2015 Fall

DNA Barcoding-> What is it?

How do we identify different species? One obvious way is morphology, the way an organism looks. This may include size, shape, and body color. Field guides or internet sites could be used to help identify a particular organism this way. However, what about organisms, like insects, that are often hard to identify strictly by morphology? That’s where a useful method called DNA barcoding comes into play.

We use the DNA barcoding technique in our lab to sample the biodiversity of insects, but we also use it to train undergraduate students in molecular biology. The purpose of this post is to describe the history as well as the science behind this technique. I will also describe how it works in our lab.

In 2003, Paul Hebert, a professor and current Director of the Biodiversity Institute of Ontario, came up with “DNA barcoding” as a way in which to identify species. DNA barcoding uses a short genetic sequence from an organism’s genome. For almost all animals, the gene region that is used is the mitochondrial cytochrome c oxidase 1 gene, or “CO1”. COI is a 648 base-pair region that codes for an enzyme that plays a major role in cellular respiration (how your body converts glucose to ATP), specifically the last step called oxidative phosphorylation. The COI gene is suitable for barcoding because its rate of mutation is fast enough to distinguish between animal species, even closely related species.

Here’s what our “pipeline” looks like:

Week 1: Students in our lab collect insects from sample plots. We have plots at a section of the city’s greenway trails as well as plots on campus. This way we can compare a disturbed urban area (campus) to a less disturbed area (greenway). After collecting in the field, the students attempt to identify the specimens using field guides and other internet resources. Here’s a great one. The insects are stored either in the freezer or in 70% ethanol.

Week 2: The DNA is extracted from the insects. This process includes initially grinding up certain parts of the insects and then going through a series of steps to isolate the DNA. We use Carolina Biological’s protocol. The samples are then stored in the freezer until the next lab.

Week 3: The DNA is amplified, or copied. During this lab we use a procedure called Polymerase Chain Reaction, or PCR. The small amount of DNA that we have extracted from the insects is replicated. We use a COI primer, which are small pieces of DNA, to amplify the DNA of interest. The PCR machine can make about 68 billion copies! This is a step that also involves using extra deoxynucleotides, a cool enzyme called Taq polymerase, and a loading dye so that we can visualize the results during the next lab. Again, the sample are stored in the freezer until the next lab.

Week 4: The DNA samples are visualized on a gel using a procedure called electrophoresis. In our case, the DNA is separated according to molecular size with the aid of an electrical field. There are many interesting applications of using gel electrophoresis. We use it to determine whether or not we have our gene of interest.

Week 5: In between week 4 and 5, our DNA samples are sequenced. During week 5, we use bioinformatics to determine our species based on our sequence with the help of a database. Students are able to compare the barcoding results with their original identification from the field guides during week 1. Students are also able to measure the biodiversity of each are (campus and greenway) using several biodiversity indices.

Two main objectives are met during this research. One, we are training undergraduate students to actually be scientists. Students need concrete examples of the scientific process from beginning to end. This research project uses a nice blend of field research and laboratory methods. The students are also given autonomy which increases learning. The second objective is to highlight the importance of biodiversity, even if it is local. Biodiversity is crucial for progress in ecological and evolutionary fields of science and also for conservation programs.

Stay tuned for our results.

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The Ecology of Fear, Part IV

Since coyotes do inhabit neighborhoods and other urban environments, humans must learn how best to live with them. In Part I of this series, we looked at the specific coyote “problem” in Iredell County. In Part II, we learned about the natural history of coyotes, and in  Part III we attempted to clear up misconceptions about coyote behavior and ecology. With this post, we will explore recommendations and suggestions on how to live with these predators.

Coyotes can be found living in every county in North Carolina yet the state has no formal coyote management plan. The reasons are pretty simple. It can be time-consuming and expensive to try to implement a removal/management plan. Individual coyotes that are found killing livestock will quickly be replaced by other individuals if they are removed from an area. This paper highlights best practices when it comes to managing potential predators of livestock. Several studies have shown that coyotes are far too resilient for periodic eradication programs. In fact, only a 10% survival rate in offspring must survive and reproduce to maintain most coyote populations. It has been estimated that if 75% of coyotes in any given area are killed each year, it would take 50 years to exterminate the population. Coyotes simply increase productivity, survival, and immigration under removal efforts. Since it does not look as if coyotes will disappear from NC any time soon, it is best for both coyotes and us that we learn how to avoid conflicts.

