The genome of a previously endangered songbird exhibits significant evidence of inbreeding, as revealed by a recent study conducted by researchers at Penn State. This finding is crucial because inbreeding can adversely affect survival and reproductive rates, thereby informing ongoing conservation strategies for Kirtland’s warblers, whose populations continue to depend on active management.
The genome of a previously endangered songbird has revealed substantial evidence of inbreeding, according to a recent investigation led by Penn State researchers. Inbreeding can hinder survival and reproductive success, making these results vital for guiding conservation measures for Kirtland’s warblers, who still need extensive management to support their populations. The study, released on December 9 in the journal Evolutionary Applications, also highlights how genetic data related to inbreeding might assist in decisions regarding the removal of species from the endangered species list.
Kirtland’s warblers, also referred to as jack pine warblers, breed solely in young jack-pine forests located in Michigan. This species nearly faced extinction in the 1970s, primarily due to habitat loss, which was further aggravated by brown-headed cowbirds that lay their eggs in the nests of other birds, including warblers, thus monopolizing resources for their own chicks. Kirtland’s warblers were designated as endangered under the Endangered Species Act of 1973. However, due to targeted and sustained conservation efforts over the years, their populations have bounced back. In 2019, the species was “delisted,” meaning it is no longer seen as endangered, although ongoing management remains essential for its survival, according to the study’s authors.
“Any time a population experiences a period with few breeding individuals, known as a ‘bottleneck,’ there is a risk of inbreeding, which can diminish the survival chances of subsequent generations,” explained Anna MarÃa Calderón, a graduate student in biology at Penn State and the paper’s primary author. “The decision to remove Kirtland’s warblers from the endangered list in 2019 was based on a study that found limited evidence of inbreeding, but the earlier tests weren’t very detailed. Our team employed advanced sequencing methods to achieve a more comprehensive understanding of genetic diversity and inbreeding potential in these songbirds.”
Like all animals, birds inherit one genome copy from each parent. Certain genetic variations can be detrimental to an animal’s survival or reproductive capability. The chance of inheriting the same harmful variant from both parents increases with inbreeding, which occurs when genetically similar individuals mate.
Earlier approaches to assessing genetic diversity—such as those cited in the delisting decision—typically focused on a limited number of specific markers, known as microsatellites, which represent only a fragment of the overall picture. However, advancements in sequencing technologies now enable cost-effective analysis of entire genomes from multiple individuals.
“If we think of the genome as a cinematic portrayal of life’s blueprint, using microsatellites is analogous to trying to understand the storyline from just a few snapshots, while sequencing the whole genome is like enjoying a full 4K movie,” remarked David Toews, the Louis Martarano Career Development Professor of Biology at Penn State and co-leader of the research project. “Sequencing the entire genome reveals a wealth of additional information, and modern technology has made this kind of analysis much more accessible.”
The research team sequenced the entire genomes of Kirtland’s warblers, along with those of two closely related species, Hooded warblers and American redstarts, which have maintained large and stable populations. They focused particularly on a parameter of inbreeding known as “runs of homozygosity.”
A location on the genome is termed homozygous when the genetic material inherited from the mother corresponds with that from the father. Runs of homozygosity (ROH) are extended segments of homozygosity, sometimes spanning millions of genetic letters. The presence of particularly long ROH suggests recent inbreeding, as these segments are more likely to arise from mating between genetically similar individuals. Conversely, fewer and shorter ROH indicate that the parents of an individual are more distantly related.
“Runs of homozygosity offer us a unique perspective into the past and can serve as indicators of a population’s genomic health,” said Zachary Szpiech, an assistant professor of biology at Penn State and co-leader of the research team. “For instance, long ROH have been linked to the survival rates of other species during their first year of life. They can also highlight harmful genetic variants, which could be significant in the conservation of the bird.”
The researchers discovered exceptionally long ROH in Kirtland’s warblers, suggesting recent inbreeding that had previously gone unrecognized in this species. They also identified numerous small to medium-sized ROH among Kirtland’s warblers while their two closely related species exhibited virtually no such patterns.
“The difference between Kirtland’s warblers and their closest relatives, which have not experienced population bottlenecks, is striking,” Toews stated. “We found no signs of inbreeding in Hooded warblers or American redstarts, whereas the inbreeding levels observed in Kirtland’s warblers are alarming. Furthermore, we detected a high frequency of potentially harmful genetic variants. This underscores how a songbird’s demographic history can influence its genetic diversity.”
The sampled Kirtland’s warblers did not show any physical deformities, but the researchers noted that the effects of inbreeding could emerge at developmental stages they did not assess, such as during migration or affect reproductive performance metrics like clutch size or hatching rates. Toews emphasized the importance of continued monitoring of these songbirds to understand better the implications of inbreeding for future conservation efforts.
“A key question surrounding Kirtland’s warblers is whether their population has historically been small or if it once thrived and then plummeted,” Calderón noted. “We can utilize ROH data to investigate the past, using rates of recombination—one method through which genomes can share information—to estimate when particular genetic combinations first appeared. Our findings reveal that most of the DNA segments within the short ROH in these birds trace back to the period between 1874 and 1954, predominantly before known population bottlenecks took place. This suggests that Kirtland’s warblers may have consistently had limited population sizes, which aligns with their specific dependence on young jack-pine forests.”
By comparing these findings with historical data on the species’ distribution and population, collected since the 1940s, researchers can gain insights into the events that have shaped these birds’ genomes. For example, the origins of many DNA segments within the longer ROH fell between 1940 and 1981, corresponding with a marked population decline beginning in the early 1940s. This bottleneck would produce a larger proportion of longer ROH. The researchers also plan to analyze the genomes of museum specimens, including birds collected as early as the late 1800s, to provide further context on critical genetic events.
“While Kirtland’s warblers are celebrated as a success story in conservation, they exhibit significant inbreeding and possess numerous potentially harmful genetic variants that could impact their long-term viability,” Calderón concluded. “Our research demonstrates that assessments of genetic health can reveal different narratives from mere population numbers, both of which must be evaluated when determining a population’s recovery and guiding conservation strategies.”
Along with Calderón, Toews, and Szpiech, the research team includes Andrew Wood, who served as a research technologist in Toews’ lab during the study and is now a postdoctoral researcher at the University of Minnesota.
This research was supported by funding from the U.S. National Science Foundation Division of Environmental Biology, the Penn State Huck Institutes of the Life Sciences, and the Penn State Eberly College of Science.
