A comprehensive new genetic and statistical study conducted by researchers at the University of Kansas reveals that two groups of scrub jays, one in Mexico and one in Texas, deserve to be recognized as distinct species. The study, published in Systematic Biology, also uses genomic data to sketch a natural history of scrub jays, demonstrating how geographic changes over millennia separated and reconnected groups of the birds, influencing gene flow between them.
“Scrub jays are blue jay cousins,” explained lead author Devon DeRaad, a doctoral student at KU’s Biodiversity Institute and Natural History Museum. “They are common backyard birds for people in the western United States, similar to blue jays who take peanuts from your feeder. They are exciting birds because they are charismatic; they will come to your feeder and interact with you. They are jays, so they are extremely intelligent, with some of the best spatial memory of any bird. They can recall thousands of locations where they’ve cached seeds and other items.”
According to the study, genetic sequencing of scrub jays collected decades ago at KU reveals evidence of two distinct new species in the genus Aphelocoma: A. sumichrasti, a “phenotypically, behaviorally, and genetically unique” endemic species of southern Mexico, and A. texana, a “Texas-endemic species of conservation concern.”
Scrub jays are blue jay cousins. They are common backyard birds for people in the western United States, similar to blue jays who take peanuts from your feeder. They are jays, so they are extremely intelligent, with some of the best spatial memory of any bird. They can recall thousands of locations where they’ve cached seeds and other items.
Devon DeRaad
While the Mexican scrub jay population was a “slam dunk” for species status, DeRaad said the Texas scrub jay population was less clear-cut.
“We weren’t sure how different it was,” he said. “It’s a bit of an isolated population on the Edwards Plateau in Texas — a restricted, small region of Texas. It was named as a subspecies so there are small phenotypic differences of size and the color, but it doesn’t look too different from the rest. But we have this great geographic sampling and we sequenced birds nearby, but off the Edwards Plateau, and they’re totally different and there doesn’t seem to be any gene flow. We did as many analyses as we could think of to rigorously prove ourselves wrong, but everything indicates this population in Texas is totally distinct and evolving on its own isolated trajectory.”
DeRaad became interested in scrub jay biodiversity after discovering that the variety of specimens in museum collections suggested that more species of scrub jay may exist than are currently recognized.
“My undergraduate adviser had previously published on this group of birds and told me that you can look at the specimens and see there are populations of Woodhouse’s scrub jay from Mexico and other places that look completely different – but they’re all recognized as part of a single species,” DeRaad explained. “My goal for my Ph.D. was to use genetic methods and sequence DNA from these birds to determine how many species there are.”
As a graduate student at KU, DeRaad accessed genetic samples of scrub jays collected decades ago by co-author A. Town Peterson, senior curator at the Biodiversity Institute and University Distinguished Professor in the Department of Ecology & Evolutionary Biology.
“He collected the specimens for his dissertation between 1989 and 1992, when people were just starting to take tissues from specimens,” DeRaad explained. “It used to be that you would collect the birds and stuff them with cotton to make museum specimens; however, skin and feathers are very stable and will keep in a drawer untreated if kept away from light and bugs. However, before DNA analysis, people did not know to save the tissue. So it’s really cool that Town published analyses on these birds using some of the earliest DNA methods about 30 years ago, and we’re able to use literally the same tissues for this study.”
DeRaad’s co-authors included Peterson, as well as Robert Moyle, senior curator at KU’s Biodiversity Institute, John McCormack of Occidental College, and Nancy Chen of the University of Rochester.
DeRaad collected DNA from scrub jays and then collaborated with the KU Genome Sequencing Core to sequence thousands of shared pieces of DNA from the birds’ genomes. DeRaad and his colleagues sought to shed light on the natural history of scrub jays and draw a more accurate evolutionary tree for the birds in addition to determining the species status of A. sumichrasti and A. texana.
For example, the researchers discovered two scrub jay species living on a genetic tree with snarled branches, revealing “complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (Aphelocoma californica) and Woodhouse’s Scrub-Jay (Aphelocoma woodhouseii) that result in discordant gene trees throughout the species’ genomes despite clear support for their overall isolation and species
Normally, evidence of interbreeding between the two scrub jay species would prevent scientists from considering them separate species, but not in this case.
“We’re coming to a more nuanced understanding of what a species is, allowing for the biological reality that evolution is more complicated than even people who study it could possibly imagine,” DeRaad said. “These lineages are constantly in the process of diverging and coming back together.”
Many “complex speciation” histories in North America, according to the authors, are the result of repeated ice ages in which glaciers split up populations, causing genetic divergence, then retreat, leaving continuous habitat where those populations could interbreed.
“It’s not easy to reconstruct that,” DeRaad said. “We don’t have a time machine, so we’ll never be able to accurately reconstruct it all minute by minute — but because we can get genomic data from thousands of pieces of DNA from all over the genome, we have much more statistical power to try to reconstruct those events than we did even 10 to 15 years ago, before sequencing technology was this good and affordable.”
