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Population Genomics of microorganisms and their hosts in health and disease

Population Genomics of microorganisms and their hosts in health and disease

Welcome to the Cornejo Lab

Our ability to understand how pathogens and hosts have adapted to each other, requires a deep understanding of how basic evolutionary processes that have shaped the genetic architecture of these organisms. In my research, we use a multidisciplinary approach that combines computational biology, population genetic/genomic analyses, phylogenetics, simple mathematical modeling, and wet lab experiments to address these issues. Developing a better understanding of the forces shaping the genetic architecture of organisms will have enormous implications on the design of strategies for the management of populations and species of interest. We use genomic data to infer the historical demographics of populations and use these demographics to better understand how selection has shaped specific regions of the genome to contribute to species adaptations.

We are interested in the inference of the evolutionary history of populations and how genomic data can be used to learn. We apply these methods to answer questions in different systems: i) Humans; ii) Bacteria; iii) Malarial parasites; and iv) Plants. Yet the questions addressed in these systems are similar in nature. Some of the questions we address in our research are:

  1. How important is homologous recombination for the evolution of traits involved in host shifts or adaptation to new environments?
  2. During which stages of the complex life cycle of organisms do we expect to find hotspots of adaptation?
  3. How has the demographics impacts the accumulation of deleterious mutations, impacting the fitness of individuals
  4. What is the demographic (population decline/growth) and selection scenario (selection coefficient, mode of selection and initial frequency) that explains the evolution of adaptive variants in populations. This question is especially important while trying to understand the evolution of disease resistance mechanisms and the evolution of virulence factors

We are experts in the generation and analysis of next generation sequencing data and we provide a great learning environment for students and postdocs with a quantitative inclination. You can learn more about what we do in our lab in the Research section.

Some of the questions currently addressed in our lab are:

  1. Can we infer from retrospective genomic analyses the demographic history of (micro)organisms and identify candidate genes that might be involved in their adaptation to their current niche (either host or environment)? How does that history corresponds to the demographic history of their host(s)?

  2. What is the evolutionary history of Theobroma cacao and what can we learn about the history of domestication of arboreal crops?

  3. What are the genetic bases of disease susceptibility? What are the difference in microbiome composition or genetics of the host that renders them susceptible to the colonization and spread of infectious diseases?

  4. What are the genetic bases of phenotypic variation in complex traits like pod color or the ability to produce offspring? These are questions that present common challenges in organisms with very distinct genomic architectures like Theobroma cacao (chocolate plants) and humans?

  5. How does the interaction of organisms modify the genomic architecture of the interacting organisms?

  6. What is the impact of overlapped generations in our inference of the demographic history of organisms?

  7. How does the recombination architecture of Anopheles gambiae shape the distribution of deleterious mutations genome-wide?

If you are interested in any of these research topics do not hesitate to contact us. For more information on the opportunities in for Undergraduate, Graduate and Postodoctoral positions visit our Opportunities section.

News of interest

Cacao in the news:

Cacao analysis dates domesticated chocolate trees back 3,600 years

The evolutionary genomics of the chocolate tree, Theobroma cacao


The lab in the WSU news


Our recent work on Gardnerella vaginalis in collaboration with Larry Forney is out (check it out)


The Cornejo Lab joins Ag1000 to help contribute to improve human health