# Blackmon Lab, Evolutionary Biology at Texas A&M University

> The Blackmon Lab studies genome structure evolution across the tree of life using computational, comparative, and experimental approaches.

## About

The Blackmon Lab is led by Dr. Heath Blackmon in the Department of Biology at Texas A&M University. The lab studies how and why genomes evolve structurally, with a focus on sex chromosomes, chromosome number evolution, and the genetic basis of adaptation. Study organisms include beetles, tomatoes, betta fish, chickens, and mammals. The lab uses three approaches: theoretical population genetics, comparative phylogenetic methods, and genetics/genomics.

## Key Research Questions

1. What evolutionary forces lead to the divergence of sex chromosomes?
2. Why does chromosome number evolve rapidly in some clades but remains static in others?
3. Is there an ideal chromosome number, and what determines it?
4. What determines the fate of mutations that expand the sex-linked proportion of the genome?
5. Are there inherent fitness trade-offs between male and female phenotypes?
6. Does the importance of epistasis vary across plants and animals?
7. How does domestication impact organisms and what can we learn about adaptation?

## Principal Investigator

Heath Blackmon, Ph.D., Associate Head, Department of Biology, Texas A&M University
- ORCID: https://orcid.org/0000-0002-5433-4036
- Google Scholar: https://scholar.google.com/citations?user=ytApUl0AAAAJ
- GitHub: https://github.com/coleoguy

## Software and Resources

- **evobiR**: R package for empirical data analysis, simulation, and teaching in evolutionary biology
- **chromePlus**: Markov models for chromosome number and binary trait evolution
- **DirectRepeateR**: Find and annotate direct repeats in genome assemblies
- **micRocounter**: Identify 2-6mer repeats in genome assemblies
- **SAGA2**: Model-averaged line cross analysis using AICc
- **Karyotype Databases**: 14,000+ records for beetles, flies, amphibians, mammals, Drosophila, and Polyneoptera
- **Epistasis Database**: 1,600+ line cross datasets from 130+ publications on epistasis in trait divergence
- **Tree of Sex Database**: 30,000+ records on sex determination systems (NESCent collaboration)

## Pages

- Homepage: https://coleoguy.github.io/
- Research: https://coleoguy.github.io/research.html
- Publications: https://coleoguy.github.io/publications.html
- Team: https://coleoguy.github.io/team.html
- Resources: https://coleoguy.github.io/resources.html
- Join: https://coleoguy.github.io/join.html
- News: https://coleoguy.github.io/news.html
- Lab Life: https://coleoguy.github.io/gallery.html
- Bio & AI CURE: https://coleoguy.github.io/biolai-cure.html
- STEGG Conference: https://coleoguy.github.io/stegg.html
- AI Concentration: https://coleoguy.github.io/tamu-ai-concentration.html
- PCM Guide (index): https://coleoguy.github.io/phylo-methods/index.html
- PCM Guide, Phylogenies: https://coleoguy.github.io/phylo-methods/phylogenies.html
- PCM Guide, Continuous Traits: https://coleoguy.github.io/phylo-methods/continuous.html
- PCM Guide, Discrete Traits: https://coleoguy.github.io/phylo-methods/discrete.html
- PCM Guide, Discrete + Continuous: https://coleoguy.github.io/phylo-methods/discrete-continuous.html
- Sex Chromosome Evolution (visual guide): https://coleoguy.github.io/sex-chromosome-evolution.html
- Coleoptera Genomics (visual guide): https://coleoguy.github.io/coleoptera-genomics.html
- Genome Structure Evolution (visual guide): https://coleoguy.github.io/genome-structure-evolution.html
- Selection in Evolution (visual guide): https://coleoguy.github.io/selection.html
- Epistasis & the Shifting Balance (visual guide): https://coleoguy.github.io/epistasis-line-cross.html
- Chromosome Evolution History (intellectual history): https://coleoguy.github.io/chromosome-evolution-history.html
- Epistasis Database: https://coleoguy.github.io/epistasis-database.html
- Circadian Period Database: https://coleoguy.github.io/tau_database.html
- CUREs Karyotype Database (63,542 records, 56 clades): https://coleoguy.github.io/cures-karyotype-database.html
- Phylogenetic Tree Explorer (interactive): https://coleoguy.github.io/phylo-explorer.html
- Citation Network (interactive): https://coleoguy.github.io/citation-network.html

