Date of Award


Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy (PhD)


Biology/Environmental Biology

First Advisor

Ron Etter

Second Advisor

Rick Kesseli

Third Advisor

Alan Christian


The deep sea is the Earth’s largest ecosystem and harbors a unique and largely endemic fauna. Although most research has focused on the ecological mechanisms that allow coexistence, recent studies have begun to investigate how this remarkable fauna evolved.. My work quantifies geographic patterns of genetic variation and investigates potential mechanisms that shape evolution in the deep ocean.

Bathymetric genetic divergence is common in the deep sea with population structure typically decreasing with depth. The evolutionary mechanisms that underlie these patterns are poorly understood. Geographic patterns of genetic variation indicated that the protobranch bivalve Neilonella salicensis was composed of two distinct lineages separated bathymetrically. Genetic diversity was greater in the lower-bathyal clade of N. salicensis than the upper to mid-bathyal clade. In a co-occurring mid-bathyal protobranch Malletia johnsoni, population differentiation was greater among samples than the confamilial lower-bathyal Clencharia abyssorum, though, genetic diversity was similar. These patterns suggest general trends do not always hold and fine scale patterns of gene flow need to be thoroughly investigated.

Little is known about the ecological or evolutionary mechanisms that might promote divergence or maintain population structure. Oxygen minimum zones (OMZs), which cover enormous regions of the deep ocean, might hamper gene flow by precluding larval dispersal. To test this, genetic patterns of the wood-boring bivalve Xylophaga washington were quantified across the northeastern Pacific OMZ. Results indicate two clades were apparent, one throughout the OMZ and one within and below it, possibly segregated by a historically stronger OMZ or other environmental factors that vary with depth. A similarly uninvestigated evolutionary factor with potentially large impacts is selection on mitochondrial DNA. Positive selection is apparent in the mitochondrial DNA of shallow water and deep-sea crabs, shrimp, and fishes, possibly related to any of the myriad factors that differ between the two habitats.

The deep sea is biogeochemically important and is highly impacted by climate change and anthropogenic factors. Genetic patterns in this habitat are very complex. This work suggests gene flow is inhibited at many scales, both across bathymetric gradients and within small bathymetric ranges.