukida group (highlighted in an inset).

Just out in Systematic Biology, we explore the role of gene flow in island phylogeography of the Solomons Black-and-white Monarch complex. doi.org/10.1093/sysb...

Up first, strong genetic structure between islands groups and weak (but present!) structure between Pleistocene-connected islands (🧵)

A five panel figure, with four showing photographs of a putative hybrid warbler between a mourning warbler and a common yellowthroat. The final panel shows an illustration of the bird by David Sibley

A three panel figure showing the genetic composition of the hybrid and the putative parental species. Two panels show points on a principal components analysis, with the hybrid falling intermediate. The final panel shows bars illustrating genome-wide admixture, with the hybrid having intermediate ancestry between the two.

I mean, the title says it all: Genetic confirmation of an “uncommon mourningthroat” (Geothlypis philadelphia  ×  G. trichas): A rare but persistent hybrid warbler. Fun stuff with @kevinfpbennett.bsky.social and Kurt Gielow, OA in @wilsonornithsoc.bsky.social!
🦉 🧪
www.tandfonline.com/doi/full/10....

A hand holding an eastern nashville warbler (Leiothlypis ruficapilla ruficapilla) during bird banding

Going to be a big month for warbler science! First out of the gates is @lannhiphung.bsky.social, with song & genomics of Nashville warblers. Eastern and western subspecies: non-overlapping and super distinct. Keep an eye on your life list 😉
🦉🧪@journal-evo.bsky.social
academic.oup.com/evolut/advan...

A poster for Else's exit seminar titled "The Role of Hybridization in the Speciation of Birds". The poster shows illustrations of several bird species (skuas and manakins) above a background of a subarctic coastline and a tropical rainforest river.

Almost PhDone! I'll be giving my PhD exit seminar in the morning (Thursday), and defending on Friday.

Patterns of Genetic Diversity Within Three California Quail Species Are Best Explained by Climate and Landscape Changes Many North American game animals experienced severe population declines during the 19th century due to market hunting. However, estimates of the timing and magnitude of these declines often rely on a...

Check out the latest paper from the CCGP on California Quail and the ecological and anthropogenic factors that impact genomic variation. Led by Phred Benham and the Bowie group: onlinelibrary.wiley.com/doi/10.1111/...

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...

🥳 My latest digest for Evolution is now available online!

Digest: Postzygotic isolation barriers stabilize a hybrid zone between two grosbeak species
academic.oup.com/evolut/advan...

Original paper: academic.oup.com/evolut/advan...

#ornithology

So great to have this work led by @devonderaad.bsky.social covered by an Evolution Digest!