More on the American Chestnut

I stumbled across some relevant links, and since I recently blogged about Chestnuts I figured I might as well post them here.

A blog discussing therapeutic vaccines from ScienceBlogs.

An article on a chestnut GMO.

PCR sneakiness

I found this little detail from a chapter of Tears of the Cheetah on whales to be quite amusing. A whale researcher named Scott Baker had done a lot of genetic work on various species of cetaceans, and had collected enough DNA sequences (mitochondrial and nuclear) to identify a random sample to species unambiguously. Using this genetic database as a reference, he covertly sampled whale meat (kujira) from Japanese and Korean fish markets. Kujira can be legally sold in these countries provided endangered species (which are legally protected) are not harvested. However, because Baker suspected that some of his samples were actually illegally harvested endangered species, he couldn't take them out of the country for analysis due to CITES Appendix I restrictions on moving tissue samples (or even DNA) across international borders. So what's a researcher to do? Simple, just replicate the DNA using PCR!!!!

Baker continued his work for several years, and discovered that 10% of the kujira sampled came from illegally harvested endangered species. Most of the meat came from minke whales, which are not endangered, but Baker did discover that 1/3 of the minke whale meat came from a small, endangered (and legally protected) population of minkes in the Sea of Japan. His results were published, and the proper authorities (the International Whaling Commision, or IWC) now use his techniques to monitor kujira meat.

I find it fascinating that DNA generated through PCR does not suffer the same restrictions as a whale's original DNA. On a molecular level they are pretty much exactly the same; the only difference is where the base pairs, etc. originated from. I'm not saying there's anything wrong with that (indeed, it allowed Scott Baker to complete his research which led to tighter controls on the harvest of whale meat), but it does illustrate the artificiality of definitions. The PCR products are still whale DNA, but because they didn't come from a whale they're not legally "whale DNA." Fascinating.

References:

O'brien, S.J. 2003. Tears of the Cheetah: And Other Tales From the Genetic Frontier. St. Martin's Press, New York, NY.

The Florida Panther

Oh, what a misleading common name it is. It implies that the Florida panther is a subspecies of Puma concolor, and indeed it was once classified as such. At one point it was even elevated to the status of being its own distinct species (Felis coryi), only to be later reassigned subspecific status. This is not, however, consistent with the genetic history of the species.

Stephen J. O'brien recounts the tale in his book, Tears of the Cheetah (I've only read 4 chapters thus far, but it is a fascinating read, written in an engaging narrative style that is easy to understand, and I highly recommend it). The previous two chapters dealt with inbreeding depression (and the historic bottlenecks that caused them) in cheetahs and Gir lions (an Asiatic subspecies), respectively. Not surprisingly, Florida panthers were also suffering from severe inbreeding depression. Mitochondrial DNA and nuclear microsatellites were used to estimate the time of the historic bottleneck which caused the genetic homogeneity of the panthers. For those not well-versed in evolution, a bottleneck occurs when a population is severely reduced in size, leading to a reduction in genetic diversity (simply due to the fact that the survivors, being only a small subset of the original population, possess only a small subset of the former population's genetic diversity). Individuals are forced to mate with genetically similar individuals (as there is no other choice), often close relatives.

So how can mitochondrial DNA and microsatellites be used estimate how long ago a bottleneck occurred? Quite simply, it takes time for mutations to accumulate and for genetic diversity to re-establish itself. Thus, cheetahs today are genetically very similar because of the bottleneck that they went through 12,000 years ago. However, some genes mutate faster than others. Mitochondrial DNA (mtDNA) does not reside in the nucleus of the cell, but in the mitochondria (organelles which supply energy to a cell, which are descended from single-celled organisms that were engulfed by the (single) cells of our very distant ancestors). Because mtDNA is separate from nuclear DNA, it doesn't benefit from the DNA repair mechanisms that are present in the nuclei of cells. Since mutations are essentially replication mistakes (or damage, but we won't get into that), and the mistakes of mtDNA don't get fixed, mutations accumulate faster than in an organism's nuclear genome. Mutations occur at a relatively fixed rate, so differences in mtDNA can be used to determine how long ago two species split from a common ancestor, or how much time has passed since a bottleneck. The situation for microsatellites is similar. Microsatellites are repeated sequences of a small number of base pairs. They exist in the nuclear genome, but are non-coding (i.e. they aren't a functional gene) and so also mutate at a greater rate than the rest of the genome.

