All posts by Opinicon

Professor of Biology and Environmental Studies at Queen's University

The HydroBall – An aquatic GIS adventure.

Madeline Healey (SWEP 2018)

The Queens University Biological Station (QUBS) strives to be one of the best field stations in North America. To enrich the resources available to researchers, QUBS recently sough to apply a new technology to improve the bathymetric maps of our local lakes. A continually evolving technology, the Hydroball® buoy was obtained for data collection at QUBS over a two week period in the summer of 2018 . The Hydroball system integrates three main components: a GNSS L1/L2 receiver, a miniature inertial motion sensor, and a single beam echosounder. The GNSS receiver measures the buoys real time position including latitude, longitude and ‘ellipsoidal height.’ The inertial sensor measures roll, pitch and heading while the echosounder measures the depth under the buoy using SONAR (Sound Navigation and Ranging) properties. The output data of these components is fed into a controller unit inside the buoy that allows up to ten soundings per second to be referenced to the seabed.

Now, you may be asking “What is a Hydroball?” At first glance it looks like something out of a Star Wars movie (BB8’s aquatic cousin?) – the Hydroball concept is actually quite simple. It is a small autonomous bathymetric buoy developed by CIDCO (The Interdisciplinary Centre for Development of Ocean Mapping; Figure 1). It is designed to map non-traditional areas such as rivers, remote locations and ultra-coastal zones. The robustness of the Hydroball instrument supports bathymetric data acquisition in turbulent waters, allowing hydrographers and companies (and field stations!) to map unknown areas with high precision and accuracy.

Figure 1. The Hydroball. A bathymetric instrument used to map and chart bodies of water in high accuracy.

Bathymetry, the study of underwater topography, is fundamental to the studies of oceans, seas and lakes. Bathymetric data, including information about the depths and shapes of underwater terrain have a range of important uses. As of the year 2000, the National Oceanic and Atmospheric Administration estimated that as much as 95% of the world’s oceans and 99% of the ocean floor remained unexplored (NOAA, 2010). The rise of technology including remote sensing and bathymetrical devices such as the Hydroball have opened up opportunities for offshore exploration. By mapping and analyzing the floors of lakes and oceans, scientists can study circulation patterns, marine biology, geophysical properties and sites. In essence, bathymetric data provide valuable information about water depth and topography of lakes and oceans, which are significant for many aspects of marine research, administration, and spatial planning of coastal environments and their resources. Bathymetric maps are increasingly important as scientists learn more about the effects of climate change on our environment.

Figure 2. A previous bathymetric image of Lake Opinicon. Similar to how topographic maps represent three dimensional features of overland terrain, bathymetric maps illustrate the land that lies beneath the water.

The data acquisition was completed during the period of of July 3rd to16th and from July 15th – 22nd thanks to the amazing team efforts of QUBS staff and members from Dr. Stephen Lougheed’s lab (QUBS Director). Many long hours were spent on the water collecting data (Figure 3), as well as in the GIS room ‘cleaning and processing’ the millions of points collected. On the boat, we used ‘Survey’ software to visualize our progress in covering the Lake Opinicon grid that we had created. A Sound Velocity Profiler (SVP) instrument was used to determine the speed sound tab which the boat was moving through the water as we were collecting data. The software, combined with the technology of the Hydroball proved to be a reliable and robust system which yielded high quality of data.

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Once data collection was completed over the time that we had the instrument, the next step was to process and clean the data. A program called ‘Depthstar’ visualized our collected data on a navigation map platform (Figure 4). From here, we scanned through point clouds of data to remove (clean) obvious anomalies in the data set. Post collection cleaning included adding Precise Point Processing (PPP) data to the raw data to georeference the points, and improving the accuracy and reliability of the data. The processed skeletal data was moved into Arc software to create the Digital Terrain Models (DEM). This process required a lot of patience (and coffee) as we collected over 6 million points over the 14 days of data collection!

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The biggest lesson I’ve learned from this project is the importance of quality data for an effective research data management plan. For data to be maximally relevant, it must be current and up to date. With such contemporary data, research organizations like QUBS are better equipped to provide accurate data for research questions. Another significant lesson learned from this project is the importance of strong organizational and communication skills. Effective communication led to a successful execution of data collection and management. Communicating questions and concerns directly with the team members allowed us to foster collaboration and to innovate and problem-solve, ultimately allowing us to attain the goals of this project.

The Hydroball project was a highlight of our summer here at QUBS. Being a part of every step of the process from data acquisition, processing, management and application was incredibly rewarding. We have definitely gained a new appreciation for sunrises above Lake Opinicon, even though it meant waking up at 4:45am to start collecting data! The final product of our work will be a detailed, high accuracy bathymetric map of a significant portion of Lake Opinicon. This information will be further used for multiple research projects at QUBS for many years to come.

Thank you to Kevin J. Wilson from CIDCO for providing us with the training and guidance to use the Hydroball at QUBS. Also thank you to Lougheed lab members and other QUBS SWEP 2018 staff for assisting in the data collection; this project would not have been possible if it wasn’t for your generous help!

Sources:

  1. US Department of Commerce, & National Oceanic and Atmospheric Administration. (2009, January 01). How much of the ocean have we explored? Retrieved from https://oceanservice.noaa.gov/facts/exploration.html
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Citizen Scientists at Work

written by 2017 SWEP intern Dayna Zunder

nesting turtle
Turtle excavating her nest in the gravel.

