Friday, January 30, 2009

Back Out To Estill Fork Tomorrow

We'll be going out to Estill Fork tomorrow to collect telescope (and scarlet?) shiners. The weather is moderating, so it should be sunny and in the low 50s F. Even so, I suspect that we'll appreciate being in insulated waders. I might also try to set up my drift net, a PVC frame holding a fine-mesh net made of organza silk. It's a passive way to sample whatever is being swept downstream such as ichthyoplankton and insects. As long as I have two tent stakes to anchor it in the substrate we may give it a whirl.

Now that I'm back on polishing the flame chub paper, Kevin came by today to talk about what maps we need for the article. He set up the maps a while back, so hopefully it will be easy to tweak them for journal format. Our plan is to have one map showing all of the historic collection sites for flame chubs in north Alabama, and a map each of Lauderdale County and Madison County showing where we did and did not find flame chubs. Hopefully the editor and reviewers will agree with my decision.

Tuesday, January 27, 2009

A More Refined Analysis Of 11-KT Experiment Data

I think I figured out the best way to analyze any influence of our experimental exposure of scarlet shiners to 11-KT. We compared the weights of 9 fish that were exposed, all under 60 mm long, to the weights of 42 wild-caught fish from Enrique's data set that were all under 60 mm long. Using an F-test to test the two data sets for homogeneity of variances, we found a statistically significant lack of homogeneity. So we used the nonparametric Mann-Whitney U-test to test the two data sets for similarity of distribution. The U-test showed that the two data sets are significantly different with p=0.04. It's not a really surprising result that fish exposed to a potent androgen like 11-KT would be heavier. The interesting thing is that we achieved this by exposing fish to it by ambient exposure in the water rather than by injecting it. I'm happy with the results since this has been a pilot project for something longer in duration and more ambitious in scope. Brittany has also been measuring the brains of our 11-KT fish, and if they turn out to be measurably different from unexposed fish I'll be doubly happy.

My editor at Endangered Species Research sent me his comments on the flame chub article. He likes it, and offered some constructive editorial suggestions. Now I have to get it back out with all figures and tables. The big challenge will be putting together a good map or two. Kevin says he's still interested in producing maps, so I have to meet with him sometime soon.

Saturday, January 24, 2009

Trying To Figure Out The 11-KT Treated Scarlets

Brittany has been working on ways to analyze the results of our 11-KT treatment of scarlet shiners. We're using 80+ wild-caught scarlet shiners from Enrique's thesis as a broad control group, since he created a large data set of length-weight relations. Below is the graph of the 11-KT scarlets vs. the much more numerous Enrique set. This is only the first step, we're going to compare only the Enrique fish less than 60 mm long since that's the maximum size of the 11-KT fish. So we'll see if we have a difference in weight at a given size. The regression lines in the figure are polynomial, which fit the data much better than linear. The Enrique fish have a lower r-squared than the 11-KT treatment because that set includes fully adult breeding males and females who we know to have different length/weight relations. So the smaller data set is likely to have an r-squared closer to the 11-KT group. But, I'll post that when it's done.

Wednesday, January 21, 2009

December Telescope Shiners

Andrew gave me the data set for the length/weight measurements of the 42 telescope shiners we collected in early December at Estill Fork. The graph is below. The interesting part of this is that there is a very high r-squared value of 0.95 for the linear relationship between length and weight. This relationship is much weaker (lower value) for telescope shiners we've collected in warm weather, during breeding season. During breeding season the females and males have very different relationships, since the females become heavy with eggs. But in December, both sexes have regressed gonads and their overall body shape/size seems to be indistinguishable. Anyway, see for yourself:

The bummer for the week is that we won't be going out to Estill Fork this Friday. I realized that I have to meet with the Dean at 1:30, so that prevents our planned trip at noon. The day is supposed to be warm, too, with temps over 60 F. But next Friday looks good in the forecast, so hopefully we can get out then.

Friday, January 16, 2009

The ASB Meeting Is In April, See You There?

This year's meeting of the Association of Southeastern Biologists is in Birmingham from April 1 - 4. I submitted an abstract yesterday to give a talk on our telescope shiner work. The title is, "Reproductive Biology of the Telescope Shiner, Notropis telescopus, in Alabama", by Stallsmith, Adrian, Holmes, Marino & Whitington. Our submitted abstract reads as follows:

Gonadal condition of the cyprinid stream fish Notropis telescopus (telescope shiner) was monitored over the course of a likely breeding season to determine reproductive schedule. The study site was at the southern limit of species range in the upper Paint Rock River valley of northeastern Alabama. Notropis species are multiple spawners with strong seasonality to gonadal size and condition. The number of maturing oocytes observed in ovaries peaked in April and May. Ripe and fully mature ovaries were found in fish collected in April, May and June. A pronounced peak in the gonadal somatic index (GSI) was found in June for both males and females. Females were found to be significantly larger than males. The average standard length of both sexes peaked in September. The evidence points to an Alabama spawning season from April to June, peaking at the end of this season.

