DOI: 10.5061/dryad.sbcc2frb9
title: Data from: Females with attractive mates gain environmental benefits that increase lifetime and multi-generational fitness

description: Resolving the degree to which environmental (direct) vs. genetic
 (indirect) benefits shape female mate choice is a long-standing challenge,
 particularly for socially monogamous species where male environmental and
 genetic contributions are difficult to disentangle. This study combines
 long-term population monitoring with quantitative genetic analyses in a
 socially monogamous but sexually promiscuous Australian songbird to
 demonstrate that female mating preferences are driven by non-genetic
 environmental benefits that increase the fitness of both the female and
 her offspring. Male Red-backed Fairywrens (Malurus melanocephalus)
 flexibly breed in either ornamented or unornamented plumage, and females
 consistently prefer ornamented males. Females paired with ornamented males
 bred earlier and allocated more to current reproduction, yet experienced
 higher survival and lifetime fitness. Furthermore, these females produced
 more grand-offspring because their early-born sons were more likely to be
 ornamented and to breed successfully than the later-born sons of females
 with unornamented partners. Quantitative genetic models showed lifetime
 fitness was best explained by parental environment rather than genetic
 effects. Mating preferences in this system are maintained by a combination
 of primary environmental benefits that increase the lifetime fitness of
 choosy females, and secondary environmental benefits that increase the
 multi-generational fitness of those females through enhanced offspring
 quality and performance.
description: We used the program NCSS (v11.0.24) to conduct all statistical
 analyses except quantitative genetic analyses. A free trial of the newest
 version of this proprietary software (NCSS 2024) is available at https://www.ncss.com/download/ncss/free-trial/. We performed the quantitative genetic analyses in R, and used the code that provided as an R script file. Detailed descriptions of all files and analyses are provided in the README file.
description: # Data from: Females with attractive mates gain environmental benefits
 that increase lifetime and multi-generational fitness ## Statistical
 Analysis - Details The published manuscript contains important details
 regarding statistical analyses. * The "Statistical analyses"
 methods section contains a narrative explanation and justification for
 analyses. * Table S3 lists the analysis type, data and variables included,
 and results from the final model for each dependent variable. Below we
 provide general information about the statistical software used, and
 specific information for each individual analysis type. **Statistical
 Software** * We used the program NCSS (v11.0.24) to conduct all
 statistical analyses except quantitative genetic analyses (see below). * A
 free trial of the newest version of this proprietary software (NCSS 2024)
 is available at
 [https://www.ncss.com/download/ncss/free-trial/](https://www.ncss.com/download/ncss/free-trial/). * This software is based upon a graphical user interface, and does not involve user-generated code. * Our settings were based on recommendations from the NCSS Documentation Manual, which is available at [https://www.ncss.com/software/ncss/ncss-documentation/](https://www.ncss.com/software/ncss/ncss-documentation/). * To ensure clarity and reproducability within this GUI-based program, we have itemized all settings for each analysis type below. **Mixed Models** Analyses were completed using the "Mixed Models-Repeated Measures" procedure. * Subject is included as a random effect * Model includes random intercept and uses Type III sums of squares * Calculation of test statistics (F, df, p) are based upon methods described in Kenward and Roger (1997; [https://doi.org/10.2307/2533558](https://doi.org/10.2307/2533558)) * Variables Tab * Response: Variable depending upon analysis (see Table S3). * Subjects: Table S3 in the manuscript lists the subject for each analysis. Most use the female ("BFID") as the subject. Exceptions include Nestling Feeding in which the pair ("Group") was the subject, and relative breeding onset day in which site/year ("SiteFirstEggDay") was teh subject. * Times: Left blank, which causes time values to be assigned sequentially. Because spreadsheets are sorted chronologically this results in accurate order assignment. * Between and Within Fixed Factors: Variable depending upon analysis (see Table S3). * Covariates: Variable depending upon analysis (see Table S3). * Pattern: "Diagonal:Random" was the starting point for all analyses. This is similar to the default "diagonal" repeated component pattern, but it adds a random subject term. The random subject term was removed if the random component parameter estimate was zero or if model simplification was necessary for proper convergence. * Force Positive