Seminars

In this talk I’ll review classic methods to calculate microbial pangenomes including assembly, annotation, and tree building. But then we’ll attempt a departure from this worn toolkit. I’ll describe how formal definitions of information derived from ecology and information theory can provide an alternative view of pangenome complexity useful for both short (pandemic surveillance) and long (systematics) time scales.

Although wolves and dogs can interbreed and produce fertile offspring, hybridization between the two is far more rare than domestic and wild populations of other species. We combined highly-sensitive local ancestry inference and phylogenomic analyses of genomes representing ~2700 ancient and modern dogs and wolves. Almost two-thirds of breed dogs have wolf ancestry within their nuclear genome from admixture that occurred nearly a thousand generations ago, and all analyzed free-ranging dog genomes carry some ancient wolf ancestry. Wolf ancestry correlates with traits like size, function, and personality characteristics. Altogether, the majority of dogs today have low, but detectable levels of post-domestication wolf ancestry that has shaped their evolution and conferred unique advantages to their survival in diverse human environments.

Any given tree has huge numbers of interactions. Insects munch leaves, fungi help gather nutrients in exchange for food, and bacteria abound. But what happens if a tree is moved out of its native range and grown on a different continent? Based on years of data on invasive species and observations of ornamentals, researchers know that non-native trees tend to have fewer interactions. The question I seek to answer is: How do non-natives, such as ornamental trees, gain or lose species interactions over years, centuries, and millennia? My research team and I are assessing this process for trees in New York City. Using contemporary sampling and historical specimens, we have found that species interactions with trees are far from static. For instance, herbivory in non-native trees has increased over centuries, but not reached the levels experienced by native species. Fungi that live in leaves of non-native trees, however, seem to have more diversity but likely less specialization compared to their counterparts on native leaves. Our results can help predict the long-term consequences for food webs of planting non-native species or native species within our cities and other landscapes.