Michael Doane

My research seeks to understand how life organizes across nested ecological scales, from the genomic landscape, where genes and epigenetic interactions form ecosystems within DNA, to the vast oceanic systems that sustain global biodiversity. Using molecular and genomic tools, I explore how these layers of biological organization—genomes, microbiomes, hosts, and environments—are interlinked, each regulating and responding to the other. This “ecosystems within ecosystems” framework, akin to a Russian doll, guides my work toward uncovering the feedbacks that connect molecular processes to ecological patterns, revealing how life’s smallest systems shape, and are shaped by, the largest. My research spans four interconnected themes:

Elasmobranch Microbiomes

Sharks and rays, like all animals, are covered in microbial hitchhikers that form intimate and essential partnerships with their hosts. I use next-generation sequencing to uncover the ecological and evolutionary processes shaping these microbiomes, examining how community composition varies across species, environments, and scales. My work has examined microbiomes of species such as the common thresher shark (Alopias vulpinus), leopard shark (Triakis semifasciata), whale shark (Rhincodon typus), large-toothed sawfish (Pristis pristis), and tiger shark (Galeocerdo cuvier).

Fish Biodiversity and Habitat Relationships

Using environmental DNA (eDNA) approaches, I study how fish communities, both cartilaginous and bony, respond to environmental gradients. Genetic markers provide a sensitive lens for detecting species and tracking changes in biodiversity across fine spatial and temporal scales. I apply these methods to regions such as the Great Australian Bight and Norfolk Island to understand how habitat structure underpins biodiversity patterns.

Shark Genomics

Sharks represent one of the oldest extant lineages of jawed vertebrates, harboring genomic traits linked to their evolutionary success. In collaboration with Oxford Nanopore, I am sequencing and characterizing the genome of the eastern grey nurse shark to explore its epigenomic landscape. This work focuses on identifying epigenetic imprinting patterns that relate to parental resource conflicts, environmental sensitivity and plasticity, population-level ecological strategies, and transgenerational responses to ecological stressors.

Microbial Oceanography

Marine microbial communities drive critical Earth system processes, nutrient cycling, carbon sequestration, and atmospheric gas regulation. My research examines microbial diversity and functional networks across physical and chemical gradients, uncovering how microbial interactions mediate global biogeochemical processes and maintain ocean ecosystem function.