Correlations: Not selected * Model (Fixed Terms): Includes all fixed factors, covariates, and interactions (see Table S3). * Intercept: Selected to include the intercept in the model. The only exception was the analysis of PC2, which properly converged only after simplifying the model by removing the intercept. * Maximization Tab * Likelihood Type: Restricted Maximum Likelihood (REML) * Solution Method: Newton-Raphson * Write Solution To: Left blank * Max Fisher Scoring Iterations = 5 * Max Newton-Raphson Iterations = 40 * Lambda = 1 * Convergence Criterion = 1E-6 * Zero (Algorithm Rounding) = 1E-12 * Variance Zero = 1E-6 * Correlation Zero = 1E-6 * Max Retries = 10 * Reports Tab * Alpha = 0.05 * All remaining options: Variable depending upon need **Multiple Regression** Analyses were completed using the "Multiple Regression" procedure. * Variables, Model Tab * Y: Variable depending upon analysis (see Table S3). * Numeric X's: Variable depending upon analysis (see Table S3). * Categorical X's: Variable depending upon analysis (see Table S3). * Default Recording Scheme: Binary * Default Reference Value: First After Sorting * Weights: Left blank * Regression Model: Includes numeric and categorical X's (see Table S3). * Reports Tab * Tests Alpha: 0.050 * Assumptions Alpha: 0.20 * Confidence Level: 95% * Select Reports: Variable depending upon need. * Report Options Tab * Variable depending upon need. **Logistic Regression** Analyses were completed using the "Logistic Regression" procedure. * Variables, Model Tab * Y: Variable depending upon analysis (see Table S3). * Reference Value: Left blank * Numeric X's: Variable depending upon analysis (see Table S3). * Default Recording Scheme: Binary * Default Reference Value: First After Sorting * Frequencies: Left blank * Validation Filter: Left blank * Regression Model: Includes numeric and categorical X's (see Table S3). * Remove Intercept: Left blank * Priors: Equal across Y Values * Subset Selection Tab * Search for the best subset from the X's: Left blank * Iterations Tab * Maximum Iterations: 20 * Iteration Termination: 0.000001 * Reports Tab * Variable depending upon need. * Report Options Tab * Confidence Level: 95% * All remaining options: Variable depending upon need **Analysis of Variance** Analyses were completed using the "General Linear Models (GLM)" procedure. * Variables Tab * Response Variable: Year2RS * Covariate Variable(s): None * Factor Variables: Son plumage, Site, Year * Factor Types: Fixed * Factor Comparisons: None * Which Model Terms: Up to 1-Way * Reports Tab * Test Alpha: 0.05 * All remaining options: Variable depending upon need **Principle Components Analysis** Analyses were completed using the "Principle Components Analysis" procedure. * Spreadsheet does not contain records with missing data for variables included in PCA analysis (missing data are omitted). * This procedure scales and centers data for each variable and presents factor scores that are scaled and centered. * Variables Tab * Variables: NestingAttempts, EggsTotal, NestlingsTotal, FledgedTotal * Data Input Format: Regular data * Robust Covariance Matrix Estimation: Not selected * Missing value estimation: None * Robust Weight: 4.0 * Maximum Iterations: 6 * Matrix Type: Correlation * Factor Rotation: None * Factor Selection-Method: Percent of Eigenvalues * Factor Selection-Value: 100 * Reports Tab * Select Reports: Variable depending upon need. * Alpha = 0.05 * Report Options: Variable depending upon need. ## Statistical Analysis - Data Files All data files are provided in CSV format. The first row of each spreadsheet contains the column names. File names indicate the dependent variables analyzed with each data file. Model details and statistical results for each dependent variable can be found in Table S3 of the associated manuscript. Spreadsheets provided only include data records that were included in analyses. Records have been omitted if they were missing data that were necessary for all associated analyses. Data does not need to be filtered prior to analysis unless stated specifically in the field descriptions for a given spreadsheet. Spreadsheets may still contain records with missing data for two reasons. First, if the spreadsheet was used for a single analysis where the a priori model did not include the variable with missing data. Second, if the spreadsheet was used for multiple analyses but the variable with missing data was not included in all of them. Missing values are represented as blanks, as recommended in the NCSS manual (see above). If the variable with missing data is included in a statistical model this program automatically omits the associated record from the analysis. Records with missing data are only included in analyses when the variable with missing data is not included in the model. Detailed field descriptions for each spreadsheet are provided below: **1.