Harmful Algal Blooms – Part 6: Finally, a Project

This semester, I’ve been working with Dr. Kenton Ross, the national science advisor at NASA DEVELOP, to understand the spectral properties of Alexandrium monilatum. I am using aspects of this work as my term project for GIS 295 and GIS 255.

In Harmful Algal Blooms – Part 5: Trouble in Data Land, I discussed the challenge of completing a mapping project when the data has lost its geospatial reference.  However, we were able to obtain approximate locations for each hyperspectral scene by estimating pixel size and lining up the time field in the hyperspectral data  with the time field in the the flight path data set. You can see the scene center lines in black on the image below.

Scene Center lines

The water in this map looks unusual. NDVI is a band ratio index used to indicate vegetation. I used ((Landsat 8 band 5 – band 4)/ (band 5+band 4)) to mask out the land  in ArcGIS. I then clipped out the unmasked water and used false color imagery (bands 6, 5 and 4) to enhance different features of the water.  The water on the right side looks thick and yellow because it is very turbid.

Once I knew where each scene was located, I analyzed each hyperspectral image individually. This is York scene 5.


The first thing I noticed was that any detail was hard to see. That’s because one side is in shadow. So, I clipped out the black edges and the bright, overly illuminated right side of the image. I also reduced my number of bands from 283 to 13 carefully selected bands in order to reduce noise and maximize the spectral signal. The resulting image is in the slide below.


The deep red swirl is the algal bloom.

I used bands 146 (710 nm), 128 (665 nm) and 85 (559 nm) to create a NIR, red, green false color composite to highlight areas with high chlorophyll.  That’s the second image in the slide.

High chlorophyll should appear red in these images, but the areas of intense blooms appeared bright yellow-green. This is because there is also a red pigment in the blooms that gives them their color.

The third image is estimated chlorophyll. I used the  ratio of band 146 (710 nm) over band 128 (665 nm) as a proxy for chlorophyll-a. Red and yellow indicate high chlorophyll, while dark blue indicates low chlorophyll. You can see that despite the red color, the algal bloom has plenty of chlorophyll.

What about the third image? I used ENVI to run an unsupervised classification. This means that ENVI sorted the pixels in the image into five groups according to their spectral properties. I then used class statistics to obtain the spectral signature of each group. That’s the big image on the left of the slide.

I repeated this procedure on seven images from the York River, four images from the James River, and one image from Mobjack Bay. The signatures in the York River were distinctive enough that we believe we are on the right track to find the spectral signature of Alexandrium monolatum.

For my GIS 295 class project, I created an web app which shows the imagery and spectral signatures at each scene. If you are a member of Northern Virginia Community College GIS group, you can access the app here. Everyone else will have to wait until we are ready to make the app public.


Moses, Wesley J.; Gitelson, Anatoly; Perk, Richard L.; Gurlin, Daniela; Rundquist, Donald C.; Leavitt, Bryan C.; Barrow, Tadd M.; and Brakhage, Paul, “Estimation of chlorophyll-a concentration in turbid productive waters using airborne hyperspectral data” (2012). Papers in Natural Resources. Paper 313. http://digitalcommons.unl.edu/natrespapers/313


Using Beetles to Learn About Past Climates

How many species are there on Earth? Nobody really knows, but one study estimated the number to be about 8.7 million and most of these species are insects.

The largest group of insects are the beetles. Beetles make up about 40% of insects and 30% of animal life. Why are there so many beetles?

Scientists used to believe that beetles had high rates of speciation, but a recent study co-authored by the awesome Dena Smith suggests that beetles might just be really good at avoiding extinction. You can read the paper here.

This resistance to extinction means that many beetle species are very old. Species living now were around millions or even tens of millions of years ago.

Beetle species don’t just live a long time, they are also fussy about where they live. They want the humidity and temperature in their homes to be just right. If it gets too hot or too wet or too cold, they move out and find another home.

