August 5, 2014

CTFS-ForestGEO Dimensions of Biodiversity USA - China Student Exchange Program

María Natalia Umaña is a student from Nathan Swenson's Lab who traveled to China to develop a Project in Xishuangbanna Tropical Botanical Garden (XTBG) funded by CTFS-ForestGEo Dimensions of Biodiversity USA-China Student Exchange Program. The following is a report she wrote about her trip when she returned: 

"Tropical forests, being important hot spots of biodiversity, harbor a significant number of rare species. Most of the plant species in tropical forests exhibit very restricted distributions and low abundances, while only few species are dominant. Why are so many species rare? Is it because rare spaces have different characteristics compared with common species? Are rare species ill-suited to the available habitats or specialized on rare habitats? These are classic questions in ecology and the main motivation of my PhD project.

In order to assess this question I am measuring the intraspecific variation in functional traits across several species with different relative abundances. Recently, as a part of my Ph.D. research, I traveled to the Xishuangbanna Forest Dynamics Plot (FDP) located in the south of Yunnan Province, China where I collected the functional trait data for seedlings in this tree community. In April 2013, 218 seedling plots were established near the 20-ha Xishuangbanna FDP. All the seedlings were monitored for growth and survival every two months. After one year, in April 2014, a team of 5 Chinese field assistants and I quantified functional trait data from every individual.
I stayed in the field station near the 20-ha FDP during my visit. This region, shaped by extensive mountains ranges, is home to a diverse tree community with over 400 species in the 20-ha plot with most of them being quite rare. During my visit I had the chance to share some time with local people who helped me with fieldwork. Although I arrived to China knowing only few words in Chinese, we were able to set up a nice team and work collaboratively in harmony. The people I met were always very kind and very hard-working. The field assistants have grown up in close partnership with nature and are very familiar with the hundreds of species located in and around the FDP. After our exhaustive field and lab work we now have an extensive data set including trait and demographic information at the individual level. With this data we will be able to evaluate how variable are traits across species with different relative abundances and how this individual level trait variation links with individual performance.

I would like to acknowledge the financial support of CTFS for this fieldwork. Specifically, the Dimensions of Biodiversity IRCN USA-China NSF grant awarded to Dr. Stuart Davies and Dr. Keping Ma funded my travel and this collaborative opportunity. I would also like to thank all of my new Chinese collaborators that were involved in this project from the laboratory of Dr. Min Cao. Specifically, t
his work would not have been possible without the help of Dr. Luxiang Lin, Cai Cai Zhang (a PhD student in Xishuangbanna Tropical Botanical Garden), Dr. Yang Jie, Zhigang Chen(field technician), Lang Ma (field technician), Zhilin Mu and Yongzheng Shen (field technician). Our time together yielded great new working relationships and friendships."

To learn more about Xishuangbanna Forest Dynamics Plot:

July 2, 2014

Harvard ForestGEO plot initial census completed!

Harvard Forest researchers, with the assistance of scientists from the Center for Tropical Forest Science (CTFS) and the Smithsonian Institute’s Forest Global Earth Observatory (ForestGEO), completed the census of woody stems within the 35 ha plot located on Prospect Hill in March 2014. Using standardized CTFS-ForestGEO methodology, Jay Aylward and field assistants Kyle Krigest and Sarah Myers have measured, tagged, painted, and mapped the final 4,400+ woody stems greater than 1 cm dbh in the remaining section of forest located in the beaver swamp in the north-central portion of the plot. 
The swamp is particularly dense, containing over 29,000 stems of winterberry holly (Ilex verticillata), highbush blueberry (Vaccinium corymbosum), witherod (Viburnum cassinoides), and maleberry (Lyonia ligustrina).  The final plot tally from Dave Orwig, Jay, and 26 field assistants was over 116,000 woody stems!  The HF ForestGEO plot is dominated by eastern hemlock (> 25,000 stems) and northern hardwood species in upland plots, and will make an excellent comparison with several other hardwood plots in North America and China at similar latitudes. This plot is part of a global array of large-scale plots established by CTFS, which recently expanded sampling efforts into temperate forests to explore ecosystem processe.
beyond population dynamics and biodiversity. The geography and size of the Harvard Forest plot (500 m x 700 m) was designed to include a continuous, expansive and varied natural forest landscape that will yield opportunities for the study of forest dynamics and demography while capturing a large amount of existing science infrastructure (e.g. eddy flux towers, gauged sections of a small watershed, existing smaller permanent plots) that will enable the integrated study of ecosystem processes (e.g., biogeochemistry, hydrology, carbon dynamics) and forest dynamics . Thus, the resulting data will integrate well with ongoing NSF-funded LTER (Long Term Ecological Research) and NEON (National Ecological
Observation Network) studies.

