Creating a Video of Vegetative Cover Sampling

As part of my graduate obligations for a course in methods of measuring and monitoring plant populations, I had to do some type of course project. Though our instructor offered several options of varying difficulty, it was clear that he really wanted someone to attempt to produce a video outlining how to do a method.

As I had done a couple of videos for other projects in the past, I was fairly certain that this would be the most difficult of the graduate project options, but after exploring my other project options, I decided to attempt the video.

So over the last few days I’ve been writing a script, planning shots, doing on-site filming, editing, and voiceover work. Then more on-site filming, more editing and more voiceover work. After several hours of dedicated editing time, I’ve finished the video.

I think it’s pretty good. It’s not great, but it’s got potential. The main challenges were equipment related. It was windy on both filming days and I don’t have fancy microphones, so we had wind noise in some of the live action clips. Despite that I was using an HD video camera that I won at a conference, the video quality wasn’t as good as I’d expected, but it was the best method of filming the video with what we had available.

Anyway, the end-result is an 8 minute video that demonstrates how to sample vegetative cover using the point-intercept method. I briefly walk viewers through what cover is, why it’s commonly measured, and how to establish random sampling locations. Then I illustrate how to lay out a transect and how to sample points using a drop rod. I discuss how to record the data and finish with a demonstration of how the recorded data can be summarized in Excel. (There’s a mistake in that section, that I caught very late in my editing and didn’t want to tackle fixing as it would have required a new voiceover that took me four takes to do the first time. See if you can spot it).

If you’re curious you can find the video on You Tube at:¬†http://youtu.be/NhcNjikpApg

Feel free to provide comments – as long as they’re positive ūüėČ

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Desert Tortoise Training

From this post title, it might appear that I took part in training desert tortoises. In reality I participated in a workshop to learn how to survey, monitor and handle desert tortoises. The 2-day workshop is conducted annually in Ridgecrest, CA by the Desert Tortoise Council and covers a tremendous amount of material including:

  • an overview of desert tortoise taxonomy, life history and threats to its survival
  • information on handling, monitoring, and surveying for desert tortoises
  • authorized egg handling and burrow construction demonstrations

One important fact we learned very early was that¬†based on DNA, geographic, and behavioral differences between desert tortoises populating the areas east and west of the Colorado River, the desert tortoise has been split into two species: Agassiz’s Desert Tortoise (Gopherus agassizii) and Morafka’s Desert Tortoise (Gopherus morafkai). ¬†With G. agassizii occurring in California, Nevada and Utah on the west side of the Colorado River and G. morakfai occurring in Arizona, and the states of Sonora and Sinaloa, Mexico. So, I guess it’s time to update our field guides.

A range map depicting this split can be seen here: http://www.usgs.gov/newsroom/article.asp?ID=2842#.UKfYG-Oe9B9

We were also instructed on desert tortoise life history, threats and legal protection. ¬†As the workshop was aimed at biologists who are working to survey, monitor and protect tortoises in the face of development, the workshop included many topics on the laws and legal framework for protection, preservation and take of the species from all of the permitting agencies that we’d potentially be working with (BLM, USFWS, CaDFG, etc.).

Our field sessions included demonstrations on:

  • how to construct protective fencing and shade structures
  • how to construct artificial burrows
  • how to relocate a nest of tortoise eggs
  • how to collect body size and condition data

We also learned how to survey for desert tortoises, including what signs to look for (scat, tracts, geophagy, burrows, etc.) after which we were given the task of surveying a plot that was pre-seeded with tortoise sign.

Finally, Desert Tortoise Council Tortoise Handling Workshops are recognized by the U.S. Fish and Wildlife Service. While a certificate of attendance does not guarantee a USFWS permit, completion of the Workshop should help with the permitting process.

A Species Diversity Map for 88,000 New World Species

This is a small sample of a species diversity map that’s an end product of our models. This was created by overlaying 88,000+ shapefiles and represents the number of species potentially present in each cell. Red is low, dark blue and purple are high (over 8,000 species per cell).

