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. We also recently published a subset of this data as the Coleoptera Karyotype Database. Beetle karyotypes are particularly powerful since they normally include information about the meiotic behavior of sex chromosomes.

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.

Google Scholar

1. Sylvester, T, Hoover, Z, Hjelmen, CE, Jonika, MM, Blackmon, LT, Alfieri, JM et al.. A reference quality genome assembly for the Jewel scarab Chrysina gloriosa. G3 (Bethesda). 2024; :. doi: 10.1093/g3journal/jkae084. PubMed PMID:38630623 .
2. Perry, A, Eddelbuettel, D, Rosenthal, G, Blackmon, H. Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short-read data. Mol Ecol Resour. 2024;24 (4):e13933. doi: 10.1111/1755-0998.13933. PubMed PMID:38299378 PubMed Central PMC10994724.
3. Burch, J, Chin, M, Fontenot, BE, Mandal, S, McKnight, TD, Demuth, JP et al.. Wright was right: leveraging old data and new methods to illustrate the critical role of epistasis in genetics and evolution. Evolution. 2024;78 (4):624-634. doi: 10.1093/evolut/qpae003. PubMed PMID:38241518 PubMed Central PMC10964199.
4. Blackmon, H, Jonika, MM, Alfieri, JM, Fardoun, L, Demuth, JP. Drift drives the evolution of chromosome number I: The impact of trait transitions on genome evolution in Coleoptera. J Hered. 2024;115 (2):173-182. doi: 10.1093/jhered/esae001. PubMed PMID:38181226 PubMed Central PMC10936555.
5. Rice, ES, Alberdi, A, Alfieri, J, Athrey, G, Balacco, JR, Bardou, P et al.. A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. BMC Biol. 2023;21 (1):267. doi: 10.1186/s12915-023-01758-0. PubMed PMID:37993882 PubMed Central PMC10664547.
6. Alfieri, JM, Hingoranee, R, Athrey, GN, Blackmon, H. Domestication is associated with increased interspecific hybrid compatibility in landfowl (order: Galliformes). J Hered. 2024;115 (1):1-10. doi: 10.1093/jhered/esad059. PubMed PMID:37769441 PubMed Central PMC10838130.
7. Alfieri, JM, Jonika, MM, Dulin, JN, Blackmon, H. Tempo and Mode of Genome Structure Evolution in Insects. Genes (Basel). 2023;14 (2):. doi: 10.3390/genes14020336. PubMed PMID:36833264 PubMed Central PMC9957073.
8. Smith, J, Alfieri, JM, Anthony, N, Arensburger, P, Athrey, GN, Balacco, J et al.. Fourth Report on Chicken Genes and Chromosomes 2022. Cytogenet Genome Res. 2022;162 (8-9):405-528. doi: 10.1159/000529376. PubMed PMID:36716736 .
9. Alfieri, JM, Johnson, T, Linderholm, A, Blackmon, H, Athrey, GN. Genomic investigation refutes record of most diverged avian hybrid. Ecol Evol. 2023;13 (1):e9689. doi: 10.1002/ece3.9689. PubMed PMID:36620416 PubMed Central PMC9817184.
10. Lotterhos, KE, Fitzpatrick, MC, Blackmon, H. Simulation Tests of Methods in Evolution, Ecology, and Systematics: Pitfalls, Progress, and Principles. Annu Rev Ecol Evol Syst. 2022;53 (1):113-136. doi: 10.1146/annurev-ecolsys-102320-093722. PubMed PMID:38107485 PubMed Central PMC10723108.