Long species durations and specific habitat requirements make fossil beetles very useful for learning about past climates, especially the Pleistocene.

The Pleistocene Epoch is defined as the time period from about 2.6 million years ago to about 11,700 years ago. Like today, the Pleistocene was a period of rapid climate change. During this time there were between 20 and 30 glacial intervals where much of the world’s temperate zones were covered in ice. These glacial intervals were separated by warmer interglacial periods when the ice receded. This map shows the Wisconsinan glaciation 18,000 years ago.Glaciation

I wanted to see if I could use GIS techniques to reconstruct Pleistocene climate using fossil beetles.  I chose two sites for my study: The Titusville Peat in Pennsylvania and Ziegler Reservoir near Snowmass, Colorado. The Titusville site is an ancient peat bog during the mid-Wisconsinan interstadial between 43.5 and 39 thousand years ago (Elias, 1999).

Ziegler Reservoir is located near Snowmass Village, a ski resort in Colorado. In 2010, work began to widen the reservoir, but the remains of a mammoth were uncovered, leading to a paleontological excavation. Numerous mastodons, mammoths, ground sloths, bison and camels as well as insects were recovered from the site. Carbon dating indicates the age of the site ranges from 126 to 77 thousand years old (Elias, 2014).Sites

I obtained the list of species for Titusville from the Paleobiology database and the species from Snowmass from Elias’s 2014 paper about the site.

I looked up species ranges using Global Biodiversity Information Facility (GBIF) and USGS’s Biodiversity Information Serving Our Nation (BISON) databases. These are sites that list museum specimens. Each record includes the longitude and latitude where the specimen was collected.

To determine climate preferences, I used two sources: The global ecological land unit map and Koppen Geiger climate zones

The global ecological land unit map was developed by esri and the USGS. It is a 250 m resolution raster containing information about bioclimate, landcover, lithology, and landforms. Here are my fossil insect species on top of the global ELU map.GlobalEco

The Koppen-Geiger climate classification was first developed in 1884. It has been revised several times, but remains the most widely used climate classification system. The system divides Earth climates into 30 zones with unique temperature, moisture and weather properties.


I used GIS a sequence of spatial joins to connect the ecological and climate data to species. I learned that 43.5- 39,000 years ago, when the Titusville Peat was deposited, Titusville was in Köppen Geiger zone Dfc, which subarctic with cool summer, wet all year. This means that winter temperatures were as low as -40 C (-40F) and summer temperatures as high as 30 C (86F) — much cooler than current climate zone Dfb (humid continental). The bioclimate was cold and wet and the dominant vegetation included needle leaf /evergreen forests.

The Snowmass data was more complicated because it represents almost 50,000 years and the site is on a mountain. On mountains, wind picks up flying insects from warmer, lower elevations and carries them to cooler, higher elevations in a process called orographic lifting.

To compensate for the long time period and the effects of orographic lifting, I divided the beetle assemblage into five time intervals and I removed all the flying beetles from the analysis.

The climate at the Snowmass site was initially similar to today’s climate. Insects suggest Koppen-Geiger Zone Dfc, subarctic with a cool summer.Over the next 2-3 intervals, the climate gradually cooled from Zone Dfc to to zone ET (tundra with no warm season). By the 4th interval, all insects indicated Koppen Geiger zone ET or tundra. But, in the last interval, the prevalence of insects from Zone Dfc indicates warming. As in Titusville, the bioclimate was cold and wet and the dominant vegetation included needle leaf /evergreen forests.

You can see the modern distribution of Dfc and ET in this map.SubArcticTundra

Using insects to model past ecosystems isn’t a new idea. But, as far as I know, no one else has used GIS to join insects to specific ecological variables for climate reconstruction. I will be presenting the more scientific version of this research at the Geological Society of America Annual Meeting in Baltimore on Tuesday, November 3.

On Shaky Ground Part 1: Earthquakes in Virginia

It’s been just over four years since a 5.8 magnitude earthquake in the Central Virginia Seismic Zone damaged the Washington Monument. That was a significant earthquake for our area.

