Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and gene flow analyses revealed three distinct Y haplogroups geographically positioned within and on either side of the Great Basin Desert. Despite close geographic proximity between populations on the boundaries of each Y haplogroup, there was extremely low Y haplogroup mixing among populations, and gene flow on the autosomes was reduced across Y haplogroup boundaries. These results are consistent with a previous study suggesting that independent degradation of a recently evolved neo-Y chromosome in previously isolated populations causes male sterility or inviability among Y haplotype lineages. Phylogeographic results supported historic contraction of MPB into three separate Pleistocene glacial refugia followed by post-glacial range expansion and secondary contact. Distinct sets of SNPs were statistically associated with environmental data among the most genetically distinct sets of geographic populations. This finding suggests that the process of adaptation to local climatic conditions is influenced by population genetic structure, with evidence for largely independent evolution in the most genetically isolated Y haplogroup.

S2CollectionInformationInformation regarding collection sites etc. Old codes are used in indexing files this file contains the link between the old and the new codes in the manuscript.Index for Plates 1-7 MPBIndex's for demulitplexing plates. File name indicates plate name. Raw sequencing data is available from NCBI: bioproject PRJNA398557IndexPlateMPB.zipRaw SNP calls for all samplesRaw SNP calls for all samples. Calls made via GATK. File in vcf formatmergedGATKsnpsPineNofilter.vcf.gzScaffold Chromosome InformationFile with scaffold information for autosomal, x chromosome and y chromosome. Scaffolds relate to the names on the MPB genomeScaffoldChromosomeInformation.zip