So there's that tangent, and now you understand how the time since a bottleneck occurred can be estimated by using “molecular clocks.” Turns out, North American pumas (not just Florida panthers) experience a bottleneck 10,000-12,000 years ago (about the same time as the cheetah). I group North American pumas together because during the course of this study, the historical scheme of 32 different puma subspecies across North and South America was essentially invalidated. Rather, 6 genetically distinct populations were found, 5 of which were South American. All North American pumas could be traced back to the single, small population that resulted from the bottleneck, and yet puma fossils in North America go back much further than this (in fact, pumas were originally a North American species that migrated to South America when the continents became connected, displacing the existing South American marsupial carnivores). So how can this be explained?

The current hypothesis is that North American pumas went extinct during the same extinction event that killed off the dire wolf, saber-toothed cats, American lion, and American cheetah, as well as other large mammals such as mastodons. As a side note, the African cheetah's bottleneck is thought to have resulted from a small refuge population that persisted in sub-Saharan Africa while the rest of the world's cheetahs—which were wide ranging in North America, Europe, Asia, and Africa—succumbed to the Pleistocene extinction event. But South America's pumas escaped this event (the extinctions were largely restricted to the northern hemisphere from what I understand). A small founder population migrated back to Mexico through Central America (small population=genetic bottleneck). This population was kept small through a combination of a geographic bottleneck (the Isthmus of Panama) and behavior—namely the fact that pumas are territorial and further northward migration was blocked off by the territories of the resident founders. The founders slowly made their way north, maintaining their status as a distinct genetic population by preventing southern cats from migrating across the Isthmus.

So all North American pumas are fairly homogenous genetically, but what about Florida panthers? They existed in a refuge of land largely unsuitable for agriculture: the cypress swamps of Florida. As cougars were extirpated from the rest of the southeast, migration to this small refuge population was (obviously) cut off. This naturally led to inbreeding depression, which was actually the cause of identifying traits used to distinguish the Florida Panther from pumas in the rest of the continental U.S. These traits included a dorsal cowlick halfway down the neck, and a kink at the tip of the tail. It's important to note that these traits were not present when the Florida panther was first described as a subspecies (before widespread extirpation throughout the east), and are actually the results of severe inbreeding. Another such consequence was cryptorchidism, a condition where one or both testicles never descend in males, leading to reduced fertility or sterility (if neither testicle descends).

A recent management decision resulted in several individuals from a Texas population (which historically overlapped with the Florida panther's range) being released into Florida. Offspring from these Texas females (which had obviously mated with male “pure” Florida panthers) did not exhibit the cowlick or tail kink, and also didn't develop cryptorchidism. The hybrids were also markedly healthier and stronger, often jumping clear over the research team after being treed by dogs (a feat that the weaker, inbred, “pure” Florida panthers were rarely able to accomplish).

I find this tale very interesting because it generates questions on where to draw the line with conservation efforts aimed at preserving the genetic integrity of small populations and/or subspecies. In the case of the Florida panther, prior to the genetic tests nobody wanted to “hybridize” them, tainting the genetic makeup of the “authentic” subspecies' population. After bringing to light that the smallest genetically distinct population was North American pumas in general, the case was made to re-introduce migrants. In the case of the Texas females, migration that existed freely before about 1900 was merely re-established.

