Thursday, December 28, 2006

A Recent heteroclitus mtDNA Sequence Bender

I've been flailing about this week trying to do five or more things at once. Over the weekend I had the chance to sit down and re-read some papers from the 1990's about Fundulus heteroclitus mtDNA diversity, the papers that set me off on this project in 1995-96. Now that Kris is making serious headway with cleaning up our sequences and plugging them into a phylogenetic tree I wanted to refresh my memory about the details of heteroclitus population structure. One key point I hadn't thought about for years (!) is that due to historical patterns of separation going back ~500,000 years, the northern subspecies, F. h. macrolepidotus, has markedly lower genetic diversity than the southern subspecies, F. h. heteroclitus, no matter how you measure it. That's generally consistent with our preliminary results, in which Cape Cod fish have little genetic differentiation (although Nantucket fish show more differences than might be expected, the whole point of this project). Our odd result to date is that Virginia Beach fish are their own distinct clade, not especially close to either northern or other southern clades. As we clean up other sequences and plug them into this growing tree I'm really curious to see how this Virginia Beach clade ends up.

We've also written some other researchers who have worked with this species, asking them for their heteroclitus mtDNA cyt-b sequences that aren't in the GenBank repository for one reason or another. Axel Meyer in Konstanz, Germany is alleged to have a New York sequence we'd dearly love to have, and a group in the Department of Environmental Science at the Virginia Institute of Marine Sciences seems to have sequences from Virginia and New Bedford, MA, fish. If anyone else is in possession of this sequenced gene from heteroclitus please contact me. I know that it's a small world of people who might have this, but if you're out there... write!

Friday, December 22, 2006

More Juvenile Scarlet Shiner Photos

On this slow university holiday I took the opportunity to further photograph very young scarlet shiners. As before, both of these shots are at 20X magnification on a digital dissecting 'scope. The 20-day-old fish is 5.9 mm long TL, and the 27-day-old fish is 6.25 mm long. The latter is also visibly better developed, with the hints of growth in various fins and deeper coloration in the chromataphore spots.

20-day-old scarlet shiner:

27-day-old scarlet shiner:

Tuesday, December 19, 2006

22-Day Old Scarlet Shiner Photograph, Plus Georgia Textbook Court Decision

I was able to sit down this afternoon with a digital dissecting microscope and take some images of one of the fish that Phil Kukulski gave me yesterday. Two of the 22-day-old fish were dead so I put them in 10% phosphate buffered formaldehyde. The image below is at 20X magnification, top-lit on a white background. The fish is 5.9 mm long from snout to the pigmented tip of the caudal (tail). The stomach/intestines is the one clearly visible internal structure without staining. The gills are also visible. They're not very well developed, but they're in the right place and fully functional. In fish larvae at this stage a key marker is the placing of the chromatophores, visible as black spots. The fish's midline is obvious, along with a heavy spotting on top of the head. I also euthanized two fish today that are 20 days old, I hope to photograph one of them tomorrow. In the next period of time we also hope to Nissl stain one or more of these fish which should highlight the nervous system. Amy isn't sure how it'll work on a whole fish, we'll soon see.

Also, this is just in from the National Center for Science Education. Anti-evolution textbook stickers will be removed from high schools in Cobb County, Georgia. Alright!

Selman v. Cobb County settled: Stickers stay out!
Selman v. Cobb County settled: Stickers stay out!
by Nick Matzke

Americans United for Separation of Church and State has just posted the following press release indicating that a settlement has been reached in Selman v. Cobb County School District. The case concerned the constitutionality of "warning label" stickers placed in the front of biology textbooks in Cobb County. The stickers were removed after a district court found them unconstitutional, but the decision was vacated by the Court of Appeals and returned to the district court for further evidence. Under the agreement reached today, the stickers will remain out of textbooks. For further background on the case, see NCSE's Selman webpage and previous NCSE news stories. NCSE was involved in the preparations for retrial and further details will be posted in the future.