To learn more about the CTFS-ForestGEO Temperate Forest Program, visit:

June 13, 2014

New ForestGEO Seminar Series

The ForestGEO seminar series is underway at the CTFS-ForestGEO headquarters at the National Museum of Natural History in Washington, DC. The first scientist to present under the new series was Yves Basset, the scientific coordinator for the CTFS-ForestGEO arthropod initiative. As the first guest speaker, Yves had an interesting and detailed talk on the diversity of bugs in rainforests, entitled "The CTFS Arthropod Initiative: monitoring rainforests arthropods". A few weeks later, the next presenter was Dr. Nathan McDowell, Staff Scientist, Los Alamos National Laboratories who presented a talk about his research, entitled "Accelerating global forest mortality". Both talks drew many ears, and generated many converstaions and collaborations on their respective topics.

The next talk will be hosted by Dr. Jennifer Baltzer from Scotty Creek Forest Dynamics Plot in Canada. Her talk is entitled "Boreal forests on permafrost: responses to climate warming". She will speak June 24th at 10am at the National Museum of Natural History.

An Aerial view of Scotty Creek Forest in Canada.
Are you traveling to Washington DC in the future and want to host a talk on forestry science? Email Delaney Rakosnik (ForestGEO Program Assistant) at with a talk topic and title. If you are in the Washington DC area and would like to know the ForestGEO Seminar Series schedule, also contact  

Learn more about CTFS-ForestGEO, visit

May 5, 2014

CTFS-ForestGEO database workshop in Singapore

CTFS-ForestGEO hosted a workshop in Singapore May 2nd - May 8th for a number of plot database managers. The workshop was organized around documentation developed to enable sites to fulfill a large part of the data management role locally with support from the CTFS-ForestGEO Systems Group. Among the plots represented at this workshop are Brunei, Hong Kong, Lambir, Pasoh, Palanan, Wanang, Bukit Timah, Sinharaja, Mo Singto, Doi Inthanon, and Huai Kha Khaeng. This workshop will focus on actively working with each plots own datasets wherever possible.

Workshop organizers Shameema Esufali and Suzanne Lao worked to introduce more advanced concepts to prepare data managers to screen and correct datasets in an organized manner.  They plan to go through the steps necessary for deriving location data from field maps using PointPicker and ImageJ, and show the latest versions of their toolkit including the dataentry system CTFSWEB, the generic form builder CTFSGDE, and the tool for correcting species allocation, TaxonEd. Some of the participants are brand new to MySQL so Shameema and Suzanne started off with a refresher (see Sandra's comments below). 

Fairoz kicks off the blog series with a recap of day 1 of the workshop in Sunny Singapore:
"Playing host to the participants from the various plots, I dropped by the Robertson Quay Hotel where they are staying to welcome them over breakfast. Saw many familiar faces and some new ones as well. Counted heads and found one to be missing.. Sandra! Found out she’ll be flying in late and will come directly to the workshop venue.
The bus took us to the west side of Singapore where the National Institute of Singapore (NIE) is located, and the venue for the workshop. Setting up individual workstations were less challenging this time round with many of us carrying our own universal adaptors and sharing around with those whose cables could not fit into the power points.

The venue for the workshop
Next came the installation of XAMPP, the latest ctfsweb version and a text editor to get us ready to start stringing together queries on our consoles. Morning was spent getting mysql running on the various operating systems on individual laptops. What a relief if was after lines and lines of sourcing and finally seeing the ‘mysql>’ line appear in the command prompt.

After a short recap on the need for database setup and simple commands, we were all punching scripts; SELECT-ing trees and JOINing tables, GROUP-ing census and ORDER-ing them alphabetically. But don’t forget to LIMIT those scripts or you might have rows and rows of data streaming down window.