Last Sunday (9/27/15) the Central Virginia Seismic Zone experienced another earthquake.  The magnitude 2.0 quake was one of hundreds of small earthquakes that have occurred in the area over the past four years. And, InsideNova feels the need to report every single one.

So, is Virginia really a seismically active area? I placed esri’s USA Earthquake Risk map on top of a topographic base map. The map shows potential ground shaking intensity from earthquakes, an estimate of the amount of damage an earthquake is likely to cause in an area.  I set the scale so the highest risk in shown in dark red while the lowest risk appears as dark blue. I added the past week’s worth of earthquakes (from esri Disater Response) to the map. You can see the our 2.0 quake in Central Virginia.

Seismic zones

Moost of Virginia falls in the medium blue range indicating a very low risk of damage from earthquakes. Our recent earthquake is small compared to the many of the other earthquakes that occurred in the U.S. last week.

It’s not surprising that the West Coast of the United States is covered in red and orange. The California, Oregon, and Washington coasts are active margins. This means that the edge of the continent coincides with the edges of one or more tectonic plates (in this case: North American, Juan de Fuca, Pacific). Geologic activity such as earthquakes and volcanoes generally occurs at the edges of tectonic plates.

The East Coast is a passive margin. The eastern edge of the North American tectonic plate is far out in the Atlantic ocean. So, geologic activity on the East Coast and most of the U.S. is relatively rare as indicated by the blue coloring.

Behind California is an area known as the Basin Range province. This is the remnant of an ancient rift zone. In the early Miocene (about 17 ma), the North American continent began to stretch and thin. But, before the continent could rift into two tectonic plates, seismic activity stopped. This left a network of faults which still responds to the stresses from activity on the West Coast. The New Madrid fault zone which underlies Alabama, Arkansas, Illinois, Indiana, Kansas, Kentucky, Mississippi, Missouri, Oklahoma, Tennessee and Texas is another example of an ancient rift zone.

But, not all rift zones are ancient. The red area in Northern New York and New Hampshire indicates activity from the St. Lawrence rift system, an active rift zone that runs along the St. Lawrence River. Perhaps one day, North America will split and a new Canadian plate will form.

If you are looking carefully you might notice that there are medium blue areas in the middle of continents far from any plate boundaries that have recently experienced larger earthquakes. Is that rifting? Does that mean we should worry?

No, it’s not rifting, but we may have reasons to worry. The cluster of earthquakes in Oklahoma includes several with a magnitude between 2.0 and 3.0. These small earthquakes have been linked to fracking rather than seismic activity. The 3.2 earthquake near Stamford, NY may also be caused by human activity. It is likely the result of water pressure from the Gilboa Dam.

Like Oklahoma and New York, Virginia has networks of ancient faults that can be reactivated by human activity. However, seismologists believe that most of our earthquakes are simply the result of old faults moving because of sea floor spreading in the Atlantic Ocean.

You can view my map here.

Where Will I Put the Bottled Water?

When we were in class on Wednesday night, Hurricane Joaquin seemed to be headed straight for Virginia. I’m pretty well prepared, but I donated last year’s bottled water stash in the spring. So, on Thursday morning, I stopped at Target to stock up on bottled water which is now sitting in the hallway because I don’t have space for it.

The latest forecasts show that I didn’t really need to rush and buy water; Joaquin isn’t likely to reach the East Coast. But, thoughts of hurricanes inspired a map.


I mapped esri’s active hurricanes and recent hurricanes as well as hurricane tracks from historic hurricanes (in blue, from Maps.com) on top of a base map. Hurricane Joaquin’s path is shown in black, while the yellow dots represent the tracks of recent hurricanes. As you can see, we might be safe from Hurricane Joaquin, but (historically speaking) it’s only a matter of time until a hurricane does hit Virginia.

You can see the ArcGIS Online map here.

I think I’ll keep the water.