https://doi.org/10.5061/dryad.k6djh9wcv

The dataset comprises R scripts and data required to reproduce the analyses presented in the manuscript:
"Multi-generation genetic contributions of immigrants reveal cryptic elevated and sex-biased effective gene flow within a natural meta-population"

Authors: Jane M. Reid, Lisa Dickel, Lukas F. Keller, Pirmin Nietlisbach and Peter Arcese
August 2023

Study population: Song sparrows (Melospiza melodia) on X̱OX̱ DEȽ (English name Mandarte island),
British Columbia, Canada, (latitude 48.6329°, longitude -123.2859°, 0.06 km²)

Files are summarised below
R scripts are annotated to explain steps and definitions of all variables
Code was written and used with R v4.2.1

Description of the data and file structure

There are two sets of files that allow the results and figures presented in the manuscript to be directly reproduced

First, the short-term (8 year) analyses of gene-drop data for immigrant and native genetic contributions for both sexes
Here, there are eight text files with the gene-drop data for each of the eight years from immigrants' arrivals, and one text file with the R script for analysis
This code generates figures 1, 2, 3, 4, 6 and S1

Data files: data.short.all.yr1.txt .... data.short.all.yr8.txt (8 files in total)
R script file: ImmContribs_GDAnalysis_Short_RCode_External_Final.R

Second, the longer-term (15 year) analyses of gene-drop data for immigrant and native genetic contributions for females only
There are fifteen text files with the gene-drop data for each of the fifteen years from immigrants' arrivals, and one text file with the R script for analysis
This code generates figure 5

Data files: data.long.all.yr1.txt .... data.long.all.yr15.txt (15 files in total)
R script file: ImmContribs_GDAnalysis_Long_RCode_External_Final.R

All variables are defined within the provided R code files, but additionally summarised below
To understand the datasets and scripts, it will be simpler to start with the longer-term (15 year) analyses
Here the models are simpler, and run faster, because they are restricted to females only

Each row of each data file considers one focal immigrant or native

ninecode = a unique identifier for each individual

allele = the identity of each individual's unique gene-dropped allele

X1 - X1000 = total counts of the individual's allele from 1000 independent gene-drops for the focal year

status: 1 = native, 2 = immigrant

sex: 1 = female, 2 = male

sex.rev = reversed sex variable: 1 = male, 2 = female. Used for easy direct estimation of male effects

cohort = the natal year of each focal individual (assumed to be the year before arrival for immigrants)

yr = number of years from arrival or recruitment (1 = year of arrival, 8 = 7 years subsequently)

natalyr = the natal year of the chicks counted in the gene drop evaluation for the focal individual (the the focal individual's natal year plus the number of years from arrival (cohort + yr))

tot.chicks.banded = total chicks ringed in the population in the focal year

exp.contrib = estimate of each individual's expected genetic contribution (the mean of each individual's N=1000 gene drop outcomes)

prop.contrib = each indivdual's proportional genetic contribution (computed as exp.contrib/tot.chicks.banded)

prop.contrib.use = prop.contrib*100

ext.prob = the probability that an individual's allele will be extinct in the focal year

In addition, we provide R scripts and data to undertake cohort specific gene-drops on the song sparrow pedigree
Running these codes is not necessary to directly replicate the results and figures presented in the manuscript (see above)
However, it shows how the gene-drop data were generated
Since the gene-drop is stochastic, running this code will not generate exactly the same results as above, but sampling variance is small given Nsim=1000 iterations
This additional code comprises one text file with the R script, and two text files with the underlying data

R script file: ImmContribs_GeneDrop_RCode_External_Final.R
Required data files: alltrip.data.cut.out.txt (pedigree data)
surv.data.cut.out.txt (survival data)

All variables are defined within the provided R code files, but additionally summarised below

ninecode = unique individual identity

gendam = identity of the individual's mother

gensire = identity of the individual's father

natalyr = natalyr2 =individual's natal year

syear = current year

age = individual's age (years)

sex = individual's sex: 1=female, 2=male

is = individual's immigrant status: 0=hatched on Mandarte, 1=immigrant

If you are interested in using the song sparrow pedigree data for purposes other than to replicate the current analyses then please contact:
Peter Arcese, Jane Reid or Lukas Keller
This allows us to manage multiple ongoing uses of the dataset
We are happy to facilitate collaborations

Code/Software

See above for summary of the R script files linked to each set of data files