Doug Fluhrer Park is a 2.85 hectare waterfront park located alongside the Great Cataraqui River, just minutes from the heart of downtown Kingston, Ontario. Aaron Sneep and I (Summer Work Experience Program interns at Queen’s) got our first taste of this newly-renovated park on a gloomy Tuesday morning in June 2018 — damp weather more typical, perhaps, of a frigid and rainy spring month. It was here that we met Mary Farrar and the Friends of Inner Kingston Harbour, a group of individuals — citizen scientists, interested in the Northern Map, Snapping, and Painted turtle species that choose to make Doug Fluhrer Park their home. Mary and her team have been visiting the park twice a day since early May, once in the morning and evening,  seeking to protect turtle nesting sites. Using a small piece of metal mesh, the group has been covering the nests for two-week periods to help prevent egg predation by local wildlife (e.g. racoons). An intricate labelling system has been devised, which makes it easy for Mary and company to determine when the nest was covered, and whether the site may be a decoy nest, perhaps built by the turtles to confuse and deceive predators.

basking
In the bay at the other side of the parking lot, three turtles basking on a log.

 

Aaron
Aaron Sneep, QUBS GIS Student stands over a nest at Doug Fluhrer Park recording the coordinates of the sit

Aaron and I met with Mary twice during the summer. The short excursion was made from our base at the Queen’s University Biological Station (QUBS), located on Lake Opinicon. We had our Trimble GPS and mapping equipment in tow. We walked around the entirety of the park and the K&P Trail with Mary and other members of the group locating covered nests in the region. The coordinates of each nest was mapped using our state-of-the art hand-held GPS unit, the Trimble GeoExplorer, with a time-correcting receiver. This additional receiver yields sub-meter accuracy for measured data points. The average accuracy of the coordinates recorded at Doug Fluhrer Park was approximately 77 cm. More than 100 turtle nests of various species were mapped within the area on the two visits made. 

Now, you may be asking yourself what all this GPS and GIS jargon is, and what its significance for this project, for QUBS, and for biology in general is. Let me try and sort a few things out for you—let’s start with the basics. GPS, which most of us are familiar with, stands for ‘Global Positioning System.’ A GPS instrument is used to determine the geographical coordinates in the field, whereas GIS (Geographic Information Systems) is a framework used to process spatial information on the computer—in our case, we use ArcGIS, the industry standard for mapping. Once the turtle nests were mapped in the field, the handheld GPS was plugged into the computer, and the data were retrieved and input into ArcMap. The coordinates were projected, using mathematical calculations to convert the coordinate system used on the curved surface of the geoid to a flat surface—this process was performed for all data recorded. Once the data were projected into the correct spatial frame, the data points were plotted, and the purpose of this project was clear. Mary and her team are determined to conserve critical turtle nesting habitat and stop the construction of the Wellington Street extension, a proposed arterial road that would run through a narrow waterfront park beside the Cataraqui River. The large population of turtles that have made their their nests in Doug Fluhrer Park are at risk, and Mary, along with many others in the community, do not believe that the extension is necessary. The Friends of Kingston Inner Harbour are huge advocates for the turtles and do not want to see them affected by this proposed construction project.

Remote sensing has become a major component in the field of biology—GIS aids researchers and scientists in storing, analyzing and displaying data more effectively and efficiently. GIS and GPS can be used in myriad studies including phytogeography, hydrology, and conservation biology. From mapping on the ground using Trimble equipment, to using the QUBS’ LiDAR data to extract information from high-resolution satellite imagery, GIS is a constantly changing field which the 2017 QUBS SWEP students delved into. We look forward to seeing what the upcoming years of students will produce and what projects they will tackle!

We thank Mary and her team for having us map the turtle nests in the Kingston region. Mary and The Friends of Kingston Inner Harbour are dedicated and passionate conservation advocates. I look forward to their many successes in the years to come.

Mary et al.
Dayna and Aaron pose with Mary Farrar and videographer Dave McCallum

Mapping Culverts at QUBS. A GIS Adventure.

By Aaron Sneep (Summer Work Experience Program – SWEP – intern 2017)

Mapping Culverts at QUBS By Aaron Sneep (Summer Work Experience Program intern 2017) Queen’s University Biological Station (QUBS) strives to be one of the best field stations in North America. To provide more resources for researchers at the station, QUBS wishes to develop a detailed, fine-scale hydrological map not only its land holdings but also adjacent lands. This summer’s field and data management technicians, Dayna Zunder and myself, have been hard at work collecting data on the locations of culverts in the region to contribute to this hydrological map (Figure 1).

Dayna at culvert
Figure 1. Field and Data Management SWEP intern Dayna Zunder posing alongside a culvert being mapped using a handheld GPS.

The culvert data will be used to complement and correct computer generated terrain models of the region produced from LIDAR (Light Detection and Ranging) data (see Figure 2). The reason we require the locations of culverts to supplement the LIDAR data is rooted in the process of LIDAR data collection. During LIDAR data collection, laser light is emitted from an aircraft flying overhead and each data point collected during the process represents a surface that reflected a laser back to the receiver. LIDAR data is often referred to as a point cloud due to the appearance of the data collected. Figure two shows an example of a LIDAR point cloud.

LiDAR
Figure 2. Side view of a Lidar point cloud for a cluster of trees. Each point in the figure represents a surface that reflected a point of laser light back to the receiver on board a plane flying at low altitudes overhead. (Sneep unpubl. 2017)

Using the point clouds, we can generate terrain models, often referred to as DEMs (Digital elevation model), or DTMs (Digital Terrain Model). With these models, we can simulate how water flows through the region (i.e. imagining how water flows from a high point in the landscape to lower elevations). However, there are concerns and caveats with this approach. The laser used during LIDAR collection cannot penetrate through solid objects such as a bridge or roadway overlying a culvert. In addition, due to limitations in spatial resolution it can be challenging to distinguish the locations of culvert openings using LIDAR data alone. Knowing the locations of culverts and bridges allows us to indicate their locations in the terrain models, and change our flow models that would otherwise appear as impediments to indicate that water is able to flow through these points in the landscape. Therefore, collecting spatial data for bridges and culverts in the region allows us to more accurately represent the flow of water through the watershed. Figure 3 shows a comparison of a DSM with and without culverts indicating where water flow can occur.

