Vegetation Sampling: an example lab

The following is adapted from a vegetation sampling lab I did in college.


In order to properly study an area, one has to know certain characteristics of that area. Studying the vegetation of an area has its many benefits. These include allowing us to understand the difference between communities, describe habitat, and understand how vegetation reacts to certain environmental gradients. In this lab, we focused on using the point-centered quarter method to characterize a forested slope.

From the data collected we can calculate average density per hectare, relative density, density, basal area, relative basal area, frequency, relative frequency, importance value, and relative importance value. These values allow us to compare characteristics among different species. This was the main objective of this lab.


This study took place on Pine Hill Alfred, NY on September 9th, 2013. Following the gas pipeline trail behinds Ann’s House on the bearing N10Wo we walked 5 meters off the gas pipeline trail. At that point we placed the center of a quadrant composed of 90o quarters. Quarters 1 and 2 faced North, 1 being on the East side. Quarters 3 and 4 faced South, with 3 being on the East side. We determined the four closest trees to the quadrant, with a diameter at breast height over 10 cm. For each tree we calculated the distance from the quadrant, diameter at breast height, and the tree’s species. The same process was repeated for a quadrate located 25 meters from the path.

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The 16 freshwater fish families

There are 16 major families of freshwater fish in the United States. Knowing which family a fish is from will help you to identify it easier. It is important to already know the parts of a fish before reading this post, you can find this information here.

  • Lepisosteidae: gar family
    • these fish have a long cylindrical body
    • they have long jaws and snouts with sharp teeth
    • notable species: spotted gar (Lepisosteus oculatus), longnose gar (Lepisosteus osseus), and alligator gar (Lepisosteus spatula)
Kaimanfische (Lepisosteus)
Florida gar (Lepisosteus platyrhincus)
  • Clupeidae: herring family
    • thin silvery fish
    • have no lateral line
    • have a saw like pectoral fin
    • notable species: gizzard shad (Dorosoma cepedianum) and the threadfin shad (Dorosoma pentenense)
American Shad (Alosa sapidissima)
  • Cyprinidae: carp and minnow family
    • mouthparts are not sucker-like
    • the largest family of freshwater fish
    • notable species: central stoneroller (Campostoma anomalum), red shiner (Cyprinella lutrensis), blacktail shiner (Cyprinella venusta), common carp (Cyprinus carpio), golden shiner (Notemigonus crysoleucas), bullhead minnow (Pimephales vigilax)

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Wildlife of Okefenokee National Wildlife Refuge

Okefenokee National Wildlife Refuge is located in South Georgia, near the border with Florida. Recently my friend and I visited to paddle around the swamp and drive around swamp island  and walk the Chesser Island boardwalk to try and see some wildlife. The refuge is 630 square miles and encompasses nearly all of the swamp and was designated as a refuge in 1937 by President Roosevelt. It is one of the best preserved freshwater ecosystems in the world and some of the swamp is a national wilderness area. In the western part of the refuge there are is a cypress swamp but in the east it opens up to a prairie land. If you rent a kayak from Okefenokee adventures its is a short trip to see both regions of the swamp. The swamp is births the St. Marys river and the Suwannee river. Okefenokee is a native american word which means land of trembling earth. Most of the “solid” ground is actually peat that is floating. This floating peat is called batteries. Overtime the batteries grow larger and area able to support trees and large animals. The swamp was formed in a saucer shaped depression that used to be a part of the ocean floor.


Captured by Lauren Schramm


Many people do not realize that fire plays an important role in the swamp. Without fire the swamp would simple become a hardwood forest. Today prescribed burns reduce the amount of fuel available fire fires. In areas where there is a natural fire regime and humans stop these fires there is a build up of organic materiel. When a fire does break out because there is more fuel, the fire burns hotter than it normally would, damaging the seed bank in the soil. This can permanently damage the ecosystem. One of the most recent fires in Okefenokee occurred in 2011 in the Honey Prairie which burned down the former boardwalk on Chester Island. This was not due to a build up of fuel however, as the parks service lets fires that were caused by lighting burn which maintaining the safety of people and structures inside the park. The new boardwalk has a built in sprinkler system. Over the 7,000 years that the swamp has existed fires occur an average of every 20 years. Currently the swamp is regenerating from the fire. Notable from the young pond cypress trees (Taxodium ascendens) that are sprouting. Trees that sprout from old stumps are common and actually grow faster than seed generated trees. This stump sprouts are called coppices.


