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Genes and climate: Hidden adaptations of an endangered flycatcher

A new study has made significant strides in the field of evolutionary biology, unveiling proof of climate adaptation at the genomic level within an endangered species – the Southwestern Willow Flycatcher. The groundbreaking research, led by postdoctoral researcher Sheela Turbek of Colorado State University, is an exceptional demonstration of a wild species adapting to its environmental conditions. 

Species across the globe are responding to changing climates through either geographical shifts or genetic changes. While experts can observe and document cases where species change locations, genetic adaptations are not as easy to trace.

How the study was conducted 

To investigate, Turbek and her team focused on the Willow Flycatcher, an endangered migratory bird native to the Southwestern United States. The research spanned over a century, comparing the genomes of modern specimens to their historical counterparts, some dating back to the late 1800s.

“We used over 200 contemporary samples from the Willow Flycatcher to scan the genetic material for specific regions of the genome associated with important environmental variables,” said Turbek. “This includes things like monthly precipitation and monthly maximum temperature. Once we identified the regions of the DNA we think are involved in climate adaptation, we extracted the genetic information from those regions in both our historical and our modern San Diego samples.”

What the researchers learned 

The findings, published in the journal Nature Climate Change, show a discernible increase in the genetic variation in the Willow Flycatcher population in San Diego, California, over the past century. Turbek theorized that the climatic changes in the region, primarily increasing humidity and precipitation, led to these genomic adaptations in the local Willow Flycatcher population.

Turbek’s study builds upon the foundational research conducted by Kristen Ruegg and her team at CSU, who had been exploring similar genetic adaptations for roughly a decade. However, it wasn’t until recent technological advancements in genome sequencing in the 2010s that a project of this magnitude became feasible.

Ruegg’s preliminary research suggested that the Willow Flycatcher, comprising four different subspecies, had locally adapted to varying climate conditions across geographical regions. 

Turbek emphasized the importance of this, stating: “The Willow Flycatcher is made up of four different subspecies, and the subspecies in the southwest has faced really precipitous population declines and was listed as federally endangered in 1995.” She pointed out the urgency in understanding these adaptive mechanisms, particularly in the face of potential climate-induced extinction.

However, historical samples often contain degraded or contaminated DNA, making it difficult to establish genetic adaptation with a high degree of certainty. This challenge was compounded by the minuscule quantity of DNA available from museum samples, often tiny clippings from a toe pad.

“Museums will send us a little clipping from a toe pad that often has really low DNA concentrations so it’s hard to acquire enough reads of the DNA to have a good idea of what the genetic code looks like,” said Turbek.

Genetic adaptations confirmed 

Nevertheless, after several years of meticulous genomic sequencing and comparative analysis between historical and contemporary DNA samples, the team finally succeeded. They unveiled compelling evidence that the Southwestern Willow Flycatcher had indeed increased its genetic variation over time.

“We think that it was actually mixing or gene flow into the population from neighboring populations that helped recover the gene pool of the Willow Flycatchers in the San Diego area,” said Ruegg.

“Human-induced climate change is really having a drastic effect on the reproductive activities of many species, and it is going to drive a lot of organisms to the brink of extinction,” said Turbek. “So, the fact that we can document this amount of adaptation over a century-long time scale is somewhat encouraging in that these birds seem to be responding to the amount of climate change that has already occurred. It can help us better predict what’s going to happen in the future, and how species might respond.”

More about the Willow Flycatcher

The Southwestern Willow Flycatcher is classified as an endangered species primarily due to habitat loss and fragmentation. This small bird, which relies heavily on riparian ecosystems (near rivers or streams) for breeding, has seen much of its habitat destroyed or altered due to various human activities.

Some of the key factors leading to habitat loss include:

Urban development and agriculture 

The growth of cities, roads, and farmland often encroaches on the riparian ecosystems that the flycatchers inhabit.

Water management

Dams, water diversions for irrigation, and other alterations of river systems can lead to the loss of the vegetation that flycatchers need for nesting.

Invasive species

Non-native plants, such as tamarisk (saltcedar), can change the structure of the vegetation in riparian areas, making them unsuitable for flycatcher nesting.

Climate change

Changes in weather patterns can further degrade the flycatcher’s habitat and lead to reduced food availability.

Predation and brood parasitism

Nest predators, such as snakes and larger birds, as well as brood parasites like the Brown-headed Cowbird (which lays its eggs in the nests of other birds, leading to the other birds raising the cowbird’s offspring), can also threaten Willow Flycatcher populations.

These challenges have led to significant population declines, leading to the Southwestern Willow Flycatcher to be listed as an endangered species in 1995.


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