DEMs
Figure 3. Left, digital elevation models (DEM) taken from a section of the Rideau trail running through the Massasauga tract of QUBS property, and on the right the same DEM supplemented with culverts and an outline of the Rideau trail. By looking at the DEM alone, it appears that the Rideau trail is a barrier to water flow. However, by knowing the locations of culverts along the trail, we know that water is able to flow under the trail and allows connectivity between the two water bodies on both sides of the trail. With this information, the DEM could be altered to more accurately model the flow of water in the region.

These models of water flow can be useful in biological research because of the important role connectivity can play in biological systems. For example, connectivity between different areas within the watershed can have implications for nutrient transport, species interactions, and dispersal and gene flow. As such, understanding hydrological connectivity within this watershed we hope will be widely applicable and encourage additional research at QUBS. There is still much work left to complete the hydrological model for this watershed, but future researchers at QUBS can look forward to using an accurate, fine-scale hydrological map to illuminate their research questions.

Fabulous Fall Fungi with a Fun Guy

Post by Art Goldsmith

Richard AaronOn October 1st and 2nd, 2015, I had the unqualified pleasure of joining the inimitable Richard Aaron, who teaches the “Fabulous Fall Fungi” workshops at the Queen’s University Biological Station (QUBS). Right, with a weapon in hand, Richard makes a point to the small class (limited to twelve people). Unlike  previous field courses that I have covered for this blog that are intended for undergraduate university students,  this one is open to anyone who is interested. It is a three-day workshop that was offered three times in 2015.  Several participants have taken the workshop several times, as it provides the ideal blend of learning and invigorating outdoor activity. As extra enticement, no two workshops yield the same set of species. If luck prevails, a carefully selected specimen may be cooked for lunch! Before attempting this on your own (eating a specimen for lunch), take the workshop at least once.

I arrived on the afternoon of the second day of the workshop. Collecting and identifying had occurred the entire day before. Both identified and yet-to-be identified specimens were spread across the tables, with Richard sharing salient tidbits about the various fungi with the class.

The Real Reason for the Knife

Richard had just cut the mushroom shown below in half lengthwise.  As you can see, the yellow flesh almost instantly turned blue when exposed to the air.  This bolete mushroom (a bolete has pores on the underside of its cap rather than gills) is called Boletus subvelutipes, which grows on the ground under hardwoods, especially oak, and conifers, particularly hemlock.

Boletus pulverulentus

 

Cantharellaceae family

Above is a Chanterelle (Cantharellus cibarius), the same kind served in fancy restaurants. Those wrinkles look like gills, but they aren’t!

Hexagonal-Pored Polypore

Above is a Hexagonal-Pored Polypore (Favolus alveolaris), which grows on dead branches and is usually seen only after the branches fall to the ground.

Turkey Tail

Above, one of the most common and most recognized polypore mushrooms, Turkey Tail, found on forest floor logs. Unlike many other common names, this one is descriptive. There are other bracket fungi (polypores) which look like Turkey Tail. There’s even a fungus without pores called False Turkey Tail which that bears a striking resemblance.

Richard Aaron 2

Above, Richard explains a central characteristic for identifying gilled mushrooms: how the gills (lamellae) attach or do not attach to the stem. The latter arrangement shown by Richard above, is termed “free gills” because the gills are not attached to the stem. And if the attachment is more narrow, this is called “adnexed”, whereas “decurrent” gills attach at a downward angle along the stem, forming an angular whorl around the stem. The other two gill attachments Richard discussed were “notched” and “sinuate”, both of which are notched along each gill edge close to the stem.

Dryad's Saddle

Above, Polyporus squamosus, a Basidiomycete commonly known as Dryad’s Saddle, which grows on hardwood stumps, logs and trees.  It is an annual bracket fungus, with the characteristic colours, flattened scales and black stem as seen in the photo of this mature specimen (immature specimens lack the black stem). Polypores, as their names suggests, have pores on the underside, which are the openings of tubes. The pores of some species can be seen with the naked eye, whereas other species require the use of a hand lens.

Brett

There are an estimated 5,000 macrofungi in Ontario (fungi that can be seen with the naked eye).  Field guides don’t cover most of these. For example, Mushrooms of Ontario and Eastern Canada covers just over 600 species. Right, workshop participant Brett, who was a great help to me and others, as he has taken the workshop before, was identifying the following mushroom, with a partial veil, rosy-coloured cap and yellow flesh: a Suillus pictus (sometimes referred to as Suillus spraguei), which is found under White Pine trees.

suillus_pictus

We’ll get back to Brett later, as he provided a photo of a magical fungal phenomenon from the local woods.

Coprinus lagopus

Above is one of the “inky cap” mushrooms, which belongs to the order Agaricales (gilled mushrooms). It is a decomposer of wood, and can be found on wood chips, sawdust, and other woody debris. As this mushroom ages, the gills liquefy into a black inky mess, and the cap quickly changes from a bell shape to a split flat cap like the one shown above.  This transformation aids in the distribution of spores, although making the species at this stage more difficult to identify. The one above was identified as Coprinus lagopus. Recent DNA studies suggest different evolutionary relationships, and it is now known as Coprinopsis lagopus, but Richard chose to use the name found in field guides in order to avoid confusion.

Panellus stipticus

Above is a very special mushroom, Panellus stipticus, which is also featured below, doing its magical thing, bioluminescence.  Yes, if you are a good mushroom detective, and find a colony of this mushroom during the day, go back at night to see the show. Thanks to Brett for taking this photo, and to Richard for sending it to me.

Bioluminescence

One peculiar characteristic sometimes used as aid in identifying fungi is odour. It so happens that a small percentage of fungi have distinct odours, reminiscent of coconut, anise, maple syrup, almond extract, coal tar, mouse, radish, cucumber, flour and more. Jennifer is seen below taking a close look at one of these, a Lobster Mushroom (Hypomyces lactifluorum), which she had collected. This unique species does indeed smell much like fresh lobster. It also has a different lifestyle, as it feeds on other mushrooms. Technically, this is not a mushroom, but a parasitic ascomycete fungus.

