Professor Alvarado's research program is motivated by understanding the molecular boundaries of biological plasticity. While genetics provides a reasonable molecular framework for certain evolutionary processes, it does not provide the entire picture. Reversible molecular processes, such as DNA methylation/RNA editing/histone remodeling can steer the function of genes in dynamic environments allowing for adaptive plasticity regardless of genetic predisposition. While a good half of a century has focused on the role of genes underlying a given trait, we know very little about how such plastic processes can influence traits and their evolution.
The Alvarado Lab is interested in the plastic molecular mechanisms that shape a genome’s response to natural changes in the environment. The Alvarado Lab primarily works with an African cichlid system Astatotilapia burtoni as well as various other animals capable of changing their body coloration (i.e.: Arctic mammals and cephalopods).
They have adopted an African cichlid model system that shows robust changes to morphology and behavior to investigate these processes. Specifically, they use the blue-yellow color morphs of Astatotilapia burtoni to understand the cellular and molecular substrates of color changes in the periphery and their subsequent effects on behavior in the central nervous system. Since behavior and pigmentation are key factors driving the speciation of cichlids in the East African Great Lakes, their work contributes to a more inclusive understanding of the molecular processes that drive adaptive speciation and trait evolution. The Alvarado lab uses an array of tools to address the following questions:
What are the plastic molecular substrates that allow an animal to change its colors? The Alvarado Lab uses various other model systems capable of seasonal changes in coloration (arctic mammals, cephalopods, teleosts) to study how pigment-bearing cells (chromatophores) function and change. This work involves profiling patterns of epigenetic function (DNAme, histone PTMs, chromatin accessibility, etc.) and functionally dissecting them with primary cell culture, (epi)genomic editing, microscopy, and pharmacology.
How does visual ecology shape neuroendocrine function? The Alvarado Lab focuses studies how different visual environments in the laboratory and natural environment can generate different hormonal profiles from neuroendocrine glands (pituitary/pineal/chromatophore lobe). This work is carried out by control of downwelling light (in the laboratory) and seasonal measurements of the ambient environment and various physiological assays. They employ the use of in vivo/ex vivo pharmacology and molecular profiling of tissue-specific transcriptomes/methylomes along with phenotyping of the ambient environment via the use of GIS and (hyper)spectral imaging.
How does animal coloration affect the behavior and vice versa? The Alvarado lab integrates how body coloration and pigmentation patterns can shape an individual's behavioral profile and its conspecifics. The Alvarado Lab primarily focuses on A. burtoni for their robust social behavior that accompanies subtle changes in their body coloration and patterns. Their lab uses video data and computer vision to follow dynamic and stable (but reversible) changes in body patterns to understand visual communication and their ties to their behavioral displays. This work focuses on the study of the reproductive/visual axis, body coloration, and its subsequent effects on social decision-making nuclei in the brain.