Data for: Tracking hybrid viability across life-stages in a natural avian contact zone
Data files
Nov 14, 2023 version files 5.26 MB
Abstract
Hybrid inviability is an important post-zygotic reproductive barrier between species, but emerging signs of reduced viability can be difficult to study across the lifespan of natural hybrids. We use a combination of long-term monitoring, extra-pair paternity and mitochondrial DNA identification in a natural hybrid zone of Ficedula flycatchers to detect emerging signs of intrinsic hybrid inviability across their entire lifespan. We evaluate possible evidence of Darwin’s corollary to Haldane’s rule, predicting asymmetries in inviability between hybrids resulting from reciprocal crosses, due to incompatible genetic factors with sex-specific inheritance patterns. We found higher hatching failure among mixed-species pairs, possibly indicating early developmental impairments associated with specific parental genetic combinations. Adult hybrids had a higher basal mortality rate than both parental species, and different age-specific mortality trajectories. There were signs of differences in age-independent mortality rates between the reciprocal hybrid crosses: hybrids with a pied flycatcher mother experienced slightly increased mortality later in life. Using an exceptional dataset with many natural hybrids tracked across life stages, we provide evidence for several emerging signs of reduced hybrid viability. Incompatibilities between alleles located on autosomes and uniparentally inherited factors such Z-linked and/or mitochondrial genes are strong candidates underlying intrinsic hybrid dysfunction in this system.
README: Data for: Tracking hybrid viability across life-stages in a natural avian contact zone
https://doi.org/10.5061/dryad.dz08kps42
This is the data accompanying the publication of "Tracking hybrid across life-stages in a natural avian contact zone" at Evolution. This record contains all datasets and code necessary to reproduce the analyses, which consists in natural records of life history traits and survival information on wild collared, pied and hybrid flycatchers in the long-term monitoring population of Öland, Sweden.
Description of the data and file structure
All mixed model analyses are described in the R Markdown file "aalund_et_al_hybrid_viability_code.Rmd", and all Bayasian based BaSTA analyses of survival in the file "aalund_et_al_hybrid_viability_survival_code.Rmd". All necessary datasets are named in the Markdown files accordingly to each analysis.
The files "adult_dispersal.csv", "natal_dispersal.csv", "nestling_mass.csv", "nestling_recruitment.csv", "nestling_survival.csv" contain individual-based data (one line per individual).
The file "hatching_dataset.csv" contains one line per nest and an individual ID for the female breeding in that nest.
The file "immigration_file.csv" contains one line per year and species with the total number of adults (all_adults), total number of immigrants (all_immigrants) and total proportion of immigrants among all adults for each year (total_immigration), as well as the detailed number of adults (all_cf/all_hycf/all_hypf/all_pf) and immigrants (cf_immigrants/ hycf_immigrants/ hypf_immigrants/ pf_immigrants) for each species (cf, pf, hypf and hycf, see below for species key) and the proportion of immigrants (column "Value") for each species (column "Type", corresponds to immigration value for each species).
The files "mass_datset_SimulatedWrongEpc.csv" and "nestling_survival_simulatedwrongepc.csv" contain the same information as in "nestling_mass" and "nestling_survival", but only for nestlings of mixed-species nests. 10% of the data has been altered in a random manner to simulate wrong assignment of species for extra-pair offspring.
The files "all_species_survival.csv", "collared.survival.csv", "hybrid_mtdna_survival.csv" and "pied_survival.csv" contain one line per individual, a record of years of birth and death when known, each year the individual was captured (1 or 0 if not present), and the species (indicated by a 1 in the corresponding column) in the "all_species" file, respectively, the maternal species in the "hybrid_mtdna" file.
Species abbreviations in the files:
CF = collared flycatcher
PF = pied flycatcher
HY = F1 hybrid between pied and collared flycatchers
HYPF: hybrid with pied flycatcher mother and collared flycatcher father
HYCF: hybrid with collared flycatcher mother and pied flycatcher father
Specific keys:
putative_species2: presumed species given the species of the parents, the first species indicates the species of the individual, the second one that of their mother.
nest_type: type of pairing (female species _ male species)
epc_rate: rate of extra-pair paternity in the nest
alive_day12: alive or not at 12 days of age
hq: habitat quality index
ld2: laying date, centered around 0 for the peak of laying for each year
nb_eggs: number of eggs in the nest
mass_d12: mass in gramms at 12 days of age
survival_rate: proportion of nestlings that survived to day 12 in the nest
mean dispersal: in meters, average distance between breeding boxes across all recorded years
natal dispersal: in meters, distance between the box where an adult individual is first recorded and the box where that individual was born.
nb_hatched: number of eggs that hatched in that nest
nb_unhatched: number of eggs that failed to hatch in that nest
Across all files, "NA" indicates missing data, when no information was available for that particular entry.
Code/Software
Code was produced using R (version 4.3.1 ), in R studio (version 2023.06.1) and RMarkdown (version ).
The following R packages were used:
tidyr (version 1.3.0)
dplyr (version 1.1.2)
ggplot2 (version 3.4.3 )
car (version 3.1.2 )
glmmTMB (version 1.1.7)
ggpubr (version 0.6.0 )
ggpattern (version 1.0.1 )
lmerTest (version 3.1-3)
sjPlot (version 2.8.15 )
Code for Bayesian survival analyses was produced using R (version 4.1.1) with the following packages:
BaSTA (version 1.9.4)
snowfall (version 1.84-6.1)