Bats living in an Arizona cave carry a genetic legacy thousands of years old

Spotted bats in an Arizona cave share maternal DNA with bats that died there 2,100 years ago, while the Southwest holds most of their variety.

An animal this hard to find sounds like one close to disappearing. Spotted bats roost alone in cliffs across western North America, and a naturalist writing in 1899 called them among the rarest mammals in the world. Yet in one cave in northern Arizona, the bats living there today carry the same maternal DNA as bats that died in that cave as long as 2,100 years ago.

The cave lies in the part of the range where the species keeps most of its genetic variety. Bats in the American Southwest carry more of it than bats at the northern edge of the range, and those northern bats may be more exposed to future change.

Faith M. Walker of Northern Arizona University led the work, with colleagues at the Smithsonian's Center for Conservation Genomics and Wildlife Conservation Society Canada. Her team read DNA from 121 spotted bats, from British Columbia to central Mexico. Many of the modern bats came from that one Arizona cave, a rare spot where the animals gather.

Why are spotted bats so rarely seen?

Each spotted bat usually spends the day alone in a crack in a cliff, within about 6 miles (10 kilometers) of water that flows year-round. Like most bats, it hunts in the dark by calling out and listening for echoes.

In an interview with Earth.com, Walker said, "Spotted bats are one of the West's hidden treasures. They have enormous pink ears, bold white spots, and echolocation calls that are within the range of human hearing, yet they are rarely encountered."

Before 1965, scientists knew of only 35 of them, and museums today hold just 95 specimens. Nobody has a solid count, and published guesses range from 2,500 to 100,000 bats.

In the U.S., the spotted bat is a species of concern, with designations that vary by state. Canada, thought to hold fewer than 1,000 adults, lists it as a species of special concern.

More than half of North America's bat species are predicted to face moderate to very high extinction risk by 2039. Climate change, wind energy, habitat loss, and a fungal disease called white-nose syndrome are among the threats.

Ancient bat DNA matches living populations

Walker's team gathered bats from three eras. Six had died in the Arizona cave and were radiocarbon dated to between 120 and 2,100 years old. Others came from museum collections going back to 1904, and 69 were caught alive between 2009 and 2013, sampled with a tiny wing clip or a cheek swab, and released.

The researchers read two kinds of DNA. One is a short stretch passed only from mother to offspring, which tracks family lines over long spans of time. The other comes from both parents and better reflects recent movement between populations.

Five of the six ancient bats carried the most common maternal type in the region. That same type turned up in 14 of the 38 living bats sampled at the cave. The sixth ancient bat differed by a single letter of genetic code, and its exact type matched two living bats from the same cave.

"As scientists, we're often looking for evidence of change, but in this case the surprise was continuity," Walker told Earth.com. "The ancient bats looked genetically very familiar."

Southwestern bats hold more genetic variety

Bats from the center of the range, around Arizona, New Mexico, and Utah, carried the most genetic variety on both kinds of DNA. Among 101 of them, the team found 26 distinct maternal types. Among 11 bats from Washington, Oregon, and British Columbia, it found two.

Central bats also carried 28 DNA variants that showed up nowhere else, while the northern bats had none of their own. A large, varied population holds more options for adapting to change, and a small, uniform one holds fewer.

The researchers tied the pattern to a northward spread as the climate warmed after the last Ice Age. On that reading, the newest arrivals at the northern edge carried only part of the variety with them.

Two groups stood apart. California bats formed a maternal line of their own, possibly cut off by the Sierra Nevada. The two bats from central Mexico differed sharply from every other group, and only one spotted bat has been detected in that region in more than 40 years.

Male bats dominate an Arizona cave

The cave held a surprise of its own. Of the 39 spotted bats caught there, 31 were male and eight were female. Researchers caught nine bat species at the cave, and six of them, including spotted bats, were predominantly male.

DNA from both parents turned up two father-and-son pairs, plus three more pairs of close relatives. The researchers found that notable because male bats are thought to do most of the traveling between populations.

Walker's team read the male-heavy count as a sign of swarming. At swarming sites, bats from many roosts gather to circle and chase one another, partly to find mates. The cave averages about 46°F (8°C), which may be too cool for mothers raising young.

Genetic differences shape bat conservation

The authors urged protection at both ends of the range. Losing local groups in the varied center could keep that variety from spreading north. The northern bats, with less variety and a small population, should be managed as a distinct group, the team suggested.

Northern bats also behave differently. Earlier tracking found bats in Arizona flying about 48 miles (77 kilometers) round trip to feed. In British Columbia, bats roosted 4 to 6 miles (6 to 10 kilometers) from where they fed.

"The genetically diverse core populations of the Southwest and the smaller populations at the edges of the range are both important, and conserving both helps maintain the species' ability to adapt and persist into the future," Walker said.

For people who share the bats' range, she said the most important step is to give their cliff habitats space and to support protection of nearby water and foraging areas.

More bat DNA is needed to fill gaps

The maternal DNA the team read is a short stretch, kept short so that old and ancient samples could be used. It traces only mothers' lines, so it can't show what fathers passed on. Sampling was also uneven, so the researchers used fewer bats from the Arizona cave in some analyses to avoid skewing the results.

At first, the team estimated more bats moving north from the central population than the reverse. When the team evened out the sample sizes, that difference disappeared.

A few founding bats, past population crashes, and plain distance could each have left the north with less variety. With the current data, the team can't tell those apart.

Walker said the next step is whole-genome sequencing, which reads a bat's entire set of DNA rather than small pieces of it. "We also need more samples from parts of the West that remain genetic blind spots, so we can see how those populations fit into the species' broader evolutionary story."

Until bats are sampled in those gaps, from northern California and Idaho to northern Mexico, it remains unclear how they connect the varied core to the less varied north.

The full study was published in the journal PLOS One.

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