Individual plasticity in response to rising sea temperatures contributes to an advancement in green turtle nesting phenology
Data files
Jan 21, 2025 version files 15.08 MB
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Alagadi_SST.nc
1.40 MB
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Climwin_SST_data.csv
798.94 KB
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Green_turtle_nesting_data_1992_2022.csv
182.30 KB
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Gulf_of_Arab_SST.nc
1.45 MB
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Gulf_of_Bomba_SST.nc
1.45 MB
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Gulf_of_Sirte_SST.nc
1.45 MB
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Individual_Phenology_Data.csv
284.24 KB
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Lake_Bardawil_SST.nc
1.45 MB
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Libyan_Tunisian_Border_SST.nc
1.45 MB
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Population_Phenology_Data.csv
1.37 KB
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README.md
16.79 KB
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SST_Data_Alagadi_29_March_29_April.csv
565 B
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TC1_Alanya_SST.nc
1.72 MB
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TC2_Tasucu_SST.nc
1.72 MB
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TC3_Southern_Cyprus_SST.nc
1.72 MB
Abstract
Phenological changes – i.e., shifts in the timing of biological events – are among the most frequently reported population-level responses to climate change and are often assumed to be adaptive and increase population viability. These may be driven by both individual-level phenotypic plasticity and population-level evolutionary and demographic changes. Yet, few studies have explored how individual-level versus population-level processes drive phenological trends. Using a 31-year dataset of over 600 individually marked nesting green turtles (Chelonia mydas), we quantify the population- and individual-level temporal change in the first nest date. Of the latter, approximately 30% is attributable to individual phenological plasticity to a rise in sea surface temperature, with females advancing their nesting by 6.47 days for every degree increase in sea surface temperature. The remaining change is almost entirely explained by individual- and population-level changes in size and breeding experience (correlates of age), as well as the number of clutches laid per season. This is the first study of individual-level phenological change in a marine ectotherm, furthering our understanding of how this and similar species may respond to rising temperatures.
https://doi.org/10.5061/dryad.8gtht76z9
Description of the data and file structure
Dataset for Proceedings of the Royal Society B: DOI: 10.1098/rspb.2024.1809
Individual plasticity in response to rising sea temperatures contributes to an advancement in green turtle nesting phenology.
Mollie L. Rickwood1, Eve Tucker1, Damla Beton2, Sophie Davey2, Brendan J. Godley1, Robin T. E. Snape1,2, Erik Postma1, Annette C. Broderick1
1 University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK.
2 Society for Protection of Turtles, Levent Daire 1, Ulus Sokak, Gönyelli, North Cyprus.
Mollie L. Rickwood: m.r.rickwood@exeter.ac.uk; Eve Tucker: evejtucker@gmail.com; Damla Beton: damlabeton@cyprusturtles.org; Sophie Davey: sophiedavey@cyprusturtles.org; Brendan J. Godley: B.J.Godley@exeter.ac.uk; Robin T. E. Snape: R.T.E.Snape@exeter.ac.uk; Erik Postma: E.Postma@exeter.ac.uk; Annette C. Broderick: A.C.Broderick@exeter.ac.uk
This file contains the data supporting the manuscript “Individual plasticity in response to rising sea temperatures contributes to an advancement in green turtle nesting phenology”. This work uses a dataset running from 1992 to 2022 of over 600 individually tagged nesting green turtles (Chelonia mydas) from Alagadi beach, Northern Cyprus. We use mixed models with within-subject centering to quantify the population- and individual-level temporal change in the nesting phenology. We find that the green turtles at our study site have advanced their phenology and that individual phenological plasticity to a rise in sea surface temperature is an important driver of this trend. However, we also show that the remaining change in nesting phenology is almost entirely explained by individual- and population-level changes in female size and breeding experience (correlates of age), as well as the number of clutches laid per season.
