Leilton Luna, postdoctoral researcher at Penn State and corresponding author of the paper, explained that when an organism’s population size drops too low because of disease or habitat loss, inbreeding can occur, which can lead to a decline in genetic diversity over time.
“Populations with low genetic diversity have a harder time evolving in response to changing environmental conditions and are at greater risk of extinction,” Luna said. “In the case of the Pennsylvania ruffed grouse, due to the sharp population decline, it certainly doesn't have the same healthy genetic conditions as it did in the past. Even so, the current levels of genetic diversity and connectivity give us great hope for the preservation of this species.”
As an initial step, the team produced the first high-quality reference genome for ruffed grouse. A reference genome, Luna said, is a representative example of a particular organism’s genes.
“This reference genome serves as a standardized genetic baseline, facilitating accurate comparisons of genome-wide diversity between individuals and populations,” Luna said. “Additionally, this genomic resource will enable us to investigate important questions, such as whether specific genetic components, like adapted genes, contribute to varying population responses to West Nile virus in different ruffed grouse populations.”
To investigate the population health of the ruffed grouse in Pennsylvania, the research team sequenced 54 individual bird genomes within habitats that were both fragmented by development and intact. The researchers examined the sequence data for evidence of gene flow, which indicates that genetic material is readily exchanged among migrating populations.
“We compared each individual to every other individual that we sampled,” Luna said. “By doing this, we were able to tell if the birds all belong to a single geographic population or to different populations, as well as how environmental factors such as habitat fragmentation and terrain elevation shape the effective dispersal of birds and, therefore, the exchange of genes.”
He said the team’s DNA analysis provided weak evidence of population subdivision across the state, although the researchers identified reduced genetic connectivity in the south, where the bird’s habitat is fragmented by human development.
“This tells us that the population may not be doing as bad as we expected,” Luna said. “It also helped us to inform wildlife managers which areas would most benefit from the development of habitat corridors. However, it is just a snapshot of the population at this particular moment. In the future, we hope to analyze the DNA of museum specimens so we can compare the genetic diversity and connectivity of today’s populations with those from before West Nile virus was present and before the habitat was so fragmented.”
Surprisingly, the team said, it also stumbled onto the presence of two genetic “anomalies,” called chromosomal inversions. These occur when a segment of DNA breaks off and then reattaches in reverse order.
“We found chromosomal inversions within some of the individuals we sampled, and these were found in individuals from across the Commonwealth,” said co-author David Toews, assistant professor of biology at Penn State.
“The data are very clear,” he said. “There are these two large chunks of the ruffed grouse genome that are highly differentiated from the rest of the genome, and they are not associated with any obvious geographic pattern among the birds. It adds a fun ruffle to the story.”