Abstract
Microbiomes contain many levels of biological information, and integrating across the levels creates a holistic understanding of host-microbiome interactions. In my research on the evolution and ecology of avian microbiomes, I use two complementary frameworks: the microbiome as a community and the microbiome as a trait of the host. We draw on classic ecological and evolutionary theory and modern statistical models to advance our understanding in each of these frameworks and then integrate what we have learned into a better understanding of host-associated microbiomes, host evolution, and microbial biodiversity. Ecological theories that bear on processes such as community assembly and metacommunities are well suited for application to microbiomes. Phylogenetic comparative methods can quantify the fit of evolutionary models and detect correlations between traits and correlations between traits and the rate of evolution; these methods allow the inference of evolutionary process from contemporary patterns.
Highlights
Microbiomes contain many levels of biological information, and integrating across the levels creates a holistic understanding of host-microbiome interactions
If the microbiome can influence the fitness of a host, we can ask how it has contributed to the evolutionary trajectory of populations, to the speciation or extinction of lineages, or to the diversification of host biology
My research is primarily interested in the ecology and evolution of the avian microbiome
Summary
Microbiomes contain many levels of biological information, and integrating across the levels creates a holistic understanding of host-microbiome interactions. To answer these questions and fully understand the processes shaping host-associated microbiomes, we need an ecological understanding of the microbiome as a community of interacting individuals (the microbe’s perspective) and an evolutionary understanding of the microbiome as a trait of the host (the host’s perspective). The debate concerning the theories of niche-based assembly and neutral assembly of communities is ongoing in the field of ecology, and I am interested in whether and how these theories are supported in avian microbiomes, across body sites with differing properties and purposes.
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