So I will SELECT ‘participants’ FROM ‘various plots’ and welcome them to the country and the workshop."

Sandra Yap shares a recap of day 2:
"I'm not the best person to describe how Day 1 went. I came in late but directly from the airport so I hope to be forgiven. I can say, however, that a few people worked late into the night on the exercises Shameema and Suzanne tested us on. Those exercises were quite a challenge especially for those who don’t regularly use mysql.  Unused muscles (in the mysql parts of our brain) had to stretch and warm up.
As I said, warming up followed us through to Day 2. We got quizzed as soon as we opened our computers :) But I think we passed with flying colors.
It’s 11:30 am and everyone is trying to set up their systems to input census data. Small groups huddled around a laptop and heads whipping right and left throwing puzzled looks seem commonplace. PCs on Windows 7 or 8 or Unix and Macs combined with capital/small letter issues are presenting a challenge this time for Shameema and Suzanne."

Dr. Sandeep Pulla provided the pictures and commentary for day 3 of the workshop:

"On day 3, folks who already had their data in the CTFS database worked on executing MySQL statements to check and fix common problems with raw data files that could not be uploaded into the database as is. They also devised clever ways to check data correctness and consistency, exercising their newly acquired MySQL skills. The rest (from Mudumalai, Hong Kong, etc.) worked on uploading their own data into staging tables. This was followed by screening and uploading these tables into the final database. Suzanne conducted a "spot the SQL error" quiz to liven things up."

Day 3 in pictures:

Participants worked very hard and ate well

MySQL expert Musalmah shares a few tips with Dr. Kamariah.

Kenneth stares at an error in phpMyAdmin hoping it would go away. He fixed it subsequently (figure not shown).

Anuttara and a guest share a light moment.

Mohaziah and Suzanne discuss the finer points of relational databases.
Something clearly blew up on Jinlong’s computer. We capture this tense moment with Shameema, Komgrich, Witchaphart, and Jinlong.

Brain fuel was in ample supply.
From their happy expressions, one would think Nik and Fairoz were playing a computer game (they were not).
Shirley in a troubled moment. Her biscuit fell down.
The bananas and other snacks were supplied by kind courtesy of Dr. Lum.

Jonathan re-emerges from his laptop (after apparently being swallowed by MySQL).

Anutarra shares day 4:
"Today the class started with the demonstration of “ctfsgde” which is about generic data by Suzanne. Then we moved on to the very important part of database management“data screening” to find errors of our plot data. However we did some practice using the database called “green” instead of “blue”. We had “cleangreen” for sql to check the errors. Coming to this step, some people started to frown. This is only searching for errors. We haven’t begun fixing them. Come on guys. We can do it. Before fixing those errors, scripts must be written. Please keep this sentence in mind. When all sql statements run successfully, data screening on ctfsweb will be done for the next step. I’d better not go to more details.

In the afternoon we went to the Southern Ridges for a field trip, starting at Mt. Faber where we could see Sentosa and the sea. We began walking from here to Henderson waves where the wave-pattern bridge locates. This bridge is the highest pedestrian bridge in Singapore. Besides you can see the height above mean sea level on the floor at several points. We kept walking until arriving the forest walk. At this point many people started to shoot a lot of photos. The forest walk is an elevated steel walkway through the secondary forest. Let’s take a look of photos from the field trip. Clear your head and mind to get ready for the next day."

Photos from the forest walk. Passing a secondary forest.

A shot from the Henderson wave bridge

At Henderson wave, the wave-pattern bridge

Group Photos


April 14, 2014

CTFS-ForestGEO Research Grants Program 2014

The Research Grants Program of the Center for Tropical Forest Science - Forest Global Earth Observatory (CTFS-ForestGEO) supports research associated with the CTFS-ForestGEO network of Forest Dynamics Plots.  A new round of research grants will be awarded in 2014. The majority of the CTFS-ForestGEO research grants will fall in the $2,000-$15,000 range.

