Wednesday, June 30, 2010

Mailing My Spring Pygmy Sunfish Letter To USFWS

I'm mailing my letter to Janet Mizzi, director of the Southeast Region of the U.S. Fish and Wildlife Service, asking for the Spring Pygmy Sunfish to receive emergency listing hearings under the Endangered Species Act. If you saw the edge of the species' habitat out along I-565 to the west of Huntsville you would too; the area is being bulldozed and leveled as a sewer line is put through. It's a typical redneck construction project with sagging mud fences and heavily silted streams, exactly what's guaranteed to kill of Spring Pygmy Sunfish in the only place they're found on the planet in Limestone County, Alabama. It could be whistling into the wind but I gotta do it. You should, too!

Saturday, June 26, 2010

Curating Darters

I realize that it's been a week since I posted. I've been distracted by helping to host visiting candidates for several of our open positions. My big advance of the week was curating darters from Estill Fork that we collected in May and June. This involves weighing, measuring and numbering each fish and placing it in its own 15 ml tube with 10% phosphate buffered formaldehyde. I hope to start examining gill arches for trematode parasites sometime in the near future. Tennessee Darters are our primary focus, and also I have a number of Rainbow Darters and Fantail Darters.

My new computer game hobby is grooming and aligning DNA sequences from Fundulus similis and F. majalis. Geneious is a surprisingly powerful program for this kind of work. To the cyt-b gene sequences I have from Dauphin Island, AL, and Key West, FL, I downloaded the only available sequences available on GenBank, three for each species, that don't exactly match mine. My sequences cover roughly nucleotide positions 350-1140 (the end of the gene), while the ones I downloaded are positions 1-990. So it's about 550 nucleotides that overlap, which makes them useful I hope. From preliminary tree building with this material the Key West sequences are markedly different from all others, with the Dauphin Island sequences distinct but not way out there. The suggestion has been made in the past that the Key West population of F. similis is deserving of subspecies designation because of some morphological distinctness. My data may support this to at least some degree (even if I think the concept of subspecies is squishy, as opposed to simply a distinct population within a species). We'll see how this plays out.

Saturday, June 19, 2010

It's Back To Bifax Extractions

I heard from Lance at IXG this afternoon. He wasn't able to get PCR results from our stippled studfish extractions, which are now pushing two years old and were stored in refrigerators rather than freezers. Since he's game to do more tries, my new task is to repeat about 15 of the extractions and get them to him soon. I admit to feeling stupid, my experience was that storing DNA in a buffer at about 4 deg. C would keep it good for a long time. The good news is that I have a bunch of extractions from years ago that I've kept frozen from a series of Fundulus diaphanus collections I made in the 90s. I'll have to throw in one of those for PCR & sequencing just to see if it'll work.

In happier news I've been curating the darter collections we've made at Estill Fork this month and last. I'm primarily interested in observering trematode gill parasites in tennessee darters, and also observing their reproductive condition. So far almost all of the snubnose darters I've examined from these collections have been tennessees rather than blacks. I also hope to look at fantail darters along the same lines.

Tuesday, June 15, 2010

New Driftnet At Estill Fork Last Friday

We went out last Friday for the last driftnet collection in our 12 month series of collections as part of Brittany's graduate project. The water was higher, murkier, faster and colder than might be expected after two days of rain. The temperature was 17 deg. C. We mostly used the original driftnet, but we also set up a new net that Ruth made to test it out. This net has two differences: the side sleeves to hold support stakes swing out in front of the net instead of to the side, and the back panel of the net itself has a vertical rather than horizontal orientation. Both of these differences seem to be successful modifications. In the photo below the new net is set in our regular collection site, with the water flow just topping the net (so it's just over a foot deep, deeper than in May). Ruth has a pattern for this net so we can make more with notice, and I have more PVC pipe for the frame. We'll see where we go with this.

Monday, June 14, 2010

So Much For Easy Bifax DNA Sequences

The cleaned PCR products I gave to IXG had no DNA when they examined the product, and the raw PCR products I brought to them this afternoon had no DNA either. I don't know what we did, but we allowed the DNA that I know was there (I have pictures! Really!) to degrade. So, tomorrow I hope to bring by our DNA extractions and let them run PCR and hopefully sequencing as they offered to do. Needless to say, we have to rethink what we're doing with DNA projects or just hire someone else to do it (which I don't really have the money for). In this case it's fairly easy, we have a total of 37 DNA samples from various fish, most Fundulus bifax.

Meanwhile, I have to finish the presentation I'm giving to the ASIH meeting in Providence about gill parasite infections in telescope shiners. This involves minor edits of the presentation Andrew gave to the Honors state finals. It should be easy (I hope!).

Tuesday, June 08, 2010

Fundulus bifax DNA Dropped Off For Sequencing

This afternoon I dropped off our first 15 purified DNA samples to be sequenced at a new company near UAH, IXG (IExpression Genes). I should know by tomorrow how it worked. Meanwhile, I've been working with the Geneious program we have to edit and align some cyt-b DNA sequences from Fundulus similis and F. majalis that I've had for a few years as part of my slow-moving project to examine population structure and differences (if any) between the two species. Two of my sequences from Dauphin Island, AL, are good, as are at least three from Key West, FL (thanks to Todd Crail some years ago for the fish). I'm edging closer to being a gene jockey.

On Friday we go out for the last driftnetting session for Brittany's project. We started it last July, but missed the February collection due to the shooting. Ruth is working on the finishing touches of a second driftnet as part of our effort to make a few working prototypes, and maybe sell them later. I know that everyone needs a driftnet in the current economy.

Wednesday, June 02, 2010

Alabama Pygmy Sunfish Action Update

I'm reposting the following from the NANFA Forum about increasing threats to the Alabama Pygmy Sunfish. Mike Sandel's description of the situation speaks for itself:

News on the ground: the Huntsville sewer line along Beaverdam Creek is nearly complete, and the wastewater treatment plant on I-565 is at least half-way complete. The wastewater treatment plant is located about 1/4 mile from Beaverdam Creek, and now I need to find out where the discharge from this system will empty. My guess is right in the middle of Elassoma territory. There has been little news from USFWS, but I have heard rumors that they are pushing for a normal listing process, as opposed to an emergency listing. This is not an indication of whether they will grant protection for the spring pygmy, it simply means they are choosing the slower of two paths which will lead to some sort of decision. In my best estimation, if they take the "normal" route, we are talking about a process that can take decades before a resolution is reached. On the other hand, the emergency listing process could take less than two years. In the opinion of every qualified biologist concerned with this situation (and anyone else who can think without dollar signs in their eyes), this listing is already 20 years overdue. The conservation measures associated with the ESA need to be in place before this area is developed. Otherwise the survival of this species will be left to the mercy of Huntsville and/or the next automobile manufacturer that shows an interest. Huntsville has been ranked among the 10 fastest growing metropolitan areas in the country. Infrastructure construction for this expansion has already begun, the remaining tracts are for sale on industrial realty sites, and we know that after the money has changed hands and facility construction has begun, USFWS will have little to say about it.

Please consider writing a letter in support of the EMERGENCY LISTING of Elassoma alabamae. These letters can come from individuals or organizations.

Send letters to:

Janet Mizzi
USFWS Southeast Regional Headquarters
1875 Century Blvd., Suite 400
Atlanta, GA 30345