Monday, December 18, 2006

The Tank-Bred Scarlet Shiner Fry Have Arrived

I met Phil Kukulski and party this morning at a gas station off off I-65 between Decatur and Huntsville, AL. They were on their way north to Indianapolis to visit Charlie Grimes after collecting fish throughout Alabama and the Florida panhandle. Lucky for me, pretty much all of the scarlet shiner fry that Phil had for me survived an extra five days of driving around since I wasn't able to meet them last Wednesday. He had three age-specific bags with fry no older than 42 days. I hope to raise most of them, and to observe growth rates. Two 22-day-old fry were dead, and I've put them in 10% buffered formaldehyde so that I can photograph them on my digital camer equipped dissecting 'scope tomorrow. We'll probably try to stain them with Nissl stain and visualize the brain and nervous system. I have no idea if this will work, but it's worth a try.

Below is a shot of the van pulling into the gas station. It's Jim Graham's "Ichthyovan", and he's at the wheel if you look very closely. Phil K is in the front passenger seat, and Todd Crail is in the back seat (not visible). The back half of the van is dense-packed coolers with serious air lines running in and around them. The expedition collected a lot of the species that you'd come to Alabama for: rainbow shiners, various Pteronotropis species, etc., species that you just can't find in Michigan.

Friday, December 15, 2006

I Might Get A Donated 4WD Truck

From a conversation I accidentally had last week, I might be able to receive the donation of a 4WD Dakota truck from a local dealership. It's a 1994 and probably only valuable to wholesalers, but for me it could be the exact right thing. The university is willing to put state tags on it and insure it, but the Biology Department (especially me) would be responsible for maintaining it. I'm ready! The sales manager at this dealership is for it, they just have to get the OK of the owner who wasn't in today. I don't even know what color the truck is(!!!). If this deal comes through I should be able to pull off monthly trips to the Walls of Jericho with few problems.

Next time I hope to be able to post our latest round of scarlet shiner brain measurements. Enrique has been measuring different brain regions of about 20 shiners so that we can hopefully pinpoint which brain structures vary in size, especially between males and females. We're using a volumetric algorithm based on length, width and depth of structures. He says he has the data but I haven't received the spreadsheets yet. It should be interesting (or have I already said that?).

Monday, December 11, 2006

It's Been Slow This Past Week, But We Have cyt-b Sequences!

I'm in the midst of final exams and realize that my fish wrangling has slowed down. But action percolates on the side. Kris has done yeoman work making our Fundulus heteroclitus cyt-b gene sequences intelligible. Unfortunately, we had to drop all of our sequences from Boston Harbor because they're just too messy to interpret honestly. These fish were the first ones I extracted DNA from back in 1995, and I may have screwed up the buffer to store the extractions in. But we do have good sequences from Nantucket, and from Oyster Pond in Falmouth, MA, on Cape Cod, to anchor our northern populations. Kris was able to find a complete mitochondrial heteroclitus genome at GenBank from a Sapelo Island, GA, fish so we have another deep South location to go with our Charleston, SC, fish. This sequence also confirms that the ~690 base sequence we're working with is both legit, and is the first stretch of the cyt-b gene. He's still working on trying to find more northeastern heteroclitus sequences in GenBank to make up for our lost Boston set. Preliminary phylogenetic trees tell an interesting story, but I'll wait to finish that thought until we start using all of our sequences rather than just one from each site.

My finals are going fairly smoothly to date. The only excitement is finding that one of my Vertebrate Reproduction students has turned in the take-home final exam full of plagiarized text. I can type almost any sentence from this exam into Google and find the source, not a good sign. So that's a zero for the final exam, resulting in a grade of F. I'm sure I'll hear wailing and gnashing of teeth in response to that.

Monday, December 04, 2006

A New Research Idea For Scarlet Shiners

I've been so distracted with teaching and a departmental job search the last week that I didn't have a chance to update. But, I'm happy to report, those distractions are lifting and a new opportunity has come along. Phil K. from Michigan has offered to give me some of the young scarlet shiners he's raised from locally collected stock (a tributary of Piney Creek in Limestone County, AL). He'll be passing through this area next Wednesday on his way south with another Michiganer for collecting near the Gulf, so he's bringing the fry to give me at an arranged meeting spot at a gas station off of I-65 near here. Sounds like a good ol' fashioned drug deal, but it's even better!

What I hope to do is take size measurements, since I know how old they are fairly closely, and also try to visualize and measure the brain. Amy suggested one of the neuron stains, so we might try to stain a few whole fish to see the whole brain (the fish are small enough that they're nearly transparent). I'm also going to raise some of them, I don't think we'll have to execute all of them(!).