First of all, seeing a coyote is not a cause for concern. If you see a coyote frequently, then you can take steps to decrease the chances of a conflict. The Urban Coyote Project recommends people follow these six steps to avoid conflicts:

1. Do not feed coyotes
2. Do not let pets run loose or be unattended
3. Do not run from a coyote
4. Repellents or fencing may help
5. Report aggressive, fearless coyotes immediately
6. Do not create conflict where it does not exist

Following these steps and using common sense when coming into contact with coyotes will benefit both parties. We certainly benefit from having these predators in our areas. Be smart.

*Since their is no coyote management plan in NC, it is extremely hard to estimate population numbers in the state. However, The North Carolina Wildlife Resources Commission does keep track of the number of harvested coyotes by hunters per year. These numbers could help us understand population dynamics from year to year. These documents can be found here.

The Ecology of Fear, Part III

This is Part III of a series on coyotes. Part I can be found here and Part II here.

Native stories about coyotes tend to focus on their mischievous and cunning behavior as well as their apparent lack of morals. Coyotes have faced intense pressure from hunters, dating back to when Europeans  first arrived in North America. Unlike wolves, cougars, and bears, coyotes have adapted and thrived in the face of persecution. How do you explain this?

Coyotes are very opportunistic, so they are sometimes active throughout the day. Typically, they are most active during the early morning and late evening hours, making them crepuscular.  It may be that in areas of high human activity, like urban environments, coyotes become more nocturnal to avoid conflict. Coyotes have the amazing ability to remain unseen by moving where terrain provides them the most cover. The video below shows a family of coyotes here in Statesville, NC, and is actually about 1.5 miles from downtown. These coyotes are most active from 1:30a.m. to 5:00 a.m.

This coyote, however, was active in the early afternoon for several days in a row in an area not inhabited by many people.

Food
When it comes to feeding, coyotes are known as ecological generalists. As their range expanded, their diet also expanded. Coyotes are really good at eating all sorts of food, including meat, fruits and vegetables, nuts, carrion, and even trash. They have been known to eat pet food off of porches. A large portion of our NC coyotes’ diet consists of small mammals, like rodents and rabbits, insects, fruits, and nut crops.

Habitat/Sociality
Coyotes could also be considered habitat generalists, meaning they can make their home in woodlands, grasslands, deserts, mountains, agricultural, and urban areas. Territories vary depending on what season it is, population in a certain area, as well as pack status. Transient coyotes, or loners, tend to roam more and may establish large territories. Coyote packs are more likely to establish a smaller territory.

Whereas wolves are highly social, coyotes are typically less social.
They do exist in packs in some areas. However, they are also found in pairs or as individuals. A “pack” is usually just a mating pair and offspring. Western coyotes tend to be a little smaller and have to avoid top predators like wolves. In places like Yellowstone, wolves have pushed coyotes into areas inhabited by people like campgrounds and roadsides. Here in the southeast, coyotes compete with grey and red foxes. They are usually dominant over both species, with grey foxes having the advantage over red foxes because they can climb trees.

The Urban Coyote Program is a long-term research project that was started in the Chicago metropolitan areas in 2000 “as a non-biased attempt to address shortcomings in urban coyote ecology information and management. The following are some major implications that this program lists from it’s research:

  • As a top predator, coyotes are performing an important role in the Chicago region. Increasing evidence indicates that coyotes assist with controlling rodent, deer, and Canada goose populations.
  • Coyotes in urban environments switch their activity patterns to be more active at night when human activity is minimal.
  • Most coyotes are feeding on typical prey items, such as rodents and rabbits, and generally avoiding trash.
  • Wildlife feeding will eventually habituate some coyotes, leading to conflicts.
  • Coyotes appear to be monogamous.
  • Coyotes are exposed to a wide range of diseases; however, to date, none of them pose a serious human health risk. In general, the coyote population appears to be relatively healthy.
  • Effective control programs target nuisance coyotes, rather than targeting the general coyote population. Coyotes removed through lethal control efforts or other causes are quickly replaced.
  • There are individuals who exhibit dangerous behavior that sometimes should be removed from the population.
  • Successful management programs include public education and outside consulting.
  • Some types of repellents, such as electronic devices employing lights and sound, may be useful for preventive control of coyotes, but more work is needed to evaluate their effectiveness and other hazing techniques.

