The Fingerprints of Survival
XSEDE Supercomputers Help UCLA-Led Team Identify Genes Associated with Surviving Climate Change
|A yellow warbler caught and measured in the field (Credit: Daniel Karp)|
By Ken Chiacchia, Pittsburgh Supercomputing Center
A UCLA-led team has found they can predict whether birds are vulnerable to climate change by comparing their genes to their changing environments. Using XSEDE supercomputers, Rachael Bay and her colleagues working with the Bird Genoscape Project found they could identify genes in the yellow warbler and the willow flycatcher that associate with recent declines in local populations of each bird. The work is a first step in understanding climate sensitivity of many species that the researchers hope will offer new tools to conservation managers.
Why It's Important:
Scientists estimate that at least 200 to 2,000—and possibly as many as 10,000 to 100,000—species of plants and animals become extinct each year, according to the World Wildlife Fund. That's likely 1,000 to 10,000 times higher than the natural extinction rate. One source of species loss is the ongoing change in climate worldwide. Because birds can fly, we might think they are least vulnerable to climate change. But it's not that simple. Brains that are hard-wired to follow migration routes may not be able to shift fast enough to keep pace with environmental change. That's why Rachael Bay of UC Davis (then at UCLA) and her colleagues there and at other institutions decided to look at the genomes—the entire DNA sequences—of bird species to see if the genes in a given population of birds could make the birds more or less vulnerable to climate change. They looked at two species of birds. The yellow warbler is a songbird common in most of the U.S. and Canada during its summer breeding season. The willow flycatcher is also common through much of the U.S. But it has an endangered subspecies in the desert southwest that promised to offer additional clues as to what genes make birds more able to withstand climate variation. To assemble these birds' genomes—a massive computational task—they turned to XSEDE via UCLA's Campus Champion, Tajendra Singh.
"One thing I really struggled with is that neither species had a previous genome assembly. That requires quite a bit of memory. We finally stumbled across XSEDE resources, which proved to be great for genome assembly. Bridges was not only good for assembly, but just about everything else we were doing."—Rachael Bay, UC Davis
How XSEDE Helped:
With Singh's help, the scientists turned to two XSEDE-allocated resources, Bridges at the Pittsburgh Supercomputing Center (PSC) and Comet at the San Diego Supercomputer Center (SDSC) at UC San Diego. The researchers needed to assemble the entire DNA sequence—the genome—for each species. In this process, known as de novo genome assembly, scientists must mix and match millions of small bits of DNA from the lab so that they connect in the proper order. That's a massive computational task requiring lots of memory, so that the machine can compare fragments of DNA to see where they overlap. Bridges and Comet in particular are useful for this task because of their "large memory nodes" offering 3 terabytes and 1.5 terabytes, respectively, of RAM. Bridges has 42 such nodes, amounting to more than 4,000 times the RAM in a high-end laptop. But Bridges' 800 "regular shared memory" nodes and Comet's 1,944 nodes also proved invaluable to the team's subsequent calculations, which involved testing the relationships between the genes their assemblies identified and variations in environmental factors. Bay also cites the systems' ease of use and the availability of relevant preloaded and maintained software as helping her, as a biologist and not a computer scientist, use the systems productively.
"We need to understand how different species of bird adapted to climate change [in the past] so we can understand how much they react to climate change in the future. We're making a simple prediction of which populations are more vulnerable to climate change in the future from an evolutionary perspective ... The question is not necessarily, ‘Will these birds die?' It's, ‘Is the place where these birds live now going to be suitable for them in the future?' In some cases, we're saying yes, in some cases we're saying no."—Rachael Bay, UC Davis
|Taking measurements on birds in the field (Credit: Jasmine Rajbhandary)|
The results of the work showed a stunning parallel between certain genes and population declines in specific parts of each bird's territory. Subpopulations with the least population loss had consistent differences in their genes compared with those that were threatened. In other words, a mismatch between predicted future climate and DNA routinely accompanied population loss. While most of the genes identified have not-yet-known functions, a few offered intriguing hints at how these genes might be working. In the yellow warbler, changes in two genes, DRD4 and DEAF1, seemed to associate strongly with climate, especially precipitation. Researchers elsewhere had had previously shown both genes associate with migration. Other scientists had also linked DRD4, in particular, to novelty-seeking behavior in primates, fish and birds. While it's too early to say for sure, Bay suspects that "good" forms of the gene may encourage exploratory behavior and the ability to disperse into new, better areas. In the willow flycatcher, populations living in hot regions, like the endangered desert subpopulation, had a different version than other populations of a number of genes previously associated with tolerance to high temperature in chickens. The scientists published their results in two papers in 2018, in Ecology Letters and Science.
It's important to remember that the variations in these genes arose in the first place as birds evolved to thrive in their habitats. Bay is tracing how each species' evolutionary history alters its ability to adapt to future changes. Also, none of these genes seem to be driving survival by themselves. Bay expects that future work will find complicated interactions between the genes that affect climate vulnerability. But the work clearly shows how a bird's DNA can be mismatched with its environment, and suggests that some variations in the DNA might help birds survive. The end goal will be a similar analysis for many bird species, offering a picture of which populations will struggle the most to keep up with the climate and so will need more active management to survive.
The work reported in Ecology Letters used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant ACI-1548562. This work was made possible by a generous gift from J. Ellis as well as funding from an NSF Postdoctoral Fellowship (to R.A.B.), NSF grant PD-08-1269 (to R.J.H.), and NSF grant IIA PIRE 1243524 (to T.B.S.), and support from M. Nicholson, the California Energy Commission grant EPC-15-043, and First Solar Incorporated.
The work reported in Science used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant ACI-1548562. This work was made possible by a generous gift from J. Ellis as well as an NSF Postdoctoral Fellowship (to R. Bay), a California Energy Commission grant EPC-15-043 (to K. Ruegg and T. Smith), a National Geographic grant WW-202R-17 (to K. Ruegg), and donation from First Solar Incorporated.