There’s something weird going on inside the plants and animals that call the Baja California peninsula home.

On the surface, everything looks as expected, but close genetic inspection of many individuals reveals a genomically distinct split between the northern and southern populations of dozens of species.

A cross-disciplinary team of researchers from the University of Arizona, the University of Oregon, Arizona State University and California State University, Sacramento received a five-year, $2.6 million grant from the National Science Foundation to study how geologic activity, rainfall patterns and climate cycles might have shaped the evolution and biodiversity of the peninsula over time.

The team, which also includes Mexican collaborators, will develop novel methods for combining and analyzing the datasets from across fields including geology, ecology and genomics.  

“Biologists say, ‘Something had to cause the pattern of divergence,’” said Benjamin Wilder, director of the Desert Laboratory on Tumamoc Hill and co-principal investigator on the project. “The leading hypothesis has been that there was a seaway through a low gap in the peninsula that connected the Pacific to the Gulf of California about 3 million years ago.”

This explanation worked its way into scientific papers and was nearly accepted until the geologists said, “‘Well, wait, there’s not evidence for that yet,’” Wilder said. This is a huge problem for the field, so Wilder and his co-authors are excited to tackle it.

“This has been our dream project,” he said.

The study will investigate three main hypotheses regarding the physical barrier of the seaway, climate and the changing landscape and rainfall patterns.

The Seaway

The researchers will first test the original hypothesis that populations could have been isolated by a physical barrier – the seaway. There are two locations near the central peninsula that might have harbored the low pass that divided the species of the north and the south.

“Our team is just torturing the heck out of the candidate sites geologically to fully reconstruct the histories of these areas,” Wilder said.

Finding Refuge

Alternatively, global climate fluctuations over the last million years could have created dynamic changes in the landscape, according to Wilder, leading to hypothesis two: Organisms retreated up and down mountaintops along the peninsula as the climate swung between cool glacial periods and warm interglacial periods.

“The desert expands and contracts as climate changes; the mountains and their diversity of habitats offer pockets on the landscape where they may be able to persist during these transitions,” Wilder said. “So the break you see could have been caused by the species retreating up into the mountains and then descending down and reconnecting with the rest of their species, but having been separated for hundreds of generations.”

Mismatched Rainfall

The nothern half of the peninsula is rainy in the winter and dry in the summer. In the south, the opposite is true. The third hypothesis assumes that opposing rainfall patterns created differences in genetic expression within species. 

This rainfall asynchrony might have isolated species through misaligned timing in reproduction or other mismatched adaptations that led to the genetic patterns observed today.

Decoding the Data

The team will scour the landscape for geological clues, test the full genomes of six different species that run the length of the peninsula, and create models to test the distribution of these plants and animals against their predictions.

The species chosen – including two plants (the pitaya agria cactus and brittlebush), two lizards (the black-tailed brush lizard and the Baja California spiny lizard) and two small mammals (the packrat and the Merriam’s kangaroo rat) – run the full length of the peninsula and are representative of the Sonoran Desert.

“Ten years ago, we couldn’t have done a project like this. We can sequence almost anything now, and it’s relatively cheap,” said Greer Dolby, an assistant research professor at Arizona State University and co-principal investigator on the study. “And now there’s a big focus on data and how you integrate it.”

The research is part of a new and growing field called geogenomics,  a term coined in 2014 to describe the use of large-scale genomic data to answer geological questions.

The team expects that after combining all the data, they’ll find that multiple causations are not just probable, but likely. Their consensus at the outset is that each these processes probably has a part to play, but they aren’t sure yet to what degree.

“One of the coolest things about this project is that it’s all about the biologists learning how the geologists see it, and we’re trying to embed the geologists in the biology,” Wilder said. “That approach has the great potential to unlock a history of evolution that has been elusive up to now.”

He also thinks there are direct conservation implications.

“This research can help prioritize where the most unique genetic diversity is geographically, which can then help policy makers prioritize for land conservation as well as help predict future responses as the climate changes.”