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Birds forced to raise kids that are not theirs- Brown-headed Cowbird (Molothrus ater)

The Brown Headed cowbird  (Molothrus ater) is a parasitic bird of North America. They used to follow the bison around and consume the insects associated with them. With the expansion of cattle in North American, the brown-headed cowbird populations have also expanded which has raised some interesting questions. Female cowbirds lay their eggs in the nests of other birds and allow those birds to raise their young. This type of parasitism is called brood parasitism. Because the cowbird is typically larger than these birds their young die in the process of raising the cowbird. Because the cowbird was not tied to a nest this allowed them to follow the bison which was a food rich source. It is unknown if they evolve this strategy to follow bison or were able to follow bison because of this strategy. They also are able to produce more eggs in a season than a typical bird, up to 3 dozen. Bird populations of the birds they parasitize have suffered as a result of this and efforts have been made to try to reduce this. Using feed designed for small birds, not spreading seed on the ground, and avoid feeding sunflower seeds, cracked corn, and millet will reduce the number of cowbirds in your area. It is important to note that the birds are covered by the Migratory Bird Act so it is illegal to remove their eggs from a nest or harm them in any other way without a permit. In some states, if they threaten an endangered species you can obtain a permit to trap the birds.


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GMOed BT corn

The following is a paper that I wrote for my population genetics class. 

Corn is a large part of the diet of North Americans. Furthermore, 15 percent of the land coverage of genetically modified crops contain Bt proteins (Hoftmann 2011). Bt corn was created because there is a high demand for corn that is damage free. Corn pests include wireworms (Elateridae sp.), cutworms (Noctuidae sp.), European corn borer (Ostrinia nubilalis), corn earworm (Helicoverpa zea), and white grubs (Phyllophaga sp.). In the past, the soil had to be treated before planting in order for the plants to be unaffected. Affected plants had stunted growth which led to a reduction in their yield. Not all pre-planting treats were effective either. (University of Kentucky) In the past, in order to deal with these pests crop rotation was also used. The areas most affected by these pests were Illinois, Indiana, Michigan, Ohio, and Iowa.


Bt corn first appeared in 1996 in Zurich Switzerland. Monsanto had the corn in development since 1992. The genes cry1Ab, bar, and bla were put into the corn. The cry1Ab gene comes from Bacilus thuringiensis, bar from Streptomyces hygroscopicus, and bla from Esherichia coli. Cry1Ab makes the crop resistant to lepidopteran species (butterflies and moths) by damaging midgut lining. It breaks down the gut wall which allows bacteria to flood into the body cavity. Bar makes crops resistant to herbicides by eliminating the activity of glufosinate in cells. It does this by acetylation. Bla detoxifies beta lactam antibiotics. This paper will focus on the bar insertion that causes resentence to pests, the Bt gene. Current the crop is used for food in 13 countries, feed in 10, and cultivation in 4 (International Service for the acqaution of agro-biotech applications.) Currently, Monsanto is working on increasing the resistance with corn rootworms (Diabrotica virgifera) and pink bollworms (Pectinophora gossypiella) (Monsanto 2015).corn_borer

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Brief overview of Phase I environmental site assessments (ESAs)

In the field of environmental consulting conducting Phase I environmental site assessments (or ESA) is very common. This is often the 1st phase in environmental due diligence. The EPA sets the standards in which this process is carried out. The report basically outlines if there is any potential environmental contamination at a site because those who own the property are responsible for it under federal Superfund law. In response to Love Canal, in which was a massive environmental disaster in Upstate New York, the government passed the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) in 1980.  This act forced the clean up of industrial waste sites and made the owners responsible for waste on their property. COnducting an ESA ensures that property owners are protected from this liability. These reports are typically done when a commercial or industrial property purchased to ensure that the buyer is not receiving an environmental disaster that will be very costly to fix. A Phase I ESA may be required from lenders, local banks, or municipalities. They may also be required when applying for a building permit, there is a change in ownership or zoning laws are changing. Sampling of air, groundwater, and soil is not conducted during a phase I ESA. This type of sampling is included in a Phase II ESA which is done if it is evidence of environmental contamination.


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North Point Bahamas

The following is adapted from my field notes on a research trip to San Salvador Bahamas. 

North Point is made of eolianites which are made of wind deposits of calcium-rich sand from the island mainland. The wet carbonate turns sold. A crust (caliche) forms on the surface and the then rest solidifies. These dunes are less than 500 years old. My professor, Fred said that sometimes the crust of the eolianites breaks and then is filled with sand which cements. It is harder than the rest of the eolianites so while the rest erodes it stays behind. Off of North Point, there is a shipwreck of a gas tanker. Fred saw a grey catbird (Dumetella carolinensis).These birds are named after their cat-like meowing sounds. Non breeding birds can be found as far south as the Bahamas. We also saw white-tailed tropic birds (Phaethon lepturus). They have very elegant long whitetails. They can be found in Hawaii as well. They don’t build nests and instead lay eggs on the bare ground. I saw several really small hermit crabs, which are also called soldier crabs (Coenobita clypeatus) taking advantage of old snail shells. This crab is one of two species that is commonly sold as pets. They are both herbivores and scavengers. 


North Point with the old gas tanker visible. Captured by Lauren Schramm.


