--------------------------------------------- # Biosphere 2 Giant Clam Valvometry Preferred citation (DataCite format): Killam, Daniel (2022). Biosphere 2 Giant Clam Valvometry. University of Arizona Research Data Repository. Dataset. https://doi.org/10.25422/azu.data.21642272 Corresponding Author: Daniel Killam, Geosciences, dkillam@arizona.edu License: CC BY 4.0 DOI: https://doi.org/10.25422/azu.data.21642272 --------------------------------------------- ## Summary The included datasets relate to the PLoS One manuscript regarding a multi- month valvometric study of giant clams in the [Biosphere 2 ocean](https://biosphere2.org/research/research-initiatives/ocean-reef-lab). * "raw valvometry data final.csv" is a large CSV with over 2.9 million rows used to inform all following analyses in the study. * "daily data merged.csv" includes daily-scale data used to conduct GAM analyses. * "minute scale valvometry.csv" is a CSV with minute-scale data used to run wavelet analysis (both raw and day-detrended versions included in Figure 7 of the publication) * "combined 15 minute data.csv" is data used to run wavelet coherence analyses * "arduino code.txt" corresponds to the Arduino code used to collect the raw data The data files enclosed are part of an open-access publication in press at PLoS One. Information on the journal article will be appended here when available. The abstract from that article: "Valvometry, the electronic measurement of bivalve shell opening and closing, has been demonstrated to be a valuable biomonitoring technique in previous ecological and environmental studies. Valvometric data has been shown to relate significantly to pollution, predation, animal stress and feeding activity. However, there is a need for valvometric techniques applicable to coral reef environments, which may provide critical insights into reef resilience to ocean warming and acidification. Giant clams are endemic to coral reefs and hold great promise as valvometric recorders of light availability, productivity and other environmental variables. Despite this promise, prior valvometric work on giant clams has been limited by the use of specialized hardware less accessible to developing countries where many coral reefs are found. Here we report on an open-source approach that uses off-the-shelf components to monitor smooth giant clam (Tridacna derasa) valve opening behavior, and tests this approach in the simulated reef environment of the Biosphere 2 Ocean. Valvometric data corroborates the influence of light availability on diurnal behavior of giant clams. The clams basked during daylight hours to expose their photosymbionts to light, and adopted a partially-closed defensive posture at night. The animals showed variations in the frequency of complete closures, with most occurring during night-time hours when the animals prioritize filter-feeding activity, clapping their valves to expel pseudofeces from their gills. Closure frequency showed a significant relation to pH and a significant lagged relationship to chlorophyll-a productivity, which are both a function of algal productivity in the Biosphere 2 Ocean tank. These results suggest that the animals fed on phytoplankton following periodic bloom events in the Biosphere 2 Ocean during the experiment. We propose that giant clams exhibit behavioral plasticity between individuals and populations, and advocate for the more widespread use of valvometry to enable comparative studies of reef environment and animal health." --------------------------------------------- ## Files and Folders "raw valvometry data final.csv": file with over 2.9 million rows used to inform all following analyses in the study. It includes the following data at 5-second resolution - datetime - Sensor1 through Sensor3: raw mV values measured from each sensor by the Arduino - zscore1 through zscore3: daily z-scores for sensor 1 through 3 "daily data merged.csv": daily-scale data used to conduct GAM analyses. Includes the following, averaged at daily resolution - date - count: number of times per day clam 3 closed its shell - chlor: daily average chlorophyll-a RFU - bga: daily average phycoerythrin RFU - pH - DO: daily average dissolved oxygen (mg/L) - light: daily average PAR levels in μmol electrons/m2s "minute scale valvometry.csv": minute-scale data used to run wavelet analysis (both raw and day-detrended versions included in Figure 7) - date - sensor3: valvometric z-scores for clam sensor 3 "combined 15 minute data.csv": used to run wavelet coherence analyses which incorporates the following data at 15-minute resolution - sensor3: valvometric z-scores for clam sensor 3 - DO: dissolved oxygen (mg/L) - pH - chla: chlorophyll-a (Relative Fluorescence Units) - PE: phycoerythrin (Relative Fluorescence Units) - light: PAR levels in μmol electrons/m2s --------------------------------------------- ## Materials and Methods The code used to generate and process the valvometric data are available open-source online at https://github.com/danielkillam/OpenValvometry --------------------------------------------- ## Contributor Roles The roles are defined by the CRediT taxonomy http://credit.niso.org/ Daniel Killam, University of Arizona: - Conceptualization - Data curation - Formal analysis - Investigation - Methodology - Project administration - Resources - Software - Supervision - Validation - Visualization - Writing – original draft - Writing – review & editing Diane Thompson, University of Arizona: - Conceptualization - Formal analysis - Funding acquisition - Investigation - Methodology - Project administration - Resources - Supervision - Validation - Visualization - Writing – review & editing Katherine Morgan, University of Arizona: - Data curation - Investigation - Project administration - Resources - Supervision - Writing – review & editing Megan Russell, University of Arizona: - Data curation - Investigation - Project administration - Resources