References:

O'brien, S.J. 2003. Tears of the Cheetah: And Other Tales From the Genetic Frontier. St. Martin's Press, New York, NY.

Powdery Mildew

We've had a lilac along the side of our house for years (rough estimate 10+?), between 2 forsythias. While I was in WA, my brother pulled up one of the forsythias (I don't remember why, but last I remember it was looking kind of runty, possibly near death) and planted another little lilac. When I got home, the new lilac had a small amount of white fungal growth on the leaves. It's gradually gotten worse, and I finally decided to look up what it was. Turns out, it's powdery mildew.

View of the whole plant

Close up of leaf.

Apparently younger plants are more susceptible, and severe cases result in curling, drying, and browning of the leaves (which this little guy exhibits). Nearly all ornamental plants can get some form of powdery mildew, but species are mostly host-specific. The mildew shows up mid to late summer, and the biggest problem with it is that it diminishes the aesthetic quality of the host plant.

The fungus itself will overwinter on fallen leaves, so I'm assuming that next year's infection could be reduced by removing the leaf litter from around the plant. Ascospores are released in the spring, and carried back to the new leaves via wind or splashed water. In sites with good airflow and well-drained soils, inoculation is less likely. Exposure to full sun also reduces the spread of the fungus. This is certainly observable in my lilacs, as the older lilac has a few lower (thus more shaded) leaves that have a small amount of fungus on them. Overall though, the older lilac largely lacks powdery mildew. Furthermore, the younger lilac is closer to the silver maple in my backyard, possibly increasing the amount of shade that it receives (the maple is south of the lilacs). Interestingly, though powdery mildew is supposed to hasten the fall senescence of the leaves, the older lilac's leaves are showing much more yellow/light green coloration than the younger, highly infected one, which is still largely dark green/crispy brown at some leaf edges.

References:

Nameth, S. and Chatfield, J. The Ohio State University Extension Fact Sheet. Plant Pathology. Columbus, OH.

Partridge, J.E. 2008. Powdery Mildew of Lilac. University of Nebraska, Lincoln Department of Plant Pathology.

Trees of Life

Western Redcedar

In the Pacific Northwest, the Western Redcedar (Thuja plicata) is often called the "tree of life." In fact, the use of it's wood and bark it's one of the defining features that represents the northwest coast indigenous cultures. Its wood is infamously rot-resistant, and since it's also easy to split it's an ideal resource, particularly in such a wet climate. Redcedar's slow decay time also makes it a very important tree ecologically, as logs persist in the understory of old growth forests (some species, including Western Hemlock, germinate almost exclusively on these "nurse logs") and in streams. Large wood is an important feature of streams because 1) the persistent wood releases nutrients into the stream slowly over time (attracting macroinvertebrates, which are then fed on by juvenile salmonids), 2) it creates a physical impediment to fast water flow, resulting in pools that spawning salmon use to rest in during their arduous journey upstream, and 3) it provides cover for juvenile salmonids as they rear in the stream.

Western Redcedar is a prevalent tree in low to medium elevations, and its cultural uses included, but are not limited to, the following:

• The wood was used to make canoes, house planks, totems, and mortuary poles.
  
• Wood was also used for such tools as arrow shafts, spear shafts, barbecue sticks, fish spreaders, bowls, dip net hooks, cradles, and coffins.
• The wood makes an excellent fuel, particularly for drying fish.
• It was said to possess healing and spiritual powers.
• Bark was used for making blankets, clothing, and baskets.

American Chestnut

If Western Redcedar was the tree of life on the Pacific Northwest coast, then the American Chestnut (Castanea dentata) was at one time the tree of life in the eastern deciduous forests. It was a dominant tree throughout most of its range, which spanned from Maine nearly to the Gulf coast, broadly following the arc of the Appalachians. It was ecologically important because it reliably produced crops of chestnuts every year. Since its functional extinction, oak species have primarily filled its niche, but oaks produce large crops of acorns some years, and small to no crops in other years. This puts stress on the myriad of species that depend on this food source, and results in wildly fluctuating populations between years. Commercially, chestnut lumber was valued for furniture, musical instruments, interiors, caskets, and fences. In addition to possessing quality wood, the chestnut's growth habit tended toward a tall, straight trunk making it extremely attractive for logging.

