Vertebrates evolved and exist in a microbial world. Yet our understanding of the eco-evolutionary mechanisms shaping communities of host-associated symbionts is limited. I seek to identify patterns within highly variable microbial communities associated with individuals, populations, species, and broader host groups, and to identify underlying processes impacting the composition of these communities.
Kirtland's Warbler with radio-tag.
Migratory bird microbiota
The evolution of flight has significant selective pressures on the gastrointestinal tract of volant animals, likely resulting in highly variable communities of host-associated microbiota, when compared to non-flying animals. It is not unreasonable to suggest these patterns may be taken to the extreme in long-distance migrants. I study the microbial phenotypic flexibility of migratory birds throughout the annual cycle and examine the extent to which microbial communities vary within and across annual cycles.
Examples of this research:
Gil et al. 2024. Journal of Avian Biology. (in press)
Skeen et al. 2023. Molecular Ecology. pdf
Skeen et al. 2021. Molecular Ecology. pdf
The evolution of flight has significant selective pressures on the gastrointestinal tract of volant animals, likely resulting in highly variable communities of host-associated microbiota, when compared to non-flying animals. It is not unreasonable to suggest these patterns may be taken to the extreme in long-distance migrants. I study the microbial phenotypic flexibility of migratory birds throughout the annual cycle and examine the extent to which microbial communities vary within and across annual cycles.
Examples of this research:
Gil et al. 2024. Journal of Avian Biology. (in press)
Skeen et al. 2023. Molecular Ecology. pdf
Skeen et al. 2021. Molecular Ecology. pdf
Fecal samples collected from Peruvian birds.
Phylosymbiosis
Phylosymbiosis is the concept that a host’s microbiota recapitulates the phylogeny of the host, suggesting that codivergence or coadaptation may be occurring between the microbiome and the host. Thus far, few studies have recovered signals of phylosymbiosis between birds and their microbiomes. I have collaborated on several studies assessing the extent to which host characteristics, including phylogenetic history, can impact the microbial composition of birds. I advance this work in my current position at University of Connecticut (described below).
Examples of this research:
Herder et al. 2023. Microbiology Spectrum. pdf
Song et al. 2020. mBio. pdf
Phylosymbiosis is the concept that a host’s microbiota recapitulates the phylogeny of the host, suggesting that codivergence or coadaptation may be occurring between the microbiome and the host. Thus far, few studies have recovered signals of phylosymbiosis between birds and their microbiomes. I have collaborated on several studies assessing the extent to which host characteristics, including phylogenetic history, can impact the microbial composition of birds. I advance this work in my current position at University of Connecticut (described below).
Examples of this research:
Herder et al. 2023. Microbiology Spectrum. pdf
Song et al. 2020. mBio. pdf
Blue-winged warbler; local Connecticut avifauna sampled for Avian IgSeq project.
Avian IgSeq
Research on wild bird microbiota is often confounded by an overabundance of environmentally sourced bacteria, which likely play no positive or negative role within the birds, yet bias analyses with their presence. So far, in studies of wild birds, no method has reliably separated ubiquitous environmental microbes from those that are managed by the host’s immune system; management implying an interaction with the host bird. In my current position I am collaboratively developing a method to assess if and how the microbiome recapitulates the phylogeny of the host by characterizing specific subsets of the gut microbial community that are managed by the immune system. If significant evidence of phylosymbiosis results from this study, this will open an entirely new avenue for studies on the ecology and evolution of avian microbiota.
Research on wild bird microbiota is often confounded by an overabundance of environmentally sourced bacteria, which likely play no positive or negative role within the birds, yet bias analyses with their presence. So far, in studies of wild birds, no method has reliably separated ubiquitous environmental microbes from those that are managed by the host’s immune system; management implying an interaction with the host bird. In my current position I am collaboratively developing a method to assess if and how the microbiome recapitulates the phylogeny of the host by characterizing specific subsets of the gut microbial community that are managed by the immune system. If significant evidence of phylosymbiosis results from this study, this will open an entirely new avenue for studies on the ecology and evolution of avian microbiota.
Field site in Cordillera Azul National Park, Peru.
Avian haemosporidians
Pathogens within Order Haemosporidia are endemic in birds and include the causative agents of the disease malaria. Avian haemosporidians exhibit a spectrum of host and geographic specificity, with cosmopolitan lineages infecting disparate avian taxa across multiple continents and other lineages restricted to a single host taxa or geographic location. These pathogens are fairly well studied in birds, yet many questions remain regarding the mechanisms that influence their distribution across geography and host taxa. I collaborate on studies of avian haemosporidians to identify phylogenetic variation in host susceptibility to infection, microclimatic predictors of pathogen communities, variation in pathogen composition throughout the annual cycle, and
macroecological factors that influence pathogen distribution
across the globe.
Examples of this research:
Wells et al. 2024. Journal of Biogeography. pdf
McNew et al. 2021. Proceedings of the National Academy of Sciences. pdf
Fecchio et al. 2021. Global Ecology and Biogeography. pdf
Pulgarin et al. 2018. Journal of Biogeography. pdf
Pathogens within Order Haemosporidia are endemic in birds and include the causative agents of the disease malaria. Avian haemosporidians exhibit a spectrum of host and geographic specificity, with cosmopolitan lineages infecting disparate avian taxa across multiple continents and other lineages restricted to a single host taxa or geographic location. These pathogens are fairly well studied in birds, yet many questions remain regarding the mechanisms that influence their distribution across geography and host taxa. I collaborate on studies of avian haemosporidians to identify phylogenetic variation in host susceptibility to infection, microclimatic predictors of pathogen communities, variation in pathogen composition throughout the annual cycle, and
macroecological factors that influence pathogen distribution
across the globe.
Examples of this research:
Wells et al. 2024. Journal of Biogeography. pdf
McNew et al. 2021. Proceedings of the National Academy of Sciences. pdf
Fecchio et al. 2021. Global Ecology and Biogeography. pdf
Pulgarin et al. 2018. Journal of Biogeography. pdf
Four species of Catharus thrushes used in migratory bird haemosporidia study
Migratory bird haemosporidia
Empirical examples of disease cycles in birds are rare yet may provide crucial insight into disease ecologies. I use time series data of avian haemosporidians to model host-pathogen disease cycles in Nearctic-Neotropical migratory birds. Using an extensive set of museum specimens, I screened Catharus thrushes collected during spring and fall migration from 1996-2019 for three genera of haemosporidians and assess seasonality and multi-year cycles in pathogen prevalence. The epizootic models generated for this study suggest that the multi-year cycles of pathogen prevalence are indicative of pathogen-driven population cycles in the host birds.
Example of this research:
Skeen et al. under review (manuscript available upon request)
Empirical examples of disease cycles in birds are rare yet may provide crucial insight into disease ecologies. I use time series data of avian haemosporidians to model host-pathogen disease cycles in Nearctic-Neotropical migratory birds. Using an extensive set of museum specimens, I screened Catharus thrushes collected during spring and fall migration from 1996-2019 for three genera of haemosporidians and assess seasonality and multi-year cycles in pathogen prevalence. The epizootic models generated for this study suggest that the multi-year cycles of pathogen prevalence are indicative of pathogen-driven population cycles in the host birds.
Example of this research:
Skeen et al. under review (manuscript available upon request)