And one last thought about my experience in court in New Hampshire in 1978. As part of a deal to get rid of us the state of New Hampshire let us all out on personal recognizance after three days. Most cases were "continued", basically dropped if we didn't do anything else in NH for the next year. A few hardcore crazies served jail time of several months because they wouldn't give police their real names. Me, I just wanted to go back and reclaim the wage slave job I had at the time in Boston.

Thursday, January 15, 2009

Kris Is On The Ball With Mummichog DNA

My big distraction earlier this week was having to go into municipal court Tuesday afternoon to fight a speeding ticket I got in November for allegedly driving 64 in a 50 zone. Luckily the cop didn't show and the judge dismissed the charges so I didn't have to do my latent lawyer routine. I realized later that I was the only one in court that day to address the judge as "your honor". I haven't been in court since 1978 when I was arrested in Seabrook, NH, during the mass civil disobedience protesting the Seabrook nuke. When I was arraigned at 5 in the morning for criminal trespass in Rockingham County, NH, I was also the only one to address the judge as "your honor". Maybe I should've been a lawyer after all? Gad, that's a terrible thought!

But back to fish... I met with Kris today and he showed me his work aligning mummichog DNA sequences. He (we) now have a reasonable number of individual sequences each of 272 base pairs in the cytochrome b gene. Even as a work in progress it's interesting; we have sequences of at least one individual from sites stretching from Maine down to Sapelo Island, Georgia, with concentrations in Charleston, SC; Virginia Beach, VA; Chincoteague, VA; and Falmouth, MA, as well as several sequences from Nantucket. We have a near outgroup in a sequence from a Fundulus majalis from the Florida Keys, and a far-outgroup in a Rivulus species. Even to the naked eye, looking at the sequences displayed in the software package Genious, the mummichogs are visibly different. We haven't put together a tree yet, but Kris basically swears that he'll one next Tuesday (I hope!). For May graduation he has to defend a thesis by the end of next month, so a certain deadline is a powerful motivator I hope.

Sunday, January 11, 2009

The Widow Creek Spill Wasn't Too, Too Bad

Luckily for everyone, the TVA was able to plug the gypsum leak from a storage pond at its Widows Creek coal plant on Friday before too much was released. So I didn't rendezvous with Anna George and others on Saturday for a Tennessee River fish survey. It was a near-miss, though. Whether TVA will respond by reinforcing its various waste storage sites is an open question. They've strongly resisted any further limitation on pollution release from their coal burning power plants, so I can't imagine they're truly humbled and ready to stop being arrogant about waste storage. I hope I'm wrong. A pleasant thought; I don't know when vacancies on the TVA Board come up since they're appointed by the President. Will Obama break with the historic practice of appointing upscale good ol' boys to the Board?

Friday, January 09, 2009

New TVA Spill In Jackson County, Alabama

News Flash! This might not be quite as bad as it could be, but TVA had made a big deal last week about how they inspected these waste ponds and they were all structurally sound. If this is bad enough, I'll probably join a survey crew on Lake Guntersville on the Tennessee tomorrow.

UPDATED 3:20pm: New Information in TVA Spill in Jackson County

January 9, 2009

WHNT NewsChannel 19 is continuing to track down the latest on a breaking news situation surrounding a TVA spill in Jackson County. A waste pond at a coal-burning power plant in northeast Alabama has stopped leaking after some spilled into a nearby creek. It's the second accident at a Tennessee Valley Authority retaining pond in less than a month. TVA spokesman Gil Francis said he didn't know the size of the spill at Widows Creek Fossil Plant on Friday.

TVA officials blamed a leaky pipe. Most of the discharge flowed into another pond but some entered Widows Creek. Francis said the leak isn't toxic. (See Official Press Release Below)

The pond contains gypsum, which is captured in the plant's air pollution control devices and is used in items like wallboard and concrete. The spill, about 30 miles southwest of Chattanooga, Tennessee, follows a December 22 dike burst at a Tennessee plant that dumped 1 billion gallons of toxic coal ash sludge.

(The Associated Press contributed to this report.)

January 9, 2009

TVA is investigating a leak from the gypsum pond at Widows Creek Fossil Plant in Stevenson, Alabama, that was discovered before 6 a.m. on Friday, January 9. The leak has stopped.

The leak from the gypsum pond flowed into an adjacent settling pond. Some material overflowed into Widows Creek, although most of the leakage remained in the settling pond.

TVA has notified appropriate federal and state authorities. TVA will perform temporary repairs to the pond. Gypsum ponds hold limestone spray from TVA's scrubbers that clean sulfur dioxide (SO2) from coal-plant emissions. Gypsum contains calcium sulfate, which is commonly used in drywall, a commercially sold construction material.

Flame Chub Article Abstract

I formally submitted the flame chub article at the publisher's web site this morning. One omission I fixed was to come up with a 250 word abstract, which I've posted below. It's actually 247 words, not including "ABSTRACT"....

