Thursday, December 17, 2015

Keeping it clean downstream

Agnetina.jpgIn peaceful streams, aquatic macroinvertebrates such as crayfish, stoneflies, and caddisflies travel over and under submerged rocks, foraging for other invertebrates, leaves, and algae. When rain falls, their world turns upside down.  At first only the surface is disturbed, but before long, runoff reaches the stream and increases its flow many fold. Silt and sand blast every exposed rock surface. At peak flow, boulders are propelled downstream by powerful currents.

How do small creatures survive such crushing chaos? They hunker down. Water-filled nooks and crannies extend deep below streambeds and far beyond river banks. These deep interstices provide a safe haven even while turbulent water pulverizes the riverbed, comparable to a storm cellar in a tornado.

Wednesday, October 14, 2015

Flat Stanley and the Centipede

Biologists sometimes field questions about a “huge scary bug” that appeared in someone’s home or worse yet on their person. Most turn out to be benign organisms that ended up in the wrong place. For me, the most common questions come in July, when male dobsonflies emerge from the Winooski River and often end up crashing into windows on the Saint Michael’s College campus where I teach. The males have impressive mandibles that look scary but are harmless to people.
Recently however, one of these questions did actually involve something dangerous. One morning I received a call from a friend and grade school teacher, who explained that she had managed to corral a very large and intimidating centipede in a plastic container at her school. I immediately emailed her a photograph of a house centipede, fully expecting that to be the end of the discussion. House centipedes commonly attract the attention of teachers and home owners. They frequently get trapped in the sink at my children’s school, and I discreetly liberate them so that they can eat real pests. However, in this case, “house centipede” was not the correct answer. I asked if the arthropod was slow moving and dark, thinking that perhaps she had found a stranded hellgrammite. No, she said, it was fast. This was getting interesting!

My friend described a centipede that was black and orange at the front, with a forked “tail” and yellow legs. Its most surprising feature was its size, a full six inches long. At this point, I asked for a photograph because the insect sounded like nothing I had encountered in Vermont. From the photograph, I determined that it was most likely a giant desert centipede (Scolopendra heros). That settled the first question, but left still many others unanswered. The school principal wanted to know if the centipede was dangerous. Were there likely to be more lurking about? Should he shut down the classroom? How does a desert centipede end up in Vermont?

I reassured them that it was unlikely to find even one such centipede in Vermont (and then less reassuringly suggested that, because one was found, they keep their eyes open). I informed the state entomologist and sent him photographs. I learned that desert centipedes give particularly nasty bites. In some cases, they can cause renal failure and even death. While death by centipede isn’t a common way to go, even in the desert, this species was certainly due some respect.

I guessed that the centipede may have come up from the desert southwest in packaging material, or perhaps through the pet trade. The truth was more surprising.  The school in question, like many Vermont schools, uses a children’s book called Flat Stanley to combine reading skills with art, geography, and just plain fun. Because Stanley is flat, he can be mailed in an envelope, and many children in schools across the world make their own Flat Stanleys and send them to friends in other places. Their friends photograph Stanley in interesting locations and return him along with local souvenirs. When my son did this, we sent Stanley to Ireland, Cyprus, and Australia.

Stanley was sent by my friend’s student to an aunt in Texas, and she mailed him back with Texas souvenirs.  The package included a map of Texas, a length of rope representing the horn span of a Texas longhorn, a piece of prickly pear cactus, and a Ziploc® bag with a hole chewed in the corner labeled, “DO NOT TOUCH – CENTIPEDE.”  Why one sends a dangerous centipede (or any centipede) through the mail is a mystery, but it certainly happened. While I can’t imagine that this centipede would establish in Vermont even if dozens were sent, it underscores the continuing need to educate the public about the dangers of moving species to new locations.

On a positive note, the school has added the now dead, preserved centipede to its invertebrate collection for classroom use. I think that speaks very well for the school that the students will learn valuable lessons from Flat Stanley’s travel companion. Perhaps it will inspire some budding entomologists?

Declan McCabe teaches biology at Saint Michael’s College. His work with student researchers on insect communities in the Champlain Basin is funded by Vermont EPSCoR’s Grant EPS-1101317 from the National Science Foundation. This article was adapted from the Newsletter of the Vermont Entomological Society and most recently circulated by Northern Woodlands Magazine's outside story.

Sunday, September 20, 2015

New semester; snorkeling; insect identification; and statistics!

A new semester; new students; and an 85 F temperature forecast for lab.  It seemed like a perfect opportunity to really experience Lake Champlain.  I bought out all of the remaining masks and snorkels from a certain local store and we were ready to go.

