Sanded cross section of bark and portion of pinyon pine core
Tag-Archive for » dendrochronology «
May 20th, 2010 | Author: sarcozona
Tree rings are fascinating and informative data, but the gazillions of formats used by different measurement and analysis programs can be a real pain in the ass. Additionally, there are a plethora of reformatting programs that all do slightly different things. Of course, many times none of them do exactly what you want. I’ve often had to feed data through 2 or 3 programs and/or write my own formatting program to get it in a usable format. Sometimes I feel like I spend more time dealing with formatting issues than actually analyzing our data.
If you aren’t having a problem with tree ring data formats, you should probably move on. If you are, hopefully this will help.
This post is going to be about some common issues I’ve had with the formatting program YUX. If you’re having trouble with COFECHA, try this.
Size problems
The first issue has to do with the size of the imported file. If it’s larger than about 52kb, YUX will crash.
Also, you can’t include more than 200 series or 4096 years without causing YUX to crash.
Mixed up data problems
If you don’t insert a character for missing data, YUX won’t give you an error, but it will seriously fuck up your data. Consider the YUX year by series output data for a set of six trees below. What we expected was the output on the left; what we got was the output on the right.
Click to embiggen
I’ve color coded each tree and its rings so you can see what’s going on more easily. Basically, YUX is sliding the tops of the series as far to the left as possible. If the last year of growth for all of your trees isn’t the same, it’ll do the same at the end of the series. We get around this in one of two ways: either we tell YUX to enter something (like NA) for the missing data (under option 3 in YUX), or we make sure the file we feed YUX is in order from longest to shortest series. The latter solution only works when the last year of growth is the same for all trees and there are no gaps within a series.
If you need more help, I recommend searching or emailing the ITRDB Dendrochronology Forum. They are remarkably helpful and very friendly in their answers to even the most basic of questions.
April 15th, 2010 | Author: sarcozona
A few weeks ago I wrote about how cool it is to be able to read the stories tree rings record, but I didn’t tell you any of those stories. However, Ed Yong at Not Exactly Rocket Science describes a very old story that’s recently been translated: the fall of Angkor. Scientists discovered two very serious droughts and some unfortunately timed flooding that likely did the powerful city in.
March 16th, 2010 | Author: sarcozona
A few weeks ago, a friend told me he was coming over with a book that I absolutely had to read. He showed up a few minutes later and launched immediately into a rapturous description of The Wild Trees.
From the Institute for Redwood Ecology
The Wild Trees is about redwood research and the people that pioneered the field. Until very recently, we had no idea what was up there and a lot of it is still a mystery.
I love popular science books, but I usually find them simply intellectually exciting and rarely get emotionally involved. This book was different for a few reasons. First of all, the scientists are portrayed as humans and the way their personal lives influence their professional lives (and vice versa) is a large part of the book. So often scientists are portrayed as dull or unnaturally obsessed, but this book shows how very human we are – from the connections we have with our families, to breakups and sex, to the awe and wonder we feel when presented with something so incredible as a redwood.
And that’s the second reason this book is so different from the normal nonfiction I read: a lot of time was spent describing the trees, the forest, and the experience of climbing the trees so that their magnificence and beauty really came through. By the end of the book, I was ready to sign up for a tree climbing class just so I could see for myself what was up there.
It was also kind of thrilling to have a sort of connection to these trees. I work with a scientist who studies redwoods and he has cores from many of these trees. To get a core, you use a special hollow drill to extract a bit of wood the size of a very, very long straw from a tree. You can sand the straw flat to see the growth rings:
Redwood rings under a microscope
I don’t study redwoods now, but I learned all about dendrochronology, or tree ring science, with redwoods. Tree rings are a fascinating archive of stress, climate, competition, and more – an autobiography of a tree, if you will. The language may be hard to interpret, but the information is there.
Every tree that is cored is given a name and most of the time the names are dull (SP032, for example). But redwoods are given names like Thor, Atlas, and Kronos. I always gave the tree a personality I associated with that name as I counted and counted and counted (and counted and counted) the rings. The Wild Trees describes the discovery of many of the trees whose cores I analyzed and what it was like to climb them, what fascinating communities live within their canopies, even human drama that occurred in their branches. I feel honored and grateful to have learned to read the stories trees tell from such ancient and stately behemoths.
January 14th, 2009 | Author: sarcozona
My mentor, cutting down a dead tree for me
I want to know how different soil types affect pinyon pine growth during drought and if there’s a difference in growth between trees that die in the drought and those that have survived so far. So I needed some cookies.
tree cookies
We had no idea that there would be two feet of snow on the ground at the site, which made working much much harder. As much as I usually hate fieldwork, you would think that I would have had a terrible time. Actually, I had a great time. Of course, that might have had a little to do with the drugs I had to take to deal with the change in elevation.
