Day 3: Highs and Lows

I woke up Tuesday morning ready for more moss- I even had a dream about moss, that I was tiny and lived in one of those Pleuridium capsules I talked about yesterday. After a hearty (and free) breakfast, I walked out to the car raring to go- the air was crisp, the sky was rain-free, and the smell of motor oil wafted across my nose. Um, what? There was a large, iridescent puddle beneath my car. Taking a peak underneath, it was clear what happened: somewhere on one of those dirt roads in East Penn, I had punctured my oil pan.

This was my payback for not renting an SUV for this trip, which probably would have cost about $400; oddly also the estimate for repairs. I was lucky that we were in Scranton, which has a VW dealership, though. They were able to squeeze me in during midday, but in the meantime I was trapped in Scranton. We did make the best of the situation, finding two populations of Funaria on opposite sides of town. After lunch at a disappointing pizza place (Donio's: home of chewy, greasy pizza), we headed back to the dealership. The estimate was actually high, which set up the rest of the day nicely.

On Day 2, we realized what kind of habitat we really needed to look for: railroad tracks. On our TOPO map, we identified the train tracks between Scranton and Ithaca, and we followed them dutifully, with amazing success. We followed the Susquahanna River north towards the New York border, and found moderately sized populations in all three counties between Scranton and the NY border. Piers and I were getting especially good at recognizing whether a particular railroad track would be promising, based on the kinds of rocks used as filler. As we entered New York, we found the tracks again north of Waverly, and driving along it, we could actually pick out where it was, based on the habitat and the bright red seta.

After Waverly, we were two counties away from Ithaca, and my advisor had given me some areas to check out near Cornell. Still, after a successful pickup in Chemung County, Piers suggested we stop just over the Tompkins County border (still about 15 miles south of Ithaca). We pulled up to the railroad tracks and Piers went left down the tracks towards a small stream, and found a few small patches. I went to the right, and... let's just say that I need to keep redefining what I mean by Mother Lode. The population was spread out over the same area as the one from Auburn, PA that I collected in the rain, about 500 feet along the tracks. This population was different- Funaria was in very large patches for this kind of moss- up to 3 feet across!

It also occured on both sides of the tracks, in an interesting habitat. On the far side of the tracks, Funaria was in smaller patches, further from the tracks than on the near side. There was also a lot of other types of moss: typical ones that occur on disturbed soil, and also a fern ally called Equisetem. A good ecologist would be able to make better hypotheses, but my guess is that Funaria is being out-competed on these soils by the other plants, and is forced further up the bank. I will be very interested to learn if the genetics of the patches with respect to their habitat. I actually collected from a third type of habitat at this location, down by the stream. Funaria doesn't usually occur in wet places, so this was an interesting find. We spent about 2 and a half hours (or, three beers in Piers Time) here, so we didn't have time to explore Ithaca that night.

We did, however, eat at an excellent Thai/Asian restaurant called Tamarind. I had the coconut soup with chicken, which I really want to learn how to make. We ended up in Ludlowville, NY, 10 miles north of Ithaca, in a really neat house. The room I stayed in was a hexagon with windows covering five of the
six walls. Needless to say, I didn't sleep much past dawn...

Miles Traveled: 150
Funaria populations: 6

Tomorrow: The southern Adirondack Mountains, ending in Maltaville, NY.

A note on Commenting

A few people have e-mailed me to ask how they can leave comments. I have left things open, so that people can leave comments with a Google account, or without. When I log out, I can choose to leave a comment as "Name/URL" which allows me to simply put my name (and a link to my favorite website) when I leave a comment.

There is still a "word verification" when you leave a comment; this is to keep spam down. Just type the word you see into the box when you leave your comment. If you have any more trouble, don't hesitate to shoot off another e-mail!

Happy posting!

Day 2: The Mother Lode

I knew very early the theme for my trip's second day: rain. It was raining when we left Bethesda, and drove (thankfully) against the traffic up to Fredericksburg, where we got back on our favorite US highway- US-15. It was a short drive up to Gettysburg, and we took the business route towards town to see what was there. Piers revealed that he double majored in biology and history, so he had interests in Gettysburg other than biology. We didn't have much time to site-see though, and headed to the Visitor's Center in the Military Park, in search of a good map. It was still under construction, and had a lot of gravelly trails headed through loose forests, so rather than get the map, we took a look around. By now the rain was pretty steady and I was soaked, so it didn't matter that I had to get a little wet to cross a small stream.

