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UI Biology Researchers Develop Tool for Identifying New Species

October 26, 2016

On the surface, the Idaho giant salamander and the coastal giant salamander look almost identical. But their genes prove they’re actually distinct species — a phenomenon biologists call “cryptic species.”

Using information about giant salamanders and other Pacific Northwest animals and plants, University of Idaho biology researchers have created a computational tool to help scientists find potential cryptic species in disjunct biomes. The tool is designed to reduce the amount of time, effort and money needed to identify new species, and in turn to conserve those species and understand the ecosystems in which they live.

“All these species that once were described as one, we find they’re significantly different genetically,” said Anahí Espíndola, a postdoctoral researcher in the UI College of Science Department of Biological Sciences. “Instead of going to the forest that has hundreds of species and checking them all, it would be useful to have some kind of predictive way to make a short list of species that could have cryptic diversity and focus on those.”

The research was funded by a National Science Foundation grant and conducted with technology provided by UI’s Institute for Bioinformatics and Evolutionary Studies (IBEST). Espíndola led the project, which also involved professor and IBEST director Jack Sullivan, associate professor David Tank and graduate student Megan Ruffley, all of the Department of Biological Sciences, as well as a graduate student and a professor from Ohio State University.

The research team began by compiling data about salamanders, tailed frogs, voles, willow trees and more from coastal and inland Pacific Northwest forests.

Over thousands and millions of years, changing climatic patterns, glaciers and geological features have divided the coastal and inland forests, but these forests are part of the same biome, an ecological community with shared characteristics. Some coastal and inland organisms that appear similar are indeed a single species; others are cryptic species.

The researchers examined Pacific Northwest cryptic and non-cryptic species to find ecological differences between the two groups, such as what rainfall patterns or temperature ranges occur in the areas the species are present. Species can evolve to fit the conditions in which they live, so cryptic species that split from each other millions of years ago and now live in different areas would likely have different ecological preferences, while populations of non-cryptic species would likely have similar preferences.

Along with ecological preferences, the researchers also used taxonomic information, with the goal of also incorporating biological characteristics of the studied species, such as reproductive mode and physiology.

Using this information, Espíndola and collaborators created a predictive tool with which scientists can input data of already investigated cryptic and non-cryptic species from the same biome, and get predictions about which unstudied species might also be cryptic in that same area. They successfully tested the model on several Pacific Northwest species, as well as species in the Baja California and Sonoran deserts, which are split by the Gulf of California.

The research and tool were published today in the journal Proceedings of the Royal Society B.

The tool will allow scientists to gather information that is useful to natural resource managers and other decision makers, Espíndola said. The research team continues to refine it, adding additional variables so it can increase its prediction accuracy.

“You can really use it as a predictive tool for understanding and identifying diversity. You want to be able to protect that diversity. For example, the Idaho salamander — if no one had ever investigated those inland populations, we’d never know it was a different species,” Espíndola said. “If you want to appropriately protect the forest in the Northern Rocky Mountains, you need to first understand what’s in there to protect it.”

The tool is also useful for scientists who study evolution and ecology. “It really informs our understanding of how species diverge and what processes lead to that,” Espíndola said.

Media Contact: 
Tara Roberts
University of Idaho Communications

About the University of Idaho

The University of Idaho, home of the Vandals, is Idaho’s land-grant, national research university. From its residential campus in Moscow, U of I serves the state of Idaho through educational centers in Boise, Coeur d’Alene and Idaho Falls, nine research and Extension centers, plus Extension offices in 42 counties. Home to nearly 12,000 students statewide, U of I is a leader in student-centered learning and excels at interdisciplinary research, service to businesses and communities, and in advancing diversity, citizenship and global outreach. U of I competes in the Big Sky Conference. Learn more at