Blackmon Lab

We study

Research

The Blackmon Lab is in the Biology Department at Texas A&M University. We have two broad areas of inquiry. The first is genome evolution, specifically sex chromosome and structural evolution. The second is the development of methods and databases that accelerate the analysis of data within a quantitative genetic or phylogenetic framework. To address these topics, we use a broad range of approaches including theoretical population genetics, bioinformatics, genomics, and molecular cytogenetics. Although we have projects involving all types of organisms, we often study beetles, and we keep several species in the lab as model organisms.

Fragile Y Hypothesis

Chromosomal sex determination is phylogenetically widespread, having arisen independently in many lineages. Decades of theoretical work provide predictions about sex chromosome differentiation that are well supported by observations in both XY and ZW systems. However, the phylogenetic scope of previous work gives us a limited understanding of the pace of sex chromosome gain and loss and why Y or W chromosomes are more often lost in some lineages than others, creating XO or ZO systems. Contrary to our initial expectations, we find that highly degenerated Y chromosomes of many members of the Coleoptera suborder Polyphaga are rarely lost and that cases of Y chromosome loss are strongly associated with chiasmatic segregation during male meiosis. We propose the "Fragile Y Hypothesis" that recurrent selection to reduce recombination between the X and Y chromosome leads to the evolution of a small pseudoautosomal region, which, in taxa that require XY chiasmata for proper segregation during meiosis, increases the probability of aneuploid gamete production, with Y chromosome loss. This hypothesis predicts that taxa that evolve achiasmatic segregation during male meiosis will rarely lose the Y chromosome.

Genetic Architecture

The pace and direction of evolution are governed by the genetic architecture of trait variation. Evolutionary biologists have disagreed about whether genes can be considered to act in isolation, or in the context of their genetic background (Fisher Wright debate). Line cross analysis (LCA) estimates genetic architecture parameters conditional on the best model chosen from a vast model space using relatively few line means and ignores uncertainty in model choice. To address these issues, we introduced an information theoretic approach to LCA, which comprehensively assesses the potential model space, quantifies model selection uncertainty, and uses model weighted averaging to estimate composite genetic effects accurately. Using simulated data and previously published LCA studies we have shown the utility of our approach to define the components of complex genetic architectures. Our analysis of 20+ previously published datasets also shows that traditional approaches have underestimated the importance of epistasis.

Insect Karyotypes

Insects exhibit variation in both chromosome number and sex chromosome systems. Insect karyotypes have been an important source of data for both taxonomic and basic evolutionary biology research. Unfortunately, this data has always been scattered among journals and dissertations that are not accessible without subscriptions. We created the Tree of Sex Database to make this data open and available to all researchers. We curate the insect portion of this database that currently has over 15,000 records and has proven to be a valuable resource to explore and test ideas about the evolution of high-level genome evolution. Recently we published a synthesis of this vast dataset and uncovered many interesting patterns and avenues for future investigations.

Chromosome Number

It has long been thought that in Eusocial insect selection to increase genetic diversity within a colony should indirectly select for increases in the number of chromosomes. To test this long-standing hypothesis, we investigated the relationship between eusociality and chromosome number across Hymenoptera. We found that solitary and social Hymenoptera do not have significantly different numbers of chromosomes. However, we did find that chromosome number evolves more quickly in social than solitary Hymenoptera. It remains unclear whether variable selection pressure or drift are responsible for this difference.

Publications

Google Scholar

2020

Ruckman, SN, M Jonika, C Casola, and H Blackmon. Chromosome number evolves at equal rates in holocentric and monocentric clades. PLoS Genetics early online open access

Hancock, ZB and H Blackmon. Ghosts of a structured past: Impacts of ancestral patterns of isolation-by-distance on divergence-time estimation. Journal of Heredity early online open access

Ruckman, SN and H Blackmon, 2020. The March of the Beetles: Epistatic Components Dominate Divergence in Dispersal Tendency in Tribolium castaneum. Journal of Heredity, 111(5), pp. 498-505. open access

