Friday, August 27, 2010

Our First View Of A Darter Gill Parasite, And More DNA

Robert and Jeremy were in the lab yesterday looking at gill arches from rainbow darters that they had set in acetocarmine stain the day before. I saw one trematode attached to a gill filament, but unfortunately the rear 2/3's of the body had been shredded by clumsy arch removal (it was their first try at it). The part I did see looked a lot different from the Dactylogyrus we've seen on shiners; the haptor (attachment) end was fluted and narrower compared to the body, and the animal was slightly larger (~400 micrometers). There is a described species of Aethycteron fluke found on rainbow darters in east Tennessee, and that's our beginning point for ID'ing the flukes we find. But as of now, I can't tell you.

Joe has re-extracted DNA from the stippled studfish we have. I hope to bring a set of 15 samples of DNA to IXG soon for sequencing. This will include 8 samples of the stippled studfish, a southern studfish, three samples of banded killifish I've had for a while and three samples of longnose killifish from St. Joe Beach, Florida. I finally broke that logjam, I hope.

Saturday, August 21, 2010

Catching Darters, Seeing Flame Chubs

I went out today with a whole new crew of students - grad students Brian and Robert, and undergrads Valerie, Eric and Jeremy. We went to the upper Paint Rock River system for two related reasons: to catch tennessee snubnose darters for our developing gill parasite research program with Robert in the lead, and to examine the Estill Fork site and one on Lick Fork as good sites for a darter micropartitioning project lead by Brian. We immediately caught about 20+ snubnoses in our first seine net haul, which was amazing, along with a juvenile blotchside logperch that we let go, some greensides, and some rainbows that we also kept. I think we have it blocked out in our heads how and where to do the microhabitat survey work there. The water today was very low, typical for August, and will certainly look very different by November. Brian was the only one who had seen darters before, so it was an introduction for everyone else.

We also stopped on our way home at Lick Fork. This is the only site in the upper Paint Rock system where I found flame chubs at an historic site in my survey 4 years ago. This particular site is where a spring field is emptied by a small, clear run that flows under the road into Lick Fork. And when we pulled up and looked at this run today I could immediately see flame chubs schooling about. This is definitely one of the best flame chub populations around. Larkin Fork at this location is generally similar to Estill Fork, but smaller and more of a riffle/run system. I think we'll use that as a second site for Brian's work. It should contain most if not all of the species present at Estill Fork, so we'll see if similar habitat is used in a similar fashion, the whole point of this work. It's also easily accessible from the road without, from what I can tell, trespassing on anyone's property in an annoying way. We'll have to sit down and formally organize what we hope to do before the project is really underway.

School has started again this past week, and it wasn't too, too crazy, luckily enough!

Thursday, August 19, 2010

Fish Coming & Going

The blacknosed dace that I sent to Wesleyan arrived in good condition last week, so I'm grateful for that. I still have to re-install Google Earth on my laptop so that I can confirm GPS coordinates they calculated for the collections I sent via a .kmz file.

And the fish coming to me are from Tony Terceira in Rhode Island. He sent me about a half dozen each of Fundulus diaphanus, F. majalis and F. heteroclitus from several sites in RI and Cape Cod, all preserved in ethanol. Especially the majalis is of immediate interest to me for the ongoing majalis/similis study.

Some new students in my lab are gung ho to go forward with extracting DNA, and I showed one of them how to do that today with a similis from St. Joe Beach in peninsular Florida. Even more immediate(!) we have to reextract DNA from our F. bifax collection for sequencing at IXG. It's real biology, I'm happy to be doing it.

Wednesday, August 11, 2010

Dace Are Off To Connecticut

I mailed off blacknosed dace to Wesleyan yesterday. Besides the Blue Spring and Flint River fish, I included 4 fish from Dutton Creek in Morgan County, AL, that we collected in 2006 on the flame chub survey. I hope these will be of interest, since they're from the southern side of the Tennessee River and may show some genetic divergence from those on the north side. Speaking of which, I still have to re-extract DNA from the stippled studfish I have....

Thursday, August 05, 2010

We Found 2 Blacknosed Dace In The Flint River System

Taito and I went out yesterday to look for blacknosed dace for the Chernoff lab at Wesleyan. It turns out that they already have fish from Blue Spring in the Paint Rock system, because I had told Mike Sandel about that spot two months ago without knowing why he and Phil Harris at Tuscaloosa wanted the fish. So, the Chernoff people asked if I could get fish from the Flint system. The one really good place I know for Flint dace is in Acuff Spring. But when we went there, it was posted No Trespassing. I guess the homeowner's association finally figured out that other people were interested in the spring which is now part of a park, and aren't especially open about it(!). So, we seined in a nearby creek connected to that spring run. We didn't find any dace, but we did find a surprising number of flame chubs. I kept a few just to examine the gills for parasites in the near future. Our next stop was the junction of Brier Fork with the main stem of the Flint at the Winchester Road bridge. I hadn't been there for a few years, and I figured that it might work even though it's a river rather than a spring run. We actually netted one YOY, along with large numbers of darters and stonerollers. Dave Webster of the TVA was also there with another guy, doing an ongoing IBI survey. He pointed out how much periphyton (algae) was growing on the substrate, which is definitely worse than before. Housing developments have hugely expanded just upstream from this site, and the effects weren't subtle. The water is still clear, but creeping eutrophication is evident. So we were off to Mountain Fork, where I haven't been for a while either. We caught lots of fish there too, but again only one YOY dace. So, that's what I'll send them, one fish from each of two locations. I hope that works for their purposes. Now it's clear to me that the Paint Rock system is in better shape with less new housing pressure.

Monday, August 02, 2010

MrBayes Analyzes The Fundulus Heteroclitus Data

And, the phylogenetic tree doesn't change much from what Kris published in his thesis using UPGMA. I'm trying to re-write the thesis for journal submission, and realized that we need another view or two of how a phylogenetic tree could be assembled from our DNA sequences. MrBayes uses Bayesian statistical techniques, different from other approaches in that it assumes one knows something about a data set and conditions, and that information can be woven in building a tree (in this case). I've been using it with my striped and longnose killifish data and it gives more plausible results than other approaches. I'll show those trees later. Anyway, with the mummichog dataset once again there is a strong north/south divide between populations, and the Virginia populations are distinct from those to the south. The larger numbers are a consensus value from the several thousand runs the program makes through the data, so 0.59 means that 59% of the program runs came up with the same solution. There are two outgroups in this tree, Rivulus (I forget which species) and Fundulus similis from Key West, FL.