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Topic	Tues lab	Thurs lab
November 24-26
Coevolution among lake organisms	Sancha de Vette	Dylan Rawlyk
Amphibian declines 1- disease	Samantha Iversen	Matt Robinson
Lakes as records of past climates	Nichole Holdbak	Carly Fleming
Effects of salmon-derived nutrients on lakes	Tamar Brinkman	Alexis Carter
Ecological speciation 1- Sticklebacks	Katy Burkholder	Andrew Leung
December 1-3
Amphibian declines 2- global change	Natalie Reichenbacher	Brandon Udy
Ecological speciation 1- Cichlids	Kathleen Foster	Nicole Bedford
Aquatic organisms and terrestrial systems	Jenna Stoner	Anne Rutherford
Irreversible change	Jana Holbrook	Crystal Lebreton
Diversity and ecosystems		Nathan McQuarrie

1. Coevolution among lake organisms

Ellen Decaestecker et al. 2007. Host–parasite ‘Red Queen’ dynamics archived in pond sediment. Nature 450: 870
Mark Urban. 2007. Risky prey behavior evolves in risky habitats. PNAS 104: 14377.

2. Causes of amphibian declines 1- disease

Johnson P.T.J., Lunde K.B., Ritchie E.G. & Launer A.E. (1999) The effect of trematode infection on amphibian limb development and survivorship. Science, 284, 802-804
Lips, K.R. (2006). Emerging infectious disease and the loss of biodiversity in a Neotropical amphibian community. PNAS 103: 3165

3. Causes of amphibian declines 1- global change

Kiesecker J.M., Blaustein A.R. & Belden L.K. (2001) Complex causes of amphibian population declines. Nature, 410, 681-684
Pounds, J.A. (2006) Widespread amphibian extinctions from epidemic disease driven by global warming. Nature 439: 161

4. Lakes as records of past climates

Smol, J. P. et al. (2005) Climate-driven regime shifts in the biological communities of arctic lakes. Proceedings of the National Academy of Sciences of the United States of America, 102, 4397-4402.
Hall, R.I. (1999). Effects of agriculture, urbanization, and climate on water quality in the northern Great Plains. Limnology and Oceanography 44: 739.

5. Ecological speciation in lake organisms 1- Sticklebacks

McKinnon, J. S., Mori, S., Blackman, B. K.. David, L.. Kingsley, D. M., Jamieson, L., Chou, J.. Schluter, D.(2004) Evidence for ecology's role in speciation. Nature, 429, 294-298
Harmon et al. (2008). Evolutionary diversification in stickleback affects ecosystem functioning. Nature 458: 1167.

6. Ecological speciation in lake organisms 2- Cichlids (choose 2)

Seehausen, O. et al. (2009). Speciation through sensory drive in cichlid fish. Nature 455: 620
Seehausen, O., van Alphen, J.J.M., Witte, F. (1997). Cichlid fish diversity threatened by eutrophication that curbs sexual selection. Nature 277:1808-1811
Barluenga et al. (2006). Sympatric speciation in Nicaraguan crater lake cichlid fish. Nature 439: 719

7. Effects of salmon-derived nutrients

Finney, B. P., Gregory-Eaves, I., Sweetman, J., Dougas, M. S. V., Smol, J. P. (2000). Impacts of climatic change and fishing on Pacific salmon abundance over the past 300 years. Science 290, 795-799
Helfield, J. M. and Naiman, R. J. (2001) Effects of salmon-derived nitrogen on riparian forest growth and implications for stream productivity. Ecology, 82, 2403-2409

8. Impact of aquatic organisms on terrestrial systems

Knight, T. M., McCoy, M. W., Chase, J. M., McCoy, K. A., Holt, R. D. (2005). Trophic cascades across ecosystems. Nature 473, 880-883.
Murakami, M., Nakano, S. (2002) Indirect effect of aquatic insect emergence on a terrestrial insect population through predation by birds. Ecology Letters 5, 333-337

9. Irreversible changes in aquatic ecosystems

Freeman et al. (2004). Export of dissolved organic carbon from peatlands under elevated carbon dioxide levels. Nature 430: 195.
Casini et al. (2008). Trophic cascades promote threshold-like shifts in pelagic marine ecosystems. PNAS 106:197. (Even though it says “marine”, it’s from the Baltic, which is a big lake)

10. Role of diversity in aquatic ecosystems

Ptacnik, R. (2008). Diversity predicts stability and resource use efficiency in natural phytoplankton communities. PNAS 105: 5134
Cardinale, B.J. (2002). Species diversity enhances ecosystem functioning through interspeci®c facilitation. Nature 415: 426.

