The goals of this project were to understand how species come into being at the level of their DNA, and to explore a case where two species have come back into contact, to see which parts of their genomes remain different and which parts become shared when they hybridize. Basic knowledge of the units of biodiversity and how they are formed – and sometimes unformed – help us understand how species adapt to a changing world and how we can protect biodiversity in the future. We focused on a common North American backyard bird, the Western Scrub-Jay, which has a distinct appearance in different parts of its geographic range, suggesting the formation of new species. Before zeroing in on the places where these incipient species come into contact, we needed to understand their history of divergence and gene exchange across their wide distribution. Engaging students at the Master’s, undergraduate, and high school level (many from underrepresented groups in the sciences), we gathered samples and determined that there are three main genetic clusters that are likely to be of species level. In practical terms, this means that the common backyard bird, the Western Scrub-Jay, will soon likely be split into three species, one along the Pacific Coast, one in the Interior United States and northern Mexico, and one endemic to southern Mexico. We also determined that there is only one location where two of these groups come into contact and hybridize, in the mountain of western Nevada. We published these results in an open access journal, BMC Evolutionary Biology, which spawned several blog posts and some social media attention. The article has already been viewed over 4,000 times, although it came out only four months ago.

             After determining the broad genetic patterns, we zeroed in on the hybrid zone in western Nevada. Here, we conducted further sampling so that we had a proper transect, i.e., sample sites went from a pure population of one species to a pure population of the other species, with sites in between representing locations with different proportions of hybrids. This work involved training two female scientists in field methods. Next we wanted to identify the parts of the genomes of these two species that were associated with their differences in appearance, so we could look at how these regions vary across the hybrid zone. To do this, we prepared four individuals from pure populations of each species for a new genomic technique that involved sequencing their entire genomes. This would assure that we were not missing any regions, which could be overlooked with other methods that only look at a subset of the genome. Whole-genome sequencing for the purpose of identifying diverging DNA regions is a relatively novel technique that has not yet been applied to many cases of bird speciation.

            After sequencing and aligning whole genomes of eight individuals, we found that there were only around 10,000 base pairs in the genome where the two species had fixed differences, meaning that all of one species had one allele and all of the other species had a different allele. This was very surprising to us because this divergence was old, and other whole-genome data we collected found around 100,000 fixed differences for more recent divergences. We are still in the process of interpreting these data, but they suggest that hybridization between species in Nevada has led to fewer fixed differences due to gene exchange. What this also means is that the differences in appearance between the species are likely to be under the genetic control of some of those 10,000 differences, nearly 3,000 of which we know are in protein-coding genes. The next step is to look at individuals across the hybrid zone and associate genotypes at t...

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