Files and variables
File: Green_turtle_nesting_data_1992_2022.csv
Description: Description: female green turtle nesting data from Alagadi beach, each row represents a successful nesting event
Variables
- Year: the year in which nesting event occurred (1992 – 2022)
- ID: the individual unique identifier of the female that laid the nest
- Date: the exact date of the nesting event
- Order: takes numeric values 1 to 6 corresponding whether the row refers to a females first, second, third etc., nest of the year
- NST.Date: i.e., nest date, this refers to the day of the year, with the 1st January being day 1 and corrected for leap years, of the nesting event
- INI: interesting interval, the number of days between consecutive nesting events, used to determine the estimated clutch frequency
- Season: whether the nesting event is in a females first, second, third etc., breeding season
- ECF: estimated clutch frequency, an adjustment of a females observed clutch frequency (the total number of clutches recorded for a female in a season) assuming one, two or three clutches had been missed when inter-nesting intervals were larger than 20, 30 and 45, respectively
- MeanCCL: a females minimum curved carapace length (CCL) calculated as the mean of three measurements taken during laying
- MeanCCW: a females curved carapace width (CCL) calculated as the mean of three measurements taken during laying
File: Population_Phenology_Data.csv
Description: Description: data for the population phenology analysis (population first, median and last nest and nesting season duration)
Variables
- Year: the year in which nesting event occurred (1992 – 2022)
- ID: the individual unique identifier of the female that laid the nest
- Date: the exact date of the nesting event
- FND: first nest date of the entire population, the day of the year, with the 1st January being day 1 and corrected for leap years, of the earliest nest recorded for the entire population
- SST: the annual mean SST in the waters adjacent to Alagadi beach between the 29th March to the 29th April
- MND: median nest date of the entire population, the day of the year, with the 1st January being day 1 and corrected for leap years, of the mean nest for the entire population
- LND: last nest date of the entire population, the day of the year, with the 1st January being day 1 and corrected for leap years, of the latest nest of a season
- NSD: nesting season duration, the length of a nesting season calculated by subtracting the FND from the LND
File: Individual_Phenology_Data.csv
Description: data for individual- and population-level phenology analysis
Variables
- ID: the individual unique identifier of the female that laid the nest
- Year_numeric: the year in which nesting event occurred (1992 – 2022) as a numeric variable
- Year_factor: the year in which nesting event occurred (1992 – 2022) as a factor variable
- FND: first nest date, the day of the year, with the 1st January being day 1 and corrected for leap years, of a females first nest of a season
- MND: median nest date, the day of the year, with the 1st January being day 1 and corrected for leap years, of a females median nest of a season
- Season: whether the nesting event is in a females first, second, third etc., breeding season
- Breeding_Experience: takes the value of 0 when Season = 1 and a value of 1 for when Season ≥ 2
- ECF: estimated clutch frequency, an adjustment of a females observed clutch frequency (the total number of clutches recorded for a female in a season) assuming one, two or three clutches had been missed when inter-nesting intervals were larger than 20, 30 and 45, respectively
- MeanCCL: a females minimum curved carapace length (CCL) calculated as the mean of three measurements taken during laying
- MeanCCW: a females curved carapace width (CCL) calculated as the mean of three measurements taken during laying
- SST: the annual mean SST in the waters adjacent to Alagadi beach between the 29th March to the 29th April
- MeanYear: the mean year in which an individual female was observed breeding
- DeltaYear: the deviation from the individual’s mean year
- MeanSST: the mean SST at which an individual female was observed breeding
- DeltaSST: the deviation from the individual’s mean SST
- MeanBreeding_Experience: an individual female’s mean breeding experience
- DeltaBreeding_Experience: the deviation from the individual’s mean breeding experience
- MeanECF: an individual’s mean ECF
- DeltaECF: the deviation from the individual’s mean ECF
- MeanMeanCCL: an individual’s mean CCL
- DeltaMeanCCL: the deviation from the individual’s mean CCL
- SST_centered: SST column values mean centered
- Year_numeric_centered: Year_numeric column values mean centered
- Breeding_Experience_centered: Breeding_Experience column values mean centered
- ECF_centered: ECF column values mean centered
- MeanCCL_centered: MeanCCL column values mean centered
- DeltaYear_numeric_centered: DeltaYear_numeric column values mean centered
- MeanYear_numeric_centered: MeanYear_numeric column values mean centered
- DeltaSST_centered: DeltaSST column values mean centered
- MeanSST_centered: MeanSST column values mean centered
- DeltaBreeding_Experience_centered: DeltaBreeding_Experience column values mean centered
- MeanBreeding_Experience_centered: MeanBreeding_Experience column values mean centered
- DeltaECF_centered: DeltaECF column values mean centered
- MeanECF_centered: MeanECF column values mean centered
- DeltaMeanCCL_centered: DeltaMeanCCL column values mean centered
- MeanMeanCCL_centered: MeanMeanCCL column values mean centered
File: SST_Data_Alagadi_29_March_29_April.csv
Description: Description: sea surface temperature data at Alagadi beach in the optimal climate window determined from climwin analysis
Variables
- Year: year of the measurement of the sea surface temperature
- Temp: the annual mean SST in the waters adjacent to Alagadi beach between the 29th March to the 29th April
File: Alagadi_SST.nc
Description Spatraster in which each layer represents the daily sea surface temperature for the waters adjacent to Alagadi (nesting beach) between 1st January 1992 and 30th September 2022. Extent: 33.34726, 33.59749, 35.31632, 35.61727 (xmin, xmax, ymin, ymax). Coordinate Reference System: WGS84. Data downloaded from E.U. Copernicus Marine Service Information (DOI: 10.48670/moi-00173).
