Season-specific impacts of climate change on canopy-forming seaweed communities

This readme file was generated on 2023-07-14 by Anthony Truong. ORCID: 0009-0005-0693-0270 Institution: San Diego State University Email: Date of data collection: Mesocosm summer trial: 2021-08-05 through 2021-09-17 Mesocosm winter trial: 2021-11-09 through 2021-12-20 Field experiment: Established 2021-07, surveyed in 2021-10 and 2021-12. Geographic location of data collection: Mesocosm experiment conducted at the San Diego State University Coastal & Marine Laboratory Institute. Collection for mesocosm experiment conducted at Navy North (32.692312 N, -117.25297W) and Navy South (32.68306 N, -117.24963 W), San Diego, CA. Field experiment conducted at Navy South (32.68306 N, -117.24963 W), San Diego, CA. This work was supported by grants received from the Cabrillo National Monument Foundation, the National Parks Service (P20AC00867), and San Diego State University ## Season-specific impacts of climate change on canopy-forming seaweed communities. File List: 1. mesocosm_parameters.csv Daily mesocosm measurements of pH and temperature for each of the three climate treatments across the duration of the summer and winter trials. 2. mesocosm_silvetia_weights.csv Measurements of Silvetia biomass taken at the beginning and end of each mesocosm trial denoted by the columns SILV_i and SILV_f, respectively. 3. mesocosm_silvetia_quantumyield.csv Measurements of Silvetia quantum yield taken at the beginning and end of each mesocosm trial. 4. mesocosm_understory.csv Measurements of understory biomass by genera taken at the beginning and end of each mesocosm trial. The following codes are used for understory genera included in the mesocosms: * CENT: Centroceras spp. * CHON: Chondracanthus spp. * CORA: Corallina spp. * LAUR: Laurencia spp. Understory biomass was categorized based on its condition and then formatted for analysis. Conditions and formatting are notified by the following where GENERA = taxa code. * GENERA_i: Initial biomass prior to start of experiment. * GENERAi+1: Initial biomass after being inflated by a dummy variable of 1. * GENERA_b: Bleached biomass at the end of the experiment. * GENERA_ub: Unbleached biomass at the end of the experiment. * GENERA_ub+1: Unbleached biomass at the end of the experiment after being inflated by a dummy variable of 1. * GENERA_f: Total bleached and unbleached biomass at the end of the experiment. * GENERA_delt: Difference between final unbleached biomass and initial biomass (i.e., x_f - x_i). * GENERA_%loss: Percentage of initial biomass that was lost across the experiment (i.e., x_delt/x_i) * GENERA_%f: Percentage of initial biomass remaining at the end of the experiment (i.e., 1 + x_%loss). * GENERA%f+1: Percentage of remaining initial biomass inflated by a dummy variable of 1. 1. mesocosm_simper.csv Modified data matrix derived from mesocosm_understory.csv for use in SIMPER analyses. 2. mesocosm_simper_environment.csv Environmental data from mesocosm_understory.csv for use in SIMPER analyses. 3. field_percentcover.csv Percent cover by genera for the field experiment taken in 2021-07 (Summer) prior to manipulations, in 2021-10 (Fall), and in 2021-12 (Winter). Grid_Count column denotes the number of grid tiles (out of 25) sampled for each plot. 4. field_simper.csv Modified data derived from field_percentcover.csv for use in SIMPER analyses. 5. field_environment.csv Environmental data from field_percentcover.csv for use in SIMPER analyses. Methodological Information: Mesocosm experiment: Three outdoor water tables (1.8 x 0.9 x 0.3 m; l*w*h) receiving flow-through seawater from San Diego Bay were designated to one of three climate scenarios: Ambient, RCP 2.6 (+1 C/-0.1 pH units relative to Ambient), and RCP 4.5 (+2 C/-0.2 pH units relative to Ambient). We elevated the temperature of the water in the tables designated RCP 2.6 and RCP 4.5 using aquarium heaters and acidified the water using CO2 injection. Data for the file "mesocosm_parameters.csv" were produced by daily measurements of temperature (nearest 0.1 C) and pH (nearest 0.01 unit) were recorded using a probe (Oakton 300 Series pH/DO meter). Measurements were unable to be recorded on days 32, 38, and 39 of the summer trial. Within each water table, we placed 20 plastic boxes (15 x 15 x 7.6 cm; l*w*h with three mesh-covered 5-cm diameter holes in each of two opposite sides for water exchange) containing grazers (six Tegula funebralis, six Lottia strigatella, six Lottia scabra, ten Littorina scutulata, and one Cyanoplax hartwegii). Understory algae (4 g of Centroceras, 10 g of Chondracanthus, 9 g of Corallina, and 2.5 g of Laurencia, 5%) was then added (these values produced column GENERA_i for the "mesocosm_understory.csv" dataset). Individuals of Silvetia compressa (72.5 1.3 g, mean SE, column SILV_i for the "mesocosm_silvetia_weights.csv" dataset) were laid over the understory species in half of the containers (Silvetia present) while the other half had no Silvetia (Silvetia absent). n=10. After allowing the experiment to run for 42 days (Summer trial: 2021-08-05 through 2021-09-17, Winter trial: 2021-11-09 through 2021-12-20), the contents of each container were collected. "mesocosm_silvetia_weights.csv": Silvetia biomass (nearest 0.1 g) was recorded using a digital scale (column SILV_f). "mesocosm_quantumyield.csv": Silvetia quantum yield was measured at five random sections (columns M1, M2, M3, M4, and M5) along the thalli of the individual using a pulse amplitude modulated (PAM) fluorometer (sensu Edwards and Kim 2010). These measurements were then averaged to estimate the quantum yield of the individual (column Average) and converted into a percentage (column Percentage). Quantum yield, a measurement of light harvesting efficiency of photosystem