Sunday, June 29, 2008

A Visit To The Tennessee Aquarium

Ruth and I spent the day driving up to Chattanooga to visit the Tennessee Aquarium. We haven't been inside the aquarium complex for years, so we figured we were due. We've always liked the original display building, now the "River Journey", and had yet to see the new "Ocean Journey".

The "Ocean Journey" displays are good, I guess much of the marine stuff isn't as interesting to me. The butterfly room is a pleasant surprise, the plants as much as the butterflies. The odd thing in that building is a shark and ray petting tank with a bunch of yellow tangs. The tangs are pretty fish, fairly hardy, but they have bone spurs on the caudal peduncle that are sharp and can inflict a nasty wound to the unwary. They seem a poor choice for a petting tank.

In "River Journey" there are still tanks devoted to various North American natives. One tank features Barrens topminnows and flame chubs. I've never seen flame chubs in a public display, so that's cool. The only topminnows I could see were some juveniles. And the darter tank had at least one blotchside logperch (Percina burtoni) along with several tangerine darters, something you don't see every day.

Tickets are $20 but it takes at least 3 hours to go through the displays so you get your entertainment value. So I approve. They also make a serious effort at education with some well designed exhibits. If you've never seen the aquarium, you should.

Tuesday, June 24, 2008

Toting Up The Bifax Project To Date

Travis has caught up with the PCR and electrophoresis of our available DNA extractions on the stippled studfish project. The fish and locations we're working with are as follows:

4 fish @Cornhouse Creek, location #1
4 fish @Cornhouse Creek, location #2
4 fish @Elkahatchee Creek
4 fish @Hillabee Creek, location #1
4 fish @Hillabee Creek, location #2
2 fish @Broken Arrow Creek
2 fish @Emuckfaw Creek
4 fish @Sofkahatchee Creek
1 fish @Channahatchee Creek
Total: 29 stippled studfish, plus:
1 F. olivaceus from Broken Arrow Creek
3 F. stellifer from the Conasauga River in Tennessee
3 F. catenatus from Estill Fork in Alabama
1 Lythrurus bellus from Cornhouse Creek
for a grand total of 37 fish that we can hopefully get good sequences for. The L. bellus, a shiner, qualifies as a serious outgroup for phylogenetic comparison. We may, of course, find other stippled studfish on our next trip through Cleburne County, AL, but I'm dubious. I also heard from Rex Strange at Southern Indiana that he has cyt-b sequences he'll give me from F. julisia and some of the other studfishes too, so that would flesh out my analysis once we get our sequences.

And I still have to write the telescope shiner project into a journal article, preferably soon!

Saturday, June 21, 2008

And At Sweetwater Creek...

This is part 2 of our trip to Tallapoosa County, AL, last Friday, June 13. After finding stippled studfish at Emuckfaw Creek we headed about 10 km to the SSE to the last remaining historic site that we hadn't visited yet, Sweetwater Creek. It turned out to be anything but sweet water. Above is a shot of Joe Scanlan, Travis and myself wading up one of the nicer stretches of this creek. Much of the creek has big clumps of algae attached to the substrate sand, with puffy organic matter covering much of the rest of the substrate. The Total Dissolved Solids (TDS) for the creek was somewhat elevated for a typical stippled studfish stream, at 29 ppm. We weren't able to determine why this creek is unpleasantly eutrophic. Joe and Travis both complained of open wounds on their skin stinging when exposed to creek water. We found no stippled studfish in this creek, mostly we found lots of small sunfish along with a few pretty shiners and a single Tallapoosa darter.

Below is a photograph Phil took of the stream's edge. The substrate is sand, a good thing for stippled studfish. But you can also see that the substrate gets darker just away from the edge due to the aforementioned puffy organic matter.

And below we emerge from bushwhacking up the creek, back to the dirt road where a wooden bridge crosses the creek.