In the early 1900's tragedy struck as the Chestnut blight (a fungus of presumabely Asian origin) decimated the species. It is functionally extinct, though you may still find specimens in the wild. The blight does not destroy the roots, and so the tree will still send up sprouts which can reach "moderate" heights (the tallest I've seen was approximately 7-8 ft. tall) before they succumb to the blight. These sprouts rarely survive long enough to produce flowers and fruits. There is some work being done to hybridize American Chestnuts with foreign species to produce a blight-resistant tree, but as far as I know success is limited and these trees are primarily used as ornamentals.

I can't remember if I read this somewhere, or saw it on a documentary, but there was an elderly man recounting the beauty of flowering chestnuts in the spring. He lamented their loss, both in an ecological sense and a personal sense, since he can never again behold that spectacle. He then went on to say that it was unfortunate how younger generations never got to witness the American Chestnut as a dominant component of eastern forests. Having never seen them, they aren't even aware of what they missed out on. He implied with deep sadness in this statement that extinctions really only hit home for the generations that witnessed them. For the majority of people, this is probably true. For some reason though, I've developed an odd emotional attachment to the American Chestnut. I get legitimately upset when I see chestnut sprouts, because I know that they'll never survive and yet they're right in front of me! It's incredibly frustrating to me, despite the fact that I've never seen a mature chestnut. I have the feeling that I'm looking at a ghost, and in some ways I am. This was a site of a mighty chestnut, and now all that remains is this spectral sprout, unnoticed by most humans as just part of the understory, and by the species that used to depend on it as just another plant that doesn't provide a source of fruit. Of course with functional extinction there's always the hope that hybridization will be successful and chestnuts can once again thrive despite the blight. But how likely is it that the tree will make an ecological comeback? There's really no way of knowing, but one thing is for certain: even if a resistant chestnut is successfully bred or engineered, it will be generations before the world sees eastern forests with an ecologically dominant chestnut.

References:

Pojar, J. and MacKinnon, A. 2004. Plants of the Pacific Northwest Coast. B.C. Ministry of Forests and Lone Pine Publishing, Vancouver, B.C.

Petrides, G. A. and Wehr, J. 1998. Peterson Field Guide to Eastern Trees. Houghton Mifflin, New York, NY.

The Legend of Sigurd and Gudrun

One idea that I have for how to proceed with this blog is to provide commentary for various things that I read. This will likely tend to fall into one of the following categories:

1. Fantasy/mythology (as is the case with this post). Generally this will mean Tolkien or occasionally something fairly unique (such as the His Dark Materials trilogy), but overall I actually don't read much fantasy. Basically I can't stand the plethora of Tolkien clones, and the fact that a lot of authors write fantasy because they're interested in it, and not because they're actually any good at it.
   
2. Science/environment. This is really broad, and may encompass anything from academic material (textbooks, primary literature, etc.) to articles in Sierra (the Sierra Club's magazine, which I happen to be subscribed to).
3. Miscellaneous. Ok, this isn't really a category but I thought I would get more specific in the above two, and now I can't think of much else that I read about with the same regularity. Some oddballs may show up every now and then, though.

Alright, enough description, and on to the meat of the post.

Recently I read Tolkien's version of the Legend of Sigurd and Gudrun, which is a re-telling of The Volsunga Saga. Tolkien drew upon various sources on the same legend, including the prose Edda of the Icelandic Snorri Sturluson, as well as the poems of the Norse Elder Edda. This was not a translation, but rather an original work which, while largely adhering to the source material, also contained a few creative alterations and interpretations of Tolkien's own invention. Indeed it was probably inevitable, since sometimes different sources on the same story contradict each other. But I'm not expert on the subject so I'll leave it at that; besides, it's explained very well in the book.