## Recent Publications (2026)

- **Copeland M, McConnell M, Barboza A, ... Blackmon H** (2026). *Dismantling Chromosomal Stasis Across the Eukaryotic Tree of Life.* bioRxiv preprint. DOI: https://doi.org/10.64898/2026.04.14.718287. Largest analysis of dysploidy rates to date (63,682 karyotypes, 55 clades). Rates vary 844-fold, and birds exceed the global median once microchromosomes are resolved.
- **Chien S, ... Blackmon H et al.** (2026). *Chromosome-Level Reference Genome of an Endemic, Endangered Long-Armed Scarab (Cheirotonus formosanus): Discovery of a Putative Y-Linked Scaffold and Demographic History.* Ecology and Evolution. DOI: https://doi.org/10.1002/ece3.73483
- **Chien S, Blackmon H** (2026). *Chromosomal Rearrangements: Tempo and Mode of Karyotype Evolution in Scarabaeoidea.* Journal of Evolutionary Biology. DOI: https://doi.org/10.1093/jeb/voag025
- **Eales JG, Copeland M, MacKenzie DS** (2026). *Peripheral and central regulation of thyroid status in teleost fish with particular reference to tetraploid juvenile salmonids and Parr-Smolt transformation.* General and Comparative Endocrinology. DOI: https://doi.org/10.1016/j.ygcen.2026.114929

## Contact

Department of Biology, Texas A&M University, College Station, TX 77843

## Interactive Tools & Databases

The lab hosts several client-side interactive tools directly on this site (no server required):

### Population Genetics Simulator
URL: https://coleoguy.github.io/subpages/popgen-sim.html
Wright-Fisher simulator supporting drift, selection, mutation, migration, bottlenecks, and sex chromosome evolution (XY/ZW). Runs entirely in the browser.

### Karyotype Databases
Six searchable, filterable, downloadable karyotype databases embedded as static HTML pages:
- Coleoptera (4,960 records): https://coleoguy.github.io/subpages/karyotype-data/coleoptera.html
- Diptera (3,443 records): https://coleoguy.github.io/subpages/karyotype-data/diptera.html
- Amphibian (2,124 records): https://coleoguy.github.io/subpages/karyotype-data/amphibian.html
- Mammal (1,440 records): https://coleoguy.github.io/subpages/karyotype-data/mammal.html
- Drosophila (1,247 records): https://coleoguy.github.io/subpages/karyotype-data/drosophila.html
- Polyneoptera (823 records): https://coleoguy.github.io/subpages/karyotype-data/polyneoptera.html
Hub page: https://coleoguy.github.io/karyotypes/
Total records: 14,037 karyotypes across vertebrates and insects.

## Phylogenetic Comparative Methods (PCM) Interactive Guide

An interactive teaching resource covering the core methods in phylogenetic comparative biology. All visualizations run client-side in the browser with no server required.

### Phylogenies
URL: https://coleoguy.github.io/phylo-methods/phylogenies.html
Covers tree reading, cladograms vs phylograms, branch lengths, tree rotation, and a fully interactive D3.js vertebrate chronogram with toggleable branch lengths.

### Continuous Trait Evolution
URL: https://coleoguy.github.io/phylo-methods/continuous.html
Brownian motion simulation, phylogenetic signal, PGLS regression. Includes live simulator (adjustable sigma, single/20-sim modes), signal comparison SVGs, and PGLS vs OLS regression visualization.

### Discrete Trait Evolution
URL: https://coleoguy.github.io/phylo-methods/discrete.html
Mk model, ancestral state reconstruction, stochastic character mapping, Pagel's test. Includes interactive Markov diagram, ASR visualization with marginal probability pies, and stochastic character mapping panels. Also covers chromePlus (R package for chromosome number evolution, gain/loss/polyploidy/demiploidy with binary trait modulation) and a comparison of maximum likelihood vs Bayesian inference with an interactive posterior/likelihood/prior canvas.

### Discrete + Continuous (ANCOVA, Pagel's Lambda)
URL: https://coleoguy.github.io/phylo-methods/discrete-continuous.html
PGLS-ANCOVA for mixed trait models, Pagel's lambda phylogenetic signal parameter. Lambda heatmap shows how the phylogenetic covariance matrix changes from no signal (lambda=0) to full BM expectation (lambda=1).