As a thunderstorm moved in on us we drove south on the dirt road to an unnamed creek indicated on the map. It was shallow, but a lot cleaner than Sweetwater Creek. Below is the three of us using my smaller, finer seine to sample one of the bigger pools on this creek. Behind me is a small dirt cliff created by several trees falling over, and their exposed root balls have created this funny pocket we're standing in. The only fish we found in this creek were huge number of small, young of the year shiners of some sort, probably pretty shiners.

Below is Joe looking intently at a seine with several of these baby shiners in it. If you click on the photo you can see it in larger scale.

I just wrote to Pat Rakes at Conservation Fisheries today asking him for some specimens of a related species, the Barrens Topminnow, Fundulus julisia so we can extract DNA for our project. Hopefully he has some available for this kind of work.

Wednesday, June 18, 2008

Return To Emuckfaw Creek

We made it back to Emuckfaw Creek in Tallapoosa County, AL, last Friday. Travis from my lab drove down with me, and Phil from the UAH Press Office followed in a UAH van for the purpose of photographing and reporting on our research. The following pictures were all taken by Phil Gentry; I realize they're the first pictures of this project that I'm in. Joe Scanlan drove up from Montgomery and met us at Emuckfaw.

We wanted to resample this creek because we hadn't found any stippled studfish there last March, when the creek was higher and we were wearing waders which limits your mobility in a creek. You really don't want to step into a hole in the creek and have cold water flood your waders. This time we went downstream from the road bridge, through fairly deep water, before we went around a bend and found a riffle system with some sandbars. And, with the sandbars, we found stippled studfish; only two, but we saw more that disappeared into emergent vegetation over really treacherous muddy/sandy sediments.

So, the first picture below shows myself and Travis holding the seine while Joe pulls out our first studfish of the day. He chased it out of the backwater to the left into the seine. This is a beautiful stretch of creek. If you look very closely you'll notice that much of the vegetation along the creek is a native rhodedendron, always a good sign.

Here's a shot of Travis and me wading downstream from this riffle system.

Setting a seine is something that seems easy but you have to do it just right, so that the lead line is tight on the bottom and the rest of the net forms a bag into which fish can be chased and snagged before they run out again. In the next shot Travis and I are setting the net in preparation for Joe to chase fish out of the backwater that produced our first studfish.

We found the second studfish about 100 m downstream from the first, along another sandbar forming a backwater pocket. Here's Joe doing the honors again, pulling a studfish out of the seine.

And, the final photo shows the first studfish of the day, probably a subadult female about 5 or 6 cm long (Phil inserted a one inch scale bar digitally). Our other fish was a fully mature male in breeding colors.

From Emuckfaw we went on to the last historic site that we hadn't sampled, Sweetwater Creek, about 7 km from Emuckfaw down a graded dirt road. This site had produced a single studfish in 1992. One of the collectors was the famous fish illustrator Joe Tomelleri. The creek looked good at first, but we quickly realized something was wrong. There were big tufts of algae growing along the bottom, and much of the sandy substrate was covered by a puffy layer of organic crud. The water stung any exposed cuts or bites, something that certainly didn't happen at Emuckfaw. We captured lots of small bluegills with the seine, not a good sign since they prefer more eutrophic water conditions than do studfish. We worked over 100 m of the creek and realized that this creek had been altered in such a way that studfish wouldn't do well. It's an open question what happened. This site is out in the middle of land used for industrial forestry, and we didn't encounter other people or see any obvious source of pollution such as agricultural chemicals. We could probably have bushwhacked upstream to see what we'd find, but we didn't really have the time for that, especially because a thunder storm was approaching. Another dead site.
We spotted another, unnamed creek on the map about 2 km from Sweetwater down the same dirt road. We drove down and found a very different creek, with shallow, clear water over gravel and sand. The creek bed was almost lined with petrified wood fossils, something I''d never seen before in Alabama. It turns out that parts of Mississippi and Alabama are the only places east of the Mississippi with petrified wood. I grabbed two small slabs and threw them in the back of my truck before we left. Before the thunder storm opened up over us we sampled a long stretch of this creek and only found young-of-the-year cyprinids, probably pretty shiners, but not a single adult. And there were lots of these baby cyprinids. The whole area was damp woodland with a thick cover of ferns on the forest floor. Lighting started cracking right over us as we finished so we jumped in our vehicles and headed out before we encountered any flooding on the road. I meant to grab more wood fossils, but it was more important to get the hell out of there while we knew we could. Our next trip will probably be to Cleburne County on the Georgia line next month to try to find new populations of studfish in the area where the Little Tallapoosa river runs into the Tallapoosa.

