Data from: Multi-generation genetic contributions of immigrants reveal cryptic elevated and sex-biased effective gene flow within a natural meta-population
Data files
Dec 21, 2023 version files 7.50 MB
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alltrip.data.cut.out.txt
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data.long.all.yr1.txt
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data.long.all.yr10.txt
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data.long.all.yr11.txt
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data.long.all.yr12.txt
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data.long.all.yr13.txt
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data.long.all.yr14.txt
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data.long.all.yr15.txt
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data.long.all.yr2.txt
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data.long.all.yr3.txt
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data.long.all.yr4.txt
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data.long.all.yr5.txt
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data.long.all.yr6.txt
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data.long.all.yr7.txt
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data.long.all.yr8.txt
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data.long.all.yr9.txt
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data.short.all.yr1.txt
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data.short.all.yr2.txt
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data.short.all.yr3.txt
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data.short.all.yr4.txt
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data.short.all.yr5.txt
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data.short.all.yr6.txt
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data.short.all.yr7.txt
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data.short.all.yr8.txt
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ImmContribs_GDAnalysis_Long_RCode_External_Final.txt
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ImmContribs_GDAnalysis_Short_RCode_External_Final.txt
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ImmContribs_GeneDrop_RCode_External_Final.txt
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README.md
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surv.data.cut.out.txt
Jan 15, 2024 version files 7.50 MB
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alltrip.data.cut.out.txt
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data.long.all.yr1.txt
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data.long.all.yr10.txt
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data.long.all.yr11.txt
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data.long.all.yr12.txt
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data.long.all.yr13.txt
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data.long.all.yr14.txt
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data.long.all.yr15.txt
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data.long.all.yr2.txt
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data.long.all.yr3.txt
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data.long.all.yr4.txt
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data.long.all.yr5.txt
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data.long.all.yr6.txt
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data.long.all.yr7.txt
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data.long.all.yr8.txt
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data.long.all.yr9.txt
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data.short.all.yr1.txt
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data.short.all.yr2.txt
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data.short.all.yr3.txt
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data.short.all.yr4.txt
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data.short.all.yr5.txt
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data.short.all.yr6.txt
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data.short.all.yr7.txt
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data.short.all.yr8.txt
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ImmContribs_GDAnalysis_Long_RCode_External_Final.R
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ImmContribs_GDAnalysis_Short_RCode_External_Final.R
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ImmContribs_GeneDrop_RCode_External_Final.R
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README.md
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surv.data.cut.out.txt
Abstract
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.
README: Data from: Multi-generation genetic contributions of immigrants reveal cryptic elevated and sex-biased effective gene flow within a natural meta-population
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
Methods
The data come from a long-term individual-based study of free-living song sparrows (Melospiza melodia) on Mandarte island, British Columbia, Canada.