Sylvester, T, CE Hjelmen, SJ Hanrahan, PA Lenhart, JS Johnston, and H Blackmon. Lineage-specific patterns of chromosome evolution are the rule not the exception in Polyneoptera insects. Proceedings of the Royal Society B 287(1935) open access

Jonika MJ, J Lo, H Blackmon. Mode and tempo of microsatellite evolution across 300 million years of insect evolution. Genes, 11(8), pp 945. open access

Hjelmen, CE, VR Holmes, CG Burrus, E Piron, M Mynes, MA Garrett, H Blackmon , JS Johnston. Thoracic underreplication in Drosophila species estimates a minimum genome size and the dynamics of added DNA. Evolution, 74 (4), pp 1423-1436. PDF

2019

Armstrong, A, N Anderson, H Blackmon. Inferring the potentially complex genetic architectures of adaptation, sexual dimorphism, and genotype by environment interactions by partitioning of mean phenotypes. Journal of Evolutionary Biology 32 (4), 369-379 PDF

Perkins, RD, JR Gamboa, MM Jonika, J Lo, A Shum, RH Adams, H Blackmon. A database of amphibian karyotypes. Chromosome Research, pp.1-7. PDF

Schield, DR, DC Card, NR Hales, BW Perry, GM Pasquesi, H Blackmon, RH Adams, AB Corbin, CF Smith, B Ramesh, and JP Demuth. The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes. Genome research, 29(4), pp.590-601. PDF

Lo, J, MM Jonika, and H Blackmon. micRocounter: Microsatellite Characterization in Genome Assemblies. G3: Genes, Genomes, Genetics, 9(10), 3101-3104. PDF

Hjelmen, CE, H Blackmon, VR Holmes, CG Burrus, and JS Johnston. Genome size evolution differs between Drosophila subgenera with striking differences in male and female genome size in Sophophora. G3: Genes, Genomes, Genetics, 9(10), pp.3167-3179. PDF

Blackmon H, J Justison, I Mayrose, EE Goldberg. Meiotic drive shapes rates of karyotype evolution in mammals. Evolution 73(3), 511-523 PDF

Passow, C, AM Bronikowski, H Blackmon, S Parsai, TS Schwartz, SE McGaugh. Contrasting patterns of rapid molecular evolution within the p53 network across mammal and sauropsid lineages. Genome Biology and Evolution 11(3), 629-643 PDF

2018

Gale, CC, E Borrego, H Blackmon, JK Harper, D Richardson, and H Song. Investigating a Photolytic Metabolite in the Nocturnal Grasshopper Schistocerca ceratiola (Orthoptera: Acrididae). Annals of the Entomological Society of America, 112(1), pp.50-55. PDF

2017

Blackmon H, Y Brandvain. Long-term fragility of Y chromosomes is dominated by short-term resolution of sexual antagonism - Genetics PDF

Blackmon H, L Ross, D Bachtrog. Sex determination, sex chromosomes and karyotype evolution in insects. – Journal of Heredity 108:1 78-93 – recommended by Faculty of 1000. PDF

Adams R, D Schield, D Card, H Blackmon, and T Castoe. GppFst: Genomic posterior predictive simulations of Fst and dxy for identifying outlier loci from population genomic data – Bioinformatics – doi:10.1093/bioinformatics/btw795. PDF

2016

Blackmon H and JP Demuth. An information-theoretic approach to estimating the composite genetic effects contributing to variation among generation means: moving beyond the joint-scaling test for line cross analysis. – Evolution 70:2 420-432. PDF

Asian Longhorn Beetle Consortium (67 Authors). Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface. Genome Biology 17:1 227 - Responsible for analysis of genome structure evolution. PDF

Ross, L and H Blackmon. Sex Determination. In R. Kliman (Ed.) Encyclopedia of Evolutionary Biology. 81-88 Elsevier Academic Press. doi:10.1016/B978-0-12-800049-6.00146-3. PDF

Adams R, H Blackmon, J Reyes-Velasco, D Schield, D Card, A Andrew, N Waynewood, T Castoe. Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution. Genome 59:5, 295-310 - Editor’s choice. PDF