Monday, June 16, 2008

Slackwater Darter Presentation Tomorrow Night

The Flint River Conservation Association (FRCA) holds its monthly meeting tomorrow night, Tuesday, June 17, 6:30 at 320 Fountain Circle in downtown Huntsville. Jennifer Schade will present findings to date of a research project hosted by FRCA on habitat assessment for the Threatened slackwater darter, Etheostoma boschungi, in tributaries to the Flint River in Madison County, Alabama. This involves both GIS assessment of possible habitat, and species associations in sampled streams. The project is funded by a grant from the World Wildlife Fund's Southeast Rivers and Streams Support Fund. Some of you may know Jennifer as a soon-to-be-graduated Masters' student at UAH. If you come, it's a potluck supper so bring something.

Sunday, June 15, 2008

Bifax In Emuckfaw Creek in Tallapoosa County

It's true, we found two there on Friday. Travis and I met Joe Scanlan there and Phil from the UAH News Office went down with us to photograph the trip for a future news item. (I hope to have pictures to post later in the week.) We started to go upstream from the road bridge, and quickly realized that there was no good habitat there; Joe described it as a "canoe river", a beautiful wide stream but with no features like sandbars preferred by stippled studfish. So we reversed field and worked our way downstream. We had to almost swim across one deep hole to get to a riffle system around the bend, which looked totally different from upstream. Steep rocky banks came down on one side, and both banks were covered by native rhododendrons. At the top of the riffle system was a sandbar with a slackwater pocket, and sure enough we were able to chase a studfish out of there into a net blocking off the exit along with a bunch of pretty shiners. We picked our way down the broken rocks in the riffle and hit another deep pool that we were just able to wade across. On the far shore was another larger sandbar with a slackwater that we had to scramble up a steep muddy/sandy bank to get onto. We could see studfish whipping around, but could only net one of them, a large male in breeding colors. And that was it for the day at Emuckfaw. But, we did catch two studfish, and just like I thought the species is still present in this stream. Most of the historic records for Emuckfaw are for one or two fish, with one of 15. So I guess we're in the typical range.

After a short lunch break we headed for a nearby stream, Sweetwater Creek, down a graded dirt road. A single record from 1992 showed one studfish collected at the site. That was more than we found. The creek was strangely odd. The sandy substrate was largely covered with thick algae or puffy sediment, and smelled funny. For the most part the small creek is standing pools connected by shallow runs and a dense, low plant canopy. The bad sign was that we caught lots of small sunfish, not typical of studfish habitat. I kept an unidentified darter, a pretty shiner and another shiner as vouchers. The stream runs through what appears to be timber plantation. We couldn't pinpoint why it seems degraded in a eutrophic way.

As a thunder storm slowly moved in on us, we decided to continue down the dirt road to another creek to the south. We found this unnamed creek and it looked good; shallow, clear, cool water running through a semi-wetland carpeted with ferns. Using our smaller, finer seine, all we found in this creek were hundreds of very young cyprinids of some sort, probably pretty shiners. Joe referred to it as a "shiner nursery", and I guess he's right, I've never encountered anything like it. The streambed was also littered with petrified wood slabs. Apparently Mississippi and Alabama are the only places east of the Mississippi with this kind of fossil. I kept two smallish ones, I'm sorry I didn't pick up more. But as we left the stream lightning was cracking closer to us and heavy rain started, so we got out in a hurry and left rather than take chances that the dirt road would become less passable with a heavy rain. Luckily it was fine.

