Population genomics of an emergent tri-species hybrid zone

Surveys of the area surrounding Prince George, British Columbia, Canada, show that all three species are sympatric, and Genotyping-by-Sequencing identifies hybrids from each species pair and birds with ancestry from all three species. Observations of phenotypes and genotypes of mated pairs provide evidence for assortative mating, though there is some heterospecific pairing. Hybridization is more extensive in this tri-species hybrid zone than in two di-species hybrid zones.

However, there is no evidence of a hybrid swarm, and admixture is constrained to contact zones, so we classify this region as a tension zone and invoke selection against hybrids as a likely mechanism maintaining species boundaries. Analysis of sapsucker age classes does not show disadvantages in hybrid survival to adulthood, so we speculate the selection upholding the tension zone may involve hybrid fecundity. Gene flow among all sapsuckers in di-species hybrid zones suggests introgression likely occurred before the formation of this tri-species hybrid zone and might result from bridge hybridization, vagrancies, or other three-species interactions.

Methods

See README for details on use of data files and scripts. Multiplexed *.fastq.gz files are described in the data processing scripts, but for re-use please see individual demultiplexed files from NCBI SRA database number SUB11950717. The pg_variants* files are called within the R PCA scripts.

Descriptions of all variables in .csv data files are included in csv_variables_descriptions.txt.

Usage notes

Canu v 1.9, Purge Haplotigs, Repeat Masker v 4.1.1, BUSCO v 5.1.2, Satsuma v 2.0, VCFtools v 0.1.16, GATK v 3.8, ADMIXTURE v 1.3.0, R, Ternary v 1.2.2, R scripts from Irwin et al. 2016 and 2018.