2015

Blackmon H, N Hardy, L Ross. The evolutionary dynamics of haplodiploidy: genome architecture and haploid viability. Evolution 69:11 2971-2978. PDF

Blackmon H and JP Demuth. The fragile Y hypothesis: Y chromosome aneuploidy as a selective pressure in sex chromosome and meiotic mechanism evolution. Bioessays 37:9 942-950. PDF

Blackmon H and JP Demuth. Coleoptera Karyotype Database. The Coleopterists Bulletin 69:1 174-175. PDF

Ross, L, H Blackmon, P Lorite, V Gokhman, and N Hardy. Recombination, chromosome number and eusociality in the Hymenoptera. Journal of Evolutionary Biology 28:1 105-116. PDF

Blackmon H and JP Demuth. Genomic origins of insect sex chromosomes. Current Opinion in Insect Science 7 45-50. – recommended by Faculty of 1000. PDF

2014

Blackmon H and JP Demuth. Estimating tempo and mode of Y chromosome turnover: explaining Y chromosome loss with the fragile Y hypothesis. Genetics 197:2 561-572. PDF

Blackmon H Coleoptera Karyotypes: The evolution of sex chromosomes and chromosome number. Newsletter of the Ontario Entomological Society 19:2 19–21. PDF

Streicher, JW, TJ Devitt, CS Goldberg, JH Malone, H Blackmon, and MK Fujita. Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs. Molecular Ecology 23:13 3273-3291. PDF

Ashman T, D Bachtrog, H Blackmon, EE Goldberg, MW Hahn, M Kirkpatrick, J Kitano, JE Mank, I Mayrose, R Ming, SP Otto, CL Peichel, MW Pennell, N Perrin, L Ross, N Valenzuela, and JC Vamosi. Tree of Sex: A database of sexual systems. Nature Scientific Data 1:140015. – responsible for 11,526 invertebrate records and all figures. PDF

2012

Blackmon H and JP Demuth. Ring Species and Speciation. Encyclopedia of Life Science. www.els.net. PDF

Resources

We devote a fair amount of our efforts to producing new datasets, software, and resources for both research and teaching. If you have any questions about these projects please dont hesitate to contact us for additional information.

Lab Meetings

Fall 2020

Teaching

Experimental Design Course: This course is intended to provide a foundation in the proper design of scientific research projects in the field of biology. A wide range of biological experiments are covered, and each type of experiment is explored with an eye toward choosing the appropriate statistical technique for analysis. By the end of the course, successful students will be able to design biological studies that are statistically tractable and perform basic statistical analyses using the programming language R.

R for biologists seminar: R is currently an essential tool for most evolutionary biologists. This seminar includes tutorials and example datasets for many basic analyses in R that are commonly encountered in ecology and evolution. The seminar starts off with the most basic steps (installation) so no prior experience is needed to use these exercises.

Foundations of evolutionary biology: An understanding of the foundational ideas that the modern synthesis of evolutionary biology is built on is essential for asking intelligent questions and understanding how your research fits into a larger understanding of life. I offered a foundations of evolutionary biology seminar course for graduate students that provided a structured environment to discuss some of the most important papers in evolutionary biology. This website contains a schedule and PDF files for all of the readings in this course.

GitHub software repository: I do most all of my development and analyses in public repositories.

GitHub Pages Tutorial

R packages

chromePlus is a collection of R functions generate markov models appropriate for the evolution of chromosome number and binary traits. These models once constructed can be fit via maximum likelihood or Bayesian MCMC methods avaialable in the package diversitree.

micRocounter is an R package to identify all 2-6mer repeates in a genome assembly. It has been optimized for speed and can calculate statitics for larger genomes in a manner of minutes.

evobiR is a collection of R functions that I have developed for different projects. The functions in this package can be loosely organized into either analysis of empirical data, simulation functions, or those created primarily for didactic purposes. A vignette demonstrating its use is available. Instructions for installing the latest version from github are available here.

