Wednesday, November 28, 2012

Aquatic Plant Species Domination - Collaborative Research Using BioBase

Contour Innovations is proud to announce a collaboration among aquatic industry leaders to better understand aquatic species domination and lake ecosystem changes over time.

FIGURE: Left map: sampling points where Eurasian watermilfoil was present (yellow) and absent (X) during a survey on Gibbs Lake, Rock Co. WI (77 acres) in summer 2012.  Points are overlain on a vegetation biovolume “heat” map from passively collected sonar data and processed by ciBioBase.  Red colors represent vegetation that is growing near the surface.  Right map: Eurasian watermilfoil “Dominance” map rendered from both species survey and biovolume data.  Areas that are yellow and red areas where Eurasian watermilfoil is dominating the plant community and growing near or at the surface.

For over a decade, point-intercept survey methodology for aquatic plants has become a standard tool for lake resource managers and researchers.  The standard methodology entails sampling a uniform grid of points on a lake noting presence absence of species at each point with a rake. It is a relatively rapid way of objectively sampling aquatic plant species communities in a repeatable fashion.  However, the methodology’s primary downfall as a standalone method is its insensitivity to abundance of plants (i.e., 1 sampled sprig gets the same weight as a large bed at any one point).  Using passive collection of aquatic plant abundance with acoustics while conducting point-intercept surveys and simple GIS overlay methodology, we are demonstrating how species presence/absence layers can be combined with complementary biovolume (% of water column occupied by vegetation) data to form a more complete survey of both species AND abundance.  Further, using both species and abundance layers, we developed a ‘dominance’ index for each species sampled and demonstrate how dominance of any or all species can be used as an aquatic plant management or lake habitat monitoring tool.  Examples from Eurasian watermilfoil and Hydrilla infested lakes are used, as well as lakes with no known invasive species.   Future applications could utilize other environmental datasets (e.g., climate, land cover & use, water quality, etc.) to model the potential and realized outcome of a host of environmental stressors on the probability that invasive species will come to dominate a water body.

Aquatic biologist Ray Valley commented, "We're excited about where this research can take us.  Collaboration among experts throughout the US allows us to draw on a wide knowledge base and study ecosystems from a broad geographic range.  As this historical centralized dataset grows over the coming years, continued collaboration will help us understand and forecast true patterns in dominance and ecosystem effects of invasive species introduction."

If you have interest in participating in this collaboration or have suggestions, please contact Ray Valley at

Participating Groups Currently Include:

Contour Innovations LLC, Minneapolis MN
University of Florida Center for Aquatic and Invasive Plants, Gainesville, FL
Wisconsin Department of Natural Resources Bureau of Science Services, Madison, WI
Minnesota Department of Natural Resources Fisheries Research Unit
North Carolina State University, Department of Crop Science, Raleigh NC

We'll keep you updated along the way!  Centralization is powerful stuff when it comes to aquatic plant research!

Monday, November 19, 2012

Lake Bottom Depth Precision and Accuracy

In an addendum to an earlier post, we continue to evaluate the accuracy and precision of BioBase depth outputs.  Lowrance has been in the depth sounding business since 1957.  They have tight factory calibration standards whereby depth should never be more than 2% different than the actual depth.  Of course then we expect depths to be spot on on hard bottom surfaces where truth can be easily measured.  But what about in mucky bottoms which are common place in many lakes, ponds, backwaters throughout the US and abroad?  With this in mind, in late May of 2012, we traveled to Pool 8 of the Mississippi River near LaCrosse WI to do some testing in a mucky, moderately dense vegetated backwater (Figure 1).  At some point we have to step back and ask, "what is the bottom of a body of water?"

Figure 1.  Vegetation cover and biovolume (% of water column occupied with vegetation) in Pool 8 of the Mississippi R. in LaCrosse WI on 5/29/2012.  Average biovolume was 30% during the survey.
The most difficult aspect of this testing was to get an objective estimate of the true depth.  In other words, where exactly did the plants end and bottom start?  Typically, investigators use a survey rod like that seen in Figure 2 to estimate actual bottom based on where they feel resistance on the survey rod.  Piece of cake over sand.  Not so easy over flocculant silt and muck or vegetative areas.
Figure 2.  Measuring bottom with a survey rod in a mucky Minnesota Lake.  Typically, the survey rod will sink several inches into the bottom before the surveyor feels resistance and judges the depth to the bottom

Many experienced surveyors will tell you that the rod will sink into the muck some distance before you feel resistance.  There is a positive correlation in the distance it sinks and how mucky the bottom is.  So, we went into this investigation expecting deeper rod depths measured than ciBioBase outputs. 