The program is intended to provide opportunities for senior researchers, post-doctoral fellows, and graduate students to utilize existing Forest Dynamics Plots and to conduct research with scientists associated with these plots. Anyone working directly in a CTFS-ForestGEO plot, analyzing plot data, or generating complementary data that strengthens CTFS-ForestGEO programs is eligible to apply. Projects can be field-oriented, herbarium- or laboratory-based, or analytical, and either basic or applied in nature. Funding is restricted to expenses directly related to field research, laboratory research, and data analysis. Examples of eligible expenses include travel, living expenses during fieldwork, supplies, and research assistance. Funds are not available for salary and/or fringe benefits of the applicant, tuition, non-project personnel, or travel to meetings. In addition, the grants program will NOT support indirect costs for institutional support. Priority will be given to early career researchers, researchers with less access to other institutional funds, and to projects that include multiple sites. Social scientists and natural scientists are encouraged to apply
The deadline for applications is Friday, June 20, 2014.
For more information, please go to the website: Applications MUST follow grant requirements as outlined at that website.

March 28, 2014

Yosemite Forest questions long-term effects of wildfires

Researcher Jim Lutz stands next to a smoldering log
In September 2013, the Rim Fire – a wildfire that began from an illegal campfire in the Sierra Nevada Mountains - burned through 1,041  sq. kms. of the Yosemite National Park, including the Yosemite Forest Dynamics Plot (YFDP). While the entire plot burned, most of the plot was spared the full force of the wildfire, burning at intensities lower than needed to kill the larger trees.  However, many trees did die.  Patches of the forest remained unburned yet some patches had considerable tree mortality. Estimates are that about 12,000 out of a total of 36,000 trees being monitored since 2009 died in the fire – mostly trees less than 10 cm in diameter.

How will this effect research at YFDP? Researchers will re-measure the plot this May, prior to the 2014 growing season to record exactly what changes the fire caused. The team will record changes in diameter of trees since the plot was established, as well as the way fire killed trees.  They will also measure changes in surface fuels and in the cover of low shrubs. Gathering this fire-related information will help answer important questions such as:, what were the relationships between trees, fuel accumulation, and tree death? How does fire affect biodiversity?  How does fire change the structure of the forest used by birds and mammals? 
YFDP researchers already perform annual mortality checks, so they will be able to monitor the long terms effects of the fire as well as the immediate effects of forest changes. The results should provide a unique understanding of how fire affects these old-growth forests.

Larger trees mostly survived
During the fire the research team worked with park fire and resource managers to provide assistance with fire planning and safeguarding park resources. The YFDP research team works with Yosemite National Park on a variety of science and management issues. This summer, the re-measurement will be carried out by a core team of four technicians - all with previous experience in the western ForestGEO plots - as well students from Utah State University, University of Montana, Washington State University, and University of Washington. Volunteers will also play a key role – just as they have in every year since 2009. The broad mission of this project is to build a science-based management of Yosemite forests through long-term research and capacity strengthening.

YFDP Research Team: Jim Lutz (Utah State University), Andrew Larson (University of Montana), Mark Swanson (Washington State University), and James Freund (University of Washington).

Click here to learn more about Yosemite Forest Dynamics Plot.

March 5, 2014

Camera traps capture images of elusive forest life

Camera traps are the latest research tool used by CTFS-ForestGEO researchers to monitor the growth and life of forests worldwide. Developed by Bart Kranstauber and Yorick Liefting, under supervision of Patrick Jansen of STRI and Roland Kays of the North Carolina Museum of Natural Sciences, camera traps are able to capture pictures of rare forest animals and birds in a non-invasive way. 

How does it work? Infrared cameras are secured to a random tree in the forest. When the camera detects a warm blooded animal is close, it begins to rapidly snap pictures. Those photos are then uploaded to a server.  Photos that are taken close to each other are automatically grouped together as they likely have the same animal or group of animals in them. A user-friendly interface then allows researchers to process these groups and identify the animals in them.  After the groups are processed, the data is available for use by researchers all over the world.

This technology has brought a new beginning to the research of various animals in the worlds forests.  The cameras work 24 hours a day. One camera can stay in the forest for 2-3 months, which rapidly increases the chance of capturing photos of the rarest species. These camera traps have even taken photos of the critically endangered Black Rhino.  To see pictures of different species photographed around the world by camera trappings, visit Smithsonian Wild.

Watch the YouTube video to see the cameras actually attached to trees in the forest.

To learn more about this innovative network, visit the Camera Trapping Database site.