The only moss of interest I found, though, was Physcomitrium pyriforme, a moss that has haunted us over the first two days. It's a member of the same family as Funaria (the Funariaceae), and from a distance (say, standing over a patch), the sporophytes look similar. However, Physcomitrium has a rather distinct capsule when examined up close: it's pyriform, as the species name suggests. Funaria, meanwhile, has a much more elongated capsule, so much so that it sometimes bends over. Anyway, same family, similar look, similar habitats mean that we both frequently bent over to examine what was ultimately the wrong moss. It's a bummer, but it eventually yielded results- after about an hour Piers found a few small patches of F. flavicans.

Since we were both soaked, we were content on staying on the highway from Gettysburg to Harrisburg. Once there he suggested we stop at a railway; it seemed like the area was a loading site, as there were a lot of tractor trailers. There was also a lot of dirty, disturbed soil, which we poked around in for a while. The main mosses here were Bryum argenteum again (which I collected from on top of gravel on an abandoned trailer), and Ceratodon purpureus, another weedy moss commonly studied for population genetics. Stuart McDaniel, who graduated from the same lab as me in 2005, did his PhD research on the species. But it's not my species, and moved on across the Susquehanna River; I didn't find either Bagel Street, nor the hat company.

The plan was to get on PA-443, which hugs the base of the Appalachian Mountains in Pennsylvania. Right as we got on it, we passed over the same train tracks as our last stop. The only way down was a "No Outlet" street called "Cemetery Road." Pretty fitting, combining our two most common destinations; perhaps that would breed good luck. We drove down it as far as we could and walked out to the tracks. Funaria, everywhere! Along a 200 foot transect, I collected 13 different patches, on both sides of the tracks. When I was done, I put them in a bag marked: Funaria: Mother Lode. If only I knew how wrong I was.

We were content to put a good bit of distance between us and the Mother Lode population, mostly since I hadn't eaten lunch yet and it was still a steady, chilly rain. After we did stop, a decision was made to take a country road, PA-895, towards Palmerton, the coal-contaminated town a bit north of Allentown, PA. We thought it would be more direct, but it was a lot more windy, and had a lot more small towns scattered around. One of them was Auburn, PA, and as we left, we went under a train tressel. Piers suggested we stop and I followed him around the sparse, blackened forest unsuccessfully (moss-wise). We then scaled the steep up to the tracks and....

...Clearly, I did not know what Mother Lode meant. This population was huuuuuuge! Now, for a moss that might be tough to imagine, but we walked about 400 feet on both sides of the train tressel and found patches all over the place, ranging from small (2 cm wide) to large (20-30 cm). One thing I found very interesting is that the setae (plural of seta: remember it's the stalk that the capsule is on) were very variable. Some of them were quite short (2 cm) while others were quite long (10-15 cm) by moss standards. One question I have about this is whether it's due to genetics, or to environment. I will have to do experiments, growing different varieties in the same environment, to determine this. If it is genetic, I will be able to determine if there is a correlation between seta height and relatedness: generally, are inbred mosses characterized by short seta?

We spent over ninety minutes at this site, and I collected 58 patches on both sides of the tracks. By the time I had gotten all the bags laid out, I then needed to measure the distances. About then, we heard a rumbling.... and a small train whisked by, sending alot of my bags flying! I was initially very mad, but then I remembered that all the bags were numbered, and Piers had placed a stick near every population as he walked by, so it was easy to put the bags back home. They (and we) were soaked through when we got back to the car, where we quickly transcribed all the info and rebagged the mosses. It was a ridiculously successful day, and we still had two hours of light left!

It was now clear that railroad tracks were the way to go. We opened our trusty Pennsylvania gazeteer to follow the tracks... and as we approached Palmerton we went where the map said we should find a choo-choo, but there was nothing. Piers asked the postmaster of scenic East Penn, PA, and he said the tracks had been removed, but there was still a trail where they used to be. We went there and searched for a while, but only found a few small patches- I'm spoiled by Mother Lodes, for sure.