My customary first lab in Community Ecology has been to test the species area relationship.  It seems like a simple enough concept: bigger area - more species, but the concept underlies important conservation biology topics such as reserve design.  The lab also provides an ideal entry point to community ecology.  Bigger areas do tend to have more species, but also a mathematical inconvenience: there are also more individual organisms.  Imagine any community with some finite number of species.  We sample 1 individual and we automatically have sampled 1 species.  As we sample more individuals we also sample more species.  Therein lies the mathematical problem: do larger areas have more species for some biological reason.....or is it just because we sampled more individuals?

On cool September days we typically wade into Lake Champlain in chest waders.  But the warm weather this year was perfect for snorkeling.  So in we went!  Snorkeling or wading, the procedure is simple enough: Find submerged rocks of diverse sizes, net them, measure them, and identify all of the attached invertebrates.

The lab has all of the ingredients necessary for an excellent learning experience: field work; sampling real communities; insect identification; data generation; analysis; writing; and the opportunity to get wet in Lake Champlain on the second day of a new semester was icing on the cake.  This year yielded a bumper crop of very tiny zebra mussels along with 24 other invertebrate species.  

By now there are 22 students writing lab reports based on the data set.  They have learned how to deal with the mathematical sampling issue using rarefaction, how and why to log transform their data set, and how to use linear regression to measure the strength of the relationship between rock area and the number of species sampled.

I'm looking forward to reading the lab reports and moving on to another successful semester in Community Ecology!

Friday, April 17, 2015

Aquatic insect your pocket

Science teachers are always on the lookout for the next idea to immerse students in hands-on science.  Collecting, identifying, and analyzing macroinvertebrate communities in streams may well be one of the most accessible and fun ways to literally immerse students in science.  Streams are ubiquitous habitats and students are often surprised to see the fascinating organisms that can be see by just picking up a rock or two.  And who doesn't enjoy cooling their feet in stream water on a hot day?

Figure 1.  Screen shot from Iphone app.         
Simply sorting invertebrates into ice-cube trays by type and quickly estimating the number of species is an easy way to get started.  Number of species is the first component of diversity.  Comparing the number of species found in two streams provides an excellent ecological lesson or could be the basis for a science fair project.    Saint Michael's College Biology students in my Community Ecology class take it several steps farther than that.  And of course they should take it farther; they are in an upper-level biology course.

Many students are interested in identifying the organisms they collect and professional taxonomic keys are readily available.  Comprehensive family-level keys designed for the mid west can be downloaded for free and work reasonably well for fauna of the north east.

Vermont EPSCoR has made an even easier tool to help with identification. Most streams and ponds host only a small subset of the organisms found in the comprehensive keys.  Using comprehensive keys requires long hours of reading detailed descriptions of arcane morphological descriptions to eliminate the large majority of organsism found in the key....but absent in your specific samples. The new tool focuses only on the organisms previously found in specific streams.  This means that a high school student collecting macroinvertebrates for the first time can identify them more accurately and in a fraction of the time it would take using traditional keys.

Figure 2.  An organism found in Brewster River.
We started by making web sites tailored to the few streams and ponds where we and our collaborating high schools sampled.  The list of streams and ponds has since expanded to include 78 sites in Vermont, New York, and Puerto Rico.  Each web site contains roughly 10 to 20 organisms making it possible to identify 95% of the organisms found at a particular site.  

Computer Science students at the University of Vermont have taken the tool one step further by developing an Iphone app.  The app can be synchronized before field work to load images from the web directly onto an Iphone.  The app can then be used at remote fields sites with or without a cellphone signal.

Students can collect an organism from Brewster River in Jeffersonville Vermont for example, pull out their cell phones or Ipads, and compare the catch of the day to a gallery of photographs of organisms found at that site (Figure 1).  A quick click on an organism's photograph reveals it's name and identification tips (Figure 2).

The web pages and Iphone app are based on a series of 138 mini web pages called templates that represent 138 different organisms that we have found in our stream and pond study sites.  The templates are like Lego bricks that can be used and reused in different stream and pond web sites.  At this point the bulk of the work has been done and it takes little time to create a new web page for a freshly sampled stream.  We can also rapidly add organisms to existing stream sites.  All new information is passed onto Iphones by synchronizing with the web sites.

I hope that this new tool can lower the taxonomic barriers a little bit and make working with macroinvertebrates in aquatic habitats a little easier for a tech-savvy generation. 


Sunday, February 15, 2015

Making trees: how are mammals related?

