Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs
Chase, Madeline; Ellegren, Hans; Mugal, Carina (2021), Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs, Dryad, Dataset, https://doi.org/10.5061/dryad.n2z34tmw6
This dataset contains SNP calls generated with GATK HaplotypeCaller followed by GenotypeGVCFs for collared, pied, red-breasted and taiga flycatchers, as well as the outgroup Ficedula hyperythra. Hard filter thresholds have been applied to the data (QD < 2.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0), and SNPs falling within annotated repeats are removed. 9 pied and 7 taiga samples with high amounts of missing data have been removed. Genotype filters for minimum depth of 5, maximum depth 200 and minimum genotype quality 30 have been applied, however sites with high amounts of missing datahave not yet been removed from this file. Only scaffolds mapping to autosomes according to the collared flycatcher reference genome are included.
Additional files contain positions of SNPs with more than 10 percent missing data for each of the species or species pairs. For species pairs, sites with greater than 10% missing data in either species were removed.
A bed file contains the coordinates of regions identified as putatively collapsed duplicates in the assembly. SNPs falling within these regions were removed from all analyses.
Knut och Alice Wallenbergs Stiftelse, Award: 2014/0044
Vetenskapsrådet, Award: 2013-8271