Connecting Populations

A Fragmented Habitat

The New England cottontail’s population has fallen in recent years as its preferred habitat – young forest and shrubland – has dwindled throughout the species’ range. This type of habitat has become fragmented across the region and today occurs in small patches subdivided by roads, development, and non-suitable habitats, including forests and fields.


New England cottontail locations (points) and genetic clusters (circles) in southern Maine and New Hampshire. Inset: Estimated NEC maximum range in region in 1960, 2003, and 2009. From Fenderson, et al, 2014, Multiscale Analysis of Gene Flow (see attachment at bottom of page).

When the population of any land animal declines in response to the loss and fragmentation of its habitat, smaller populations (sometimes called sub-populations) may survive in remaining habitat patches, with ever-increasing distances between those patches. The resulting loss of connectivity among subpopulations may affect the species’ ability to persist in the future.

In most wildlife species, members of a given population (most often males) “disperse,” or move out of the population in which they were born and travel until they find a new population to join, where they can mate and reproduce. New England cottontails are believed to disperse as far as 1 to 3 miles from the place of their birth. If they find good protective cover to use while dispersing, they may avoid predators – foxes, coyotes, bobcats, hawks, owls – and successfully join and add their genetic material to a neighboring population of New England cottontails.

As populations lose connectivity, fewer individual animals can successfully disperse between habitat patches, and genetic material cannot be freely exchanged. As a result, individuals may lose genetic material important for their survival, and both they and the population as a whole may become less able to adapt to changes in the environment, such as the appearance of a certain kind of predator or a new disease.


Connectivity corridors between two isolated New England cottontail populations in southern Maine and New Hampshire. Red-orange shading highlights powerline corridor west of and parallel to I-95, offering potential for genetic exchange. From Amaral, et al, 2016, Anthropogenic Habitat Facilitates Dispersal (see attachment at bottom of page).

Animals in separate, isolated habitat patches may also begin to inbreed, since there are too few unrelated individuals to choose from as potential mates: parents may breed with young, siblings or half-siblings with one another. Inbreeding renders members of the population less fit by enhancing the effects of harmful genes. For example, inbreeding can lead to reproductive abnormalities, lower the survival ability of young, and increase vulnerability to infectious disease.

Today, the lack of connectivity among populations is affecting the New England cottontail in many parts of its six-state range.

Conservationists and scientists are working together to create habitat that will maintain and improve connectivity among New England cottontail populations. They’re also studying how cottontails disperse and move across the landscape. And they are researching the rabbits’ genetics – both that of small populations, and of the species as a whole – to learn whether and how much the New England cottontail’s genetic make-up has changed over time.

Conservation Genetics

Dr. Adrienne Kovach is a conservation geneticist with the University of New Hampshire’s Department of Natural Resources and the Environment. Kovach, her graduate students, other conservation geneticists, and state and federal biologists are studying how landscape features, both human-created and natural, affect the way New England cottontails disperse from one population to another, and how those populations either remain in touch or lose connection. (See Attachments, below, for a recent report on her research results.)

Says Kovach, “We need to increase and refine our knowledge of New England cottontail dispersal patterns so that conservationists can develop habitat management and restoration strategies that will increase the connectivity of remaining populations – something that will, in turn, improve the species’ genetic health and ensure its persistence into the future.”

Her research has focused on four tasks:

Determine how to best conduct fecal pellet sampling to learn where New England cottontails live. In the laboratory, Kovach and her students and colleagues identify DNA from fecal pellets (droppings) collected by field biologists to determine whether the pellets were deposited by New England cottontails, eastern cottontails (a non-native species that now exists in greater numbers regionwide than the native New England cottontail), or snowshoe hares. From these pellet sampling surveys, conservationists learn where New England cottontails persist within their historic range, and how they are distributed across the landscape.

Monitor populations of New England cottontails on selected sites and develop techniques to measure the genetic response of those populations to management actions creating more or better young forest and shrubland habitat. This research explores how biologists can best set up transects (pathways to be walked through occupied habitat) to maximize the information gained from pellets deposited by New England cottontails. This research reveals that field crews typically need to do two surveys of a given site to get the most accurate results concerning population abundance. As conservationists take steps to create or improve habitat, further sampling can reveal whether cottontail numbers increase and local populations expand.