#Eggs.FemaleAge.csv** This spreadsheet was used to analyze the number of eggs laid and to test for assortative pairing by age. | Column | Description | | ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Group | Breeding group ID number | | AuxPresence | Presence of non-breeding auxiliary in group. Categorical. "Y" if group had 1+ auxiliary "helpers". "N" if group had 0 auxiliary "helpers". | | BFID | Breeding female ID number | | BFAge | Breeding female age in years | | BMAge | Breeding male age in years | | BMPlumage | Breeding male plumage color. Categorical. "Red/black" is ornamented plumage. "Brown" is unornamented plumage. | | FirstEggDay | Day of the year when first egg of listed group was laid. Days start at January 1 of a given year (0) and continue until end of the field season, which is typically January of the next year. Thus values can exceed 365. | | Site | Abbreviation for field site location | | Year | Field season. Year at start of season is used to denote entire season (even after Dec 31). Season typically ends in January. | | EggsTotal | Number of eggs laid by group. Includes all nests for that group in that year. | **2.PCA.PC1.PC2.csv** This spreadsheet was used to conduct a principal components analysis (PCA) of correlated measures of female reproductive effort. It was also used to analyze the resulting principal components. | Column | Description | | --------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Group | Breeding group ID number | | Site | Abbreviation for field site location | | Year | Field season. Year at start of season is used to denote entire season (even after Dec 31). Season typically ends in January. | | AuxPresence | Presence of non-breeding auxiliary in group. Categorical. "Y" if group had 1+ auxiliary "helpers". "N" if group had 0 auxiliary "helpers". | | BFID | Breeding female ID number | | BFAge | Breeding female age in years | | BMAge | Breeding male age in years | | BMPlumage | Breeding male plumage color. Categorical. "Red/black" is ornamented plumage. "Brown" is unornamented plumage. | | FirstEggDay | Day of the year when first egg of listed group was laid. Days start at January 1 of a given year (0) and continue until end of the field season, which is typically January of the next year. Thus values can exceed 365. | | NestingAttempts | Number of nesting attempts by group. Includes all nests for that group in that year. | | EggsTotal | Number of eggs laid by group. Includes all nests for that group in that year. | | NestlingsTotal | Number of nestlings produced by group. Includes all nests for that group in that year. | | FledgedTotal | Number of fledglings produced by group. Includes all nests for that group in that year. | | PC1 | Factor scores for the first principal component from PCA of NestingAttempts, EggsTotal, NestlingsTotal, FledgedTotal. This loaded positively with all variables and was interpreted as reproductive effort. | | PC2 | Factor scores for the second principal component from PCA of NestingAttempts, EggsTotal, NestlingsTotal, FledgedTotal. This loaded positively with number of fledglings but negatively with number of nesting attempts and eggs. It was interpreted as reflecting lower renesting rates after successfully fledging young. | | PC3 | Factor scores for the third principal component from PCA of NestingAttempts, EggsTotal, NestlingsTotal, FledgedTotal. This did not meet the Kaiser criterion for inclusion (Eigenvalue &gt; 1) and was not statistically analyzed. | | PC4 | Factor scores for the fourth principal component from PCA of NestingAttempts, EggsTotal, NestlingsTotal, FledgedTotal. This did not meet the Kaiser criterion for inclusion (Eigenvalue &gt; 1) and was not statistically analyzed. | **3.NestlingFeeding.csv** This spreadsheet was used to analyze the relative contribution of each parent to feeding nestlings. | Column | Description | | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------ | | Group | Breeding group ID number. Used as repeated subject in mixed models analyses. | | Day | Day of the year when observations were made. Days start at January 1 of a given year (0) and continue until December 31 (364). | | Site | Abbreviation for field site location | | Sex | Sex of parent. Categorical. "F" is female, "M" is male. | | AuxPresence | Presence of non-breeding auxiliary in group. Categorical. "Y" if group had 1+ auxiliary "helpers". "N" if group had 0 auxiliary "helpers". | | BMPlumage | Breeding male plumage color. Categorical. "Red/black" is ornamented plumage. "Brown" is unornamented plumage. | | Age | Age of parent in years | | StartHours | Hours after sunrise when observations began | | NestlingAge | Age of nestlings in days | | NumNestlings | Number of nestlings in the nest | | FeedingScore | Measure of total food delivered to nestlings. Calculated as (# feeding visits x average prey size). | **4.FoodPerNestling.PreySize.csv** This spreadsheet was used to analyze the average quantity of food that parents delivered to each nestling and the average size of prey items females fed to their nestlings. | Column | Description | | ---------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------ | | Group | Breeding group ID number | | Day | Day of the year when observations were made. Days start at January 1 of a given year (0) and continue until December 31 (364). | | Site | Abbreviation for field site location | | AuxPresence | Presence of non-breeding auxiliary in group. Categorical. "Y" if group had 1+ auxiliary "helpers". "N" if group had 0 auxiliary "helpers". | | BFAge | Breeding female age in years | | BMAge | Breeding male age in years | | BMPlumage | Breeding male plumage color. Categorical. "Red/black" is ornamented plumage. "Brown" is unornamented plumage. | | StartHours | Hours after sunrise when observations began | | NestlingAge | Age of nestlings in days | | NumNestlings | Number of nestlings in the nest | | FemaleAvgFoodSize | Average size of female prey items. Scale from 1 (smaller than parent bill) to 4 (at least 3 times larger than parent bill). | | TotalFeedingScore | Measure of total food delivered to nestlings. Calculated as (# feeding visits x average prey size). Feeding score of both sexes combined. | | TotalFeedingScorePerNestling | Average food received per nestling. Calculated as (TotalFeedingScore / NumNestlings). Feeding score of both sexes combined. | **5.NestlingMass.FledgingRate.BreedingOnsetDay.csv** This spreadsheet was used to analyze nestling mass, the percent of nestlings that fledged, and female breeding onset day. | Column | Description | | ---------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Nest | Nest ID number | | Group | Breeding group ID number | | FirstNestForYear | Specifies whether this was a group's first nest in a given year. Categorical. "Y" if first nest for a group in a given year. "N" if group had 1+ nests earlier that year. Used to filter data for Breeding Onset Day analysis (only included "Y"). | | AuxPresence | Presence of non-breeding auxiliary in group. Categorical. "Y" if group had 1+ auxiliary "helpers". "N" if group had 0 auxiliary "helpers". | | BFID | Breeding female ID number | | BFAge | Breeding female age in years | | BMAge | Breeding male age in years | | BMPlumage | Breeding male plumage color. Categorical. "Red/black" is ornamented plumage. "Brown" is unornamented plumage. | | Site | Abbreviation for field site location | | Year | Field season. Year at start of season is used to denote entire season (even after Dec 31). Season typically ends in January. | | NestlingBandAge | Age of nestlings in days when they were banded | | NestlingBandDay | Day of the year when nestlings were banded. Days start at January 1 of a given year (0) and continue until end of the field season, which is typically January of the next year. Thus values can exceed 365. | | FirstEggDay | Day of the year when first egg of listed nest was laid. Days start at January 1 of a given year (0) and continue until end of the field season, which is typically January of the next year. Thus values can exceed 365. | | NumNestlings | Number of nestlings in the nest | | PercentNestlingsFledge | Percent of nestlings that fledged. Calculated as (number of fledglings / number of nestlings). | | AvgNestlingMass | Average mass (grams) of nestlings at the time they were banded. | **6.RecruitmentRate.GrandOffspring.csv** This spreadsheet was used to analyze the rate of offspring recruitment (measured as survival to year after birth) and the number of grand-offspring produced by sons in the year after their birth. | Column | Description | | -------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | BFID | Breeding female ID number | | Year | Field season. Year at start of season is used to denote entire season (even after Dec 31). Season typically ends in January. | | Site | Abbreviation for field site location | | AuxPresence | Presence of non-breeding auxiliary in group. Categorical. "Y" if group had 1+ auxiliary "helpers". "N" if group had 0 auxiliary "helpers". | | BFAge | Breeding female age in years | | BMAge | Breeding male age in years | | BMPlumage | Breeding male plumage color. Categorical. "Red/black" is ornamented plumage. "Brown" is unornamented plumage. | | FirstEggDay | Day of the year when first egg of listed group was laid. Days start at January 1 of a given year (0) and continue until end of the field season, which is typically January of the next year. Thus values can exceed 365. | | NumFledged | Number of fledglings produced by group. Includes all nests for that group in that year. | | NumRecruited | Number of offspring alive the year after birth. Includes all nests for that group in that year. | | NumMaleRecruits | Number of male offspring alive the year after birth. Includes all nests for that group in that year. | | PercentFledglingsRecruited | Percent of fledglings that were alive the year after birth. Calculated as (NumRecruited / NumFledged). Includes all nests for that group in that year. | | TotalSonRS | Number of grand-offspring produced by sons in the year