Sitting beside a small stream in the southwestern Adirondacks, Spencer Bruce clipped a tiny brook-trout fin and placed it in a small container. The fin is one of more than a thousand he has collected in recent years from waters in New York State for a genetic study.

Studying the genetic makeup of fish may provide clues to how resilient a population is to climate change and other environmental problems. In the Adirondack Park, several cold-water species of fish are thought to be at risk from climate change. Besides brook trout, they include lake trout and round whitefish. Other aquatic species, including amphibians and loons, also could be at risk.

A researcher at the New York State Museum, Bruce believes heritage-strain brook trout that have evolved in the Adirondacks for thousands of years are better suited for dealing with a changing climate than certain strains of stocked trout that lack genetic diversity. Heritage trout are believed to have large gene pools that contain traits that helped them survive past environmental challenges, such as droughts and serious fluctuations in temperature.

“Genetic diversity translates to adaptability,” Bruce explained. “That means that populations have a better chance of withstanding invasions from parasites, disease, competing with non-natives, or changing with the environment, such as climate change or warming waters.”

Bruce is looking at two measures of genetic diversity: allelic richness and heterozygosity. Allelic richness refers to the overall number of genes in a population. A specimen is heterozygous when it has two or more versions of a gene.

“For example, if you have brown eyes and also carry the gene for blue eyes, you are heterozygous,” Bruce said. “If you have brown eyes and just carry the gene for brown eyes, then you are homozygous. So a population that is heterozygous basically has more variations. That’s one measure of diversity.”

Bruce said heritage-trout populations generally are characterized by heterozygosity and allelic richness.

The state Department of Environmental Conservation has identified eleven strains of heritage trout (including several used in stocking), but Bruce and other scientists believe that there are other heritage strains in small, remote streams.

Research to better understand and protect brook trout is important because their numbers have diminished dramatically in the last few centuries. In addition, brook-trout fishing is a key economic driver for the Adirondacks every spring. Once perhaps the most plentiful fish in the Adirondacks, the wild brook trout has declined because of loss of habitat, overfishing, acid rain, competition with non-native fish, and warming waters. Statewide, only 5 percent of watersheds that historically contained wild brook trout still do, according to the Eastern Brook Trout Venture, a coalition of government agencies, conservation organizations, and scientists that works to protect the fish.

Some scientists and environmental advocates fear that climate change could wipe out many of the remaining wild populations. In June, the Environmental Protection Agency released a report predicting that brook-trout fishing could disappear by 2100. The report stated that warming temperatures would eliminate cold-water habitats that brook trout prefer in the Adirondacks.

Dan Josephson, an aquatic biologist based in Old Forge, does not dispute that warming temperatures would seriously impact brook trout, but he doesn’t expect them to disappear by 2100. He said the EPA report did not take into account other factors, such as the availability of cold-water refuges in deep lakes and spring holes in streams. Yet, he warns that brook trout could disappear from waters that lack refuges.

“If it’s ten degrees warmer fifty years from now or whatever they’re predicting, there will be no brook trout in those shallow lakes,” Josephson said. “They won’t survive it.”

Josephson, who is a researcher for Cornell University, said brook trout stand a better chance of surviving climate change in stratified lakes – generally, deep lakes with cold water on the bottom. A study in the early 1990s that analyzed data from the Adirondack Lakes Survey Corporation found that 170 brook-trout lakes and ponds were stratified, 173 were weakly stratified, and 234 weren’t stratified. The lakes that are weakly stratified or not stratified (70 percent of the total) are considered very vulnerable to climate change. However, trout might hang on in stratified lakes.

In a study in Global Change Biology in 2012, Josephson and four other scientists concluded that warming temperatures in a shallow lake diminished brook-trout reproduction. The study was done between 1998 and 2010 at a private lake near Old Forge. The researchers found that trout spawned later than usual in the fall following a summer of elevated temperatures. They also found that trout created fewer spawning beds for their eggs, perhaps because they lacked the energy to do so. Brook trout create spawning beds with their tails in gravelly areas. On this lake, the beds were on groundwater springs along shorelines.

The study warned that the delay in spawning in the fall could cause a timing mismatch in the spring between young fish and their main source of food, zooplankton. The scientists hypothesized that eggs could hatch later in the year, whereas many plankton would emerge earlier in the year because of warming temperatures in the spring.

Moreover, the study said warmer temperatures caused trout to expend more energy and slowed development of reproductive organs. In 2005, when temperatures were unusually high, the researchers observed no spawning beds, suggesting that no trout were born the following year. Brook trout can rebound from a poor reproductive year, the study said, but several bad years in a row would jeopardize their population.