Hypomyces lactifluorum

Fungi grow everywhere.  They are a universal life form, making up a large proportion of the Earth’s living mass.  Below is a gilled mushroom that grows on conifer cones, particularly white pine and Norway spruce, and also on magnolia cones: Baeospora myosura. The convex shaped cap is crowned with a papilla (literally, a nipple), a characteristic shared with many small, gilled mushrooms, particularly in the genus Inocybe.

Baeospora myosura

After supper, we waited until sundown and then gathered in the lab.  Once we were all seated in one corner of the lab, we gathered the sticks that hosted the Panellus stipticus. The lights were then turned off, and our eyes slowly adjusted to the dark. After a few minutes the Panellus stipticus was passed from person to person so we could see the light show (as shown in Brett’s photo above) close up. I must say this was a moving and mystical experience, one of the highlights of a glorious summer.

Afterwards, we went to the seminar room, where Richard played Taylor Lockwood’s tantalizing film, Spirits of the Forest, about his (Taylor’s) global search for as many species of bioluminescent mushrooms as he could find. It capped the perfect day.

You may find more about Taylor Lockwood, his film and his quest here.

The collecting continued the next day.  Richard wrote to me to say that by the end of the workshop, 161 species had been identified. This is just shy of the record 165 species found in one of the 2014 workshops. Of the 161 species, 33 had not been found in any of the previous workshops.

I followed the participants out on Cow Island as they collected.  Here, Karl is seen collecting two mushrooms for his basket. Ekky (short for Ekkehard) joined us to take a look. Their first guess, which proved to be correct, was that these were Boletus edulis, which is a great find (as this species is a choice edible).

Northern Toothed Fungus

As we left the trail, I took the above photo of a most impressive Northern Tooth Fungus, Climacodon septentrionalis. The Latin name translates as “Northern stair tooth”, alluding to the teeth on its underside, its staircase pattern of growth, and occurrence in the northern hemisphere. It forms massive (35 cm. high and 25 cm. wide is not unusual) clusters each year on wounds of standing hardwood trunks, especially maple.

We reached the Raleigh J. Robertson Biodiversity Centre in time for lunch, which included some especially tasty Oyster Mushrooms we had collected, along with several other species (Richard emailed to say that the class sampled five different species over the three days of the workshop). After lunch, I bid my adieus to Richard and his students. Thanks, Richard for an especially illuminating time. We will see you next Fall at QUBS!

Richard Aaron showing two Galerina autumnalis (the current name is Galerina marginata, but only occurs in the most recent field guides) which everyone should get to know. This small gilled mushroom commonly grows individually or in groups on decaying hardwood and conifer stumps and logs, especially in Fall. It is deadly poisonous thus providing its suitable common name, Deadly Galerina.
Richard Aaron showing two Galerina autumnalis (the current name is Galerina marginal, but only occurs in the most recent field guides) which everyone should get to know. This small gilled mushroom commonly grows individually or in groups on decaying hardwood and conifer stumps and logs, especially in Fall. It is deadly poisonous thus providing its suitable common name, Deadly Galerina.

Ecologically Yours

By Art Goldsmith

August 19, 2015

Another fine summer day in August found me in the company of Grégory Bulté and his Ecology Field Course. Grégory is an instructor at Carleton University’s Biology Department, and according to the university’s website, he is:

“…broadly interested in the ecology, evolution and conservation of animals.”

What this does not tell you is that Grégory’s enthusiasm and knowledge about the life around Lake Opinicon and the wetlands bordering the lake, are boundless.

Officially the course is called “Field Ecology & Natural History” and this year was offered to 12 students during the last two weeks of August at QUBS.

Grégory, with his blue t-shirt in the foreground, here supervises the survey of some of the animals that live along the shores of Lake Opinicon, some rarely being seen at all. The purpose of this field study is to learn about the diversity of the lake and surrounding lands.

Grég raises the trap. The mysteries of the lake are revealed

Turtles, fish, frogs and snakes are briefly captured, photographed, identified and then released. Lake Opinicon is home to some less common turtles, like the Northern Map Turtle (Graptemys geographica) and the Eastern Musk Turtle (Sternotherus odoratus). Note the excellent Latin species names, “geographica” and “odoratus”. They are both so descriptive of the animals. Map Turtles are named for the markings on their shells, which are reminiscent of the lines of a topographical map. Musk Turtles are also called Stinkpots, because they emit a stinky liquid from their musk glands when disturbed.

A Northern Map Turtle swims for the camera. (Photo by Grégory Bulté)
A Northern Map Turtle swims for the camera. (Photo by Grégory Bulté)

Below is a photo by your blogger of a very shy Musk Turtle taken at Lake Opinicon a few years ago. It is rare to see one out of the water. They do, on occasion, emerge onto a snag that angles out of the water, like this one, usually in an area that is well hidden. These are small turtles, usually less than 13 centimetres long. Map Turtles are among our larger turtles. Females in Lake Opinicon have measured up to 26.5 cms long and males up to half of that length. They are often seen basking on larger rocks in our rivers and lakes in Eastern Ontario.

Musk Turtle

This photo of Grég tells us about the joy of the field course. It captures the underlying good feelings from learning in the field. The photos that follow were all taken by or provided by Grég.
This photo of Grég tells us about the joy of the field course. It captures the underlying good feelings from learning in the field. The photos that follow were all taken by or provided by Grég.
The lake, the sky and the clouds dwarf the class as they check a trap. Many fish were in this trap. The majority are sunfish, mainly Bluegills and Pumpkinseeds (Lepomis spp.)
The lake, the sky and the clouds dwarf the class as they check a trap.
Many fish were in this trap. The majority are sunfish, mainly Bluegills and Pumpkinseeds (Lepomis spp.)
Many fish were in this trap. The majority are sunfish, mainly Bluegills and Pumpkinseeds (Lepomis spp.)
Every grade-school kid's first ecology lesson... big fish eat little fish, in this case, a fingerling Bass is swallowing a neighbour not that much smaller than the Bass.
Every grade-school kid’s first ecology lesson… big fish eat little fish, in this case, a fingerling Bass is swallowing a neighbour not that much smaller than the Bass.