Revisiting the North Etiwanda Preserve

Sage Scrub Chaparral

Sage Scrub Chaparral

When I studied population biology in junior college we conducted our field work in a large expanse of land along the alluvial fan that drained the San Gabriel Mountains to the Inland Empire valley below. Our specific field site was a 750+ acre area containing coastal sage scrub and coastal sage chaparral plant communities that were intersected by riparian corridors of alder, willow and occasionally sycamore trees.

Coastal sage scrub is a type of ecoregion that is located along the southern and central coast of California. It is important because is an endangered ecosystem that contains many unique species that occur nowhere else in the world (endemic), a number of which are endangered species. Coastal sage scrub is imperiled because it is also located on highly valued coastal real estate and threatened by human development.

Coastal sage scrub occurs from sea level to 1500 feet in elevation, along the coastal and inland valley foothills where coastal fog moderates the climate. Habitat contains sparse, low-growing soft, aromatic shrubs that range from dull-green to gray-green in color. In hot, dry summer months, shrubs often lose their leaves and become dormant as an adaptation to drought tolerance. They become green and vibrant again when winter rains arrive.

Some characteristics species in coastal sage scrub communities include:

Federally recognized threatened and endangered species include the California gnatcatcher (Polioptila californica), the San Diego banded gecko (Coleonyx variegatus abbottii ), the cactus wren (Campylorhyncus brunneicapillus), Merriam kangaroo rat (Dipodomys merriami), flannel-mouthed sucker (Catostomus latipinnis), western patch-nosed snake (Salvadora hexalepis), and cheese-weed moth lacewing (Chrysoperla spp.). Thirteen plant species of the coastal sage scrub are also recognized as threatened or endangered. (1)

A few years later the area began rapidly developing and our field area was threatened by a series of housing developments. Through the efforts of many people who fought to see the area protected to stem the decline of chaparral and coastal sage communities, a 762 acre section was set aside as a reserve. The area lies between the developed portions to the south and the national forest to the north and is protected on the southern end by a very wide power transportation corridor that serves as a buffer between the two land uses.

Welcome Sign

Welcome Sign

After several years of being away from this site, I recently revisited it yesterday afternoon and was surprised to see signs pointing the way to the preserve as I drove to the parking area. I was further surprised to see a dozen cars in the parking area at 3 pm on a Tuesday. When I last visited the site, it was protected, but still the completely undeveloped area that few people ever ventured into.

Trail Map

I quickly saw that the preserve has since been enhanced with formal trails, interpretive signs, and a few scattered picnic sites. It was now a popular place for hiking due to its cultural and recreational significance. Many people were taking a new trail that lead to a side canyon that contained a waterfall and shade beneath the alder trees. Others hiked around the lower portion of the preserve stopping at gazebos and interpretive signs.

While it was strange to see so many people in a place I used to walk around without seeing a soul, I was thrilled to see that the plant communities I fondly remembered were still there and appeared to be thriving. Walking through the scrub and chaparral I was transported back in time to my first population biology class, awestruck by the sight and smell of white sage and asking myself the same questions about the distributions of the plants I encountered along my hike.

Walking along one of the trails I saw massive shifts in the vegetation communities along a 1-mile length. Vegetation changed from stands that were dominated by white sage, to stands co-dominated by chemise and buckwheat containing little white sage. Walk a little further and the vegetation became co-dominated by black sage and sagebrush. Along this stretch I could not detect a difference in soil texture or aspect. So the sudden shifts of vegetation may the result of secondary successional processes where fire and floods disturb the vegetation and a different plant community begins growing in the areas that were disturbed. The overall pattern looked like waves of different vegetation along the hillside that was fascinating and worthy of more examination. Some of those communities are shown in the photos below.

Preserve Facing North West

Preserve Facing NW

White Sage

White Sage

White Sage Community

White Sage Community

Chemise and Buckwheat

Chemise and Buckwheat

Black Sage and Sagebrush

Black Sage and Sagebrush

Alder Riparian Woodland

Alder Riparian Woodland

Intersecting what I used to think was scorching hot chaparral (I’ve since lived in Arizona, so I have a new definition of hot) are wonderfully different riparian habitats containing cool, lush, shade tolerant species and – water. Water is a powerful force in these regions, winter rains and spring meltwater can move large amounts of water down the mountain through these canyons. Occasional fires remove vegetation and later rains bring floods that break trees and push large granite boulders downstream too. ¬†These processes cause regular disturbances in the canyons and adjacent lands, and the vegetation is always in some state of recovery. The dense canopy of alder trees in the canyon bottoms is evidence of that those areas were previously disturbed, new trees grew to replace those that were killed, but self-thinning has not yet completed restructuring the tree stand.