The lake in question is one of four private lakes near Old Forge that Cornell researchers have been monitoring for more than a decade. In a new study, postdoctoral researcher Mariah Meeks is looking at how fish in the four lakes respond to warming waters. She puts trout into water tanks with different temperatures – some at ambient temperatures, others warmer – and then tests their organs to see how they respond.

“Our hope is that by looking at this, then we’ll be able to find some markers, some genetic markers, [and] that we can then go out and do a broader survey of other populations,” she said. “We’re hoping to be able to develop a tool that will allow us to kind of assess which populations are going to be able to maybe have this [genetic] makeup to be able to withstand warmer temperatures better than other populations.”

Although some brook trout might be able to withstand warming waters, Meeks cautioned that brookies aren’t likely to become warm-water fish. “I’m not saying that there’s somehow super populations that can somehow exist in warm bathwater,” she said. “We’re just saying … there may be populations that do better than others. It’s a relative thing in response to thermal stress.”

Waters that warm likely will be more hospitable to other species of fish, such as bass, northern pike, and yellow perch. These fish often out-compete brook trout for food and spawning habitat. However, it’s not clear how climate change will affect these other species. For instance, a study released this summer found that yellow perch are having less success reproducing in Lake Erie because of warming water.

A report released last winter by the Adirondack Nature Conservancy warned warming temperatures pose a threat to the Park’s lake trout, a fish that requires cold (below fifty-five degrees), well-oxygenated water. With a few exceptions, New York’s native lake trout are restricted to lakes deeper than thirty feet and located north of the forty-third parallel (roughly, the Adirondack Park’s southern boundary).

Typically, lake trout dwell in the lower depths of stratified lakes. In summer, the oxygen at these depths is limited but sufficient for the fish to survive. The oxygen gets replenished in late fall after the surface water cools, becomes denser, and sinks just before the ice starts to form. The water remains mixed until the following spring, when it settles into layers again shortly after ice-out, again replenishing oxygen in the lower depths. As the months pass, the amount of oxygen dwindles. If climate change continues to lengthen summers and shorten winters, as expected, the deeper regions of lakes likely will have less oxygen in the late summer and fall than they do now.

Josephson said the loss of lake trout could have a big impact on an aquatic ecosystem. In many waters, lake trout are an apex predator, feeding on smaller fish such as suckers, minnows, and smelt. In the absence of lake trout, the populations of the prey fish could grow, and this might diminish the number of brook trout, which compete for the same food as the prey fish. The loss of lake trout may not be felt as keenly in lakes where other large predators dwell, such as invasive pike and bass.

Brook and lake trout are just two of many aquatic species threatened by climate change. Another iconic species – the common loon – is expected to all but disappear from the Adirondack Park by the end of the century, according to a National Audubon Society report released last fall.

The loon breeds during summer in Canada and the northern United States and winters along both the east and west coasts. As temperatures rise, the loon is expected to abandon the southern portion of its range and breed farther north. Audubon’s climate model predicts that by 2080, the loon will no longer be found in 56 percent of its summer range and 75 percent of its winter range in North America.

Loons prefer large, clear lakes and ponds in order to spot fish. They often nest on islands or floating bogs, which are at risk of disappearing with warming temperatures.

“The biggest lesson learned with the habitat report is that we’re going to have to work harder at protecting the habitat that’s important to the birds,” said Erin Crotty, a former state environmental commissioner who now heads the New York chapter of Audubon.

Insects and amphibians, such as salamanders and frogs, are at risk because the winter snowpack is expected to be smaller and droughts are expected to be more frequent. That means there will be fewer vernal pools for them to breed in during spring.

The Adirondack Park is dotted with bogs and fens, but these wetlands could become overrun by forests in the future, according to a 2012 National Wildlife Federation report, “Assessing the Vulnerability of Key Habitats in New York.”

The wetlands are dominated by such flora as mosses, sedges, and dwarf shrubs, including leatherleaf, sheep laurel, bog laurel, and Labrador tea. Black spruce and tamarack trees also are common. A fen differs from a bog in that it is fed by groundwater and is less acidic.

The report warns that droughts and higher temperatures could dry out the wetlands, opening the way for more trees. “It is possible that all boreal bog habitats [including fens] could be eliminated from the state by future climate change,” it states. “At the least, they indicate a great reduction in the current extent of the habitat type, with it surviving as isolated, smaller patches at higher elevations at the most northernmost part of New York.”

Bogs and fens are habitat for a variety of wildlife, including spruce grouse, moose, and numerous species of boreal birds such as the olive-sided flycatcher and bay-breasted warbler.

“The lowland boreal remains central to our sense of what the Adirondacks are. It is what the Adirondacks have that the lowlands around us don’t have,” wrote Jerry Jenkins in Climate Change in the Adirondacks. “And, as with the high mountains, it is one of the reasons that we perceive the Adirondacks as deeply and essentially northern.”