We called it a day without getting to Palmerton. I don't think I'll regret it, as I slave away under a microscope this summer, measuring the thousands of plants we collected today. Tomorrow's plan: Ithaca is Gorges! It's a short, 2-hour drive from Scranton to Ithaca but we'll be taking our time, snaking along US-11 which apparently runs along a railway, and then over to some sites near Cornell that Jon Shaw suggested. The forecast calls for a lot less rain, but also a lot less temperature. Sounds like a multi-layer day.

Miles Traveled: 200
Funaria Populations: 4

Day 1: "This is a weed, right???"

So, I have some bad news. I packed the wrong USB-cord, so I won't be able to include pictures in my updates. Don't worry though, I'm taking plenty!

Today, we started off from Durham at 8 AM and headed up US-15 from Oxford. The name of the game was: find some cemeteries! I admit, it is a little odd to be walking around a cemetery looking for moss, but they do seem to have a great assortment of mosses. Many cemeteries don't have very high grass, and near the headstones or on clear dirt are great places to find moss growing. I usually stuck to the outskirts of the cemeteries, letting Piers wander around among the graves. The only collection I made all day from one was next to a headstone marked only with a name; I assumed that it was just a placeholder.

We stopped along the John H. Kerr Reservoir near the border of North Carolina and Virginia. There was a state park on the NC side, and it looked really promising. Funaria is a first-colonizer of recently burned-over soils, and campgrounds are usually a good bet. This campground featured a bunch of 10'x10' squares populated by a single table (wooden sitting platforms and a stone top), along with a circular metal fire pit. Some of the squares had obviously not been populated for some time, as they had moss growing even on top of the stone table! However, there was no Funaria.

We moved on north, to the Occoneechee State Park, because Piers had previously collected Funaria flavicans near a parking lot. Rather than pay $4 for a day pass, we convinced the ranger that we just need to get a GPS point, and so we couldn't stay long. Sure enough, we parked next to the entrance to the aptly named "Mossy Creek Trail," and in the grass next to the gravelly lot there were four small patches of F. flavicans! "Well, you can't call the trip a bust anymore," said Piers, unfortunately foreshadowing the rest of the day.

We stopped at many forest trails and cemeteries on our way north through Virginia, including the one I mentioned earlier, where I collected Bryum argenteum, at a cemetery near Sheppards, Virginia. After a few more sites (unsuccessful for Funaria but Piers collected a lot), we stopped for lunch in Farmville, VA. I didn't see many farms, and I must admit I was feeling a bit frustrated at this point. I said to Piers, "We're sure this thing is a weed, right?" Of course, it is, but Piers responded equally sardonically, "well, that's the danger of being a specialist... generalists always find what they're looking for!"

North of Farmville we came across some railroad tracks and a lumber yard a few miles north, near the town of Dillwyn. I turned in to check it out, intending to look mostly at the railroad tracks. Driving closer to a large building we noticed a man sitting in a forklift staring at us, so we slowly backed out towards the main road. Before we went to check out the RR tracks, I looked at a grassy area that led up this large ramp, at the end of which was an odd looking contraption that probably filled passing trains with sand, with a dispenser dangling precariously over the tracks. This will probably make more sense when I have a picture. Anyway, beneath my feet were clearly stems of Funaria! I collected many patches of the moss up the ramp, over about 200 feet. It was exciting, and I wanted to find more quickly, but it was getting late and we had a lot of miles to cover before spending the night at Sam's in Bethesda.

We only stopped once more, at another cemetary in Fluvall County, VA, where I collected an interesting moss, Pleuridium. It occurs on clay just like Funaria flavicans often does, but rather than having sporophytes with a long seta (the stalk), Pleuridium has barely any seta at all. The result is that the capsules, which release the spores for the next generation, are immersed, and they can't go all that far. It would be interesting to study the population dynamics of this species. But, another thesis for another lifetime, I guess.

We got in at Sam's at 9 PM, and happily chowed down on some chicken parm subs, due to a rare fit of initiative in picking a place to eat without three hours dicussion.... Overall a pretty successful first day, since I don't want to burn out collecting tons of stuff early on! Tomorrow's plan: make our way back to US-15, and take that to Gettysburg and Harrisburg, before turning east towards the coal-smelting town of Palmerton, and a final resting place near Scranton, PA.