May 28th, 2008 | Author: sarcozona
Carbon dioxide levels have been increasing since the industrial revolution and have been increasing really really fast since the 1950s. You’ve all seen the hockey stick graph.
I’ve been looking at pinyon pine tree rings for the past year and think there might be something going on with increasing CO2 and what the rings are doing. So I’ve got a stack of papers to read through and thought I’d share some of them with all of you.
Carbon dioxide is pretty good for plants because plants need carbon for photosynthesis. We’re interested in what higher levels of CO2 will do to plants because if plants are growing more and eating more carbon dioxide it could help slow down global warming. But giving most plants most places extra carbon dioxide doesn’t seem to do much in the long run because plants need lots of other things to grow, like nitrogen and water, and carbon isn’t usually the most limiting. It’s the same for you: it doesn’t matter how many vegetables you eat if there’s no water.
But what about plants where carbon might be a limiting factor for growth? Carbon can be limiting in hot, dry places because to get carbon, plants have to lose water. Plants have little tiny pores in their leaves called stomata. They have to open these to let in CO2, but water escapes whenever they’re open. A lot of plants that live in hot, dry places have evolved a different kind of photosynthesis to deal with this.
Another place carbon might be limiting is at very high elevations. Atmospheric CO2 concentrations decrease with increasing elevation. That means that in the same amount of space there’s less CO2. This happens to all gases. Flagstaff is above 2000 meters. When people move here, they have a hard time breathing for awhile because of the lower oxygen concentration.
Lamarche et al. looked at tree rings in the 1980s of bristlecone pine growing at 3100 meters. They found that the trees had increasing growth since about 1840. Initially they thought that this was due to warmer temperatures, but then when it cooled down in the 60s, the trend kept going and even accelerated. So, the faster growth wasn’t due to hotter temperatures.
But was it caused by higher CO2 levels? Plants can only use so much CO2, no matter how much is available. Like at Thanksgiving dinner, there’s lots of food available, but you can only eat so much. In the 1960s, CO2 was between 223 and 230 ppm at 3500 meters. For spruce, that concentration is well below what it considers CO2 saturation and so is probably well below what bristlecone considers saturation.
While the authors didn’t really have enough data from enough places to say for sure CO2 makes trees growing at high altitudes grow more, what they do have certainly suggests it.
This paper is over 20 years old, so we’ll see what more recent papers have found…
LAMARCHE, V.C., GRAYBILL, D.A., FRITTS, H.C., ROSE, M.R. (1984). Increasing Atmospheric Carbon Dioxide: Tree Ring Evidence for Growth Enhancement in Natural Vegetation. Science, 225(4666), 1019-1021. DOI: 10.1126/science.225.4666.1019
January 07th, 2008 | Author: sarcozona
I use a program called COFECHA to help crossdate trees. COFECHA uses some old school formats developed for punch-cards. Excel, which I used to make changes to ring widths, does not like these formats. There are lots of programs for changing formats, but it’s all a bit confusing.
Many dendrochronology programs produce and use Compact/Precision formats. When crossdating trees with the program COFECHA, it is often useful to convert Compact/Precision formats to formats recognized by spreadsheet programs like Excel and then convert back to Compact/Precision formats to run through COFECHA. So for any other confused dendrochronologists out there, here’s a method that works for me.
Compact/Precision format looks like this when you open it with notepad:
ira 11946 170 200 216 755
ira 11950 529 332 405 342 384 760 647 363 556 466
ira 11960 288 431 490 124 827 282 319 248 441 1082
ira 11970 1601 498 992 1407 850 1053 1356 951 1145 1621
ira 11980 1756 1381 1397 1626 1868 2739 2447 2250 1684 1942
ira 11990 1401 1390 861 1389 1158 1421 1454 1040 -9999
Sometimes the numbers seem to run together, but each line will start with a series identifier and each series will end with -9999.
Convert file from Compact/Precision to tab delimited .txt file with program YUX. Open .txt file with Excel and make necessary changes, being sure to save as a tab delimited .txt file. Convert to Compact/Precision format with program CASE, being sure to save the new file as a .rwl. COFECHA should be able to read this file.
If you get COFECHA output that only includes the title or part of the desired output, try playing around with the print options in COFECHA. If COFECHA produces a completely empty output file, try copying and pasting the information from your .rwl file into an existing .rwl file and saving it as a new .rwl file.
All programs can be downloaded from the Ultimate Tree Ring Web Pages run by Henri Grissino-Mayer.
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