### Birth-Death Tree Simulator
URL: https://coleoguy.github.io/phylo-methods/bd-simulator.html
Interactive birth-death tree simulator using the Gillespie algorithm. Runs two independent simulations with identical λ (speciation) and μ (extinction) rates, showing how stochastic macroevolutionary processes produce very different tree topologies and diversity. Adjustable sliders for λ, μ, and crown age. Visual: gold=surviving lineages, grey=extinct lineages, red dots=extinction events, teal dots=extant tips. Paired panels illustrate how the same net diversification rate (r = λ − μ) can yield very different outcomes.

### Likelihood Ridges in Discrete Trait Models
URL: https://coleoguy.github.io/phylo-methods/likelihood-ridges.html
Guide to a numerical challenge in Mk-model maximum likelihood estimation: high rate parameters proportional to trait spread across the tree can fit data nearly as well as the true MLE, creating a flat ridge in likelihood space at biologically unrealistic values. Explains why MCMC with priors or multiple starting points matters, and what happens when optimization wanders into this region. Includes interactive likelihood surface visualization and links to discrete trait methods.

## Chromosome Number Evolution, Intellectual History

A standalone editorial page tracing a century of ideas on karyotype evolution: cytological foundations (Stebbins, White), the population genetic challenge (Lande), the hybrid speciation synthesis (Rieseberg), and the probabilistic methods era (Mayrose ChromEvol, Zenil-Ferguson BiChroM/ChromoSSE). Ends with open questions and the Blackmon Lab's contributions. Newspaper-style two-column layout. Links to karyotype databases, chromePlus, and the PCM guide.
URL: https://coleoguy.github.io/chromosome-evolution-history.html

## Citation Network

An interactive force-directed graph of the lab's publication network. Nodes are papers, sized by citation count and colored by year (gold to teal). Edges connect papers that share co-authors. Built with D3.js, fetches data from OpenAlex by ORCID. Supports pan/zoom, hover tooltips, node dimming, and click-to-DOI. Includes a stats overlay (paper count, total citations, connections) and a color/size legend.
URL: https://coleoguy.github.io/citation-network.html

## Visual Guides to Evolutionary Biology

In addition to the Chromosome Evolution History page and the PCM interactive guide, the lab hosts several long-form visual guides covering core topics in evolutionary biology:

### Sex Chromosome Evolution
URL: https://coleoguy.github.io/sex-chromosome-evolution.html
A visual guide to sex chromosome evolution, from ordinary autosomes to the X, Y, Z, and W chromosomes that determine sex across the tree of life. Covers identification methods (cytogenetics, sequencing), Ohno's law, Y/W degeneration, dosage compensation (XCI, hypertranscription, incomplete compensation in ZW systems), and turnover. Includes interactive diagrams, phylogenetic distribution of sex determination systems, and key papers.

### Coleoptera Genomics
URL: https://coleoguy.github.io/coleoptera-genomics.html
A visual guide to beetle genomics. Covers reference genomes across coleopteran families, Stevens elements (ancestral chromosomal units), dosage compensation in beetles, population genetics of pest and model species, and the genomic basis of extraordinary species richness. Links beetle karyotype databases to modern genome assemblies.

### Evolution of Genome Structure
URL: https://coleoguy.github.io/genome-structure-evolution.html
A visual guide to the evolution of gross genome structure: chromosome fusions, fissions, whole-genome duplication (polyploidy), demiploidy, and the forces that shape karyotype evolution across the tree of life. Covers meiotic drive, drift, and selection on chromosome number. Includes interactive diagrams and links to karyotype databases and chromePlus.

### Selection in Evolution
URL: https://coleoguy.github.io/selection.html
A visual guide to selection, covering natural, artificial, sexual, background, and indirect selection on recombination modifiers. Spans Darwin to modern population genetics. Includes interactive fitness landscape visualizations, the breeder's equation, and key papers from Fisher, Wright, Haldane, and Hamilton through modern quantitative genetics.

### Epistasis and the Shifting Balance
URL: https://coleoguy.github.io/epistasis-line-cross.html
A visual guide to epistasis, line cross analysis, and Wright's shifting balance theory. Covers types of epistasis (magnitude, sign, reciprocal sign), the Wright-Fisher debate, the joint-scaling test, SAGA/SAGA2 (information-theoretic line cross analysis), and empirical evidence from over 1,600 datasets. Includes interactive fitness landscape diagrams and the full intellectual history of the debate.