Because of climate change, the Adirondacks may lose that part of its identity.

SIDEBAR: Even Pristine Lakes Are At Risk

Even the intact aquatic ecosystems may be no match for climate change. Wolf Lake is considered a “heritage lake” by scientists because of its pristine condition, yet it has been impacted more by warming than have four other nearby lakes.

The State University College of Environmental Science and Forestry (ESF) has long-term lake-ice records for five lakes (Wolf, Deer, Arbutus, Catlin, and Rich) on its Huntington Wildlife Forest in Newcomb. Scientists reviewed the dates of ice formation on the lakes from 1975 to 2007 for a 2012 report in the journal Climate Change. The data showed that median ice-in dates for all five lakes shifted from November 28 to December 9, while the median ice-out dates shifted from April 28 to April 23.

The ice season decreased on all five lakes, but the largest change occurred on Wolf Lake, which had twenty-one fewer days of ice cover by the end of the study.

Wolf Lake contains no exotic species and has not been negatively impacted by acid rain. Analysis of its sediments indicates Wolf Lake is in much the same condition it was before the Adirondacks were settled.

The study states that changes in lake ice lead to a variety of ecological impacts. “In the lake ecosystem itself, loss of ice cover may cause shifts in water chemistry, thermal strata, biotic communities, and a variety of related ecosystem processes,” according to the study.

The shorter ice season may lead to an earlier onset of thermal stratification, which in turn results in less oxygen later in the season for deep-dwelling fish such as brook trout and lake trout. It also means more sunlight reaches the water, lengthening the growing season of aquatic plants and raising water temperature. Combined with higher ambient air temperatures, these changes could eventually make lakes less suitable for cold-water species such as brook trout and lake trout and more suitable for warm-water species such as bass.

“There’s no evidence of human impact on the lake. It’s a little tiny pocket of untouched ecology,” said ecologist Colin Beier, an ESF professor. “But of the lakes we looked at, it shows the most change, both in the timing of the ice forming and melting, and in its shrinking duration. Conservation efforts are probably helping to protect it, but conservation is not a panacea.”

“Climate change is a game-changer in conservation,” he said. “There are places where you’ve done everything you can to protect these ecosystems and you think they’re safe. They’re not.”

SIDEBAR: Getting Back In The Flow

Over the last few centuries, roads and human development in the Adirondacks have fragmented aquatic habitats, severing natural corridors for fish and wildlife.

Culverts on rivers and streams are a prime example. They can become barriers for fish when water levels drop below the height of the pipes in summer—the very time of year when brook trout swim upstream to find cooler water in shaded tributaries.

The Adirondack Nature Conservancy and Ausable River Association have partnered with town and state agencies to replace a number of problematic culverts in the Ausable River watershed. The new structures don’t include pipes. Instead they leave the area under a bridge wide open to allow water to flow in its natural streambed. So far, culverts have been replaced on two tributaries on River Road in Lake Placid and on one tributary on Lenny Preston Road in Wilmington.

Brook trout prefer temperatures between roughly fifty and sixty-five degrees. During the 2014 summer, conservancy scientists found the temperature in the Ausable River to be sixty-nine degrees, whereas the temperature in nearby tributaries was fifty-eight degrees.

“The Ausable has seen a lot of warming here in the main stem, warming that has exceeded what a threshold for a brook trout is,” said Michelle Brown, a biologist with the conservancy. “So in a place like this where a main stem is reaching those levels of temperature it’s really critical that a species can move upstream and find cold-water refuge.”

The warming in the main stem of the West Branch of the Ausable River has occurred for a number of reasons. Because of development, its shorelines are not shaded as much as in the past. Plus, summers stretch out longer than they once did. With increasing temperatures predicted for this century, river temperatures are expected to rise even more, making fish passage more essential.

The culverts are designed to be more resilient to flooding, which is expected to be more frequent with climate change. In the past, the pipe culverts would clog up with debris and cause water to flood over roads, sometimes washing away pavement.

Photos, from above: Scientist Spencer Bruce, right, collects brook trout for his statewide genetic study (photo by Mike Lynch); a brook trout (Mike Lynch); a brook trout has its fin clipped for a genetic study (Mike Lynch); an Adirondack loon (Jeff Nadler); a new culvert on Roaring Brook in Lake Placid (Erika Edgley / Adirondack Nature Consevancy photo); and an illustration by Jerry Russell.

This story originally appeared in the Adirondack Explorer, a nonprofit newsmagazine devoted to the protection and enjoyment of the Adirondack Park. Get a full print or digital subscription here.