So now I've hit all of the historic studfish sites on my list except for those in the mainstem of the Tallpoosa River. It seems that several creeks in Tallapoosa, Coosa and Randolph counties have good populations, along with the disjunct Sofkahatchee Creek in Elmore County. But we haven't encountered a new population yet. I hope to make a trip in July to Cleburne County, way upstream almost to Georgia, to see if any streams near where the Little Tallapoosa runs into the Tallapoosa contain previously unknown stippled studfish populations. I have no idea what to expect since I've never been to that area before. But until then we have work to do with running PCRs and starting to sequence amplified DNA.

Wednesday, June 11, 2008

Update To The Last Entry...

The stippled studfish DNA shown in the last entry's PCR gel photo is from Elkahatchee Creek in Coosa County and Broken Arrow Creek in Tallapoosa County. This expands our geographical coverage of Tallapoosa creeks. When we meet for this Friday's collecting trip Joe Scanlan will give me 6 ethanol preserved studfish from Sofkahatchee Creek in Elmore County. This is the only known population in the Coosa River drainage, with an unknown history. Looking at their DNA may explain their history as an anomalous population.

Tuesday, June 10, 2008

New, Improved PCR; Really.

Travis has achieved an impressive 7 for 7 in the PCR amplification of stippled studfish DNA. Below is the most recent run, seven lanes on the left of studfish DNA and a DNA ladder on the right. In about the middle of the gel vertically is the 7 amplifications, all of them about 850 base pairs of DNA. It's a simple enough process at this point, but I'm glad we're getting consistent product with our new reagents. (I'll try to avoid posting more gel photos, it's certainly been overdone...)
In the egomaniac department, I noticed that someone started a wikipedia entry for me. I'm honored; I'll have to link it to the UAH entry.

Sunday, June 08, 2008

I Submitted My Flame Chubs Article

It's true, I finally submitted it, but I didn't entirely mean to. I sent the 11 pages of text without maps or tables to the editor of the journal Endangered Species Research to ask him if the article looked at all like anything they'd like, and he sent it on to their freshwater fishes editor. So we'll see. Hopefully they won't think I'm retarded or anything; before I make a push to produce maps to support our story I want to see what the journal thinks. This is an article I'd like to get out since we finished most of the work by the end of 2006. I know it's a good story; the species was found in 18 of 53 historic sites, so I'd say that something is affecting the fish and it's disappearing.

This Friday we return to the Tallapoosa system looking for stippled studfish in several streams. With this trip we should wrap up all of the historic sites on my list, except for the river sites that we can't reach. From there it should be largely a matter of running DNA samples and interpreting what if any pattern we find.

Thursday, June 05, 2008

Most Of The Scarlet Shiners Are Still Alive...

... after I added 11-KT suspended in ethanol to their tanks last Friday. I'd pulled out the filter pads in the hanging filter boxes so that the 11-KT wouldn't be removed too quickly. But, by Sunday when I came in, several of the tanks had clouded up and several of the young scarlet shiners were dead in a few tanks. I had to consolidate all of the surviving fish (8) exposed to 35 ng of 11-KT in one tank, and all of the surviving control fish (5) in another tank. Interestingly, the two groups of fish in tanks exposed to 15 ng of 11-KT (10) were fine, so they're still in two separate tanks with 5 fish each. If I try this again in the future I've got to get purer steroids not in ethanol so I won't take a chance on crashing the biological filtration in the tank. I guess even 2 ml of ethanol in a 10-gallon tank can have a bad effect; after all the years I've kept fish I've never added ethanol to a tank(!) so now I think I can offer free advice: don't do it! So my ideal experimental design is compromised, but I'll keep going to see what happens over time with the surviving fish.

We'll be going back to the Tallapoosa system next Friday. Joe Scanlan can meet us, and I hope to finally finish visiting sites in Tallapoosa County. Joe is bringing 6 stippled studfish captured in Sofkahatchee Creek in Elmore County, preserved in ethanol, to give me for DNA extraction. And of course we still have lots of lab work to do, but at least the PCRs are working better than before. And that's all you can hope for.