### Epistasis Database
URL: https://coleoguy.github.io/epistasis-database.html
Interactive database of 1,600+ line cross datasets from 130+ publications, quantifying the relative contributions of additive, dominance, and epistatic genetic effects to trait divergence across plants and animals. Includes cumulative distribution plots, ternary (additive/dominance/epistasis) visualization, searchable/sortable data table with individual dataset downloads, and full citation list. Replaces a former Shiny application; runs entirely client-side.

### Circadian Period Database
URL: https://coleoguy.github.io/tau_database.html
Searchable database of 1,634 free-running circadian period (tau) measurements across the tree of life. Includes species, common name, tau value, light regime, sex, and citation for each record. Client-side with filtering and download.

## AI-Native Biology Program

The Blackmon Lab is building AI-native workflows for evolutionary biology. Full program overview:
URL: https://coleoguy.github.io/ai.html

### TraitTrawler, Autonomous Literature Mining
URL: https://github.com/coleoguy/TraitTrawler
A general-purpose autonomous pipeline that searches PubMed, OpenAlex, bioRxiv, and Crossref for scientific papers, retrieves full-text PDFs through a 12-source cascade (DOI content negotiation, PMC, Unpaywall, OpenAlex, publisher URLs, Europe PMC, Semantic Scholar, CORE, bioRxiv/medRxiv, Internet Archive, DOAJ, browser-based institutional access), extracts structured trait data with mandatory double-entry verification, and writes validated records to CSV. Generalizes the lab's earlier domain-specific karyotype agent to any trait, any clade.

### AI as Lead Investigator
An experiment in research autonomy: a Claude-powered agent that formulates hypotheses about claw evolution, selects comparative methods, runs analyses, interprets results, and drafts a manuscript. Manuscript in preparation.

### Biology and AI CURE
URL: https://coleoguy.github.io/biolai-cure.html
Course-Based Undergraduate Research Experience (Spring 2026) where students conduct original evolutionary biology research using phylogenetic comparative methods and AI-assisted analysis.

### AI in Biology Concentration (Texas A&M)
URL: https://coleoguy.github.io/tamu-ai-concentration.html
Formal degree concentration at Texas A&M, 10 semester hours of AI-focused coursework in Biology BS and PhD programs.

## Public Data Sources for Evolutionary Biology

A curated directory of major open-access databases and repositories used in comparative and evolutionary biology research. Organized by category: trait databases (AVONET, PanTHERIA, TRY), occurrence/taxonomy (GBIF, iNaturalist, ITIS, NCBI Taxonomy), phylogenies (Open Tree of Life, TreeBASE, TimeTree), genomics (NCBI, Ensembl, UCSC), and repositories (Dryad, Zenodo, Figshare). Each entry includes a brief description and direct link.
URL: https://coleoguy.github.io/subpages/data-sources.html

## Research Glossary

Plain-language definitions of core concepts in the Blackmon Lab's research areas: phylogenetics and comparative methods, chromosome and karyotype evolution, population genetics, and genomics. Terms include: birth-death model, Mk model, Brownian motion, PGLS, phylogenetic signal, sex chromosome, B chromosomes, fixation probability, coalescence, and more. Aimed at upper undergrads and early grad students entering the field.
URL: https://coleoguy.github.io/subpages/glossary.html

## Phylogenetic Tree Explorer

Interactive D3.js-based phylogenetic tree viewer. Users paste or upload a Newick string and optionally a CSV/TSV trait file. Supports three layout modes: cladogram (equal leaf spacing), phylogram (branch lengths proportional to evolutionary distance), and radial (fan layout). Includes clade collapsing/expanding on click, hover tooltips with node info, trait-based tip coloring with legend, zoom/pan, and SVG export. Demo data shows a beetle phylogeny with habitat traits. Client-side, no server required.
URL: https://coleoguy.github.io/phylo-explorer.html

## BIOL 682: Communication in the Biological Sciences

Course materials for BIOL 682, scientific writing, storytelling, peer review, and revision in the biological sciences. Includes downloadable PDFs on common writing flaws in life sciences manuscripts, structured revision prompts, example revision responses, and peer review guidelines.
URL: https://coleoguy.github.io/subpages/biol682.html