after their birth. Includes all nests for that son in that year. | | AvgSonRS | Average number of grand-offspring produced by sons in the year after their birth. Calculated as (TotalSonRS / NumMaleRecruits). Includes all nests for all sons in that year. | **7.BreedingOnsetDay(Site/Year).csv** This spreadsheet was used to analyze shifts in female breeding onset day in response to average breeding onset on that site in that year. In other words, it analyzed the extent to which females advanced breeding in "early-breeding" years. | Column | Description | | --------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | BFID | Breeding female ID number | | Site | Abbreviation for field site location | | Year | Field season. Year at start of season is used to denote entire season (even after Dec 31). Season typically ends in January. | | BFAge | Breeding female age in years | | BMAge | Breeding male age in years | | BMPlumage | Breeding male plumage color. Categorical. "Red/black" is ornamented plumage. "Brown" is unornamented plumage. | | AuxPresence | Presence of non-breeding auxiliary in group. Categorical. "Y" if group had 1+ auxiliary "helpers". "N" if group had 0 auxiliary "helpers". | | SiteFirstEggDay | Day of the year when the first egg was laid at a given site in a given year. This gives a unique value for each site/year from which repeated observations are made. This variable (which indicates site/year) is used as the repeated subject in mixed models analysis. Days start at January 1 of a given year (0) and continue until end of the field season, which is typically January of the next year. | | SiteAvgEggDay | Average day of the year when groups in a given site/year laid their first egg. Days start at January 1 of a given year (0) and continue until end of the field season, which is typically January of the next year. Thus values can exceed 365. | | FirstEggDay | Day of the year when the first egg of listed female was laid. Days start at January 1 of a given year (0) and continue until end of the field season, which is typically January of the next year. Thus values can exceed 365. | **8.OffspringPlumage&RS.csv** This spreadsheet was used to analyze the plumage color and reproductive success of first-year males based upon their developmental environment. | Column | Description | | --------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | ID | Male offspring ID number | | Site | Abbreviation for field site location | | HatchYear | Field season of birth. Year at start of season is used to denote entire field season (even after Dec 31). Season typically ends in January. | | FledgeDay | Day of the year when fledged. Days start at January 1 of a given year (0) and continue until end of the field season, which is typically January of the next year. Thus values can exceed 365. | | NumFledged | Number of birds that fledged from natal nest. | | AuxPresence | Presence of non-breeding auxiliary in natal group. Categorical. "Y" if group had 1+ auxiliary "helpers". "N" if group had 0 auxiliary "helpers". | | BFAge | Mother age in years during offspring hatch year | | BMAge | Social father age in years during offspring hatch year | | BMPlumage | Social father plumage color during offspring hatch year. Categorical. "Red/black" is ornamented plumage. "Brown" is unornamented plumage. | | GeneticFatherPlumage | Genetic father plumage color during offspring hatch year. Categorical. "Red/black" is ornamented plumage. "Brown" is unornamented plumage. | | GeneticFatherPlumage1stYear | Genetic father plumage color during the genetic father's first breeding season. Categorical. "Red/black" is ornamented plumage. "Brown" is unornamented plumage. | | Year2Plumage | Male offspring's plumage color in first adult year. Categorical. "Red/black" is ornamented plumage. "Brown" is unornamented plumage. | | Year2RS | Number of offspring produced in first adult year | **9.BodyCondition.csv** This spreadsheet was used to analyze changes in female body condition across the course of the breeding season. Body condition was estimated from fat stores. | Column | Description | | ----------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | BFID | Breeding female ID number | | Site | Abbreviation for field site location | | Year | Field season. Year at start of season is used to denote entire season (even after Dec 31). Season typically ends in January. | | AuxPresence | Presence of non-breeding auxiliary in group. Categorical. "Y" if group had 1+ auxiliary "helpers". "N" if group had 0 auxiliary "helpers". | | BFAge | Breeding female age in years | | BMAge | Breeding male age in years | | BMPlumage | Breeding male plumage color. Categorical. "Red/black" is ornamented plumage. "Brown" is unornamented plumage. | | EarlyVSLate | Stage of the breeding season. Categorical. "Early" = prebreeding (before any eggs had been laid on the study site). "Late" = after Dec 1 (breeding typically concludes by early January). | | Fat | Fat stores seen in the