• Wed. Jun 7th, 2023

Grad student makes use of information science to discover biological diversity


May 26, 2023

Utilizing information science applied to plant and animal records at all-natural history museums, UO graduate student Jordan Rodriguez is locating new methods to study the evolution of essential proteins.

As an undergraduate, Rodriguez embarked on a study project seeking at the biases and limitations of biodiversity records from all-natural history collections and databases like iNaturalist. That function led to a current publication in Nature Ecology and Evolution.

Now she’s a graduate student in biology professor Andrew Kern’s lab at the UO, employing machine finding out approaches to trace the evolution of protein diversity.

“I realized the statistical energy of functioning with significant information, but my initially study expertise truly set the stage for understanding the hidden pitfalls of information,” Rodriguez mentioned.

Possessing millions of information points can be really valuable, she mentioned, but only if you fully grasp the data’s limitations.

Rodriguez’s path to computational study began in the Ruth O’Brien Herbarium at Texas A&ampM University-Corpus Christi, exactly where she helped digitize a collection of plant specimens. Alongside biologist Barnabus Daru, now a professor at Stanford University, Rodriguez started exploring the coverage gaps in unique kinds of all-natural history information.

“We have access to an abundance of information out there on what species are living exactly where,” Rodriguez mentioned, from legacy museum collections to field observations captured in on the web databases. “But a thing we’d began to observe was that in places usually identified as biodiversity hotspots, like the Amazon rainforest, there seemed to be a mismatch in between what the information was telling us and what biology was telling us.”

Most all-natural history records fall into a single of two categories. Vouchered records are physical specimens, like these observed in museum and herbarium collections. Observational records are records of a sighting without the need of a physical specimen to back it up.

Thanks to the rise of smartphone apps like iNaturalist and eBird, there’s been an explosion of observational records in current years. With these tools, everyone — scientist or not — can snap a image of a plant, insect or bird and document the sighting in a public database.

Rodriguez and Daru looked at additional than a billion records and analyzed how the vouchered and observational datasets varied across unique groups like plants, birds and butterflies.

The unique collection approaches “lead to these intriguing variations in how separate information sets represent international biodiversity,” Rodriguez mentioned.

Each vouchered and observational information had gaps in coverage, Rodriguez and Daru report in their paper. Each sorts of information sets had been additional probably to report species in straightforward-to-access places: close to roadsides, close to airports, at reduced elevations.

And they had been each biased towards specific kinds of species. Persons are additional probably to capture a image of a plant with a showy flower than the grass ideal subsequent to it, Rodriguez mentioned.

But the coverage gaps had been higher for observational records, possibly mainly because vouchered records are usually collected additional deliberately by researchers on field collection trips. Vouchered records also had richer representation across time, with additional balance across years and seasons. Citizen scientists are additional probably to be snapping images of serendipitous wildlife observations on a warm sunny day than in the winter, Rodriguez noted.

In spite of these drawbacks, observational records nonetheless have a location, she mentioned. They’re specifically valuable for animals and endangered plant species, exactly where it is advantageous to record a sighting without the need of killing something. And mainly because they are less difficult to gather, scientists can access a substantially higher quantity of information points. Observational and vouchered records “are functioning in concert,” Rodriguez mentioned.

Rodriguez hopes that her function will encourage scientists to believe about the limitations of the information set they’re employing and account for doable bias in their outcomes. Her lately published study points to certain methods these biases show up in all-natural history information sets of numerous plant and animal groups. But the lessons carry into other information-focused fields.

Now at the UO, Rodriguez is shifting away from all-natural history study and rather focusing on population genetics, also employing a significant information method.

The undergraduate study project “gave me expertise with approaches and tools improvement in bioinformatics, functioning with billions of information points and attempting to fully grasp the statistics,” she mentioned. As a graduate student, “I knew I wanted to remain in a computationally focused lab.”

She’s lately joined Kern’s lab, a computational biology study group that is element of the UO Information Science Initiative and the College of Arts and Sciences. There, she’s begun an exploratory project applying artificial intelligence to biological information, to disentangle the evolution of the complete set of proteins in humans, chimps, mice and rhesus monkeys.

Utilizing machine finding out tools related to the technologies behind ChatGPT, she hopes to fully grasp additional about the price at which proteins are evolving in these animals.

“So substantially prospective lies at the intersection of machine finding out and evolutionary concerns,” Rodriguez mentioned.

Scientists have a wealth of genetic sequence information, and deep finding out models could be capable to uncover new insights from it. Whilst such approaches take specific talent in handling and understanding information, she noted, “this is the future of evolutionary study.”

By Laurel Hamers, University Communications
—Top photo:
Jordan Rodriguez

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