Blackchin Shiner

Two of the many representatives of the Cyprinidae family (minnows and carp) in Lake Opinicon. Above is the Blackchin Shiner (Notropis heterodon) and below is the Golden Shiner (Notemigonus crysoleucas).  The Blackchin Shiner is native to the Great Lakes‒St. Lawrence basin. It is a small fish, rarely exceeding 6 cms.  The Golden Shiner may grow up to 30 cms., although most are in the size range pictured below.  This popular bait fish is native to much of eastern and central North America and has been accidentally introduced well beyond its native range.

Golden Shiner

Frogs abound in and around the lake.  The first two photos, above, feature a frog that rarely leaves the water, the American Bullfrog (Lithobates catesbeianus). Our largest frog in Ontario, the Bullfrog is very aggressive with other frogs—and anything else that moves!  The third photo, above right, is a Green Frog (Lithobates clamitans). This is also a large, mostly aquatic frog, which is frequently mistaken for the Bullfrog. Note the clearly visible ridges running down the sides of this frog’s back.  These ridges are distinguishing marks of the Green Frog. Below left is a photo of a Leopard Frog (Lithobates pipiens). Leopard Frogs travel far from the water during the summer months and return to overwinter in lakes and ponds. Below top centre is a Wood Frog (Lithobates sylvaticus), distinguished by facial side masks. Scrunched up on the Milkweed leaf, below right, is a Grey Tree Frog (Hyla versicolor), our loud summer frog. Its call is often mistaken for a bird. As the Latin name suggests, the Grey Tree Frog changes colour to match its surroundings for better camouflage. The Green Frog and Leopard Frog photos were taken by Art Goldsmith. The remaining four photos were taken by  Grégory Bulté.


The other group of common, and usually hidden, amphibians is the salamander (above lower row).  The three species above are best seen in early spring when spring melt waters and warm rains form ponds and pools where many salamanders breed in the evening hours. These salamanders spend most of their time dug into the soil or beneath rocks and fallen tree limbs in moist forests where they hunt for invertebrates. The three of Ontario’s 12 species shown here are, from left, Blue-spotted (Ambystoma laterale), Spotted (Ambystoma maculatum), and the lung-less Eastern Red-back (Plethodon cinereus). The latter is a member of the Plethodontidae family.  The species in this family have no lungs, and therefore are restricted to moist, terrestrial habitats where they breed and lay their eggs.  The other two Ontario members of this family are the Two-Lined and the Dusky Salamanders, neither of which have been recorded at QUBS.


For a slight change of focus, we look at a few reptiles.  Above are two photos of a Northern Water Snake (Nerodia sipedon sipedon) that posed for students.  This common reptile is found in and around ponds, lakes and rivers throughout the southeastern portion of Ontario.  Below is a much rarer species, the Eastern or Grey Ratsnake (Pantherophis spiloides), an effective predator of rodents and other small animals. The large tracts of conservation lands protected by QUBS are vital to the Ratsnake’s  survival as the population in the Rideau Lakes is threatened; whereas in southern Ontario, it is endangered.

Grey Ratsnake

Of course, the underpinnings of any functioning ecosystem are its wealth of native plants and fungi, both macroscopic and microscopic. Fungi make up a very large percentage of the Earth’s biomass.  Then there are the invertebrates—the huge diversity of arthropods in Eastern Ontario, and the other invertebrate phyla—all forming the base of food and energy production for all of us vertebrates.  The previous blog post featured the entomology field course and just a sample of the insects to be found in the area around QUBS.  Here are a few more insects , other invertebrates and a small sample of the local plants.

Note that fungi will be the subject of my next post, Richard Aaron’s Fabulous Fall Fungi field course.

Widespread throughout North America and ecologically significant in our lakes, ponds and marshes, the Yellow Pond-lily (Nuphar lutea), pictured above left provides shelter, food and stabilization for many animals, including some of the aquatic invertebrates. To the right of the Pond-lily is a typical dragonfly (Order Odonata) nymph. The next photo is a freshwater crustacean (possibly the Waterlouse, a species of the genus Asellus, Order Isopoda). On the far right in this sequence of four photos, one of our Leech (Hirudinea) species is pictured.  Healthy ponds and lakes are teeming with these and many other invertebrates, zooplankton and phytoplankton, which provide the basic food for all larger species.

A Jagged Ambush Bug female (Phymata americana) munches on a fly, while two male Ambush Bugs attempt to mate with her.  All of this is happening amongst tiny Goldenrod (Solidago spp) flowers.  This is a LOT of biology in one photo!
A Jagged Ambush Bug female (Phymata americana) munches on a fly, while two male Ambush Bugs attempt to mate with her.  All of this is happening amongst tiny Goldenrod (Solidago spp.) flowers. This is a LOT of biology in one photo!

Laetiporus sulphureus

We will explore in great detail the world of the fungi in our next post. I didn’t see this fungus (above) during the fungi course though.  The Laetiporus sulphureus, which has a preference for Red Oak,  has several common names, including Sulphur Shelf and Chicken-of-the-Woods.

Above, these are aquatic Leaf Beetles, Donacia sp.,  mating and another common aquatic invertebrate, a Damselfly nymph (Odonata).

Monarch Butterfly caterpillar

We are not seeing as many of these on Milkweed as we have in the past.  In a walk with two other naturalists recently, we thought it would be approrpiate to change the name of the Common Milkweed to Monarch Flower, to honour this plant which hosts the Monarch Butterfly caterpillar, like the one shown above.