Ecological benefits?
As highlighted above, coyotes do seem to benefit ecosystems. In some areas, coyotes may act as keystone species and help regulate populations of other species. Domestic cats may kill as many as 4 billion native birds per year in the U.S. This recent study shows that coyotes may help native bird populations by eliminating cats from certain areas, or at least causing cats to avoid certain areas.

Because coyotes are here in Statesville, and because they do benefit local ecosystems, we will take a look at best ways to avoid conflict with these animals in Part IV.

 

The Ecology of Fear, Part II

You could not have asked for a better morning in the valley they call the Lamar. The air was cool and crisp with a slight breeze that had a “bite” to it. All was well because we had plenty of clothes and coffee. However, it did not take us long to realize that all may not be well with the pair of coyotes that we had been observing for the past hour.

The coyotes had suddenly encountered an unwanted visitor in the form of a wolf. This was especially dangerous for a couple of reasons. Gray wolves are much larger and more powerful than coyotes, so the coyote pair could be in danger of losing their lives. This particular wolf was also in close proximity to the coyotes’ den where the pups were hiding.  As we watched the coyotes attempt to chase and/or distract the wolf, we wondered aloud about how these two species of canines have interacted, and co-evolved, through thousands of years.

The video below shows the last half of this particular interaction.

There are currently at least seven (maybe as many as 10, depending on how you split or lump species) members of the taxonomic genus Canis that are included within the Canidae family. The coyote of North America, or Canis latrans, is one of those. This link shows the current list of species and subspecies.

Phylogeny of canid species. from Genome sequence, comparative analysis and haplotype structure of the domestic dog Kerstin Lindblad-Toh et al. Nature 438, 803-819 (8 December 2005) doi:10.1038/nature04338
By Sminthopsis84 (Own work) [CC BY-SA 4.0 (http://creativecommons.org/licenses/by-sa/4.0)%5D, via Wikimedia Commons
File:C. dirus, C. lupus, C. rufus, C. latrans, C. anthus & C. aureus skulls.jpg
Skulls of dire wolf, grey wolf, red wolf, prarie wolf, African golden wolf and reed wolf.
By Max Hilzheimer, John C. Merriam & Edward Alphonso Goldman [Public domain or Public domain], via Wikimedia Commons

Canidae ancestry can be traced back to a genus of carnivorous mammals named Miacis. Species in this particular genus were about the size of a weasel and appeared during the late Paleocene around 56 million years ago (Heinrich et al.). Even though the coyote is actually more primitive than the gray wolf (C. lupus), they both have had a long history of competitive and antagonistic interactions in North America. Therefore, the interaction we witnessed that cold morning in June was nothing new, historically speaking, to either of the species.

Wolves hunt in packs and typically specialize in large prey. They usually rely on tiring out their prey by a long chase (Mech 1974). In contrast, coyotes are mainly solitary hunters that kill small mammals by pouncing and shaking them (Bekoff 1977). However, coyotes did not always hunt small mammals. In fact, there is research that shows that during the Pleistocene, coyotes did, in fact, hunt and kill larger prey (Meachen et al. 2014). One reason they hunted larger prey was simply because Pleistocene coyotes were larger in size than present day coyotes. It was probably during the end of the Pleistocene (between 11,500 and 10,000 years ago) that a decrease in food supply and the megafaunal extinctions led to a shrinkage in coyote size and a niche shift (Meachen and Samuels 2012 and Meachen et al. 2014). After animals like sloths, camels, horses, and llamas went extinct, there were fewer large prey species for the coyotes to eat. The dire wolf (C. dirus), probably the coyote’s biggest competitor during that time, also went extinct. Being large was not really an advantage for coyotes anymore, which is why ecologists observe this shift to smaller coyotes in the fossil record (see here for a quick explanation of natural selection).

During the past several centuries, coyotes have benefited significantly from humans. Coyotes hunted small prey successfully in the western plains of the U.S., but then early settlers pushed west and hunted wolves to extinction and did major damage to other carnivores like mountain lions and bobcats. Coyotes thrived because they reproduce faster than their competitors and are more opportunistic feeders. The spread of agriculture also played a major role in coyote explansion (Kays, Curtis, and Kirchman 2009). Coyotes had (and still have) no trouble exploiting the environmental changes caused by people. Eastern coyotes, especially, have shown they have no trouble adapting to urban areas that are heavily populated by humans.

