DOI: 10.5061/dryad.k6djh9wcv
title: Data from: Multi-generation genetic contributions of immigrants reveal cryptic elevated and sex-biased effective gene flow within a natural meta-population

description: Impacts of immigration on micro-evolution and population dynamics
 fundamentally depend on net rates and forms of resulting gene flow into
 recipient populations. Yet, the degrees to which observed rates and sex
 ratios of physical immigration translate into multi-generational genetic
 legacies have not been explicitly quantified in natural meta-populations,
 precluding inference on how movements translate into effective gene flow
 and eco-evolutionary outcomes. Our analyses of three decades of complete
 song sparrow (Melospiza melodia) pedigree data show that
 multi-generational genetic contributions from regular natural immigrants
 substantially exceeded those from contemporary natives, consistent with
 heterosis-enhanced introgression. Further, while contributions from female
 immigrants exceeded those from female natives by up to three-fold, male
 immigrants’ lineages typically went locally extinct soon after arriving.
 Both the overall magnitude, and the degree of female bias, of effective
 gene flow therefore greatly exceeded those which would be inferred from
 observed physical arrivals, reshaping the eco-evolutionary implications of
 immigration.
description: The data come from a long-term individual-based study of
 free-living song sparrows (<em>Melospiza melodia</em>) on
 Mandarte island, British Columbia, Canada.
description: # Data from: Multi-generation genetic contributions of immigrants reveal
 cryptic elevated and sex-biased effective gene flow within a natural
 meta-population 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