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Chinook salmon that migrate in spring, fall are more alike than scientists thought

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Oct. 30 (UPI) — Traditionally, spring-run and fall-run Chinook salmon have been classified as two separate subspecies, or ecotypes, but new genetic analysis suggests the two groups are much more similar than they are different.

According to the new study, published this week in the journal Science, the migration patterns of spring-run and fall-run Chinook salmon are dictated by differences in a small snippet of DNA in their genomes.

“Understanding the genetic basis of ecotypic differentiation in salmon provides a solid framework for predicting the outcome of different management actions,” study co-author John Carlos Garza, professor of ocean sciences at the University of California, Santa Cruz, told UPI in an email.

Scientists previously observed evidence that members of the same Chinook salmon lineages switch between fall and spring migrations. The new research showed spring-run and fall-run Chinook salmon are indeed two versions of the same fish, like a brother and sister with different colored hair.

When researchers compared the genomes of spring-run and fall-run Chinook salmon, they discovered two versions of a set of genes in a part of the genome scientists dubbed the Region of Strongest Association, or RoSA — an E version for early migration and L version for late migration.

Because these versions, or variations, feature a handful of switched-around genes — not just one — they’re called haplotypes.

And since salmon offspring inherit a chromosome from both their mother and father, they can boast one of three different RoSA haplotypes: EE, LL or EL. Since these haplotypes trigger different behaviors, or traits, they’re also referred to as genotypes.

When researchers sampled and analyzed more than 500 salmon caught by the Yurok Tribe in the Klamath River Estuary of Northern California, they found no overlap in the migrations of fish with EE and LL genotypes.

Researchers found EL fish tended to overlap mostly with spring-run fish, but some EL fish were also found migrating alongside fall-run salmon. The abundance of EL fish, they said, suggests fall-run and spring-run salmon regularly interbreed.

As part of the study, researchers analyzed genetic samples from post-spawning salmon carcasses in a handful of rivers throughout northern California, as well as Oregon’s Siletz River. The survey turned up EL genotype fish in every river where both spring- and fall-run salmon are found.

“We also performed an elegant simulation analysis that found that the proportion of combinations of gene variants inside and outside of the core region found in the genomes of Klamath salmon could not have arisen through interbreeding in the period of large-scale human manipulation of the basin,” Garza said. “So it is a natural process that has been going on for a long time.”

The survey data and genomic modeling also proved the ecotype variations present among Chinook salmon evolved at least 180 years ago. That’s good news for the project of salmon conservation in the Klamath River, the researchers said.

For decades, damming has prevented a spring run in the upper reaches of the Klamath River Klamath River.

As the construction of dams depleted cool water refuges in the Klamath, spring-run salmon, which must spend the summers in freshwater, were depleted. But the latest research suggests the migration pattern has been preserved in populations of nearby salmon.

“The finding that the E haplotype is highly conserved across Chinook salmon lineages — i.e. it is much more similar in those lineages than the rest of the genome — means that the same ancient mechanism underlies the early migration phenotype throughout our study area,” Garza said.

That means a spring run can be reestablished — once their habitat has been restored via major dam removals — by introducing or cross-breeding fish carrying the E lineage into a predominately fall-run population.



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Scientists program robot swarm to count penguins

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Oct. 28 (UPI) — Penguins occupy ecosystems increasingly vulnerable to climate change. Tracking their abundance and distribution is vital to the project of tracking global warming’s ecological effects — but counting penguins is difficult work.

To make the task of tallying the size of penguin colonies a bit easier, researchers recruited the assistance of not one robot, but a whole swarm of bots.

“The idea actually grew out of a conversation at my sister-in-law’s wedding,” Mac Schwager, an assistant professor of aeronautics and astronautics at Stanford University, told UPI in an email. “I met our co-author Annie Schmidt at the wedding, and learned that she studies penguin populations in Antarctica, and one of their key challenges was counting the penguins.”

“I told her I worked with autonomous groups of drones that could be used to take images for counting the penguins,” Schwager said. “At that point, it was clear that we had a great research synergy.”

Researchers typically use a single drone to conduct aerial surveys of penguin colonies, but the process is slow and requires a lot of time, effort and skill from the drone pilot.

In collaboration with Schmidt and her team of biologists, Schwager and Stanford grad student Kunal Shah programmed a swarm of drones to autonomously survey penguin colonies.

The team of scientists described their novel solution in a new paper published Wednesday in the journal Science Robotics.

“Our main technical innovation is our path planning algorithm, the computer program that decides where each drone should go and when,” Schwager said. “Existing methods typically plan paths like a lawnmower, or a vacuum cleaner, going back and forth over the survey area.”

“It turns out, other paths can be much more effect, in the sense that they can take the same images while requiring less back-tracking, and while making sure that the drone is close enough to the base camp to make it back safely with the remaining battery life.”

Previously, it took scientists three days to survey Antarctic penguin colonies using a solitary, hand-piloted drone. The robot swarm programmed by Schwager and his colleagues completed surveys in just two to three hours.

Time is precious in Antarctica, where animals are often on the move and weather can quickly take a turn for the worse. But speed isn’t the swarm’s only advantage. The self-piloted robots also offer reliability.

“If one drone fails, the other drones can take up the slack and still finish the survey,” Schwager said.

