Scientists are keeping a cautious eye out for the seasonal return of piping plovers — those tiny shorebirds whose fragility keeps stretches of beach off limits to humans on Long Island and much of the Atlantic coast this time of year.

This latest cause for concern for the federally protected species is a natural disaster that took place last fall in the Bahamas, more than 1,100 miles away.

Long Island serves as an important breeding ground for the species. Of the fewer than 4,000 to be found along the Atlantic Coast, nearly 800 come to New York, mostly Nassau and Suffolk counties, each summer to mate.

An estimated quarter of the Atlantic Coast population winters in the Bahamas, with a bulk along the northern part of Andros island and nearby unpopulated islands known as Joulter Cays. Berry Islands, about 35 miles northeast, also host a significant population.

Enter Hurricane Matthew, which struck Andros over two days in October as a Category 3 and 4 storm, pushing winds from 96 mph to 156 mph over the region. The storm and surge destroyed homes, knocked out power and eroded beaches.

It also hit during prime piping plover wintering season.

advertisement | advertise on newsday

“The storm surge caused about 15-foot waves,” said Matt Jeffery, deputy director of the International Alliances Program for National Audubon Society. “It pushed them under water and they had no place to hide.”

Some birds were forced up into the winds. “It’s unclear that they made it,” Jeffery said.

Before the storm about 324 piping plovers had been documented on Andros and the Joulter Cays. Afterward, the number fell to 120 birds.

“Each time we’ve gone back there’s been less and less and we’ve been back three times this winter,” Jeffery said. “The teams — they looked everywhere they could look.”

Some birds may have left to migrate north, but “it’s not looking good,” he said.

To understand why that matters here, consider that the birds are like dual citizens.

“You have to think about the entire life cycle,” said Caleb S. Spiegel, a wildlife biologist with U.S. Fish and Wildlife Service in Massachusetts, who has taken part in international census efforts.

Surveys over the past 11 years have found that while many of the birds spend their winters from North Carolina to Texas, as much as half the population flies internationally, to places like the Bahamas, Cuba and Turks and Caicos.

Protections in the United States do not extend to other places but managing and protecting the species means knowing all its risks.

“We sometimes joke they’re Bahamian birds because they spend most of their lives there,” said Anne Hecht, an endangered-species biologist with U.S. Fish and Wildlife Service in Massachusetts. “It’s a shared resource. We have an obligation on both sides of the resource to make sure they are conserved.”

advertisement | advertise on newsday

Hecht said it’s too soon to know how the population was affected. “We have reasons to be concerned but we’re a long way from making any conclusions about the effects of the storm,” she said. “We’re watching carefully.”

Locally many managers say it’s too soon to know.

Things will become more clear when the state Department of Environmental Conservation does its annual plover census from June 1 to June 9 to count the population.

“They’re still just getting here and setting up,” DEC’s regional wildlife manager Michelle Gibbons said.

In general, before this year, plover numbers had been increasing. Last year, the state recorded 381 pairs in Nassau, Suffolk, Queens and Brooklyn, with the bulk here on Long Island. In 2013, the number was 289 pairs.

advertisement | advertise on newsday

These small birds typically weigh less than 3 ounces and they like to roost in overwash areas and wide open sand flats — perfect places for humans to off-road, sunbathe and hang out.

Development, recreation, beach nourishment, predators, invasive species and natural events can harm them. In their first year, only about half of all fledged birds survive.

“It is a species that has a lot of threats,” Hecht said.

The Bahamian government, in part because of the plovers, have designated two key roosting spots as sanctuaries or important bird areas.

The nests — called scrapes until there are eggs — are small indentations in the sand with a collection of rocks and shells, said Annie McIntyre, environmental manager for the Long Island region of New York State Parks.

“They can be hard to find,” she said. “The mantra for plover monitoring is wait, watch and listen.”

Jones Beach State Park is home to the largest concentration of breeding plover pairs in New York. Each year, the park is home to about 35 to 40 breeding pairs.

So far this year, 20 pairs have been spotted.

“I’m not concerned yet,” McIntyre said, adding that another 10 pairs could be spotted in the coming days, based on past experience. “It means they’re still setting up.”

Other groups say the same.

“It’s hard to tell,” said Amanda Pachomski, the Long Island bird conservation manager for Audubon New York, which monitors six private sites on the North and South shores. “It is still early.”

Scientists are quick to point out that the storm may have also done some good by cutting down dunes and removing trees, making more space for the plovers to nest.

On Fire Island, since superstorm Sandy hit in 2012, a breach in the barrier island has become a popular plover nesting spot.

“It seems like maybe we have a few more nests than last year,” Fire Island National Seashore wildlife biologist Lindsay Ries said. “Our site seems to be recruiting new pairs, which is a really good thing. We’ll have to see how it plays out.”

Experts say Hurricane Matthew is a good example of why the species needs to be protected and managed so it can handle mortality events.

“Breeding is the engine for your next generation of the species,” Hecht said. “It won’t take very long if we stop protecting them for this species to plummet.”