Angel G. Rivera-Colón

It has been really useful. I was able to redo a whole suite of MK analysis in my barnacle data in minutes!

Thanks to Andy for spearheading this project and to the KR colab for their feedback. Keep an eye out for future publications from the lab using MKado!

MKado is written in Python can be easily installed using pip. Its only dependencies are widely used Python libraries (Numpy, Scipy, etc).

Also, the docs have tons of examples on how to use the software and interpret the results. Check them out: mkado.readthedocs.io/en/latest/

MKado can also generate publication-ready plots, including volcano plots showing NI and MK test significance and asymptotic curves showing the fit of the asymptotic MK test. Here's an example in human-chimp orthologs:

Given the need, Andy spearheaded the development of MKado, an unified, all-in-one tool for MK tests. MKado runs both standard and extended versions of the test. It takes aligned coding sequences as input and can analyze thousands of genes in parallel. It can run >12k genes in under 1 minute!

Clara and I independently needed to run MK tests for some of our projects, but we had a problem: there was no single unified tool to run the test, and particularly, it's extensions (e.g., asymptotic MK, polarized MK). Same for MK-related statistics like NI, DoS, alpha, etc.

Check our new preprint from the KR-colab with @ramencult.bsky.social and Andy Kern:

MKado: a toolkit for McDonald-Kreitman tests of natural selection

doi.org/10.64898/202...

Molecular Ecology Molecular Ecology is an international journal for research using molecular genetic techniques to address questions in ecology, evolution, behavior and conservation.

Hello! Molecular Ecology is now on @bsky.app!
Follow us for updates about Molecular Ecology and Molecular Ecology Resources publications, as well as special issues, events, and awards!
onlinelibrary.wiley.com/journal/1365...

Nominations are open to the annual 𝗠𝗼𝗹𝗲𝗰𝘂𝗹𝗮𝗿 𝗘𝗰𝗼𝗹𝗼𝗴𝘆 𝗣𝗿𝗶𝘇𝗲!
The award recognizes the work of outstanding scientists for their contribution to the field of molecular ecology. Nominations are due on 𝟮𝟰 𝗔𝗽𝗿𝗶𝗹 𝟮𝟬𝟮𝟲.
Read more: onlinelibrary.wiley.com/page/journal...

Society for the Study of Evolution Site description

Are you a grad student attending #Evol2026? Submit your talk for the SSE Hamilton Award for Outstanding Graduate Student Presentation! Finalists will present their talks during the virtual portion of the meeting. Apply during registration. Deadline April 15! shorturl.at/qDIP4 @evolmtg.bsky.social

Water off a manakin’s back: How sexual and natural selection shape plumage coloration in manakins Plumage coloration mechanisms shed light on introgression patterns.

New story on the Avian Hybrids blog!

Water off a manakin’s back: How sexual and natural selection shape plumage coloration in manakins
avianhybrids.wordpress.com/2025/12/10/w...

Based on the Science Advances paper by Haw Chuan Lim et al. | #ornithology

Today in robots.

github.com/matplotlib/m...

crabby-rathbun.github.io/mjrathbun-we...

Estimating Organism Abundance Using Within‐Sample Haplotype Frequencies of eDNA Data Environmental DNA (eDNA) provides powerful insights into species presence and community composition but remains limited in its capacity to infer species abundance or population structure. Here, we sh...

🧬 My haplotype paper is out!

We show that deviations between within-sample and population-level haplotype frequencies can be used to estimate how many individuals contributed to an eDNA sample.

No tissue references needed, just metabarcoding data and some population genetics.

#eDNA #PopGen

Charles Darwin Quote I hate a Barnacle as no man ever did before, not even a Sailor in a slow-sailing ship.

Don’t forget the barnacles! www.azquotes.com/quote/1095192

The missing data problem in population genomics and statistical methods to address them The “Missing Data” problem is prevalent across all statistical inference, owing to the “absence of some part of a familiar data structure” (Efron 1994). Po

I wrote a short op-ed in @genetics-gsa.bsky.social G3 this month’s issue on missing data problems in population genomics that I’ve been thinking about for a couple of years. Lemme know your thoughts! Comments/suggestions/ideas welcome! doi.org/10.1093/g3jo...

My sculpture of an acorn barnacle—a crustacean!—in steel, bronze, and sterling silver, sitting on a white background. My hand touches the steel barnacle shell and provides scale (barnacle is just a bit smaller than my hand). The barnacle’s filter feeding legs (cirri) are spread dramatically wide.