The package SAGA2 is a collection functions to ease and hopefully improve the quality of line cross analysis of genetic architecture. The overall goal is to allow for an easy and straightforward implementation of model averaged analysis using AICc. A vignette demonstrating its use is available. Instructions for installing the latest version from github are available here.

Databases

Karyotype Databases: Karyotypes are a highly variable and complex trait that offers an opportunity to detect changes in genome organization, uncover phylogenetic history, and distinguish cryptic species. The current databases contains more than 8,000 records for amphibians, coleoptera, and polyneoptera. The databases allows users to select the records that they wish to retrieve based on either taxonomy or trait values and builds customized tables of the results in a new window.

The Tree of Sex Database: this is a product of a working group sponsored by the National Evolutionary Synthesis Center which sought to compile all information on sex determination systems across the tree of life. To date, we have collected over 30K records including more than 10K invertebrates. Much like the Coleoptera Karyotype Database, our goal is to make this data widely available allowing researchers across the globe to use data that was previously difficult to collect.

Other

I recently built a cluster consisting of 26 Raspberry Pi 4Bs. I have assembled some notes to guide anyone else through this process

I have assembled some links to graduate student funding opportunities for graduate students.

Lab Members

Principal Investigator

Heath Blackmon

Heath Blackmon received his PhD in the Demuth lab at the University of Texas at Arlington in 2015 while studying the evolution of sex chromosomes and karyotypes in Coleoptera and invertebrates. He then transitioned to a postdoc for two years at the University of Minnesota. While there he collaborated with Emma Goldberg and Yaniv Brandvain on projects spanning population genetics and macroevolution. Heath opened his own lab at Texas A&M University in the fall of 2017. CV - October 2019

ORCID iD iconhttps://orcid.org/0000-0002-5433-4036

Research Staff

Tahmineh Esfandani joined the lab in 2020 as a research scientist. She earned a Bachelors degree in Cellular and Molecular Biology from Iran and followed this with a masters in genetics and bioinformatics from Trinity College in Ireland. She has a broad background including managing a large mouse colony and extensive wetlab experience working in core facilities at the University of Oregon. Tahmineh is involved in a range of project focused on sex chromosome evolution.

Cark Hjelmen

Carl Hjelmen joined the lab in 2019 as a postdoctoral researcher. Carl's previous work has examined the evolution of genome size and the dynamics of Y chromosome decay across drosophila. He will be working on projects that examine the strucutral evolution of genomes and extending his studies of sex chromosomes in a genomic context. Carl's website

Graduate Students

Terrence joined the lab as a biology Ph.D. student in 2017. He is currently exploring the relationship between sexual systems and rates of chromosome evolution in Phasmatodea. Terrence has broad interests in evolutionary biology. He is working to develop a project that will allow him to combine field work with his interest in the evolution of genome complexity and structure.

Michelle joined the lab as a genetics Ph.D. student in 2018. She is currently working on a project examining the dynamics of microsat evolution across hexapods. Michelle has broad interests and extensive experience in forensics. Michelle's website

Jamie Alfieri joined the lab in 2020 as a PhD student in Ecology and Evolutionary Biology, and is co-advised with Giri Athrey. Jamie's previous work has examined the effects of disturbance (urbanization and scavenger exclusion) on invertebrate community ecology. Jamie is broadly interested in connecting genome structure to organism function and community diversity.

Undergraduate Students

Johnathan joined the lab in 2018 and is working on algorithms for genome analysis. John has one first author paper for an R package micRcounter that he built. This software does rapid inference of microsatellite content from genome assemblies. He also is a coauthor on several other lab projects.

Alli joined the lab in 2020 and is working on a project focused on building new genome assemblies.

Kayla joined the lab in 2019 and is working on a project that is focused on the dynamics of autosome sex chromosome fusions. Kayla has previous research in Tribolium castaneum. While she was still in high school she worked in the Demuth lab at UT Arlington where she was focused on mitochondrial introgression and phosphine resistance.