Hay field

Hay fields, as in the stunning photo above, are an excellent habitat to collect a wide diversity of insects and other Arthropods.  Lastly, the Grégory Bulté Ecology Field Course class of 2015.

Ecology Field Course class of 2015

The Bugman Cometh

By Art Goldsmith

August 11-12, 2015

I spent quality time on two fine August days with THE Bugman of Ontario, Marvin Gunderman, an Entomology professor at McMaster University in Hamilton, Ontario. Each year, a maximum of 14 very fortunate students spend two weeks with Marvin and two very motivated co-instructors, one of whom is a very capable entomologist and photographer, while the other is a crop plant specialist.

The course is officially called “Field Entomology & Ecology“. Students receive a full Ontario Universities course credit for completing the course. For more information visit http://fieldentomology.com/.

After lunch on the first day, I found a Hickory Tussock Moth caterpillar (common at QUBS, but not in the upper Ottawa Valley, where I live).

Immediately, I showed the caterpillar to Dave, who identified it. Dave travels to QUBS from his job at the National Museum of Denmark, where he is the Collection Manager for Diptera (flies).

First thing in the morning, students gather around Marvin to take the long, long trek down the QUBS road to the first collecting site of the day, meadows and fields a-buzz with a diversity of insect life.

First thing in the morning, students gather around Marvin to take the long, long trek down the QUBS road to the first collecting site of the day, meadows and fields a-buzz with a diversity of insect life.

Only seconds have elapsed, and Marvin's keen eye has spotted a worthwhile insect model amongst the Goldenrods.
Only seconds have elapsed, and Marvin’s keen eye has spotted a worthwhile insect model amongst the Goldenrods.
Collection nets
The happy troop, collection nets in hand (except for course instructor Dave, centre) troops off down the road in search of their quarry.
Reaching the meadows, Marvin stops and surveys the scene, looking for the best and richest microhabitat to find a rare insect, or, at least, an insect representative of one of the more esoteric orders.
Reaching the meadows, Marvin stops and surveys the scene, looking for the best and richest microhabitat to find a rare insect, or, at least, an insect representative of one of the more esoteric orders.
Jeremy, above, describing the REALLY big beetle that got away.
Jeremy, above, describing the REALLY big beetle that got away.

Tales in Horse Poop

We ecologists and naturalists are an easily distracted lot. We bring new meaning to the word “FOCUS”. Indeed, who could resist focusing on a very large Arachnid, which had decided to occupy equine waste. Certainly, Marvin could not resist. Nor could I. Marvin is seen below, fancy home-made diffuser and flash at the ready with super macro lens to take a photo to record the sighting. Initially identified as a “Nursery Web” spider, the evidence later pointed to one of many Wolf spiders (family Lycosidae), which are indeed close relatives of the Nursery Web spiders (family Pisauridae) and it does take a close inspection of the arrangement of the multiple eyes to sort out. Our largest Canadian spiders are members of these two families.

Marvin 3

Fortunately, my own photo, below, does show the arrangement and decided the identification.

Lycosidae

Inspired by this impressive Lycosidae, for comparative purposes I went onto the QUBS wharf to find the most commonly seen Pisauridae, the Dock or Wharf Spider, which has caused a few “starts” in many cottage vacationers in southern Canada.  It took me seconds to find a half dozen, and another hour to get a decent photo of these shy creatures (below).

Pisauridae


All students are required to bring cameras that are able to take macro photos (i.e., lenses which are able to get very close to a small object like an insect).

Simonne taking a photo for a record of an insect on a thistle flower.
Simonne taking a photo for a record of an insect on a thistle flower. All students are required to bring cameras that are able to take macro photos (i.e., lenses which are able to get very close to a small object like an insect).

Alex

Above, Alex demonstrates the capture and preservation of an insect specimen.  Students are required to create a collection of the most common insect orders, and to arrange and identify their specimens, as shown below.  Pins are used to secure specimens onto Styrofoam.

Pins

Gunderman Course

Right, Skippers are common and diverse butterflies throughout North America. One of the most common Skippers that we see in late summer is the European Skipper (Thymelicus lineola), an exotic species from Europe that came to North America in the early part of the 20th century, when agriculture was planting a lot of Timothy grass (Phleum pretense), also from Europe. Until this summer, I often overlooked Skippers, assuming most were European. I found that many native Skippers still abound, such as the Crossline Skipper (Polites origenes). European Skippers are orange in colour. This Crossline Skipper is dull with a very faint pale band, clearly visible in this photo.

Cicada

Above, one of the students was able to capture a newly emerged Cicada, the “warm-days-of-summer” buzzing True Bug, of the order Hemiptera. We have only one species in Eastern Ontario, the Dog Days Cicada, Neotibicen (Tibicen) canicularis.

And what else is in all of those jars the students used for collecting?  Like the Diptera (the insect order that includes all of the flies, collectors will also find a lot of Coleopterans (the Beetles insect order). During late summer days in fields like the one in which we were collecting, there are many members of the Silphidae, Carrion Beetles, such as  the one pictured below, feeding on insects. So far in North America, there are less than 50 species of Carrion Beetles described. Perhaps one of the budding entomologists on this course will describe many more in the future.

Carrion Beetle

Click on this link to learn more about the Silphidae (Carrion Beetles).

I was distracted by a very large spider (our SECOND spider distraction of the afternoon. See “Tales in Horse Poop” above for another scintillating story, which even Marvin could NOT resist). Female spiders are generally much larger than males. Therefore, I expect this is a female Shamrock Spider (Araneus trifolium), as it was just under an inch in length.  Unlike the two spider families discussed under “horse poop”, which hide and surprise prey, this one is an orb weaver.

Shamrock Spider


Boathouse

I took a break from the lab chemicals to visit the QUBS wharf, above.  I was after the Wharf Spider, and I also was fortunate to see a common dragonfly of Eastern Ontario, the Black-shouldered Spinyleg (Dromogomphus spinosus), below.