The book is comprised of two main parts, both in verse: The Lay of the Volsungs which tells the tale of Sigmund, and his son Sigurd, and The Lay of Gudrun, which occurs after Sigurd's death and follows his widow, Gudrun, and the conflict of the Niflungs (her brothers, Gunnar and Hogni) with Atli (historically, this is Attila the Hun). Tolkien follows the style of Norse eddaic poetry which, as the Foreword to the book points out, differs from that of the Old English epic poetry that I was more familiar with. In one of his lectures, Tolkien himself noted that "in Old English breadth, fullness, reflection, elegiac effect, were aimed at. Old Norse poetry aims at seizing a situation, striking a blow that will be remembered, illuminating a moment with a flash of lightning-and tends to concision, weighty packing of the language in sense and form..."

Reading it was a bit of an adjustment, as scenes would change with little in the way of contextual transition. The beginning in particular was difficult, as it dealt with the actions of gods (namely Odin and Loki), and I'm not terribly familiar with Norse mythology. It's definitely a subject that I'd like to read up on more. Fortunately, I still have the books from my Middle Ages and Middle Earth class (yes, I got to take a class on Tolkien in college), including The Volsunga Saga and Poems of the Elder Edda. It's strange how, in a way, I've come full circle with my reading of Norse poetry. In the class we looked at a few of the poems (Otr's Ransom comes to mind) with respect to the influence they had on Tolkien's writing (specifically The Hobbit and LotR, as Tolkien's Lays on the Sigurd legend hadn't yet been published). Essentially, they shed light on our source material, which was Tolkien's Middle Earth. Now I've read Tolkien's own version of the Norse legend, and I look back at that ancient, original source material to see how Tolkien has influenced it ("it" being the legend, in the sense that he's now contributed to it).

References

Tolkien, J.R.R. 2009. The Legend of Sigurd and Gudrun. ed. Tolkien, C. Houghton Mifflin Harcourt Publishing, New York, NY.

Where do we go from here?

I haven't really been updating this blog all that much. I think part of it is because its subject matter tends to be very general, and quite frankly random, so I always struggle with what exactly to write about. Of course the larger issue is that I suspect that very few people actually read this blog, and I thus don't have much motivation to update. Perhaps if I posted more consistent subject matter more people would check it regularly.

I spent a good part of the day reading a D&D blog (for those that aren't familiar with the game, D&D = Dungeons and Dragons). That tempted me to focus on D&D, but at the same time few of my friends actually play or are interested in the game, and I currently am not playing in a campaign, nor am I DMing one. While reading through the blog (Grognardia, in case anyone is curious), I found myself gravitating toward posts on the author's ongoing campaign. This, in turn, really made me want to DM my own long-term campaign, but alas player availability is seeming to be an issue. If I actually manage to get a campaign going that would be the perfect opportunity to start a D&D related blog, but at the same time I almost think that this blog isn't the appropriate venue for such an endeavor. Namely because I would still like to use this for random musings, thoughts, and reports.

I really wish that blogs had an easy way to categorize subject matter by post title. For example, at the top of my blog (under the title) there would be links for "topics" (or something, I don't care what it would be called) so I could click on "D&D," "environment," "trip reports," etc. and all posts within that category would show up. Likewise, each topic would have its own url so if I wanted to link someone to my D&D blog, for example, on the Wizard's of the Coast forums, I could do so without them having to sift through all of my other random posts. I suppose I could always create a second blog (since D&D is different enough from my more...academic interests to justify it), but I really like the title "The Chamber of Mazarbul".

So I guess the take home message is that I would like to start updating this blog more regularly. Hopefully that will attract more readers. I'm just trying to figure out what direction I'm going to take with it. Some posts will soon follow as I test the waters.