Julia joined the lab in 2018 and is working on a theory project to understand the evolution of alternative forms of meiosis.

Alejandro joined the lab in the fall of 2020 and will be working on computational and theoretical projects.

Ellena joined the lab in the fall of 2020 and will be working on computational and theoretical projects.

Chandler joined the lab in the fall of 2020 and will be working on computational and theoretical projects.

Kate joined the lab in the fall of 2020 and will be working on computational and theoretical projects.

Alumni

Sarah joned the lab in 2019 to finish up a masters in EEB before heading to Florida to work on her Ph.D. Sarah has broad interests in evolution and behavior. While in the lab her work focused on understanding the genetic underpinnings of dispersal behavior in Tribolium castaneum.

Nathan was first an undergraduate researcher in the lab for two years and since his graduation in December 2019 has transitioned into a technician position until he begins gaduate school in September of 2020. Nathan has broad interests in population and quantitative genetics as well as phylogenetics. Nathan's website

Riddhi Perkins joined the lab as an undergraduate researcher in 2018. She quickly proved herself so organized and ambitious that she became a part-time lab manager as well. Riddhi's current research projects are focused on understanding the dynamics of chromosome evolution across amphibians.

Andrew was a mathematics major and in the lab from 2017-2020 he published a great paper on line cross analysis methods and is now working in the finance industry.

Paulina was in the lab from 2018-2020 and worked on several different beetle projects.

Eleanor was in the lab from 2018-2020 and worked on a genome size evolution project.

David was in the lab from 2018-2020 and worked on a sexual antagonism project.

Amy was in the lab from 2018-2020 and worked on a sexual antagonism project.

Mayra was in the lab from 2018-2020 and worked to create new genetic resources in Tribolium.

Roberto was a summer intern graduate student in the summer of 2018. He worked on a phylogeny project.

Calendar

If you need to scedule an appointment with me the best approach is to pick a time that is not currently blocked out and then email me asking to meet at that time. I am not guranteed to be in my office unless you let me know you will be coming by (I often work in coffee shops!)

Lab News

For the latest happenings check out our twitter feed below.

Joining the lab

We are always seeking new students that can bring diversity, enthusiasm, and dedication into the lab.

We believe strongly in the importance of creating an inclusive supportive environment for all lab members. To achieve this we ask all lab members to sign a document that makes explicit our expectations for all lab members. This document includes the following statements:

  • I will participate in weekly lab meetings and journal clubs.
  • I will attend departmental and IDP seminars.
  • I will prepare for our regular progress/pitfalls meetings
  • I will proof-read manuscripts from other lab members.
  • I will maintain a set of lab notes, including directories of data, annotated codes and versions, detailed methods. Lab notes will be sufficient to reproduce results without additional instructions.
  • I will participate in general lab responsibilities (beetle maintenance, maintain common areas, community outreach events).
  • As a graduate student I will be available in the lab/office most days from 9:00 – 17:00.
  • As an undergraduate researcher I devote a minimum of 10 hours a week to research and I will make a two semester commitment to work in the lab.
  • I value diversity in intellectual background, race, sex, and identity.
  • I will treat all others with respect and dignity.
If you are interested in joining the lab please email Dr. Blackmon (blackmon@tamu.edu) to schedule a meeting.

Lab Pictures


Evolution Conference 2019


Riddhi decorated the lab door for us


Late night tacos after collecting


Searching for tiger beetles in Willcox AZ


Michelle Jonika's award winning artwork


No beetle is out of reach with this net


Bernice


Looking for Mordellidae


East Texas collecting trip


I'm too slow


Prada in West Texas


Setting up lights for a night of collecting


LT checking the sheets for bugs


2019 collecting during monsoons in AZ was productive


Lots of these signs around field sites in AZ


Inaugral Aggie Vets Who Code Class


Abbi caught a lot of giant millipedes


Checking out aliend artifacts in Roswell


Terrence finding the only shade in White Sands


Nellie was one of our first lab members


Movie night


Carl sand surfing


Social distancing but still spending time together


Terrence checking out a tarantula