furcular hollow during capture. Scale from 0 (no fat) to 3 (bulging) in 0.5 increments. | **10.Survival.csv** This spreadsheet was used to analyze female survival from her first breeding season to the following year. All included females are one year old. | Column | Description | | ------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------- | | BFID | Female ID number | | Site | Abbreviation for field site location | | Year | Field season. Year at start of season is used to denote entire season (even after Dec 31). Season typically ends in January. | | AuxPresence | Presence of non-breeding auxiliary in group. Categorical. "Y" if group had 1+ auxiliary "helpers". "N" if group had 0 auxiliary "helpers". | | BMAge | Breeding male age in years | | BMPlumage | Breeding male plumage color. Categorical. "Red/black" is ornamented plumage. "Brown" is unornamented plumage. | | AliveNextYear | Specifies whether bird survived to the following year. Categorical. "Y" if survived to the following year. "N" if did not survive to the following year. | **11.Lifespan&LifetimeRS.csv** This spreadsheet was used to analyze female lifespan and lifetime reproductive success. | Column | Description | | -------------------- | ------------------------------------------------------------------------------------------------------------------------------------------- | | BFID | Female ID number | | Site | Abbreviation for field site location | | BirthYear | Field season of birth. Year at start of season is used to denote entire field season (even after Dec 31). Season typically ends in January. | | PercentMatesRedBlack | Percent of all mates across lifetime that had red/black plumage | | Lifespan | Maximum age in years | | LifetimeRS | Number of offspring produced across lifetime | # Quantitative Genetic Analysis - Details The published manuscript contains important details regarding quantitative genetic analyses. * The "Quantitative genetic analyses" methods section contains a narrative explanation and justification for the analyses. * Table S1 displays results from this analysis. ## Quantitative Genetic Analysis - Code File We performed the quantitative genetic analyses in R, and used the provided script file to estimate quantitative genetic variance components for total genetic offspring using MCMCglmm. A description of the code is below: **QGenScript.Final.Sep24.R** This file contains the R script used for quantitative genetic analyses. The code contains annotations that describe the purpose of each set of commands and explain possible errors and their interpretation. We conducted quantitative genetic analyses in R using the most updated versions of the program and loaded packages available at the time (analyses completed on September 4, 2024): * R (v4.4.1; [https://www.R-project.org](https://www.R-project.org)) * MCMCglmm (v2.36; [https://doi.org/10.32614/CRAN.package.MCMCglmm](https://doi.org/10.32614/CRAN.package.MCMCglmm)) * remotes (v.2.5.0; [https://doi.org/10.32614/CRAN.package.remotes](https://doi.org/10.32614/CRAN.package.remotes)) ## Quantitative Genetic Analysis - Data Files Data files used in quantitative genetic analyses are provided in both RAT and CSV formats. Users should only use one file type when running code (do not load both). RAT files are preferentially used by Program R, and thus the code provided loads the RAT files. However, the code provides annotation that can be used to instead load CSV files if preferred by users. ID numbers in each file have been modified to indicate birth year. Sequential numbers representing years from 1996 (0) to 2011 (15) were added before the 4-digit bird ID number (e.g. if bird 1389 was born in 2003, that bird would be listed as 71389). Thus, ID number simultaneously identifies the bird and its birth year. Missing values in the spreadsheets below are represented by "NA". Detailed field descriptions for each spreadsheet are provided below: **AllTotalGenOff.csv** This is the primary data file. This same data is also provided in .Rat format. | Column | Description | | --------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | animal | Offspring ID | | Sire | Genetic father ID | | Dam | Mother ID | | SocSire | Social father ID | | MatGen | Mother ID | | PatGen | Genetic father ID | | Sex | Sex of bird. "F" is female, "M" is male. | | FirstYear | Field season when bird was first monitored. Year at start of season is used to denote entire field season (even after Dec 31). Season typically ends in January. The first year a bird is monitored is not necessarily that bird's first year alive (if the bird was not observed during its birth year). | | Site | Field site location | | TotalGeneticOffspring | Number of genetic offspring produced across lifetime | **DougPed.csv** This data file only contains a pedigree. This same data is also provided in .Rat format. | Column | Description | | ------ | ----------------- | | animal | Offspring ID | | Sire | Genetic father ID | | Dam | Mother ID |