Dataset.

Data from: Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281344
Digital.CSIC. Repositorio Institucional del CSIC
  • Friis, Guillermo
  • Fandos, Guillermo
  • Zellmer, Amanda J.
  • McCormack, John E.
  • Faircloth, Brant C.
  • Milá, Borja
genolike_map20_q20_snp16_maf002_ind32_430K.beagle Input file of genotype likelihoods in Beagle format (.beagle.gz) for PCANGSD analysis. ORJUSTRUx8_biall_dp450_q40_perpopmiss075_hwe00001_maf002_LD02_neutral01 Dataset of 16,858 independent neutral SNPs from 64 samples in vcf format for STRUCTURE analysis. ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_noZ_neutral01 Dataset of 15,209 neutral SNPs used in the PCA intended for population structure correction in the redundancy analysis (RDA). ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_noZ Dataset of 15,252 SNPs used in the redundancy analysis. ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_sel01_BAYESCENV Subset of 49 SNP outliers identified with BayScEnv for the second redundancy analysis in the manuscript. ORJUGEO_coords_ALLSAMPLES Table of sample location and geographic coordinates for all sequenced samples of the study. ORJUGEO_coords_ClimVariables Sample data and WorldClim environmental data (Fick, S.E. and R.J. Hijmans, 2017. Worldclim 2: New 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology.) for each one of the samples included in the genotype-environment association analyses., The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA) while controlling for population structure. Analysis of genome-wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (i) drift in geographic isolation, (ii) differentiation along continuous selective gradients, and (iii) isolation by adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci., Peer reviewed
 
DOI: http://hdl.handle.net/10261/281344, http://datadryad.org/stash/dataset/doi:10.5061/dryad.0nb2307
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281344

HANDLE: http://hdl.handle.net/10261/281344, http://datadryad.org/stash/dataset/doi:10.5061/dryad.0nb2307
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281344
 
Ver en: http://hdl.handle.net/10261/281344, http://datadryad.org/stash/dataset/doi:10.5061/dryad.0nb2307
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281344

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281344
Dataset. 2018

DATA FROM: GENOME-WIDE SIGNALS OF DRIFT AND LOCAL ADAPTATION DURING RAPID LINEAGE DIVERGENCE IN A SONGBIRD

Digital.CSIC. Repositorio Institucional del CSIC
  • Friis, Guillermo
  • Fandos, Guillermo
  • Zellmer, Amanda J.
  • McCormack, John E.
  • Faircloth, Brant C.
  • Milá, Borja
genolike_map20_q20_snp16_maf002_ind32_430K.beagle Input file of genotype likelihoods in Beagle format (.beagle.gz) for PCANGSD analysis. ORJUSTRUx8_biall_dp450_q40_perpopmiss075_hwe00001_maf002_LD02_neutral01 Dataset of 16,858 independent neutral SNPs from 64 samples in vcf format for STRUCTURE analysis. ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_noZ_neutral01 Dataset of 15,209 neutral SNPs used in the PCA intended for population structure correction in the redundancy analysis (RDA). ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_noZ Dataset of 15,252 SNPs used in the redundancy analysis. ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_sel01_BAYESCENV Subset of 49 SNP outliers identified with BayScEnv for the second redundancy analysis in the manuscript. ORJUGEO_coords_ALLSAMPLES Table of sample location and geographic coordinates for all sequenced samples of the study. ORJUGEO_coords_ClimVariables Sample data and WorldClim environmental data (Fick, S.E. and R.J. Hijmans, 2017. Worldclim 2: New 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology.) for each one of the samples included in the genotype-environment association analyses., The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA) while controlling for population structure. Analysis of genome-wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (i) drift in geographic isolation, (ii) differentiation along continuous selective gradients, and (iii) isolation by adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci., Peer reviewed





1106