File: Gulf_of_Arab_SST.nc
Description: Spatraster in which each layer represents the daily sea surface temperature for the Gulf of Arab (foraging site) between 1st January 1992 and 7th October 2022. Extent: 28.94322, 29.19345, 30.80213, 31.10308 (xmin, xmax, ymin, ymax). Coordinate Reference System: WGS84. Data downloaded from E.U. Copernicus Marine Service Information (DOI: 10.48670/moi-00173).
File: Gulf_of_Bomba_SST.nc
Description: Spatraster in which each layer represents the daily sea surface temperature for the Gulf of Bomba (foraging site) between 1st January 1992 and 7th October 2022. Extent: 22.98775, 23.23798, 32.55765, 32.8586 (xmin, xmax, ymin, ymax). Coordinate Reference System: WGS84. Data downloaded from E.U. Copernicus Marine Service Information (DOI: 10.48670/moi-00173).
File: Gulf_of_Sirte_SST.nc
Description: Spatraster in which each layer represents the daily sea surface temperature for the Gulf of Sirte (foraging site) between 1st January 1992 and 7th October 2022. Extent: 16.43173, 16.68196, 31.20339, 31.50434 (xmin, xmax, ymin, ymax). Coordinate Reference System: WGS84. Data downloaded from E.U. Copernicus Marine Service Information (DOI: 10.48670/moi-00173).
File: Lake_Bardawil_SST.nc
Description: Spatraster in which each layer represents the daily sea surface temperature for the waters adjacent to Lake Bardawil (foraging site) between 1st January 1992 and 7th October 2022. Extent: 33.09704, 33.34727, 31.00276, 31.30371 (xmin, xmax, ymin, ymax). Coordinate Reference System: WGS84. Data downloaded from E.U. Copernicus Marine Service Information (DOI: 10.48670/moi-00173).
File: Libyan_Tunisian_Border_SST.nc
Description: Spatraster in which each layer represents the daily sea surface temperature for the waters adjacent to the Libyan-Tunisian border (foraging site) between 1st January 1992 and 7th October 2022. Extent: 11.42714, 11.67737, 33.15955, 33.46049 (xmin, xmax, ymin, ymax). Coordinate Reference System: WGS84. Data downloaded from E.U. Copernicus Marine Service Information (DOI: 10.48670/moi-00173).
File: TC1_Alanya_SST.nc
Description: Spatraster in which each layer represents the daily sea surface temperature for the waters adjacent to Alanya (foraging site) between 1st January 1992 and 7th October 2022. Extent: 30.94506, 31.24534, 36.57027, 36.87122 (xmin, xmax, ymin, ymax). Coordinate Reference System: WGS84. Data downloaded from E.U. Copernicus Marine Service Information (DOI: 10.48670/moi-00173).
File: TC2_Tasucu_SST.nc
Description: Spatraster in which each layer represents the daily sea surface temperature for the waters adjacent to Tasucu (foraging site) between 1st January 1992 and 7th October 2022. Extent: 33.89777, 34.19805, 35.96838, 36.26932 (xmin, xmax, ymin, ymax). Coordinate Reference System: WGS84. Data downloaded from E.U. Copernicus Marine Service Information (DOI: 10.48670/moi-00173).
