10.5061/DRYAD.Q573N5TH7
Cuevas, Angelica
0000-0003-0862-4582
University of Oslo
Ravinet, Mark
University of Nottingham
Sætre, Glenn-Peter
University of Oslo
Eroukhmanoff, Fabrice
University of Oslo
Intraspecific genomic variation and local adaptation in a young hybrid species
Dryad
dataset
2020
FOS: Biological sciences
Passer sparrows
hybrid species
WGS
genomic incompatibilities
hybrid constraints
Genome evolution
The Research Council of Norway*
297137
The Swedish Research Council and the European Union Marie Sklodowska
Curie Action *
2011-302504
The Research Council of Norway
297137
2020-11-30T00:00:00Z
2020-11-30T00:00:00Z
en
https://doi.org/10.1101/732313
77773138 bytes
4
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Hybridization increases genetic variation, hence hybrid species may have
greater evolutionary potential once their admixed genomes have stabilized
and incompatibilities have been purged. Yet, little is known about how
such hybrid lineages evolve at the genomic level following their
formation, in particular their adaptive potential. Here we investigate how
the Italian sparrow (Passer italiae), a homoploid hybrid species, has
evolved and locally adapted to its variable environment. Using restriction
site-associated DNA sequencing (RAD-seq) on several populations across the
Italian peninsula, we evaluate how genomic constraints and novel genetic
variation have influenced population divergence and adaptation. We show
that population divergence within this hybrid species has evolved in
response to climatic variation, suggesting ongoing local adaptation. As
found previously in other non-hybrid species, climatic differences appear
to increase population differentiation. We also report strong population
divergence in a gene known to affect beak morphology. Most of the strongly
divergent loci among Italian sparrow populations do not seem to be
differentiated between its parent species, the house and Spanish sparrows.
Unlike in the hybrid, population divergence within each of the parental
taxa has occurred mostly at loci with high allele frequency difference
between the parental species, suggesting that novel combinations of
parental alleles in the hybrid have not necessarily enhanced its
evolutionary potential. Rather, our study suggests that constraints linked
to incompatibilities may have restricted the evolution of this admixed
genome, both during and after hybrid species formation.
Genomic DNA was purified from blood samples. Double digestion of the
genomic DNA for ddRAD sequencing was performed using EcoR I and MseI
restriction enzymes. Molecular identifier tags were added with PCR
amplification. Library pools were size selected for fragments between
500-600bp. The size selected library pools were then sequenced using an
Illumina Nextseq500 machine and the 1x75bp sequencing format. A series of
genomic tools were used to filter raw reads and call variants, vcftools,
plink, bcftools, GATK, among others. Here we provide the VCF files and
final data files generated from statistical analysis. As well as the
scripts used to analyse the data. Scripts for processing the raw reads to
obtain final VCF are included as well as the scripts used for the
statistical analysis and final figures found in the study. All files used
in the R scripts are also provided.
The README.txt file explain the different categories of files and those
used by the scripts.