Whole genome sequence of the behaviorally polymorphic white-throated sparrow. 1: Mapping genes for sociogenomics

Chromosomal inversions are thought to lead to adaptation and speciation as they reduce recombination thereby protecting favorable genetic linkages. If this is the case, it is predicted that beneficial combinations of genes associated with fitness be located within chromosomal inversions. Here, we use whole genome sequencing and mapping with bacterial artificial chromosomes (BAC) to understand how gene arrangement leads to the morphological, behavioral, and physiological differences exhibited by two morphs of the white-throated sparrow (Zonotrichia albicollis). In this species, both sexes occur as white or tan morphs that have adopted alternative life-history strategies. Morph is determined by the presence or absence of a large rearrangement, which limits recombination of the second autosome. We have amassed 25 years of detailed data on this species making it possible to identify the genetic, epigenetic, and environmental bases of behavior. To begin these analyses we generated a high-quality 1Gb reference genome with N50 contig length of 104kb and scaffold length of 4.9Mb. We then used high-resolution BAC mapping to anchor the genome, and in doing so we were able to identify the breakpoint in this chromosome as well as several other smaller rearrangements of gene order. Despite considerable synteny in avian genomes, evolutionary analyses indicate minimums of 11 rearrangements between white and tan morphs, 35 rearrangements between chicken and sparrow, and 26 rearrangements between zebra finch and sparrow. Morphs of the white-throated sparrow provide a unique opportunity to study intraspecific genomic differences, which have resulted from two separate, yet linked evolutionary trajectories - such results can transform our understanding of the evolution of genomes as well as highlight the importance of inversions as drivers of evolution.