Chromosomal inversions from an initial ecotypic divergence drive a gradual repeated radiation of Galápagos beetles
Data files
May 02, 2024 version files 16.13 GB
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elevated_Fst.bed
523 B
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inversions.bed
397 B
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RADseq_1SNP_NEUTRAL.vcf
4.25 MB
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RADseq_1SNP.vcf
5.22 MB
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RADseq_all.vcf
77.44 MB
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README.md
2.21 KB
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WGS_all.vcf
16.04 GB
Abstract
Island faunas exhibit some of the most iconic examples where similar forms repeatedly evolve within different islands. Yet, whether these deterministic evolutionary trajectories within islands are driven by an initial, singular divergence and the subsequent exchange of individuals and adaptive genetic variation between islands remains unclear. Here, we address this issue using a gradual, repeated evolution of low-dispersive highland ecotypes from a dispersive lowland ecotype of Calosoma beetles along the island progression of the Galápagos. We show that repeated highland adaptation involved selection on multiple shared alleles within extensive chromosomal inversions that originated from an initial adaptation event on the oldest island. These highland inversions first spread through dispersal of highland individuals. Subsequent admixture with the widely distributed lowland ecotype resulted in polymorphic dispersive populations from which the highland populations evolved on the youngest islands. Our findings emphasize the significance of an ancient divergence in driving repeated evolution and highlight how a mixed contribution of inter-island colonization and within-island evolution can shape parallel species communities on islands.
README: Chromosomal inversions from an initial ecotypic divergence drive a gradual repeated radiation of Galápagos beetles.
https://doi.org/10.5061/dryad.jsxksn0j4
Description of the data and file structure
The zip file contain vcf files to conduct the analyses shown in the manuscript 'Chromosomal inversions from an initial ecotypic divergence drive a gradual repeated radiation of Galápagos beetles.' It contains SNP data based on i) RAD sequencing (n=121) or ii) whole-genome resequencing (n=33). A reference genome is available on NCBI (see below). Sample information can be found in table S4 in Supplementary Information of the manuscript. For detailed information on how the vcf files were created (aligning, variant calling, filtering, ...) we refer to the Material and Methods section in the manuscript.
RADseq (SbfI restriction enzyme)
- RADseq_all.vcf: a vcf file containing all SNPs across all RADtags (n=17,651 SNPs)
- RADseq_1SNP.vcf: a vcf file containing a single randomly selected SNP per RADtag (n=1,135 SNPs)
- RADseq_1SNP_NEUTRAL.vcf: a vcf file containing a single randomly selected SNP per RADtag, but RADtags located in genomic regions of elevated between-ecotype divergence (FST > 0.1) (see Structural variant analysis in manuscript) and RADtags containing an outlier SNP in at least two within-island ecotype comparisons (see* Outlier loci detection* in manuscript) were discarded (n=900 SNPs)
WGS
- WGS_all.vcf: a vcf file containing SNPs of 33 resequenced specimens (n=15,569,155 SNPs)
- Elevated_Fst.bed: bed file with scaffold name (1st column), start position (2nd column) and end position (3rd column) of regions with elevated Fst values (>0.1) (see *Structural variant analysis *in manuscript for more details)
- Inversions.bed: bed file with scaffold name (1st column), start position (2nd column) and end position (3rd column) of regions that were identified as chromosomal inversions (see *Structural variant analysis *in manuscript for more details)
Sharing/Access information
Raw DNA sequences have been deposited in the NCBI SRA (PRJNA706924). The assembled genome is available at NCBI (JAGJTL000000000).