September 23, 2014

CTFS-ForestGEO grant project report from KC Cushman at Barro Colorado Island, Panama

CTFS-ForestGEO Grants Program recipient, KC Cushman, has been researching her grant proposal “Improving estimates of biomass change in buttressed trees using site-specific tree taper models" in Panama, Thailand, Singapore and Colombia. She recently completed her project and the following is her report:
KC with a buttressed tree in Khao Chong, Thailand
"The amount of biomass stored in any tropical forest can change over time as trees grow, produce new seedlings, and die. Measuring how tropical forest biomass changes over time is important for understanding the global carbon cycle; if tropical forests increase in biomass over time they act as a carbon sink (if trees are growing more than they are dying, on average), but if tropical forests decrease in biomass over time they act as a carbon source (if trees are dying more than they are growing, on average).

CTFS plot in Amacayacu, Colombia.
The diameter measurement height of
each tree is marked in yellow paint.
One tool for studying biomass change is measuring tree diameters in forest plots, such as those in the Center for Tropical Forest Science network. Diameter measurements taken at 1.3 m height are converted to an estimate of total biomass using equations developed in previous research. All trees in a plot are remeasured regularly to determine changes in biomass.
Picture of a tree, a 3-D model
of the same tree constructed
from 43 pictures using
Agisoft PhotoScan, and
trunk outlines extracted from
the 3-D model point using the
program Cloud Compare

However, the prevalence of buttressed trees in tropical forests presents some challenges for this approach. Trees with buttresses are not cylindrical at 1.3 m height, so their diameters are measured higher on the trunk. This practice creates a bias because tree trunks tend to decrease in diameter with height, or taper. Therefore, diameter measurements taken above 1.3 m height will be smaller and yield a lower value for biomass. The magnitude of biomass underestimation in a forest can change over time because measurement heights are often moved up a tree as it grows. This is problematic because biomass appears to change, but the change is not caused by real forest processes. In a previous study on Barro Colorado Island, Panama, we found that biomass trends change significantly after correcting for changing measurement heights in diameter data. Biomass decreased over time in uncorrected data but increased over time in corrected data (Cushman et al. 2014).

Walking to the plot in
Huai Kha Khaeng, Thailand
This year, I had the opportunity to follow up on our preliminary study on BCI through research supported by the CTFS-ForestGEO Research Grants Program. I visited four other CTFS plots to compare tree taper in different forests: Amacayacu (Colombia), Bukit Timah (Singapore), Huai Kha Khaeng (Thailand), and Khao Chong (Thailand). In this study, I am also using a novel tool to measure trees by creating 3-D models from digital pictures using Agisoft PhotoScan. I took 30-60 photos of each of approximately 100 trees per plot to create a model of each tree.  I am using these models to measure characteristics of trunk shape at each site, such as how diameter and trunk circularity change with height. Results from trunk shape measurement can then be used to improve estimates of biomass change when diameter measurement heights change over time.
Field Station at
Huai Kha Khaeng, Thailand

I am thankful to have had the opportunity to visit these plots and meet other researchers through the CTFS-ForestGEO network. This work would not have been possible without the support and guidance of collaborators Helene Muller-Landau, Stuart Davies, Sarayudh
Bunyavejchewin, Alvaro Duque, Somboon Kiratiprayoon, and Shawn Lum, and the assistance of Pablo Ramos, Paulino Villareal, Emily Francis, Juan Sebastian Barreto Silva, Gabriel, Pitoon Kongnoo, Mohamah Fairoz, Jonathan, and Reuben in the field."

To learn more about CTFS-ForestGEO, click here

September 5, 2014

2014 CTFS-ForestGEO Dimensions of Biodiversity Workshop

The 2014 NSF-funded CTFS-ForestGEO Workshop was held last month at the Xishuangbanna Tropical Botanical Garden (XTBG) in Yannan Provine in China . It was the fourth of five annual research workshops over the period 2011 to 2015 focused on "Diversity and Forest Change: Characterizing functional, phylogenetic and genetic contributions to diversity gradients and dynamics in tree communities". The program is co-supported by the Dimensions of Biodiversity Program of the US National Science Foundation (DEB-1046113) and the National Science Foundation of China.

Over 55 scientists from 20 countries worked in small groups to address specific research topics. The focus was on both individual plot analyses and cross-plot comparisons, and included studies of forest carbon dynamics, spatial patterns in species diversity, and forest growth and mortality. The workshop culminated in the presentation of over 40 different research projects on the final day of the workshop. Manuscripts derived from the work are now being prepared.

The gathering of many partners from across the CTFS-ForestGEO network also provided an important opportunity to advance current and future collaborations on the science of the world’s forests. While in China, scientists also enjoyed a tour of the Xishuangbanna Plot and a canopy hike in Greestone Forest.

August 25, 2014

2014 Research Grant Program awardees

The 2014 cycle of the CTFS-ForestGEO Research Grant Program was competitive. Approximately 35 interesting and diverse proposals were submitted from all over of the globe. Each proposal was read by network scientists, and ranked according to scientific merit, contribution to the network, educational contribution, and status of the Principle Investor (PI) to determine an overall rank. 5 proposals were selected for funding. Find a summary of each funded proposal below.  

Carlos Jaramillo, a Staff Scientist at STRI, submitted Pollen flora of the Amacayacu 25 Ha Plot: adding a geological time scale dimension to SIGEO plots, The research will take place at Amacayacu National Park, Amazons, Colombia.

Matthew Craig, a PhD student at Indiana University submitted A new framework for quantifying drivers of soil carbon dynamics within and among forests. The research will take place at Lilly Dicky Woods, SCBI, SERC, Tyson Research Center,  Wind River.

Jan Ng, a PhD student at University of California-Davis submitted Assessing shifts in tree spatial patterns following reintroduction of fire disturbance in the Yosemite Forest Dynamics plot. The researched will take place at Yosemite Forest Dynamics Plot in California, USA.

Owen Lewis, an Associate Professor at Oxford University submitted Linking botanical and entomological datasets: A seed trap network for the Wanang 50-ha plot. The research will take place at Wanang, Papua New Guinea.

Jian Zhang, Postdoc at University of Alberta submitted See forests from drones: testing the potentials of drones in CTFS long-term monitoring network. The work will take place in Dinghushan, China.

To learn more about the CTFS-ForestGEO network, visit

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 SIGEO 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 processes 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 CTFS-ForestGEO, click here.

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