Miles Traveled: 315
Funaria Populations: 2

An Epic Field Trip

One main motivation for starting this blog was to post updates from my first research field trip of grad school. Originally this trip was planned for after the semester, in about Mid-May. However, my advisor and I realized that Funaria, the genus I'm looking for, matures a bit earlier than we had previously thought. If they fully mature before I get there, they'll release their spores and be useless to me. So the whole field trip was moved up to... next week. Starting tomorrow.

I'm looking for populations of Funaria across a wide range, like the Northeast US. There are two objectives:

1) To examine the genetic structure of populations- how related are populations from NY to populations in Virginia? Remember, we're talking mosses here, so you have to think on a really small scale- is there a lot of mixing across the Eastern US, or are populations isolated?
2) How variable are populations? Moss can increase in numbers in two ways: either through sexual reproduction and spores (which fly through the wind to land on new soil), or vegetative reproduction. The latter would produce a population that is, essentially, one clone. This question is interesting if you're inclined to think about philosophical questions such as: What is an individual.

The other objective on the trip is to collect two species of moss: Funaria hygrometrica, and Funaria flavicans. These species are related, and it is possible that they can hybridize. If I can collect populations where both species occur, I may be able to find evidence that genes have been exchanged between the species. If this is true, it would open up a whole set of questions for my thesis, regarding the field of speciation. Briefly, the principles of natural selection make predictions about how species form and how they remain distinct. For closely related species, there is often something preventing them from crossing, which typically results in unfit offspring.

Both species of Funaria grow in similar areas: disturbed, sunny soil. For example, the first population I sampled was right next to the Duke greenhouse:



It's right there near those piles of dirt. It's most "natural" habitat is in recently burned areas, but mostly during this trip I will be look for cemeteries, forest paths, and railroad tracks. When they are completely mature and ready to release their spores, they're actually pretty distinctive, having a bright orange color that stands out from the surrounding grass or other moss:



My guide will be Piers Majestyk, who is a post doc in the lab and an excellent field bryologist and taxonomist. He's real laid back and should be fun to travel with, and I'm looking forward to learning a lot from him. This trip is small potatoes for him, as later this year he's going to be gone for three months, collecting a tropical moss genus (Daltoniaceae) from: Ethiopia, India, Nepal, Philippines, and Hawaii. That's intense.

So, where am I going? Here's the preliminary plan:

Sunday night: Bethesda, MD
Monday night: Scranton, PA
Tuesday night: Ithaca, NY
Wednesday night: Saratoga Falls, NY
Thursday night: Providence, RI
Friday and Saturday night: Hardyston, NJ
Sunday night: Salisbury, MD

Of course, that's just the sleeping places (200 years from now, there may be historic sites: Matt Johnson slept here!). There are a few interesting places I'm targeting:

Day 1: Central Virginia. I'll be taking the long way to the DC area, up US-15 rather than I-95. This way, we'll be able to stop at sites that look promising- cemeteries, open fields, forests that look recently burned.
Day 2: Pennsylvania: We'll leave the DC area and return to US-15, which goes through Gettysburg on its way to Harrisburg. One place I'm looking forward to exploring is Palmerton, PA, which is further east near Allentown. Over 100 years ago, it was the site of a coal smelter, and half the mountain near Palmerton has very contaminated soil. The southern half of the mountain, meanwhile, is clean. If I can find Funaria on both sides, there could be different population dynamics depending on the contamination.
Day 3: Ithaca: My advisor spent a lot of time at Cornell and Ithaca College in the 1980s, and so he is familiar with the areas. He's suggested some filtration ponds near Cornell's campus, and some hills near Ithaca to explore.
Day 4: Southern Adirondack Mountains: This is probably my best chance to find Funaria in a "natural" environment, one that won't be too terribly disturbed by humans, which could make it a good comparison to other, more disturbed populations.
Day 5: Vermont, New Hampshire, Massachusetts: We'll end this day in Providence, and hopefully collect Funaria from at least once site in each state I pass through.
Day 6: Rhode Island, Connecticut: Most of this day will be catching up with friends/family in Providence, with some bryologizing on the side :-)
Day 7: Sussex County, NJ: I may be biased, but I'm hoping there's an interesting population or three here, so that I can have a good excuse to go home to "study." We'll be hitting up High Point State Park and Stokes State Forest, perhaps also Wawayanda.
Day 8: Central/Southern NJ or Delaware. This will depend on how successful we've been, but one plan would be to visit some small parks in New Jersey, as well as the Pine Barrens. Another plan would be to head down the middle of Delaware towards Saisbury, MD. I already have an extensive collection from near Middleton, DE, but further down the penninsula could be interesting as well.
Day 9: Eastern North Carolina. Piers says that some of the swamps/parks in northeast North Carolina have been undercollected. While there may not be Funaria, it will be good to end the trip on a high note for the Duke Herbarium.

