Using environmental DNA and occupancy modeling to estimate rangewide metapopulation dynamics of the endangered tidewater goby eucyclogobius spp.

Author

Chad M. Martel, Humboldt State UniversityFollow

Graduation Date

Summer 2019

Document Type

Thesis

Program

Master of Science degree with a major in Natural Resources, option Fisheries

Committee Chair Name

Andrew Kinziger

Committee Chair Affiliation

HSU Faculty or Staff

Second Committee Member Name

Andre Buchheister

Second Committee Member Affiliation

HSU Faculty or Staff

Third Committee Member Name

Nicholas Som

Third Committee Member Affiliation

HSU Faculty or Staff

Keywords

eDNA, Environmental DNA, Occupancy modeling, Metapopulations, Tidewater goby

Subject Categories

Fisheries

Abstract

Conservation of species is most effective when metapopulation dynamics are well understood and incorporated into management plans, allowing managers to target conservation efforts where they will be most effective. The development of environmental DNA (eDNA) methods provides an efficient and highly sensitive approach to generate presence and absence data needed to elucidate metapopulation dynamics. Combining sample detection histories from eDNA surveys with occupancy models that account for non-detection can offer unbiased estimates of rangewide metapopulation dynamics. However, traditional occupancy models do not allow direct evaluation of the drivers of site occupancy, extinction, and colonization. Herein, I utilize a novel dynamic multiscale occupancy model that accounts for non-detection to estimate rangewide metapopulation dynamics and their drivers in an endangered fish, tidewater goby Eucyclogobius spp., a genus endemic to California estuarine habitats. I collected rangewide eDNA data from 190 sites (813 total water samples) surveyed from two years (2016 and 2017) and analyzed the data using a dynamic multiscale occupancy model. Rangewide, estimates of the proportion of sites that were occupied varied little between 2016 (0.524) and 2017 (0.517). Although I uncovered stability in the number of sites that were occupied across the two study years, there was evidence for extinction and colonization dynamics. Rangewide estimates of extinction probability of occupied sites (0.106) and colonization probability of unoccupied sites (0.085) were nearly equal. The consistent rangewide occupancy proportions combined with the presence of extinctions and colonization suggests a dynamic equilibrium between the two years surveyed. There was no latitudinal gradient or regional differences in extinction and colonization dynamics across the tidewater goby geographic range. Assessment of covariate effects on metapopulation dynamics revealed that colonization probability increased as the number of occupied neighboring sites increased and as distance between occupied sites decreased. I show that eDNA surveys can rapidly provide a snapshot of a species distribution over a broad geographic range, and when these surveys are paired with dynamic multiscale occupancy modeling, they can uncover rangewide and regional scale metapopulation dynamics and their drivers.

Citation Style

AFS

Recommended Citation

Martel, Chad M., "Using environmental DNA and occupancy modeling to estimate rangewide metapopulation dynamics of the endangered tidewater goby eucyclogobius spp." (2019). Cal Poly Humboldt theses and projects. 323.
https://digitalcommons.humboldt.edu/etd/323