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Freshwater Fish

Ichthyology is the study of fish which includes both saltwater fishes and freshwater fish. Freshwater fish are endothermic vertebrates meaning their temperature is regulated by the environment and they have a backbone. They breathe via gills and move with fins. All species have their own range and is typically limited by factors like prey, cover, suitable water temperatures, and dissolved oxygen levels. Generally, certain types of fish are likely to be found in certain habitat types. Darters and shiners, for example, prefer swift following stream with riffles while sunfish, bass, catfish, and suckers like prefer pools. Gar, bowfin, and perch prefer backwater as it has low dissolved oxygen. Fish can be found at all levels of the food chain from bottom feeders to apex predators. Fish can also be broken down into groups based on their tolerance to pollution. The amount of pollution tolerant fish, immediate and pollution sensitive fish can be used to determine the water quality in an area.

A rainbow trout (Oncorhynchus mykiss), photo credit: my dad, Stowe, Vermont. 

Biologists commonly use two methods to study fish; electroshocking and seining. Here I will discuss seine for riverine species. Larger seines are used in marine environments for more commercial purposes. Seining involves taking a vertical net, that has weights on the bottom and floats on the top and dragging it through the water. The net is then flip upward, trapping any fish that were in the area. You can easily make your own seine with netting and plywood. To seine properly it is best to have at least three people, tow to drag the net and one to pull fish out of the net and place them in a bucket to identify species. Electroshocking or backpack shocking is way more fun and productive than seining, however, you do need a permit to do so. If you have the necessary permits someone puts on the shocking device which is similar to a backpack. The device holds a car battery so it is very heavy but once the battery is placed in the backpack the backpack it typically waterproof. The backpack has a tail and a wand. When turned on there is an electrical field between the two elements. The stunned fish float up to the surface and the net holders scoop them up. The fish often recover very quickly and you have to act fast to scoop them up. For some reasons, surface area I think, larger fish are more impacted by being shocked. It is important to wear waders while shocking and not touch the water to protect yourself.


Once you have a fish in hand it is important to know what certain terms mean to help identity it. There are 16 major families of freshwater fish. In the next Taxonomy Tuesday post, I will be going to the families.

  • Lateral line: a sensory organ that runs horizontally along the fish
  • The dorsal fin is the fin on the top of the fish
    • this is composed of
      • the spines, which is the frontmost flap and
      • the soft rays which is the flap behind the spines
  • Caudal fin: the tail fin
  • Pectoral fin: the fin most similar to an arm
  • Pelvic fin: located in the bottom middle of the fish
  • Anal fin: the fin opposite of the soft rays
  • Barbels: the whisker type organs found on a catfish
  • Adipose fin: a meaty hump found on the rump of some fish


Thriving in the swamp- Marsh Rabbit (Sylvilagus palustris)

While on a boardwalk in Okefenokee National wildlife refuge, which is in South Georgia, my friend and I heard chewing noises. After waiting patiently, a tiny rabbit with short ears and small paws appeared out of the bush! It was a marsh rabbit (Sylvilagus palustris). Marsh rabbits are a species of rabbits that are adapted to live in wetlands. There is also a species called swamp rabbits (Sylvilagus aquaticus), but they the largest species of rabbit in the Southeast and weight between 4 and 6.5 pounds. The ranges of the two species do not entirely overlap which is how I figured out I had seen a marsh rabbit and not a swamp rabbit. You can see marsh rabbits in southeast Virginia, southern Georgia, eastern Alabama, and the Florida peninsula. The largest population is found in the Dismal Swamp. There is a subspecies, Lower Keys marsh rabbit (Sylvilagus palustris hefneri), which is found in south Florida. The subspecies has darker fur and has a different sized skull than the regular marsh rabbit. The subspecies is considered by IUCN to be critically endangered and is federally listed as endangered. Most of these rabbits can be found on Big Pine and Boca Chica keys. Because of its conservation status, there is more information available about the Lower Keys marsh rabbit.


Marsh Rabbit. Captured by Lauren Schramm. Okefenokee National Wildlife Refuge


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Avian eggshell formation- how a lack of calcium leads to fragile eggs

Many birds, more specifically passerines (order Passeriformes), rely on different sources of calcium for skeletal growth and store calcium in their bodies, a necessity for their ability to form strong eggs during the eggshell formation process. Near human settlements birds and in areas with high qualities soils, birds tend to have more access to the calcium that they need. Because of the importance of calcium passerines often ingest snail shells in areas in which the soil is calcium deficient. The most common source of calcium is snail shells followed by calcareous grit, bones, eggshells, and other sources.  Soil can be calcium deficient can be caused by acid precipitation which removes calcium from the soil. Most passerines are unable to ingest their much-needed amounts of calcium due to the scare amounts of nutrients in the habitats that they live in. This results in the development of thin fragile eggs that are unable to hatch thus affecting the bird population in various habitats.


 Burgundy snail (Helix pomatia): a common European species


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