And then, back to Durham. My aim is to write interesting things that happen on the trip, and when I have internet access, update frequently, so check back soon!

Accidental Bryology

Back in December, the first-year grad students felt bored and slightly lost as we sat in a banquet hall at Washington Duke Inn. It was the Biology Department Retreat, although it was a very loose interpretation of the word "retreat," since we were about 200 yards from campus. An idea was born that day, though, that the first-years should have a real retreat of our own, and we were granted some funding to go someplace special. Although I voted for the Duke Marine Lab, the winning place was the Mountain Lake Biological Station. I'm sure the knowledge that Dirty Dancing was filmed at the nearby Mountain Lake Hotel swayed a few of the female voters. It's located at the edge of the Appalachian mountains near Blacksburg, VA, and I must say I'm glad we chose the spot, the weather was great and we had the whole place to ourselves.

Since I'm taking a Bryology class this semester, I've gotten in the habit of taking my collecting bag wherever I go. It's complete with my GPS, Camera, small paper bags, and pens. It also contains a 14x hand lens, which others have lovingly referred to as a "nerd beacon," as you can always tell a naturalist from the small lens draped around his neck. Throughout the day, I kept looking for Funaria in its customary places: near old campfires, along the edges of the paths. Plenty of moss everywhere, but no Funaria. That was fine, and I had fun telling the laboratory-stricken among us all about bryophytes. Later in the day, there was a movement to hike up to Bear Cliffs, which is a sheer cliff-face that overlooks all of the Piedmont of central Virginia.

I am not very well suited for field biology in the mountains. I learned this back in March when our Bryology class went to the Highlands Biological Station, up in the NC mountains. Climbing uphill was tough on me, and to try and keep up I would hunch over and hurry upwards, which ruined my back for a few days afterwards. Most of it is because I'm out of shape, and I'm working on that. The MLBS, meanwhile, is at 3800 feet, and these "Bear Cliffs" were at 4100 feet, so there was a bit of a climb to come for me. My back and legs screaming, I eventually made it up to the top, about 15 minutes after everyone else:



My GPS disagreed with the elevation listed on the sign, but that wasn't a primary concern. This picture was taken across a crevice that had a sheer drop of 100 feet or so, and I had to negotiate around to finally get to the flat-topped rock where everyone was sitting. I said hello and then wanted to take in the view, which was striking:



I then sat down on the rock to enjoy the view (and catch my breath), and I leaned back. One hand found rock behind me, but the other went into something moist and squishy. Alarmed, I spun around and let out a high pitched "Cool!" that caused the others to look at me very weirdly. Here's what I saw:



Funaria! On the top of this mountain! I whipped out my collecting bags and my knife and carefully sampled the population. The trip up the mountain was definitely worth it. When I got back to Duke, I was telling my advisor about this and his colleague across the hall declared afterwards: "A success, of Accidental Bryology!" Indeed, it was.

Matt's Moss Work: A Primer

Welcome to Gametophyte Junction. Here, I will be making (hopefully) frequent updates on my progress through grad school. Most who know me, visiting this site, already have a very vague idea of what I'm doing: evolutionary biology of mosses. This site is intended to give a more in-depth view of what the crap I'm spending my mid-twenties doing. It's also a place for me to practice boiling down my research to layman terms, and hopefully also a place for me to come back to in a few years to observe how wide-eyed I was as a first-year grad student. So, feel free to say hi in the comments, and please: ask questions! If you're interested, then I'm doing a good job making it sound interesting, and that would make me happy. Anyway, I thought I'd start with a short overview of what I'm working on and the kinds of questions I'm interested in. I'll probably go into further detail on lots of these things in future posts, so stay tuned!