Black-shouldered Spinyleg


Marvin 4

Back on the trail, the intrepid class receives Marvin’s wisdom, above, before spreading out to capture insects in a very different habitat, the wetlands around Cow Island. Below, course instructor Jen, who annually takes leave in order to help Marvin deliver this course, briefly glances up before returning to her insect detective work.

Jen

Above left, enthusiasm abounds as students collect water insects, like the Water Scorpion (Genus Ranatra), a predatory insect, in the right-hand jar, above right.

Jen and Dave

Later that evening, Jen and Dave take a moment to pose for this awesome photo (above), after a job well done. Meanwhile, below, the incredibly handsome duo of Marvin Gunderman, and your blogger, Art Goldsmith, take a brief millisecond break from their very serious taxonomical deliberations. Note Marvin’s “insect” t-shirt and Art’s hand lens!

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The annual show of tree leaf colour

Constance Nozzolillo, BA Hon., MA Queen’s, PhD UOttawa
Retired Professor of Biology, UOttawa

Life member of the Phytochemical Society of North America, emeritus and founding member of the Canadian Botanical Association and the Canadian Society of Plant Biologists, emeritus member of the Botanical Society of America and the American Society of Plant Biologists, member of Groupe Polyphenols

As the end of summer nears, the green leaves of our deciduous trees undergo a change in colour.  Those of some become a brilliant red like the red maple while others change to a yellow or golden colour like the birch and all of them ultimately become a brown colour.  Despite the economic importance to our tourist industry of the autumnal display of colour of the trees in our forests, relatively little scientific study has been made of this annual phenomenon.  As a result, we are subjected in the newspapers and on websites to an imaginative description of the process too often only distantly based on established facts.  Of a half dozen of the many websites turned up by a Google search of “autumn color”, not one explanation conforms entirely to the present incomplete state of knowledge.  However, in the past two decades, ground-breaking work in the north-east USA and in northern Sweden has yielded a deeper understanding of the coordinated processes ongoing in the leaves as deciduous trees prepare for winter.

The reason for the autumnal change is variously attributed to lower light, cool temperatures, or various other environmental factors, although many descriptors have now grasped the fact that daylength is significant.  In point of fact it is not the daylength itself that is important.  The trees and shrubs recognize the increasing length of time between sunset and sunrise, i.e. the dark period, as the summer progresses and thus begin to make preparations for winter survival. They are able to do this because of an invisible blue-green pigment called phytochrome in their cells.  This pigment serves as a timepiece, enabling the plant to ignore the suggestion of warm autumn days that summer may never end and to realize that ambient temperature is not a reliable marker of the seasons. Thus the process called leaf senescence is begun.

Autumn_Scene_Bulte_October_2014
Autumn scene at the Queen’s University Biological Station. Photo by Grégory Bulté.

The colour change of the leaves is only one of many processes going on as the leaf senesces but it is the one most obvious to us.  The green leaf of the maple and other trees contains several pigments in addition to phytochrome.  Most visible are the green chlorophylls present in tiny intracellular structures called plastids.  These pigments are the key to our survival on earth because of their ability to trap the energy of sunlight for food production by the leaf.  Also present in the plastids but masked by the chlorophylls are several kinds of orange and yellow pigments called carotenoids, a name derived from the Latin name of the orange carrot root.  Over the course of a few days or weeks, the green of chlorophyll disappears.  The carotenoids also are destroyed but not so rapidly as the chlorophylls, thus the leaf becomes a yellow colour. They are yellow, not orange, because the xanthophylls, the yellow carotenoids, are three times more abundant than the carotenes , the orange carotenoids.  At the same time, the leaves of some species begin to produce red-coloured pigments called anthocyanins.  (These are the same pigments that are in the healthful blueberry and cranberry fruits we are encouraged to eat.)  If nearly every cell of the leaf contains these pigments in high concentration, the leaf will be a brilliant red colour like those of the red maple, the carotenoids again masked from view.  If the concentration is low, the leaf will appear orange like those of the sugar maple because we see the red of the anthocyanins mixed with the yellow of the carotenoids.  Thus the orange colour seen in sugar maple leaves is not due to orange carotenoids as frequently stated, even in some botanical textbooks, but to the mixing of the primary red and yellow colours. Didn’t we all learn that as kids?  Newly formed carotenoids do result in a red colouration in some species that retain their leaves in winter, red cedar being an example.

Since the above discusses the mixing of colours, at this time I will also point out that there are some tree leaves that produce anthocyanins all summer, a horticultural variety of Norway maple for example.  It cannot be ignored that the leaves of these trees are very dark in colour, and certainly not a clear green.  That is because nearly all the light passing through the leaf tissues is absorbed by the mixture of pigments thus yielding a very dark purplish or blackish colour.

How the annual disappearance of an amount estimated to be a billion tons of the green chlorophylls is brought about has been subjected to rigorous study only in the past three decades.  Some popular reports state that chlorophyll is broken down and remade all summer long, that it is “used up” in the photosynthetic act.  It is true that chlorophyll is easily broken as evidenced by the rapid bleaching of the leaves of an over-wintered houseplant abruptly put out into bright spring sunshine, but a leaf properly adjusted to bright light conditions does not bleach.  One of the roles of the carotenoids is to protect the chlorophyll from such destruction.  And of course, new chlorophyll must be made as new leaves are formed on the tree or to replace that damaged due to excessive light exposure, but the deliberate breakdown of chlorophyll in a senescing leaf seems to be a one-time event.  It is now known to be a highly controlled, multi-step process associated with major changes in the structure of the plastids.  An important result for the tree is the release of nitrogen, the most essential element for plant growth, from the proteins to which the chlorophylls had been attached.  The removal of this nitrogen from the leaf for storage in the trunk or other parts of the tree before the leaf falls off is a significant activity.  Results available to date demonstrate that trees vary considerably in their ability to do this.  Some are able to remove as much as 80%, whereas others remove relatively little before the leaves fall. Surprisingly, the nitrogen bound into the chlorophyll molecule itself is not made available for transport and so remains in the fallen leaf.

