The unifying theme of our research is to develop a comprehensive understanding of the mechanistic and functional basis of phenotypic variation and adaptations in natural and domesticated populations. This research is valuable, not only for understanding the genetic basis of traits, but also in the broader context of finding solutions to real world problems, for example, disease resistance in hots, or host preference in infectious disease vectors.

Domesticated animals, like chicken, are tremendous models to deconvolute important details about how genes contribute to particular phenotypes, especially in the case of complex traits. Chicken also occupy key positions in the global health, food security and sustainability equation, due to their direct relevance to human health and well being.  The main areas of emphasis in our lab are described below:

1. Phenotype X Genotype

Identifying individual genes, mutations and functional interactions that control important adaptive phenotypes  is the one of the major puzzles in biology. Characterizing sequence variation in genes and regulatory elements underlying traits has great importance in a variety of contexts – such as understanding disease resistance, or skeletal muscle deformities, host-seeking behaviors in disease vectors. In our lab we are interested in using crossing experiments coupled with next-generation sequencing approaches to unravel the genetic basis of complex traits. Avian traits of particular interest to our lab are disease resistance, degenerative myopathies and behavior.

At present we are applying whole genomic and functional datasets to characterize the basis of Woody Breast in broiler chicken.

2. Comparative *Omics

The explosion of sequencing technologies and computational tools has given us the unique opportunity to use comparative approaches to understand how organisms function in at various levels of organization. Our lab is currently involved in whole genome sequencing and assembly of three avian genomes. Ultimately, we use this as a pathway to enable new discoveries about the molecular mechanisms that drive important traits in birds (and other taxa).

In addition to comparative sequence analysis, we also use transcriptome sequencing to tease out functional differences that define a phenotype. The natural progression of this work will lead us to explore how components of the metabalome, or the epigenome, for example,  interact with other system components in explaining functional differences between phenotypes, populations or species.

A major area foci of work in this category currently is the discovery and categorization of structural genome variation in the genus Gallus

3. Evolutionary/Population Genomics

A major thread of inquiry in my past work has been  reconciling the genetics and demographic history of populations.  Deciphering the evolutionary history of populations can be challenging, especially when we do not have access to samples spread across time,  This is a recurrent problem in fields as varied as conservation genetics and vector biology.

My recent work on Anopheles mosquito populations in Equatorial Guinea has demonstrated that Approximate Bayesian Computation is a powerful approach to understand population genetic change in mosquito populations (Athrey et al, PLoS Genetics). Current collaborative projects in this domain are focusing on understanding population history of two malaria vector species in Kenya, in the context of vector control program, and especially the spread of insecticide-resistance alleles in the population.

At present we are working on understanding population genetic trends in captive population, inbreeding, and effective size changes in populations with a known history of bottlenecks.

4. Microbiome x immune interaction

An astonishing number of bacteria colonize the gut of vertebrates. The diversity of the microbiota and the variability across individuals is only beginning to be explored now, but their role in determining or detracting from the health of the individual is still poorly understood. One of the foci of our research is to understand how components of the avian innate immune system  interact with the gut- microbiota in the context of infection. Current work in this area in our lab is looking at the avian gut microbiome, especially functional enrichment as it relates to specific effects on avian immunity.

One research emphasis under this topic has been to understand factors directing microbiota acquisition in birds, specially in poultry environments.

5. Avian Circadian 

The circadian system is a system of endogenous rhythms that regulates a large number of behavioral, physiological and molecular processes. The Avian circadian system is distinct in its organization, compared to mammals, but also more relevant as a model of vertebrate circadian, compared to mice models. In our lab we use the interaction between photoperiods and photo intensity in establishing and entraining the avian circadian, and in elucidating the genetic, functional and epigenetic consequences of circadian disruption.

At present we are working on the role of extended photoperiods in disrupting the circadian system, and in characterizing the consequences of such circadian disruption on microbiota disruption, and metabolic dysfunction.