The genus of moss I'm going to be working on is called Funaria, which looks like this:
It's a very common, small, weedy type moss that grows in all kinds of disturbed habitats: recently burned forests, roadsides, sidewalk cracks, etc. It is a monoicious moss, which means it has produces both male and female parts, eventually releasing egg and sperm from the same plant. I'll try to avoid jargon as much as possible, and so I'll refer to this condition as being "bisexual." It will probably get me blocked by filters, but that's okay, it keeps the riffraff out. It's also very closely related to the species Physcomitrella patens, which recently became the first moss to have its entire genome sequenced. That's going to make a lot of what I'll be doing a lot easier.


To explain what it is I'll be doing with this moss, you'll have to take a trip with me back to basic bio:

Most organisms are diploid; they have two copies of every chromosome for most of their life cycle- this is true of all animals and most all plants. The organism you see (whether it's a dog or a tree) is diploid. All organisms, when they sexually reproduce, reduce their chromosome number to "haploid" to make sperm and egg, which then fuse to produce a new diploid individual. In plants, the haploid stage lasts a bit longer, with multicellular haploid structures forming from which the sperm and egg are derived. This is called an "alternation of generations," and in mosses, it is to the extreme. In the Funaria picture, the green tufts at ground level are the haploid stage- a bisexual "gametophyte" that produces both sperm and egg
(gametes). These fuse just like in any organism and produce a diploid individual- in the picture, that's the green glob on the end of a long white stem. Inside the green glob, meiosis occurs, producing haploid spores that are released to grow into new gametophytes.


Ok, so a couple of interesting things going on here, one of which is the issue of inbreeding. One of the fundamental rules of evolutionary biology is that inbreeding is bad... very bad. Recently,
the entire diploid genome of DNA-helix discoverer James Watson was sequenced, and he was found to have 12 lethal mutations... but he only had one copy of those mutations, and because they were recessive (like blue eyes), he is able to survive. But he most likely shares many of
these 12 mutations with his sister, and if they were to inbreed, the child would not survive, because the chances are very high that the child would have two copies of a lethal mutation. In evolutionary terms, this decreased "fitness" due to inbreeding is known as "inbreeding depression," and is the measure of decreased fitness that is caused by related individuals mating.


So, back to the moss. Remember I said that Funaria is bisexual, and produces both egg and sperm on the same plant- these egg and sperm will be (genetically) completely identical to one another, and if they fuse to produce a diploid, it will immediately have two identical copies of every gene, including any recessive mutations. This could be very bad news for the diploid offspring, if the mutations are lethal or even simply disadvantageous. So, one of the basic questions I want to ask is what relationship is there between relatedness and fitness in a moss. I'll be growing moss from different populations together to see if there is an effect- do related individuals produce unfit offspring, and do unrelated individuals produce more fit offspring? I'll be measuring relatedness by using a DNA-fingerprinting technique known as microsatellites- short regions of DNA repeat the same thing over and over, and it varies from individual to individual how many copies there are. By comparing the patterns of the numbers of copies in the offspring, I can estimate how related its parents were.

The other major part of my research involves the components of mating success. Many studies have been done looking at this topic in other organisms, under the umbrella of sexual selection. Briefly, this kind of selection typically involves animal species which evolve specialized characters that are most related to finding mates. For example, deer bull antlers are characteristics by which does select their mate- the bigger the antler, the higher probability of mating. Similarly, cardinals which are bright red have a better chance at mating. There are a few hypotheses regarding why such traits evolve, but I'm more interested in which traits are important, rather than why. When we see a patch of moss like pictured above, what traits of a particular individual give it a higher chance of mating? I will also be testing hypotheses with my mosses using a combination of field research and experimental studies, such as having two male mosses compete over a single female, and measuring the offspring to determine who got the girl.

Well, I think that's a good start. Stay tuned for more hot moss on moss action! I mean, serious science.