Riparian Waterfall

Riparian Waterfall

Alder Woodland

Alder Woodland

The Southern California coastal sage scrub and chaparral communities are a wonderful place to explore with very interesting ecology that is worthy of protection and study. I’m happy that the North Etiwanda Preserve exists and look forward to continued visits.

 

 

For more information about the North Etiwanda Preserve see: http://sbcnep.org/

Photos of common coastal sage scrub and chaparral plants (from the nearby Cal State San Bernardino campus) can be seen at: http://biology.csusb.edu/PlantGuideFolder/

Finally, more information about coastal sage scrub and chaparral can be found at: http://www.eoearth.org/article/California_coastal_sage_and_chaparral

Happy exploring !

(1) From: http://www.eoearth.org/article/California_coastal_sage_and_chaparral

Night Blooming Cerus, Peniocereus greggii

The Night Blooming Cerus, or Queen of the Night, (Peniocereus greggii) is a Sonoran Desert cactus that most of the year would be virtually impossible to find. It’s main stem is a thin, dull-green to brown stalk that resembles the branch of shrubs like the palo verde, Ironwood, or creosote bushes that it normally grows beneath.

What makes this cactus special is that on certain summer nights the plants in each population produce large blooms synchronously – with some plants producing numerous flowers, some producing one and some none at all. The flowers open at sunset and last for one night, withering in the morning sun.

The flowers are produced only at night, are mostly white, about 3 inches wide and are strongly scented (though some people apparently cannot smell them). The flowers have long floral tubes and are pollinated by hawk moths (Sphingidae) which fly hundreds of yards between different plants in search of nectar. In return they exchange pollen between individuals.

The Night Blooming Cerus is actually not a cerus at all. When cacti were first collected and categorized they were lumped into one genus named ‘Cactus’. Later, taxonomists determined that there were several groups of cacti and split the plants into groups like Opuntia (beaver tail cacti), mammillaria (fish-hook cacti), Cerus (columnar cacti) and others. In the newer classification many columnar cacti were lumped into the Cerus genus, the Night Blooming Cerus being one of them – hence it’s name. However later work further subdivided plants in the Cerus genus into more groups. Columnar cacti like the Giant Saguaro remained in the genus Cerus, but vine-like cacti like the Night Blooming Cerus were moved into a new genus named ‘Peniocerus’, where the species is currently classified.

In Arizona and New Mexico, the Night Blooming Cerus is a protected or endangered species that has seen much of its habitat lost to agricultural and urban development. In addition, its future is dependent upon hawk moths which themselves are vulnerable to impacts from nearby development. For example, where pesticides are heavily used in agricultural areas adjacent to desert habitat, the hawk moth populations can be greatly reduced, such that few remain to pollinate the Night Blooming Cerus to help maintain the cactus’ population size.

Photos from the 2012 Night Bloom at Tohono Chul Park:


All images on this page copyright 2012 by John Donoghue II. All rights reserved.

For more information, see:

Mobile Apps for Naturalists

Project Noah LogoSince nearly everyone carries a smartphone these days, we can now carry a small library worth of field guides with us inside our phones so we never miss an opportunity to identify an interesting organism. With this in mind, here are a few mobile applications that are today’s field ecologist or naturalist should¬†definitely consider having on your smartphone.

Merlin – Merlin is the Cornell Laboratory for Ornithology’s new bird identification app. Answer five simple questions about what bird you’re seeing and Merlin will¬†come up with a list of possibilities based on both the answers to your questions and your location. Merlin is able to make highly educated guesses using its database of more than 70 million observations from the eBird citizen-science project.

Journey North – The¬†Journey North app engages students in a global study of wildlife migration and seasonal change. Focused for K-12 students, users record and submit their observations while they are in the field and¬†share their own field observations with classmates across North America. Students can use the app to track the coming of spring through the migration patterns of monarch butterflies, robins, hummingbirds, whooping cranes, gray whales, bald eagles‚ÄĒ and other birds and mammals; the budding of plants; changing sunlight; and other natural events.¬†(iPhone, Android).