Bamfield talk

UCSD Lecture 1

UCSD Lecture II

Common problems with Lake Papers
Read this to do better on your Stream Paper

Lab paper marking scheme

Notes for Lakes data from Katsky:

1. The Thurs abiotic data are now posted (previously missing).

2. Jon has posted the Floroprobe data, no analyses need to be done on this data, they are similar to the abiotic data in that you have measurements across a variety of depths. This data should be displayed in the same way as the abiotic data graphs and can be discussed qualitatively. Be sure to keep your formatting (graphs and tables) consistent throughout the paper.

3. Be careful with your error bars – what are they (SE?, Standard deviation?), if all the error bars on a graph look exactly the same size they are probably wrong, and need to be recalculated in excel (remember S.E. = std. dev/sqrt(n))

4. Keep in mind that lack of statistical difference is not the same as saying there is no difference.

5. I will be in the stats lab from 2-4pm Tuesday and Thursday next week for help with stats or questions, though there is no required lab. Please make use of my time.

6. your stream papers will be returned to you on Monday

7. Tuesday's Phosphorus tukey results are incomplete

8. Thursday conductivity graph is incorrect

9. watch error bars - especially on the secchi data and phyto. data (and possibly others - remember, if all your error bars are the same size something is wrong)

10. Phytoplankton data has a number of flaws - you can use the tuesday data but the error bars are incorrect. the thursday analyses are incorrect, and I believe that the labelling on some graphs are incorrect, as are the diversity measures. Check through this data - you may have to reanalyze things.

Developing your hypotheses – base your report on ALL (or almost all) of the info available – look at the graphs, see how things tie together – how does temperature relate to O₂ (choose EITHER % saturation or mg/l)? How does the depth of the thermocline relate to light penetration and exposure of the lake to wind? How does light penetration relate to phytoplankton vertical distribution? How does phytoplankton abundance relate to the nutrient content of the lake and O₂ distribution? How do zooplankton fit in? Are there consistent differences between lakes with and without fish, and what does this say about top-down effects? Are the differences between lakes related to nutrients (using the links mentioned above and whatever else you can think of), and what does this say about bottom-up effects?

- you are trying to tie all these data together into a complete story – do they fit with what you know about eutrophic and oligotrophic lakes, and fish vs. fishless lakes? Where they do not fit, can you explain the deviation in terms of anything else you measured or observed? Tie these into concepts you learned in lecture.

All of these will be in your paper (yes, I know it is a lot, this will be a big paper. It is important to structure it in a logical way – e.g. organize it into sections for different kinds of data, abiotic, phytoplankton, etc., and be as concise as possible). Describe in your intro how you expect a lake to work (e.g. if you have lots of nutrients you expect…., if you have fish you expect…., etc) and come up with specific predictions for each lake, knowing that Deer lake is eutrophic and has fish, and that the other lakes are more oligotrophic and Loon and Gwendoline have fish but Shirley doesn’t.

Make use of Katsky’s time during the lab slots this week (from 2-4 Tues and Thurs). ASK FOR HELP- IT WILL SAVE YOU TIME AND SUFFERING LATER ON AS WE CAN STEER YOU AWAY FROM MISTAKES.

Data notes from Katsky! Important!

Here are the graphs and analyses of the stream data for the Tuesday and Thursday Labs. Some things to note:

You can use any of the graphs/data you choose (ie it does not matter which lab you are in), but it is your responsibility to make sure it is correct.
Drift samples – the ‘day’ drift samples were collected over a 7 hour period, whereas the ‘night’ drift samples were collected over 13 hours – therefore we had to scale the densities of these samples to make them comparable. WE WERE NOT ABLE TO SCALE SPECIES RICHNESS OR DIVERSITY, therefore the statistical comparison of day to night samples produces biased results – leaving the nets in for a longer time will increase sample species richness and possibly diversity. Keep this in mind when writing your report, perhaps you can still make some qualitative comparisons…
There was an error in the chemistry raw data – this was found and corrected in the Thursday lab data (use this data preferentially)
No post-hoc tests (eg Tukey’s HSD) were done to determine where the differences (if any) were, these need to be done where significance was found. You can do additional ANOVA’s or t-test to determine this. Or it can be done in JMP after the 2 way ANOVA by pulling down the red arrow beside the factor (eg Stream or Habitat or stream*habitat) and selecting ‘Tukey’ – in the output the values in red indicate where the differences lie.
We are missing the fish data for the Thursday lab.
Because the tuesday lab was cut short we did not have a chance to standardize the graphs – therefore if you use these graphs you must make them all look alike before you hand in your paper, or you may choose to use graphs produced in the Thursday lab.
Comparatively, Allouette is a high flow stream, Marion is intermediate, and Stream 2 and 4 were very low flow.
Be sure to check for errors in the data/analyses – although these graphs were done by the class as a whole it is your individual responsibility to be sure that what you hand in is correctly analyzed and displayed.

Good Luck!