Dataset DOI: 10.5061/dryad.jm63xsjpz

Description of the data and file structure

The findings of this paper are drawn from a mark-recapture and genotyping study carried out on a focal island population of brown anole lizards (Anolis sagrei) within the Guana Tolomato Matanzas Natural Estuarine Research Reserve in Florida. Although animals in this population have been tracked between 2011 and 2025 from a long-term ongoing study, this dataset primarily focuses on the individuals in the 2015-2018 cohorts, their survival, reproductive fitness, and parent ages. In this study, we evaluated the effects of parental age on offspring fitness. We tested for both maternal and paternal age effects on the fitness of sons and daughters.

Based on the methods, the dataset provided illustrates individual identity of animals (e.g., ID, Sex, Cohort) and information on parents, as determined by genetic parentage (e.g., Parent ID, Parent Age, Parent Cohort). The dataset includes four fitness measures of individuals (S_1_1_spring, survival to adulthood; off_count_year_1, First year reproductive success; tot_off, Lifetime Reproductive success; longevity, total lifespan of individuals). The size of individuals is also included to examine effects of parental age on offspring growth. 

Files and variables

File: "RM_sires.csv"

Description: The following variables are present in the dataset.

Variables

• ID: Animal ID; Unique identifying ID number given to each captured individual.
• Sex: Sex (Categorical variable, M = male, F = female)
• Sire: Sire ID; Unique identifying ID value given to the individual's father.
• Dam: Dam ID; Unique identifying ID value given to the individual's mother. NA values indicate that a mother could not be genetically assigned
• Cohort: Hatch year; Assignment based on the year in which the individual was known to be born (e.g., a cohort 2015 individual would have hatched in the year 2015).
• S_1_1_spring: Survival to an individual's first reproductive year, first census (spring); binary (0 = died; 1 = survived). Determined by mark-recapture censuses (e.g., determined to survive if captured in this census or any census after).
• off_count_year_1: total number of genetically assigned offspring during the individual's first reproductive year
• tot_off: total number of genetically assigned offspring across an individual's lifetime
• Sire_Birth_Year: The cohort (hatch year) of the father
• Age: The age (in years) of the father in the year that the offspring hatched
• Fitness_Measured_Year: The year that the offspring reached reproductive maturity and fitness could begin to be measured for the individual
• SVL_0_4__fall: Measured snout-vent length (mm) during the individual's natal year, 4th census (fall). NA values indicate missing size data.
• SVL_1_1_spring: Measured snout-vent length (mm) during the individual's first reproductive year, 1st census (spring). NA values indicate missing size data.
• Longevity: The number of censuses across which an individual survived throughout its lifetime, including any censuses in which an individual was missed between captures (e.g., a cohort 2015 animal that only survived to the spring 2016 census would be scored as 1, whereas a cohort 2015 animal that survived to the fall 2016 census would be scored as 4, regardless of whether it was also captured in the early summer 2016 and late summer 2016 censuses)

File: "RM_dams.csv"

Description: The following variables are present in the dataset.

Variables

• ID: Animal ID; Unique identifying ID number given to each captured individual.
• Sex: Sex (Categorical variable, M = male, F = female)
• Sire: Sire ID; Unique identifying ID value given to the individual's father. NA values indicate that a father could not be genetically assigned
• Dam: Dam ID; Unique identifying ID value given to the individual's mother.
• Cohort: Hatch year; Assignment based on the year in which the individual was known to be born (e.g., a cohort 2015 individual would have hatched in the year 2015).
• S_1_1_spring: Survival to an individual's first reproductive year, first census (spring); binary (0 = died; 1 = survived). Determined by mark-recapture censuses (e.g., determined to survive if captured in this census or any census after).
• off_count_year_1: total number of genetically assigned offspring during the individual's first reproductive year
• tot_off: total number of genetically assigned offspring across an individual's lifetime
• Dam_Birth_Year: The cohort (hatch year) of the mother
• Age: The age (in years) of the mother in the year that the offspring hatched
• Fitness_Measured_Year: The year that the offspring reached reproductive maturity and fitness could begin to be measured for the individual
• SVL_0_4__fall: Measured snout-vent length (mm) during the individual's natal year, 4th census (fall). NA values indicate missing size data.
• SVL_1_1_spring: Measured snout-vent length (mm) during the individual's first reproductive year, 1st census (spring). NA values indicate missing size data.
• Longevity: The number of censuses across which an individual survived throughout its lifetime, including any censuses in which an individual was missed between captures (e.g., a cohort 2015 animal that only survived to the spring 2016 census would be scored as 1, whereas a cohort 2015 animal that survived to the fall 2016 census would be scored as 4, regardless of whether it was also captured in the early summer 2016 and late summer 2016 censuses)

File: "WYmcdat3.csv"

Description: The following variables are present in the dataset.