Unemployment

This whole being unemployed thing is starting to get old. It was nice for the first 3ish weeks of being at home. Now I'm just getting antsy. Ideally, I'd like to get a seasonal position with UPS being a "driver's assistant." They hire them during the holiday season to essentially grab packages from the truck and run them up to people's houses. I can't imagine that it saves enough time to justify the position (especially since the pay is quite decent, $13/hour from what I hear), but I'm not complaining. Someone somewhere must have done a cost/benefit analysis, and I guess it would be cheaper to pay a bunch of seasonal employees than to send out more trucks to make up for the increased volume of packages. In any case, thus far this is the only position I've really applied for yet, though I have been looking for jobs in the general area. Soon I'll have to lower my standards. Not having a car makes it harder.

In the not as near future, I'm working on applying to a position in the Sierra Nevada doing bird research as part of a field crew (possibly supervising). The pay is pretty good considering that these positions tend to just be living stipend + housing, but this one is $1800-$2700 per month with free housing and work vehicles provided. And I would basically get to go backpacking in the Sierra Nevada and count birds! My lack of previous experience with mist netting, point counting, etc. is unfortunate, but I'm going to apply anyways and see what happens. That would be mid-April until August. I'll also probably look into seasonal work at a national park, most likely the Smoky Mountains. In either case, I hope to have a car by that point. Which means that the pressure is on to get a crappy job and make some money. At least AmeriCorps is taking care of my loans for a while yet :D

I don't have much of an idea of when I'll be applying for grad school. It's partially because I'm not sure if I want to go for a Master's or a Ph.D. I love research, but it can be stressful and time consuming, especially if I ended up going into academics. I just don't necessarily like the idea of having my career monopolize most of my time. I don't want to be a slacker, but I also would like an appropriate amount of leisure time. You only live once, why let your job dominate your life? Even if you love your job, variety is good. I guess I'm leaning toward going for the Master's first, and seeing how that goes.

Coast to coast...

I'm back home in OH after my road trip from WA. And a week and a half after I got back, I went to Maine to visit Liz. So in the last couple of months I've been to the beaches of Olympic National Park (Pacific) and Acadia (Atlantic). Good stuff :) But yeah, I don't think I feel like posting a lengthy trip summary, so I'll just list where I went on the way back.

Started out climbing Mt. St. Helens. Next we went to Olympic NP and hiked up the Hoh River Trail up to the Blue Glacier on Mt. Olympus. Then we went to the beach and did a day hike near Lake Ozette (Cape Alava to Sand Point). Then came North Cascades, and the trail we were going to do was on fire. So we did another trail but hiked out early because of rain (despite being on the east side!). So we got to Idaho early, visited Julie's friend Simon, and then visited another of Julie's friends in Bozeman, Montana before heading out to Yellowstone. Backpacked in the Lamar Valley (wolf hotspot, but we unfortunately never saw one) and then headed to Grand Tetons for a day hike. On the way back east we stopped at Badlands NP for an overnight, and then spent nights in Wisconsin and Chicago (with Mike!).

Acadia was fun too; I drove up there with Dawn for basically a long weekend (her grad school schedule didn't allow for a longer trip; oh well). 15 hour drive, and we drove through the night, got there at 7 pm on Thursday morning and napped while Liz went to work. She's doing environmental education in the park.

Ummm...yeah those were really short, lame trip summaries but I don't really feel much like typing right now.

3...2...1...Offblast!

I fly back to WA today. Computer access will be limited, if not nonexistent. Aug 25th I climb Mt. St. Helens. Then it's off to Mt. Rainier NP, Olympic NP, N. Cascades NP, somewhere in Idaho, possibly Yellowstone, etc. That last part hasn't exactly been planned out yet :) Be back some time in late September, possibly with a long entry about the trip. And pictures, assuming my camera makes it :/