For now, Schwager’s swarm of drones only take pictures. The counting is done back at base after the survey has been completed and the photographs downloaded onto computers. But in the future, Schwager said the drones could use artificial intelligence to count penguins as they go.

Schwager has previously programmed robotic swarms to track the movement of people and cars on the ground in order to analyze pedestrian and vehicular traffic patterns, and he thinks similar algorithms could be adopted to track animal movements.

“The system could also be used to survey forests and other landscapes for wildfire risk, a problem that is very close to home right now for us at Stanford,” he said. “We could also use the drones to survey construction sites, mining sites, agricultural fields, to assess damage after a natural disaster, or to help find lost hikers.”

Biologists and study co-authors Schmidt and Grant Ballard are currently testing the drone aerial survey system in Antarctica. Meanwhile, Schwager and his colleagues at Stanford continue to make tweaks to the system to help the drones make better in-flight decisions and avoid collisions with birds or drones that have gone astray.

“We are passionate about using teams of autonomous drones to help us to understand and take care of the natural environment around us,” Schwager said.



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Fight judges favor aggression over skill, study shows

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Oct. 28 (UPI) — Often to the chagrin of fans and competitors, wrestling matches, boxing bouts, mixed martial arts and other types of combat competitions are frequently decided by judges.

That’s bad news for competitors that rely more on skill than vigor. New research suggests judges are more likely to award victory to aggressive fighters than skilled fighters, all else being equal.

For the study, published this week in the journal Biology Letters, researchers analyzed data collected from 550 men’s and women’s mixed martial arts contests organized by the Ultimate Fighting Championship.

The data included the percentage of strikes that landed firmly and accurately, a measure of skill, as well as the number of strikes attempted per second, a measure of vigor or aggression.

Regardless of the match conclusion, whether decided by knockout or judges’ decision, the data showed the victor was the more vigorous fighter. However, the correlation between vigor and victory was strongest for matches decided by the scores of the judges.

Fighting skillfully wasn’t entirely discounted. The data showed addition of skill enhanced the advantage of vigor, but the research showed vigor was the most important factor for fights decided by the judges.

“MMA is a fast paced sport and one of the suggestions from our research would be that judges may find vigor easier to assess than skill,” lead author Sarah Lane, postdoctoral research fellow at the University of Plymouth, said in a news release. “That, in turn, leads them to overvalue it when making their decisions, especially in longer fights where one fighter tires more quickly and the disparity in vigor is easier to spot.”

“The advance of technology such as instant replays could potentially counter this, but until they are employed more regularly rate of attack is likely to remain the most important performance trait for victory by decision,” Lane said.

The research was funded by the Biotechnology and Biological Sciences Research Council, which supports studies focused on the role of skill in animal contests.

Most of Lane’s time is spent studying hermit crab fighting, but the authors of the latest paper suggest their analysis of human fights could have implications for understanding physical competitions among animals.

There aren’t typically knockouts in fights between rival animals. Often, males joust and tussle to demonstrate their physical dominance to would be rivals and mates. Like in boxing, a competitor’s performance is subjective.

“Human combat sports provide a unique scenario in which to explore how performance traits such as skill and vigor are perceived, both by participants and observers,” said study co-author Mark Briffa.

“However, because of the obvious communication issues, very little is known about the accuracy with which fighting animals more widely judge the abilities of their rivals,” said Briffa, a professor of animal behavior at Plymouth.



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Graphene-based memory resistors could pave the way for brain-based computing

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Oct. 29 (UPI) — Researchers have created a new computer component capable of toggling between 16 possible memory states — the kind of computing versatility provided by brain synapses.

The new component, called a graphene field effect transistor, described Thursday in the journal Nature Communications, could pave the way for advances in brain-inspired computing.

Modern computers are exclusively digital, featuring two states: on-off or zero and one. Engineers at Penn State University are working to build a computer that replicates the brain’s analog nature, capable of hosting many different states.

If a digital computer’s information processing components work like a light switch, toggling only between on and off, then an analog computer is like a light dimmer.

Scientists have been investigating the potential of brain-based computing for decades, but analog computers have been overshadowed by the advances in traditional computing power. However, the rise of big data and smart devices like self-driving cars has highlighted the need for more computing efficiency.

“We have powerful computers, no doubt about that, the problem is you have to store the memory in one place and do the computing somewhere else,” lead researcher Saptarshi Das, an assistant professor of engineering science and mechanics at Penn State, said in a news release.

All the movement of information required by the bifurcation of memory to logic in modern computers puts a strain on speed. It also requires more spaces. Das and his research partners estimate that their graphene field effect transistor can help eliminate this bottleneck.

“We are creating artificial neural networks, which seek to emulate the energy and area efficiencies of the brain,” said study first author Thomas Shranghamer.

“The brain is so compact it can fit on top of your shoulders, whereas a modern supercomputer takes up a space the size of two or three tennis courts,” said Shranghamer, a doctoral student in the Das group.

Brain synapses can be quickly reconfigured to create a variety of neural network patterns. Likewise, the new graphene field effect transistor, formed by a one-atomic-thick layer of carbon atoms, can be used to control 16 possible memory states.

Researchers were able to reconfigure the transistor, effectively toggling between memory states, by applying a brief electric field to the graphene layer.

“What we have shown is that we can control a large number of memory states with precision using simple graphene field effect transistors,” Das said.

Das and his research partners are now looking to work with semiconductor companies to attempt to scale-up the production of the new technology.



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