Use genetic data collected through in-patch monitoring to chart genetic diversity, relatedness, and inbreeding. Sophisticated DNA testing can help scientists calculate “allelic richness” in individual animals and small populations. Analyzing DNA from fecal pellets and body tissues lets conservation geneticists learn whether and how closely New England cottontails may be related in a given population or across a broader area.

Use genotype data to characterize fine-scale population genetic structure, movement patterns, and dispersal of New England cottontails. Working with Kovach, former graduate student Lindsey Fenderson identified three to five genetically distinct New England cottontail populations in southern Maine and the Seacoast region of New Hampshire, between which gene flow no longer is taking place, although it did in the past. (See Fenderson, et al, attachment below.) Genetic variation in each population is low, as are effective population sizes: fewer than 50 individuals, which is thought to be the minimum number of rabbits needed for a population to sustain itself over a short term. In contrast, some New England cottontail populations in western Connecticut and eastern New York – where ample interconnected habitat still exists – show greater genetic variation and may support substantially greater numbers of rabbits.

Cottontail Movements

As field biologists monitor radio-collared rabbits (both New England cottontails and eastern cottontails living within the New England cottontail’s range), they learn more about movement patterns for each species. Amanda Cheeseman is a Ph.D. candidate in the State University of New York College of Environmental Science and Forestry. In a study in New York’s Hudson River valley, Cheeseman found that the vast majority of movements by New England cottontails were less than 500 meters; to date, the farthest a radio-collared rabbit has ventured is nearly 4 kilometers (2.5 miles), with nine other collared rabbits moving less than 1.5 kilometers (about 1 mile). In Connecticut, a team of biologists led by Dr. Howard Kilpatrick, with the Connecticut Department of Energy and Environmental Protection, observed both New England and eastern cottontails moving as far as 1 mile through older forest to occupy new young forest habitat created by timber cutting.

In the lab, Kovach and her colleagues, including former graduate student Katrina Amaral, are using genetic information to evaluate the kinds of landscape features that influence movement and gene flow among New England cottontail populations. (See Attachments below to learn more.)

They identified heavily trafficked roads, areas developed by humans, and mature forest as significant barriers to dispersal and connectivity. Forested wetlands and rivers also represented barriers to cottontail movement.

powerline habitat

Powerlines offer cottontails corridors to use in moving across the landscape, with shrubs shielding rabbits from predators./C. Fergus

Grassy and weedy fields, used as travel corridors by many other kinds of wildlife, seem to be too open to offer good dispersal corridors for New England cottontails, which need shrubs that offer enough overhead protective cover for them to successfully disperse.

Two natural landscape features allow cottontails to move across the land: shrubby patches and shrubby wetlands. Human-created features that help cottontails disperse and populations remain connected include powerlines with shrubs, shrub-grown roadsides, and railroad rights-of-way that support shrubs.

“Roads have a dual influence on cottontail gene flow,” Kovach says. “Rabbits will move parallel to a roadway if there’s enough good habitat along its edge. But it’s hard for them to safely get across a road and avoid being hit by a vehicle, so roads can also represent a formidable barrier to dispersal and connectivity between neighboring populations.”

Powerline Corridors Important Habitat Features

Kovach characterizes powerline corridors as “important features linking geographically isolated habitat patches and populations.” These manmade features offer conservationists an excellent opportunity to create, refresh, and maintain shrubby habitat that will allow rabbits to move across the landscape.

In different parts of the New England cottontail’s range, conservationists are working to ensure gene flow in the species by making habitat in key places. Preserving and creating corridors of young forest and shrubland will help keep populations connected, allowing dispersal and exchange of individuals and genetic material among different populations. In the future, conservationists may need to translocate, or move, animals from one population to another to maintain the health and continued existence of isolated populations.

Read more about Dr. Adrienne Kovach's conservation genetics research.