File: TC3_Southern_Cyprus_SST.nc
Description: Spatraster in which each layer represents the daily sea surface temperature for the waters adjacent to the Southern Cyprus foraging site between 1st January 1992 and 7th October 2022. Extent: 32.64662, 32.9469, 34.36333, 34.66427 (xmin, xmax, ymin, ymax). Coordinate Reference System: WGS84. Data downloaded from E.U. Copernicus Marine Service Information (DOI: 10.48670/moi-00173).
File: Climwin_SST_data.csv
Description: environmental data required for climwin analyses
Variables
- date: date of sea surface temperature (SST) measurement (in dd/mm/yyyy format) from 01/01/1992 to 31/08/2022
- Alagadi: SST at Alagadi beach, the nesting site
- Egypt: the mean daily SST between the Gulf_of_Arab and Lake_Bardawil
- Turkey-Cyprus: the mean daily SST between TC1, TC2 and Southern_Cyprus
- WestLibya: the mean daily SST between the Libyan_Tunisian_Border and the Gulf of Sirte
- GOB: mean daily SST at the Gulf of Bomba
NA: Not applicable
Code/software
Analyses were conducted in R version 4.3.0 (R Core Team. 2023).
Phenology analyses can be replicated using the following:
Data_Preparation.R
Description: This script contains a summary of the data (e.g. how many individual females are included in the dataset, how many nests were observed etc.). Here we also create a population-level phenology dataset comprising of the first, median and last nest date of the entire population. We also create two separate individual-level datasets, one for the first nest date and one for the median nest date of each female, in each of her breeding years. On these individual-level datasets, we perform within-subject centering, finding the mean of each predictor (Year, SST, breeding year, ECF and CCL) for each female and then the deviation from this mean for each observation. These values are also mean centered.
Figure_2_Population_Phenology.R
Description: This script contains the analysis of the population’s phenology outlined in Methods section “Modelling nesting phenology” and the findings are presented in the Results section “Population nesting phenology”.
Figure_3_Contribution_of_predictors_to_change_in_FND.R
Description: This script contains analysis underlying the results presented in the Results section “Individual-level nesting phenology”. Here we use the glmmTMB R package (Brooks et al., 2007) to perform within-subject centering following Van De Pol and Wright (2009).
Individual_Phenology_Effect_of_SST_BE_ECF_Size.R
Description: This script contains analysis underlying the results presented in the Results section “Individual-level nesting phenology”. Here we build on an approach by Ellner et al., (2011) to quantify how much of the within- and among-individual temporal trend in the FND is explained by each of the predictors.
SFigure_1_Percentage_of_nests_observed_each_year.R
Description: This script contains the code behind Figure S1, showing the proportion of nests each year that were observed versus unobserved.
SFigure_2_Boxplot_of_FND_with_increasing_season_number.R
Description: This script contains the statistical analyses comparing the FND between breeding years, showing that there is a significant difference between the first breeding year to all subsequent breeding years.
SFigure_6_Temporal_change_in_predictors.R
Description: This script shows the statistical analyses behind Figure S5, showing the temporal change in each of the predictors (SST, breeding experience, ECF and CCL).
Climwin analyses can be replicated using the following:
Climwin_Analysis.R
Description: Contains the climwin analysis for the population FND and MND and the individual FND and MND. Here we also compare the strength of the climate signal from all the foraging grounds and also the nesting beach. See Supplementary Methods for climwin analysis Table S1 and S2, Figure S3 and S4.
Comparison_of_SST_in_climate_windows.R
Description: This script contains the statistical analyses comparing the various climate windows identified for the population FND and MND and the individual FND and MND.
SST_Data_Preparation.R
Description: This script contains the preparation of the SST data downloaded from E.U. Copernicus Marine Service Information (DOI: 10.48670/moi-00173). This involves grouping the foraging sites identified by Bradshaw et al., (2017) and Snape et al., (2022) into 4 broadscale foraging areas and finding the mean daily SST. A data frame is created containing the daily SST for all sites that will be used for the climwin analysis.
Packages and versions
- cowplot 1.1.1
- climwin 1.2.3
- dplyr 1.1.4
- glmmTMB 1.1.10
- ggplot 3.5.1
- lme4 1.1.33
- patchwork 1.1.2
- terra 1.7.83
- tidyverse 2.0.0