Merry #Crustmas to all who celebrate! Hoping you are firmly attached to people you love, are able to scoop up large amounts of food, and can hide in an impervious shell when the social situation requires it ❤️

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

Barnacles the size of a small human fist piled into a museum jar

Big ol’ jar of the whale #barnacle Coronula diadema collected from a humpback whale that stranded in Massachusetts in 2016. Our museum has the whale skeleton as well! #crustmas

I'm recruiting a Ph.D. student for Fall 2026.

Interested in comparative studies and trait evolution in fishes?

Send me an email with a CV and research interests. Please take a look at my website (jcorush.github.io ) for more information about my research.

#hybridization #minnows #mudskippers

Putting on my hat as @asn-amnat.bsky.social ASN President for a minute for a string of announcements, please share widely!!!

1. Student research awards are open for applications, to fund research expenses for 10 graduate students ($2000 each)
nam10.safelinks.protection.outlook.com?url=https%3A...

Early Career Scientist Awards 2026 Application to the UW-Madison Evolution Seminar Series - Early Career Scientist Awards.

Wisconsin Evolution is accepting applications for our Seminar Series' Early Career Scientist Award. Come share your evolution research and visit UW-Madison's evolution community. Open to grad students and postdocs (<5 yrs post PhD) from outside UW-Madison.

Apply by Dec 15th here: shorturl.at/4a4O6

Chuck Schumer Helps Pull Democrats Back From Brink Of Courage

Chuck Schumer Helps Pull Democrats Back From Brink Of Courage

that panel from Watchmen

some years, Circulatory System Walking Through the Kitchen Day just completely sneaks up on you

📣📣📣 CONSERVATION GENETICS WORKSHOP -
Few more spaces left!

ConGen Population Genomic Data Analysis Course
🧬💻💡
University of Pretoria, South Africa 🌍
7-14 December + field trip to Kruger NP!
🦁🐃🐘🐆🦏

More info & registration here: www.umt.edu/congen/africa/

GBE | Hemoglobin-Gene Cluster Deletions in Antarctic White-Blooded Icefishes Facilitated by Transposable Elements Analyzing numerous genome assemblies of notothenioid fishes, Desvignes et al. demonstrated that in Antarctic white-blooded icefishes, the only vertebrates living without hemoglobin, the two hemoglobin gene clusters were lost independently from one another by different genomic mechanisms, although both mechanisms incriminate transposable and repeat-like elements.

@notothentoma.bsky.social @arcolon14.bsky.social & @jpostlethwait.bsky.social show how Antarctic white-blooded icefishes, the only vertebrates without hemoglobin, independently lost hemoglobin cluster genes, driven by TEs and repeats.

🔗 doi.org/10.1093/gbe/evaf184

#genome #evolution #TEsky

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

Reference genome bias in light of species-specific chromosomal reorganization and translocations - Genome Biology Background Whole-genome sequencing efforts, have during the past decade, unveiled the central role of genomic rearrangements—such as chromosomal inversions—in evolutionary processes, including local a...

📌 New publication out:

Reference genome bias in light of species-specific chromosomal reorganization and translocations

TL;DR - We show that the choice of reference genome biases the detection of structural variants and popgen stats. Navigate carefully - 🛳️ 😬

link.springer.com/article/10.1...

Do you know anyone with an interest in pursuing a PhD studying the genetics, development, and evolution of skeletal morphology and life history? If so please encourage them to apply to work with me through any of the University of Illinois' EEB or PEEC programs. 1/4 🧪🦷🦴🐭🐒

Top left: Results of genome-wide association study (GWAS) for sex in E. caeruleum, E. radiosum, and E. spectabile showing sex chromosome turnover has occurred repeatedly. Top right: Phylogeny showing sex chromosome turnover in darters and non-darter percids. Chromosome 9 is the putative ancestral sex chromosome, shared by Perca flavescens and multiple members of the orangethroat darter complex (e.g., E. spectabile, E. pulchellum). Bottom: Schematic depicting repeated turnover of sex chromosomes as a mechanism to resolve mitonuclear conflict and promote speciation.

First pop gen paper from our lab! We find repeated evolutionary turn over of sex chromosomes in darters contributes to reproductive isolation. Turnover may be an escape hatch to resolve mitonuclear conflict & neo sex chromosomes evolved via a rare recessive mutation. www.biorxiv.org/content/10.1...

Looking forward to the awesome @elliecat.bsky.social’s lecture today in our EEB seminar series! “Not All Bad News: Minor Genomic Impacts of Population Declines in Brown Bears” Noon Pacific in the Gold Auditorium, Shiley Biosciences Center. See ya there!

Dept of Plant Biology at UIUC hiring in any subdiscipline of Mycology and/or Plant-Fungal Interactions tenure-track faculty position at the assistant professor level.
Apply by Oct 31, 2025. For complete details including salary and benefit information, visit go.illinois.edu/PlantBiolfac...