DOI: 10.5061/dryad.rv15dv4mz
title: Data from: Adaptation and plasticity of <em>Nannochloropsis</em> sp. in response to seasonal and geographic climate variation

description: This dataset contains the raw files and R code describing the
 pre-processing and analysis of a common garden experiment used to quantify
 the plasticity and adaptive responses to seasonal and geographic climate
 variation of Nannochloropsis, a microalga commonly used in biotechnology.
 An initially monoclonal strain was grown outdoors across four locations in
 Hawaii (Cyanotech), Texas (Qualitas Health), California (UCSD), and New
 Mexico (NMSU). Following 17 and 22 months of cultivation outdoors, we
 collected samples during winter and summer, respectively, and we compared
 strains’ growth from the four sites across temperature and light gradients
 in the laboratory.
description: <strong>Experimental design:</strong> We tested the
 performance of each strain compared to the baseline strain in 24-well deep
 well plates (VWR, Radnor, PA, USA) exposed to temperature (5°C, 10°C,
 15°C, 20°C, 25°C, 30°C) and light (100% = 100 µmol
 m<sup>-2</sup> s<sup>-1</sup>, 50% = 50 µmol
 m<sup>-2</sup> s<sup>-1</sup>, 10% = 10 µmol
 m<sup>-2</sup> s<sup>-1</sup> and 5% = 5 µmol
 m<sup>-2</sup> s<sup>-1</sup>)
 gradients. Each strain was inoculated in three
 replicate wells 24 times (for each treatment combination of light and
 temperature). We randomized the position of the plates and replicates in
 plates and used sterile distilled water in well A1 of each plate, as well
 as culture media in empty wells to confirm there was no
 cross-contamination across wells. We collected samples for optical density
 on day 0, 1, 3 and 5. OD<sub>750</sub> was measured on 1:1
 diluted sample using a Tecan Infinite 200 PRO microplate reader (Tecan,
 Männedorf, Switzerland). <strong>Calculation of
 growth rates and statistical analyses:</strong> Cultures were grown
 for 5 days, and their growth rates calculated from the slope of
 OD<sub>750</sub> increase during the exponential growth phase
 (i.e., the first 3 days of growth) and used as our measure of performance.
 We constructed thermal and light performance curves (TPC and LPC)
 respectively using generalized additive models (GAMs) from the package
 “mgcv”. We quantified the effects of the site (baseline, Hawaii, Texas,
 California, and New Mexico) and seasonality (winter and summer) on growth
 rate by comparing models with site-specific or global TPCs/LPCs. For TPCs,
 each light treatment was analyzed separately, whereas for LPCs, each
 temperature treatment was analyzed separately. To select for the best
 fitting model, we used Restricted Maximum Likelihood (REML). Within each
 light/temperature treatment and using season or site as the grouping
 parameters, we applied GAMs comparing three nested models, (i) Model 1:
 the “simplest” model using a single global smoother fitting all data; (ii)
 Model 2: a model with a global smoother and a parametric term (i.e., site
 or season), allowing different intercepts for each group (site or season);
 and (iii) Model 3: a model providing different smoothers for each group
 and a parametric term for each group-specific intercepts. Models were
 selected based on the lowest Akaike information criterion (AIC). The
 anova.gam function performed Wald tests to determine the significance of
 each parametric and smooth terms. We avoided overfitting data and made
 sure that every model had a gaussian (bell shape) curve as expected for
 TPC/LPC when possible, by limiting wiggliness. We used R version 4.2.2 for
 statistical analyses. All differences were considered significant when p
 &lt; 0.05.
description: # Data from: Adaptation and plasticity of *Nannochloropsis* sp. in
 response to seasonal and geographic climate variation Dataset DOI:
 [10.5061/dryad.rv15dv4mz](https://doi.org/10.5061/dryad.rv15dv4mz) ##
 Description of the data and file structure This is a project analyzing
 thermal and light performance curves in a common garden experiment of
 different strains growing outdoors. Following 17 and 22 months of
 cultivation outdoors, we collected samples during winter and summer,
 respectively. There is the baseline strain (cryopreserved), and the field
 strains: Hawaii (Cyanotech), Texas (Qualitas Health), California (UCSD,)
 and New Mexico (NMSU). The files are: * TLG_May22.csv * TLG_Oct22.csv -
 TLG_code_compiled.R The R code has been tested and run on MacOS using R
 version 4.3.2. It needs the packages specified at the beginning and the
 two csv files TLG_May22.csv and TLG_Oct22.csv. To run, make sure to
 download both TLG_May22.csv and TLG_Oct22.csv and place them in a working
 directory that will host the rest of the generated files and plots. ###
 Files and variables #### File: TLG_code_compiled.R **Description:** The R
 code that uses both TLG_May22.csv and TLG_Oct22.csv to process data,
 create growth curves, estimate growth rates, run GAMs, and create plots.
 #### File: TLG_May22.csv **Description:** the winter collection dataset
 ##### Variables * Plate: the number of the plate from 1 to 24 * Map: the
 random map from 1 to 4 followed for that specific plate *
 Sample: information about the content of the sample, if H2O (water),
 Site_Replicate, or Blank * Lab: information about the Site or if to be
 excluded * Temp: temperature treatment in degree C = "5",
 "10", "15", "20", "25",
 "30" * Light: light treatment in % = "100",
 "50", "10", "5" * Replicate: samples were
 tested in three replicates R1, R2 and R3 * Day: day since common garden
 experiment started from 0 to 5 * OD: raw optical density at 750 nm *
 Water_OD: water optical density at 750 nm used as the blank * Fluor: raw
 fluorescence * Water_Fluor: fluorescence of water as the blank *
 DilutionFactor_OD: dilution factor for optical density *
 DilutionFactor_Fluor: dilution factor for fluorescence *
 Corrected_OD: final optical density after subtracting water OD and
 applying dilution factor * Corrected_Fluor: final fluorescence after
 subtracting water OD and applying dilution factor #### File: TLG_Oct22.csv
 **Description:** the summer collection dataset ##### Variables *
 Plate: the number of the plate from 1 to 24 * Map: the random map from 1
 to 4 followed for that specific plate * Sample: information about the
 content of the sample, if H2O (water), Site_Replicate, or Blank *
 Lab: information about the Site or if to be excluded * Temp: temperature
 treatment in degree C = "5", "10", "15",
 "20", "25", "30" * Light: light treatment in
 % = "100", "50", "10", "5" *
 Replicate: samples were tested in three replicates R1, R2 and R3 *
 Day: day since common garden experiment started from 0 to 5 * OD: raw
 optical density at 750 nm * Water_OD: water optical density at 750 nm used
 as the blank * Fluor: raw fluorescence * Water_Fluor: fluorescence of
 water as the blank * DilutionFactor_OD: dilution factor for optical
 density * DilutionFactor_Fluor: dilution factor for fluorescence *
 Corrected_OD: final optical density after subtracting water OD and
 applying dilution factor * Corrected_Fluor: final fluorescence after
 subtracting water OD and applying dilution factor ## Code/software
 Both TLG_May22.csv and TLG_Oct22.csv can be read using microsoft excel.
 TLG_code_compiled.R requires R software.