Accurate and precise results in mucky, vegetated bottoms

After 30 points measured with the survey rod, we compared the results with the ciBioBase depths measured in the same location.  We were pleased to see very high precision with a Coefficient of Determination (R^2) of 0.94 and a systematic difference in depth of only 4.9" (Figure 3).  The depth of 4.9" was quite possibly the average depth where we first felt resistance of the survey rod.  The upshot here is that ciBioBase depth outputs are highly precise, consistent and accurate even in mucky vegetated bottoms.
Figure 3. Accuracy and precision of ciBioBase depths measured against depths collected with a survey rod in the mucky, vegetated backwaters of Pool 8 of the Mississippi River near LaCrosse, WI.

Thursday, November 1, 2012

Mapping is Easier with Passive Collection

I remember the days when you had to schedule an hour out of your field day to “set up” and “take down” your mapping set-up.  Wires, an echosounder, a transducer, a GPS, a PC to run everything all had to be set up and configured (Figure 1).  Most importantly, equipment had to be secured by creatively fashioned brackets, booms, and working platforms so you didn’t lose a $4,000 part.  Many horror stories over the years have been told by colleagues who forgot “Righty” was “Tighty” and as a result dropped an expensive piece of fish structure in the drink!

Figure 1.  Elaborate set up of wires, brackets, and working platforms needed to operate the  hydroacoustic systems of yesterday
Needless to say, life during this period was about dedication.  A dedicated survey boat.  Dedicated surveys.  Dedicated staff to run the equipment.  Dedicated staff to analyze the data.  Dedicated staff to oversee that “Righty” made “Tighty” (ok, maybe not that bad).  But still, the expense and logistics of such dedication kept hydroacoustic mapping out of the reach of most water and fisheries resource entities.

With advances in consumer sonar technology, GIS and cloud-computing, now anyone can create high quality bathymetry, vegetation, and bottom hardness maps and datasets with a $700 Lowrance Depth finder, a canoe, and access to the internet with a subscription to ciBioBase (Figure 2).

Figure 2. A 3.6-acre storm water retention pond mapped in 30-min (upload processing time = 10-min) using a canoe and a portable Lowrance HDS-5.  Red lines are the actual traveled track along which data were collected and uploaded to ciBioBase for the generation of the bathymetric map.
Who needs dedication anyway?

No needs for a dedicated boat. The unit can be made portable with no larger than a 12” by 8” footprint (Figure 3).  The transducer(s) and optional GPS can be mounted on a bracket available from Cabelas (Figure 4).  This set up can then be put on a range of vessels from a canoe to a large cabin cruiser.  It can be checked out and passed around by lake association subscribers taking turns mapping the lake on which they live if they don’t already have an HDS.

Figure 3.  Lowrance HDS units can be made portable a variety of different ways to fit your budget and  sampling needs.
Figure 4. Example portable mounts for transducers 
No needs for dedicated surveys. Whether you are a lake association member drinking cocktails (while staying under the legal limit of course) on pleasure cruise on your pontoon or a biologist going point-to-point sampling species of plants, passively recording sonar data requires no work outside of hitting “record,” inspecting the screen for signal quality (i.e., a clear picture), and uploading the data when you return from the field.  ciBioBase algorithms rigorously evaluate the quality of each signal and filter poor outputs (Figure 5).  Back in the day, the staff hydroacoustician had to do this.  Computers do this now.

Figure 5.  Example of automated data quality filtering by ciBioBase.  In the top example, bass tournament anglers were rapidly hopping from spot to spot.  Vegetation detection becomes unreliable at speeds greater than 12 mph.  Consequently, outputs are not generated at speeds that exceed this threshold.  In the bottom example, depths were shallower than 2.4 feet and thus not mapped because of detection errors in depths shallower than this threshold.  However, manual waypoints can be added in these locations within users' ciBioBase account.
No need for dedicated staff trained in hydroacoustics and GIS.  Although ciBioBase offers much for the Hydroacoustic and GIS aficionados via data exporting and importing into their favorite data analysis software, training in hydroacoustics and GIS is not a prerequisite for creating good outputs and datasets.  Hydroacoustics and Geostatistics are not new or “soft” sciences that are so variable and complex that they can’t be automated (i.e., ecology).   The basic physics of sound traveling through water and reflecting off of various objects has been well understood for decades.  Concepts and applications of kriging (originally developed in the gold mining industry) are almost as old and well understood.  Accordingly, ciBioBase automates the interpretation of acoustic signals, creation of a GIS map layers, and standard summary reports.

Dedication in almost every aspect of life is an admirable virtue for which we all should strive.  However, when it comes to mapping lakes, rivers, or ponds, ciBioBase lowers the prestige of this virtue.  Indeed, there will always be a well-placed need for dedicated mapping.  However, we feel opportunities for understanding the dynamic nature of aquatic habitats will be missed if data are not logged while engaging in other activities on the water.  This is non-dedication at its finest!