The status of many freshwater fish species in the species-rich southeastern United States is surprisingly poorly known. Vulnerable species found in smaller streams in the region have not received adequate research attention. The flame chub, Hemitremia flammea (Cyprinidae), is included among a group of stream species considered to be “narrow endemics” susceptible to habitat alterations due to growing human population. The obligatory habitat is spring-fed streams sensitive to human activities. The species has a patchy range primarily in the Tennessee River Valley in Alabama and Tennessee. The conservation status of H. flammea is poorly documented. The NatureServe global status of the flame chub is G3, Vulnerable, and the Alabama state status is S3, Vulnerable. Reflecting the poor knowledge of the species’ status, the International Union for the Conservation of Nature (IUCN) Red List Category is DD (data deficient), a change from earlier listing of Rare. This study is intended as a presence or absence survey of H. flammea at historic location sites in north Alabama based on holdings records of the University of Alabama Ichthyology Collection in Tuscaloosa, Alabama. Fifty three sites in 9 counties in the Tennessee River drainage with an historic record of H. flammea presence were visited and sampled by seining. One or more H. flammea were found at 18 of these sites. Two strongholds remain for the species in Alabama. The first is much of the Cypress Creek system in Lauderdale County. The other is in the Flint River system in Madison County.

Wednesday, January 07, 2009

Alright, The Flame Chub Manuscript Has Been Accepted!

I heard from the Senior Editor of the journal Endangered Species Research this morning. She had forwarded my flame chubs manuscript to a potential article editor in Ontario, and he said it should be accepted and that he'd be willing to work on it to kick it into final shape. So, that was surprisingly easy. It's always an ego boost to have an article accepted. Hopefully we can turn this around quickly and have it posted on their web site. In the time since when I originally submitted the article in June I have some new observations to weave in.

I had a staggered lab meeting with four students today about what we're going to do in my lab this semester. Everyone had agreed to a 2 o'clock meeting, but of course two of them realized this morning that they did indeed have a class conflict. So it wound up as a 2 X 2 meeting. We're going to start by measuring the brains of the scarlet shiners from the 11-KT experiment, and also measure and examine the gut contents of the telescope shiners we caught last month at Estill Fork. We have a trip to Estill Fork scheduled for January 23, weather allowing, for another batch of telescopes and scarlets. We have to visit Limestone Creek, too, in the near future.

Tuesday, January 06, 2009

The Flame Chub Crusade Continues, Too

I hadn't heard about my flame chub manuscript that I submitted last June to the journal Endangered Spec. Rsch. so I sent an email to the editor. Boy was he embarrassed, it had basically disappeared as he had forwarded it to an editor in Kenya who seems to be MIA(?). So I've resubmitted to another senior editor. The joke is that it's not a completely finished manuscript, I was looking for their input that it's something they're interested in so I could finish the range maps / tables to fit their format. In spite of this I still want to publish it with them since I think it covers the appropriate field.

I'm having a lab meeting with students in my lab tomorrow afternoon at 2 to organize this semester's work. We'll get back on the scarlet & telescope shiner track which will take several forms. And we've got to get on to sequencing stippled studfish DNA. Kris is now ready to write up his results with mummichog DNA sequencing, which I think will be worth it. No big breakthroughs, but it will expand upon what is known about mummichog population structure and by inference recent evolutionary history. I'll definitely keep you posted.

Thursday, January 01, 2009

The Black Darter Crusade Continues

I've made more headway on this article, which now has a name (see below). A round of heavy editing and proofreading has it down to a total length of 37 pages. This includes a bunch of figures of histology images showing details of ovarian and testicular structures. Hopefully the editors see fit to include these figures in some form, the work that went into them damn near killed Rachel(!). I'm just about happy with it, and from here I show it to the two other co-authors who don't know yet that they are co-authors. Anyway, following is the title and abstract --

Reproductive Development in the Blacksided Snubnose Darter, Etheostoma duryi, in North Alabama

Reproductive development in the percid fish Etheostoma duryi (subfamily Etheostomatinae) was studied in two north Alabama populations in the Tennessee River drainage. Sites chosen for comparison were urban Town Creek, near downtown Athens in Limestone County, and rural Limestone Creek, in Madison County. Because of the small body size of this species the study uses a histological approach which has not been used in population studies of the Etheostomatinae. Microscopic and macroscopic methods were utilized to study gonadal development and investment. Town Creek fish were larger than Limestone Creek fish. Reproductive investment, as measured by gonadosomatic index, relative gonad mass and the proportionality coefficient, increased in both sites (and for both sexes) toward the time of peak spawning. However, there were no significant differences between the sites in reproductive output for either sex. Total number of oocytes differed significantly between populations, possibly attributable to differing body sizes. Clutch size and mass were not significantly different between sites. Reproductive maturation occurs from January until the peak in late March and April at both sites.