DOI: 10.5061/dryad.jm63xsjpz
title: Parental age effects on offspring fitness in a wild population of a short-lived reptile

description: As organisms age, the fitness of the offspring they produce can decline,
 which is often attributed to parental senescence. However, few studies
 have tested for effects of parental age on offspring fitness in wild
 populations or in short-lived vertebrates, and only recently have studies
 begun to examine such effects in male and female offspring independently.
 Here, we use five generations of mark-recapture and genetic parentage data
 from an island population of a short-lived lizard, the brown anole (Anolis
 sagrei), to test for effects of maternal and paternal age on the survival
 to adulthood, first-year reproductive success, longevity, and lifetime
 fitness of their offspring. We tested for effects of maternal and paternal
 age on components of offspring fitness using two methods: 1) “within-year”
 analyses of parents of different ages within the same annual reproductive
 season, and 2) “within-parent” repeated-measures analyses of the same
 parents at different ages across successive reproductive seasons. Our
 study adds to the growing literature suggesting that negative effects of
 parental age on offspring fitness may not be as prevalent as once thought,
 particularly in wild populations.
description: # Parental age effects on offspring fitness in a wild population of a
 short-lived reptile Dataset DOI:
 [10.5061/dryad.jm63xsjpz](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](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](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.i13[https://doi.org/10.18637/jss.v082.i13](https://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/](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](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](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](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](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.01686[https://doi.org/10.21105/joss.01686](https://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