Variables

• ID: Animal ID; Unique identifying ID number given to each captured individual.
• Sex: Sex (Categorical variable, M = male, F = female)
• Cohort: Hatch year; Assignment based on the year in which the individual was known to be born (e.g., a cohort 2015 individual would have hatched in the year 2015).
• Sire: Sire ID; Unique identifying ID value given to the individual's father. NA values indicate that a father could not be genetically assigned.
• Dam: Dam ID; Unique identifying ID value given to the individual's mother. NA values indicate that a mother could not be genetically assigned
• S_1_1_spring: Survival to an individual's first reproductive year, first census (spring); binary (0 = died; 1 = survived). Determined by mark-recapture censuses (e.g., determined to survive if captured in this census or any census after).
• tot_off: total number of genetically assigned offspring across an individual's lifetime
• off_count_year_1: total number of genetically assigned offspring during the individual's first reproductive year
• off_count_year_2: total number of genetically assigned offspring during the individual's second reproductive year
• off_count_year_3: total number of genetically assigned offspring during the individual's third reproductive year
• Sire2: Short-hand Sire ID; Unique identifying ID number given to the individual's father. NA values indicate that a father could not be genetically assigned
• Dam2: Short-hand Dam ID; Unique identifying ID number given to the individual's mother. NA values indicate that a mother could not be genetically assigned
• Sire_cohort: The cohort (hatch year) of the father.NA values indicate that a father was not genetically assigned.
• Dam_cohort: The cohort (hatch year) of the mother. NA values indicate that a mother was not genetically assigned.
• Sire_Age: The age (in years) of the father in the year that the offspring hatched. NA values indicate that a father was not genetically assigned.
• Dam_Age: The age (in years) of the mother in the year that the offspring hatched. NA values indicate that a mother was not genetically assigned.
• s11_2: Survival to an individual's first reproductive year, as determined by whether the individual was assigned an offspring during that reproductive year; binary (0 = died; 1 = survived).
• Sire_surv: The lifespan (in years) of the father, as determined by mark-recapture censuses. NA values indicate that a father was not genetically assigned.
• Dam_surv: The lifespan (in years) of the mother, as determined by mark-recupture censuses. NA values indicate that a mother was not genetically assigned.
• Longevity: The number of censuses across which an individual survived throughout its lifetime, including any censuses in which an individual was missed between captures (e.g., a cohort 2015 animal that only survived to the spring 2016 census would be scored as 1, whereas a cohort 2015 animal that survived to the fall 2016 census would be scored as 4, regardless of whether it was also captured in the early summer 2016 and late summer 2016 censuses)
• SVL_0_4_fall: Measured snout-vent length (mm) during the individual's natal year, 4th census (fall). NA values indicate missing size data.
• SVL_1_1_spring: Measured snout-vent length (mm) during the individual's first reproductive year, 1st census (spring). NA values indicate missing size data.

File: "genotypes.csv"

Description: The following variables are present in the dataset.

Variables

• ID: Animal ID; Unique identifying ID number given to each captured individual.
• percent_genotyped: Percent of loci successfully genotyped for a given individual (out of 215 total SNP loci)
• GTseq_locXXX: The individual's genotype at the specified locus. A 0 indicates that a genotype could not be determined at the specified locus.

Code/software

We used RStudio to wrangle and analyze data. The following is the complete list of packages we used in analyzing and plotting the data. The Rcode used to analyze the dataset to reproduce analyses and figures in the paper is available for download. The data file "RM_sires.csv" corresponds with the Rcode "WP_Sire_DRYAD.R", the data file "RM_dams.csv" corresponds with the Rcode "WP_dam_DRYAD.R", and the data file "WYmcdat3.csv" corresponds with the Rcode "WY_DRYAD_FINAL.R."

• emmeans: Lenth R (2023). _emmeans: Estimated Marginal Means, aka Least-Squares Means_. R package version1.8.5, https://CRAN.R-project.org/package=emmeans.
• ggplot2: H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
• psych: Revelle, W. (2022) psych: Procedures for Personality and Psychological Research, Northwestern University, Evanston, Illinois, USA, https://CRAN.R-project.org/package=psych Version = 2.2.9.
• lmerTest: Kuznetsova A, Brockhoff PB, Christensen RHB (2017). “lmerTest Package: Tests in Linear Mixed Effects Models.” _Journal of Statistical Software_, 82(13), 1-26. doi:10.18637/jss.v082.i13https://doi.org/10.18637/jss.v082.i13.
• lme4: Douglas Bates, Martin Maechler, Ben Bolker, Steve Walker (2015). Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software, 67(1), 1-48. doi:10.18637/jss.v067.i01.
• car: John Fox and Sanford Weisberg (2019). An {R} Companion to Applied Regression, Third Edition. Thousand Oaks CA: Sage. URL: https://socialsciences.mcmaster.ca/jfox/Books/Companion/
• patchwork: Pedersen T (2023). _patchwork: The Composer of Plots_. R package version 1.1.3,https://CRAN.R-project.org/package=patchwork.
• readr:  Wickham H, Hester J, Bryan J (2023). _readr: Read Rectangular Text Data_. R package version2.1.4,https://CRAN.R-project.org/package=readr.
• dplyr: Wickham H, François R, Henry L, Müller K, Vaughan D (2023). _dplyr: A Grammar of Data Manipulation_. R package version 1.1.2, https://CRAN.R-project.org/package=dplyr.

• DHARMa: Hartig F (2022). _DHARMa: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models_. R package version 0.4.6, https://CRAN.R-project.org/package=DHARMa.

• glmmTMB: Mollie E. Brooks, Kasper Kristensen, Koen J. van Benthem, Arni Magnusson, Casper W. Berg, Anders Nielsen, Hans J. Skaug, Martin Maechler and Benjamin M. Bolker (2017). glmmTMB Balances Speed and Flexibility Among Packages for Zero-inflated Generalized Linear Mixed Modeling. The R Journal, 9(2), 378-400. doi: 10.32614/RJ-2017-066.
• tidyverse: Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019). “Welcome to the tidyverse.” _Journal of Open Source Software_, 4(43), 1686. doi:10.21105/joss.01686https://doi.org/10.21105/joss.01686.

Access information

Other publicly accessible locations of the data:

• NA

Data was derived from the following sources:

• Data was collected as a part of this study