BirdLog– I have been wanting a good mobile field notebook application for birding for quite a while. I even went so far as to build my own database to sync between my phone and laptop. BirdLog, is better. Developed in cooperation with the Cornell Lab of Ornithology, BirdLog helps you record and submit your latest bird sightings from the field. Moreover, your sightings contribue to the eBird database and provide data for thousands of amateurs and scientists who study birds. Among its many features, BirdLog allows you to create lists even when there is no cell coverage, keeps a running total of the number of species on your checklist, and plots the exact location of your sightings using your phone’s GPS. (iPhone, Android)

Nature’s Notebook – The National Phenology Network (NPN) has just released the mobile apps for Android and iPhone that let you record phenology¬†(the annual timing of events such as flowering) observations in the field. Fill out a very short form and submit your information for use by scientists everywhere. While many people and applications are set to record when events like flowering start, knowing when they stop is just as important, as it helps tell¬†scientists¬†whether the growing season is getting shorter or shifting. So,¬†one important component of the Nature’s Notebook application is that you can also use it to collect when plants have yet to flower or have stopped flowering, are showing new leaves or have dropped their leaves.¬†(iPhone, Android)

Leafsnap – You can use Leafsnap to help identify plants. Simply use the application to snap a photo of a leaf and it will be uploaded to their servers where sophisticated image recognition software will combine the leaf’s photo with your location (from your phone’s GPS) to suggest possible matching species.¬†(iPhone, Android)

iBird – iBird is the definitive application for identifying birds. It loads the contents of several bird guides onto your phone, combining drawings, photos, recordings of bird calls, range maps and other information to help you lookup any bird and identify its species. iBird loads all of this information on your phone, so you can use it in areas with no internet access. With iBird, there’s really no need to carry a thick bird guide around anymore.¬†(iPhone, Android)

National Audubon Mobile Field Guide Apps РThe National Audubon Society offers a suite of applications for smartphones that contain field guides to birds, mammals, reptiles, fish, insects, trees, wildflowers, and mushrooms. (iPhone, Android)

My Nature Animal Tracks – When all you have is evidence that an animal was present, you can use My Nature Animal Tracks to identify the animal by examining their tracks and scat using this handy app. (iPhone)

PhenoMap РHelp scientists study changes in phenology (the annual timing of events such as flowering) by snapping photos of when natural plants in your area bloom. Fill out a very short form and upload your sighting to the University of Chicago and the National Phenology Network for inclusion into their phenology database. (iPhone)

ProjectNoah РEarn merit badges for being a citizen scientists and help the larger scientific community by logging your sitings of species in your neighborhood, on trails, etc. The information submitted by tens of thousands of citizen scientists is used to help study species diversity and distributions and other questions. (iPhone, Android)

These are just a few of the many exciting and helpful mobile applications that can assist your field excursions and reduce the number of field manuals you carry. While I’ve tried to introduce some very good and popular applications, this list is by no means complete.¬†If you know an app that should be on this list, please add a comment below.

Create QR Codes Using the Google Chart API

For some of you this might be old news, but I wanted to create a QR Code for a poster presentation for an upcoming ecology conference (since all the cool people are using QR Codes these days). In searching for a way to generate one, I learned that you can easily create a QR Code using the Google Chart API.

To create a QR Code, simply enter the following URL into your web browser’s address bar:

http://chart.apis.google.com/chart?cht=qr&chs=200×200&chl=
(but don’t press enter yet, see the next step)

Before pressing enter, complete the API command by entering the URL of the location you want to generate a QR Code for after the chl property and equal sign (chl=) at the end of the link above.

For example, the complete API command you would enter into your web browser’s address bar¬†to generate a QR Code for a link to this blog would be:

http://chart.apis.google.com/chart?cht=qr&chs=300×300&chl=http//www.geoapplications.com

This creates a 300 x 300 pixel QR Code. To generate different sizes, simply modify the chart size property (chs) to a different pixel size. For instance if I wanted to generate a larger version of the same QR Code above, I could enter:

http://chart.apis.google.com/chart?cht=qr&chs=500×500&chl=http//www.geoapplications.com

Happy QR Coding.