And what is the purpose, if any, of synthesizing new complex chemical structures like the anthocyanins?  Scientific study directed to answering this question has begun only in the past few decades and provides some evidence to indicate that the red pigmentation may protect the leaf from the damaging effects of light so that more of the valuable nitrogen and other nutrients can be transferred to the trunk.  Another question frequently asked is “Won’t the process of anthocyanin synthesis require energy that the leaf will no longer have freely available because of the loss of chlorophyll?”  Of course energy will be required both to make the anthocyanins and also to transport the nutrients but this energy can be provided by “burning” the residual sugars in the cells of the leaf in the tiny “furnaces” called mitochondria.  These bodies provide the energy necessary for the activities of every living cell, plant or animal.

And how are the red pigments made?  Contrary to statements frequently made in the past, these red pigments are not present in the leaf blade during the summer in the green leaf, although the leaf stalk may be red in some species, but are made anew in the autumn in those species equipped with the necessary genes.  That fact is now recognized in most popular explanations.  The answer usually provided to the “how” question, however, completely ignores the current state of knowledge of the process by stating that the sugars remaining in the leaf as a product of photosynthesis are converted into anthocyanins.  This may sound reasonable especially since some sugars are incorporated into the final structure.  However, innumerable studies over the past several decades have shown that building of the part of the anthocyanin molecule that is responsible for the red colour involves sugars only as a source of energy to drive the process.  It occurs in the cytoplasm of the cell in a tightly coordinated multi-enzyme process, the final step of which is to add one or more sugars.  Only then is the molecule so formed called an anthocyanin.  It does not leave the cell in which it is formed but is deposited into the vacuole, a large sac filled with a slightly acidic watery solution that occupies most of the cell volume.  The amounts of anthocyanins subsequently produced depend on many factors, including temperature, light exposure, and nutrient status.  Scientific studies back up the observation that bright sunny days and chilly nights result in the best display of colour.  A current “fashion” in popular explanations is to add that “chilly” cannot include sub-zero temperatures, but a touch of “jack frost” overnight does wonders to enhance the colouration of our hardy native species!  It is true that freezing will kill the leaf cells but no one seems to have tested the frost hardiness of our maple leaves.  If the weeds in our gardens can survive overnight temperatures of -1C or -2C with no ill effect, it seems logical that so can the leaves on a native tree.  On the other hand, in warm weather, especially if the days are overcast, much of the chlorophyll remains and little of the red pigments is made.  As any casual observer may note, more red colour is present in parts of the tree fully exposed to sunlight.  It is important to keep in mind that a typical leaf is comprised of many individual cells each responding more or less independently to its environment.  Although the overall process of preparing for winter is synchronized and ultimately leads to leaf fall, some cells may retain normal functioning much longer than others.  Thus the colour of the leaves is not the same in all parts of the tree or even in all parts of the same leaf.

While all these colour changes are ongoing, the leaves are prepared for the phenomenon familiar to us as leaf fall.  Preparation for separation from the tree is done so as not to leave an open wound at the point of attachment.  An impermeable corky layer, called an abscission layer, is gradually built across the base of the leaf stalk. Such a layer is obviously incompatible with the already-mentioned desirability of removing as much as possible of the valuable nutrients in the leaf for storage in the trunk; how can nutrients be moved past an impermeable layer?  The solution lies in the fact that the tissues through which the nutrients are moved, the vascular tissues which make up the veins of the leaf, are the last part of the leaf stalk to be cut off.  The statement usually made in popular explanations is that the sugars (sucrose, the sugar we put in our coffee, is the form in which sugars are transported in the plant) are trapped in the leaf by this layer and are thus available for conversion to anthocyanins.  But is it true that sugars are indeed trapped?  How long into the autumn is water carried into the leaf?  And how long does the part of the veins responsible for moving nutrients out of the leaf remain functional?  All we know for certain is that finally the leaf is held onto the tree only by the veins which ultimately break off to allow it to float away. Its point of departure is marked by a characteristic leaf scar that can be used to identify the tree in winter, its smooth corky surface marred by the broken remnants of the vascular tissues.

And now we come to the matter of the final brown colour seen in the fallen leaves and also in leaves of some species that are still attached as in the white oak, for example.  Again, explanation of the brown colour on websites is highly variable and mostly unrelated to the probable truth.  There is no brown pigment already present in the tree leaves under discussion, or at least none that any phytochemist has isolated and reported on.  The most likely cause of browning is the phenomenon familiar to anyone who has left a slice of apple or potato exposed to air.  The exposed surface soon becomes brown because the tissues of apple and potato contain an abundance of colourless phenolic substances that are polymerized by enzymes to yield a brown shade.  (There is now a genetically engineered variety of apple and another of potato that do not brown when cut, but will anti-GMO activists manage to prevent them from reaching the market?  Personally, I hope not!)

Tree leaves also contain a complex mixture of phenolics, most of them formed at various steps of the same pathway that leads to anthocyanins as well as the enzymes noted above.  Notable among them are two classes of vegetable tannins, condensed tannins, polymers of catechins whose synthesis branches off at a late stage of the pathway and hydrolysable tannins that are polymers of gallic acid combined with glucose.  (The chemistry of these compounds is exceedingly complex but that has not prevented their use over countless centuries in the production of leather from animal skin!) Thus there are ample compounds available for the browning phenomenon to occur in senescing leaves.
Our trees must maintain the delicate balance of retaining normal functioning of the leaves for as long as possible consistent with making adequate preparations for winter!  Beginning the process of leaf senescence too soon will rob the tree of the ability to make food during the warm days of autumn but, on the other hand, starting too late may result in an abrupt cessation of all metabolic activity due to a killing frost before the tree has time to recover nutrients from its leaves.