Figure 1.  An 1837 sketch from Charles Darwin's notebooks.
How do scientists tell what organisms are related to other organisms?  It's not easy to go back in time and visit with the common ancestor of chimpanzees and humans for example, so we need some approaches to place organisms into natural groups.  This was precisely what the Swedish biologist Carl Linnaeus first attempted in a 12 page publication called  Systema Naturae in 1735.  By 1758, the tenth edition included descriptions of 12,100 plants and animals.

Modern biologists are just as concerned with appropriately grouping related organisms as was Linnaeus.  Since the time of Darwin we have used tree diagrams to represented the relationships among related organisms (Figure 1).  Humans and chimpanzees for example can be placed on the tips of branches that can be followed back to a larger branch that represents the ancestor we share in common.  To see how we are related to monkeys, bats, dogs, or sharks, we'd have to track back closer and closer to tree trunk and then trace paths back out along more distant branches.  The length of that branch-tracking journey represents the distance of the relationship between any two organisms on the tree.

When I started teaching evolution at Saint Michael's College I wanted an authentic activity that students could complete to make an actual evolutionary tree.  It's quite frankly boring to simply study trees completed by others and memorizing the branching patterns seems utterly pointless.  My quest was for a prepared procedure that would walk students through the actual process used by evolutionary biologists to make the trees that we call phylogenies.

Figure 2.  Data from 2015 Saint Michael's College students.
My quest was fruitless and so I wrote my own student-accessible procedure based on the techniques used by professional biologists.  My students use a collection of real and replica mammalian skulls.  They come up with a laundry list of observable skull characteristics: canine teeth, forward facing eyes, snouts, notches, grooves, and whatever traits they can come up with and clearly communicate to their class mates.  Each skull is then scored for each trait: "1" represents "present"; "0" represents "absent".  A subset of this year's data is shown in Figure 2 and from it you can see that bobcats, and lynx have tiny molars and Y-shaped premolars that are not found in the other organisms on this subset of the larger list.  These unique traits together with many others can be used to infer that bobcats and lynx are related.

Figure 3.  The arbitrary starting tree; click to enlarge.
This year we measured 46 traits from 26 mammals and then placed the mammals on an arbitrarily drawn tree (Figure 3).  I describe the starting tree as "arbitrary" because no attempt was made to place related organisms on adjacent branches: bobcats share a branch with polar bears and sheep for example.  Obviously this is not ideal and more importantly, it suggests that tiny molars evolved bobcats, and again in lynx, and evolved independently three more times in lions, cougars, and Bengal tigers.  It makes more logical sense that tiny molars evolved in some ancient cat and that the trait was passed down to modern cats.  If this is true we should expect to see this traits in other cats and indeed we do see exactly that in the two other species we have in our collection: house cat and caracal cat.  Scientists call this "the principle of parsimony": why invoke 5 evolutionary events when just 1 is needed to explain the data.

We refer to the gain or loss of traits as "transitions" and we used software to count the 251 transitions needed to explain the arbitrary tree.  My students then move branches around on the tree and the software automatically recalculates the number of transitions.The goal is to generate the most parsimonious tree, or the tree with the smallest number of transitions.  This becomes competitive as student groups report out on their shorter and shorter trees during the lab session.  As a homework assignment, the students compare their trees to trees published by evolutionary biologists.  This places their work in the larger context and I have found that the comparisons generally fare very well.  As a result of writing this blog I think I'll ask my students to use their trees, together with published trees to write several hypotheses about the traits of skulls they have not yet seen.  Sounds like a whole new lab!
Figure 4.  A tree made based upon the observed skull traits.

What I don't tell my students is that the software has a feature that does the work automatically.  The software is unbiased; it won't place the polar bears near the brown bears just because that might make most sense.  Instead, the software makes groups that minimize the number of transitions and generates a tree based solely on the data (Figure 4).  This data-based tree requires 121 transitions and places organisms together in ways that very closely match the tree of life, a phylogeny generated by professional biologists.

Importantly, 15 students dreamed up 46 traits without consulting published work and without reference to what some other biologist might think of as a 'good trait'.  They worked in groups and the only criteria for choosing traits were: that they could communicate the trait to their peers; the trait should occur in at least 2 skulls; the trait could not occur in every skull.

This is our third year running this experiment.  We use different skulls each year to keep it interesting.  The list of traits that students come up with changes each year also.  If other teachers would like to run this exercise on skulls or on other organisms you can find all of the needed information in this short paper.

Figure 1 from Wikimedia Commons.  Other figures generated at Saint Michael's College.