Coyotes can now be found in every county here in North Carolina. They can hunt, eat, sleep, and raise their pups in cities. They are even hunting deer, filling a niche left open by the red wolves (C. lupus rufus) that once roamed here. A recent study showed that from 2006-2009, coyotes were definitely responsible for 37% of South Carolina’s fawn deaths and could have been responsible for as much as 80% of fawn deaths (Kilgo et al. 2012). As highlighted in Part I of this series, Iredell County residents in North Carolina have become quite familiar with the coyote. In 2008, Iredell County Animal Services and Control sent out this publication. It states that at one point in the past, foxes were in so much demand for hunting that someone transported coyotes from Virginia into Iredell County to replace them. Hurricane Hugo, which came through the county in 1989, supposedly demolished the coyote pens, and they all escaped into the wild. Judging by how fast coyotes have spread into other counties throughout North Carolina, it is unclear whether this single event helped coyotes spread into the area faster than they normally would have. What is clear is that coyotes are here, they are doing well, and they are not going anywhere any time soon.

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Bekoff, M. 1977. Canis latrans. Mammal Species, 79:1-9.

Heinrich, R.E., Strait, S.G., and Houde, P. 2008. Earliest Eocene Miacidae (Mammalia: Carnivora) from northwestern Wyoming. Journal of Paleontology, 82: 154–162.

Kays, R., Curtis, A., and Kirchman, J. 2010. Rapid adaptive evolution of northeastern coyotes via hybridization with wolves. Biology Letters, 6:89-93.

Kilgo, J., Ray, S., Vukovich, M., Goode, M., and Ruth, C. 2012. Wildlife Management, 76:1420-1430.

Meachen, J., Janowicz, A., Avery, J., and Sandleir, R. 2014. Ecological Changes in Coyotes (Canis latrans) in Response to the Ice Age Megafaunal Extinctions. PLoS ONE 9(12): e116041. doi:10. 1371/journal.pone.0116041

Meachen, J. and Samuels, J. 2012. Evolution in coyotes (Canis latrans) megafaunal extinctions. PNAS, 109: 4194-4196.

Mech, L. D. (1974). Canis lupus. Mammal Species, 37:1-6.

The Ecology of Fear, Part I

“Coyotes are wreaking havoc in one area county…attacking animals and scaring people.”

Ecologists describe “ecology of fear” as prey behavior changing due to the presence of predators (Ripple 2004). For example, the presence of wolves in a certain area may cause the elk not to stay and forage as long as they would if the wolves were absent. In this article (and the ones that follow), we refer to the ecology of fear as predator presence in an area, especially a neighborhood, striking fear in the local residents.

Coyotes have taken up residence in all of North Carolina’s 100 counties. Not only are they surviving, but they are thriving. During our annual camera trap study, in which we put up trail cameras to survey wildlife, we have gotten quite a few pictures of coyotes within city limits. As they increase in density, their range decreases, and they matriculate into urban areas. This increases the likelihood that they will come into contact with humans. Iredell county, and in particular Statesville, has not been able to avoid this conflict. Just look at this news article from 2012. One dog attacked by a “pack” of coyotes is how it describes the event. Look at the following quotes from area home-owners concerning the rising coyote population:

“This problem is getting out of control.”

“It’s very scary.”

“I don’t really want to kill them or anything like that. Let’s just catch them and relocate them where they need to be, not so much in the middle of a city and the public where someone can get hurt.”

These are real fears from real people. How do we address these “nuisance” problems and deal with these fears? The one thing wildlife biologists can say for sure is that these canines are not going away anytime soon. To properly address this issue, we first need to learn all we can about the coyote, Canis latrans. In this series, we will try to bring clarity to several misconceptions about the eastern coyote so that we can all learn to live with them.

In Part II, we will delve into the natural history of coyotes. We will learn how they developed genetically. We will also learn how they came to live in North Carolina. Part III will attempt to clear up misconceptions about coyote behavior and ecology. Finally, part IV will explore recommendations and suggestions on how to live with the predators.