II, is recorded as a ratio (nearest 0.01) of variable fluorescence (Fv) to maximal fluorescence (Fm) and its unit is [PSII]. "mesocosm_understory.csv": Understory biomass (nearest 0.01 g) was recorded using a digital scale and further partitioned into bleached (column GENERA_b) and unbleached (column GENERA_ub) biomass. Column GENERA_f is the total bleached and unbleached biomass for the respective genera. Columns labeled with a +1 have had their respective values increased by a Bray-Curtis dummy variable of 1. Column GENERA_delt is the difference between final unbleached and initial biomass. Column GENERA_%loss is the proportion of GENERA_delt to GENERA_i. Column GENERA_%f is calculated as 1-GENERA_%loss, and represents the proportion of remaining biomass relative to initial. "mesocosm_simper.csv": All GENERA_%f+1 columns from the "mesocosm_understory.csv" dataset were moved into a new .csv file for SIMPER analysis. "mesocosm_environment.csv": Columns Season, Canopy, and Climate from the "mesocosm_understory.csv" dataset were moved into a new .csv file for SIMPER analysis. Field Experiment: Experimental field plots were established at Navy South. Plots measured 0.15 x 0.15 m and contained an adult Silvetia individual. We crossed Silvetia Canopy (High, Partial, None) with the initial state of the Understory (Full, Cleared) and assigned each plot randomly to one of the six resulting treatments; n=10. Plots assigned to Silvetia None treatments had the Silvetia occurring with the plots trimmed to the holdfast. Plots assigned to the Silvetia Partial treatments had the Silvetia trimmed to a single thallus layer while Silvetia High plots were unmanipulated. However, because 1) we observed large within treatment variation and 2) the Full and Partial Silvetia Canopy treatments provided similar canopies, we pooled Full and Partial Silvetia treatments into a single Silvetia Present treatment and compared this pooled treatment to the Silvetia Absent treatment. To manipulate the understory assemblages, the existing assemblages in half of the plots of each Silvetia treatment were removed using scrapers and chisels (Understory Cleared treatments) while the assemblages in the other half were left unmanipulated (Understory Full treatments). "field_percentcover.csv": We measured the percent cover of each genus within the plots using 25-point intercepts within 0.15 x 0.15 m quadrats once before manipulations in Summer (2021-07) then twice after manipulations in Fall (2021-10) and Winter (2021-12). Genera four letter codes: CENT = Centroceras spp. CHON = Chondracanthus spp. CORA = Corallina spp. GAST = Gastroclonium spp. GELI = Gelidium spp. GIGA = Gigartina spp. GRAC = Gracilaria spp. JANI = Jania spp. LAUR = Laurencia/Osmundea spp. LOME = Lomentaria spp. MAZZ = Mazzaella spp. PLOC = Plocamium spp. PTER = Pterygophora spp. RHOD = Rhodymenia spp. SILV = Silvetia compressa ULVA = Ulva spp. BARE = Bare rock OTHER = Unidentifiable genus/species "field_simper.csv": All genera percent cover columns from the "field_percentcover.csv" dataset were moved into a new .csv file for SIMPER analysis. "field_environment.csv": Columns Season, Canopy, and Understory from the "field_percentcover.csv" dataset were moved into a new .csv file for SIMPER analysis. Statistical Analysis: All data were analyzed using R-Studio and Primer + PERMANOVA 7. Prior to analyses, data were checked for normality and heteroscedasticity using Shapiro-Wilks and Levenes tests, respectively. For the mesocosm experiment, measurements of quantum yield required square-root transformation to meet assumptions of normality. Silvetia biomass and measurements of quantum yield within the mesocosms were compared among the three climate treatments using separate one-way ANOVAs (for each season). This was done as separate analyses rather than a two-way ANOVA that included season as a factor because the experimental mesocosms were broken down, cleaned, randomized, and reassigned with new assemblages prior to the winter trial. Tukeys HSD post-hoc tests between pairs of climate treatments were then used when the ANOVAs returned significant differences. To visualize shifts in the understory algal assemblages between the Climate and Silvetia canopy treatments within each trial, Principal Coordinates Analysis (PCoA) was used to map similarities in the algae comprising each assemblage. Two-way PERMANOVAs were then used to determine if the assemblage shifts differed between the Climate and Silvetia canopy treatments. Due to a high number of zeroes for certain taxa in the Silvetia Absent treatments, the data were square-root transformed and the PERMANOVAs were run with a zero-inflated Bray-Curtis similarity indices using a dummy variable of 1. A priori post-hoc permutation tests were then used to examine pairwise differences in the assemblages between Climate and Silvetia canopy treatments. SIMPER analyses were used to identify the relative contribution of each understory taxon to assemblage dissimilarity between treatments. As discussed above, these analyses were run separately for the summer and winter trials. For the field experiment, a three-way PERMANOVA was used to assess differences in the understory communities (based on percent cover) between Silvetia canopy treatments, Understory treatments, and Seasons. Unlike the mesocosm experiments, season was included as a factor because the field experiment was run continuously. Following the PERMANOVA, a priori permutation post-hoc tests were used to determine differences in understory assemblages between the Silvetia canopy treatments within each Understory treatment and season. SIMPER analyses were used to determine the percent contribution of each general to the observed differences. All analyses were evaluated at an -level of 0.05. ``` ```