Ichthyology

Students in the 2013 Ichthyology posing in front of their candy phylogeny

Instructor: Joshua Drew

1013 Schermerhorn Ext.

212 845-7807

email – jd2977@columbia.edu

Twitter: @Drew_Lab

Graduate TA: Emily Chou

Email: EC3158@columbia.edu

Meeting Time: M & W 8:40-9:55

Location: Schermerhorn 1015

Office Hours: Wednesday 10:30-11:30

Textbook (recommended)

The Diversity of Fishes, 2^nd Edition – Helfman, Collette, Facey & Bowen

Objectives: The purpose of the course is to understand how the ecology and evolution of fishes influence our ability to conserve aquatic biodiversity.

Grading:

Mid-semester Lecture Exam

1 @ 100 points 100

Assignments (Candy Lab, Shark Tooth Lab, AMNH Scavenger Hunt)

3 @ 50 points 150

Critical Viewing/Writing of Aquatic Documentary

2 @ 100 points 100

Lecture Final

1 @ 100 points 100

Term Paper

1 @ 100 points 100

Readings leader

1 @ 100 points 100

Discretionary / Participation Points 50

Total-700 points

Laptop Policy:

Over the years I’ve noticed that many students are taking notes in class using a laptop. That’s fine, in theory. I have also noticed, however that the second I stop speaking, students start checking email, watch videos, shop on-line etc. Not only is this a waste of your money, but these activities also tend to distract even the must assiduous student.

Overwhelming evidence suggests that students learn better when they take physical notes. This is especially true in classes Ichthyology where not all of the material could be easily transcribed in Word or Powerpoint. For example recent articles in Scientific American, The Washington Post, and the New York Times have summarized a suite of scientific papers showing the performance enhancements of taking notes the old fashioned way.

I am also keenly aware that for some students taking notes using pen and a notebook can represent physical impediment to learning, so I am not doing an outright ban. You can use a laptop if you want to. However I would like you to try it for two to three weeks and see if your retention is improved. You are spending a lot of money coming to Columbia and I’d like you to get the most out of our shared time here.

Assignment Group 1: Labs:

We will be having three labs that will take place in both the class and at home. The first will be focusing on the phylogeny of candy, the second will be looking at shark teeth evolution and the third will be a scavenger hunt at the AMNH.

Assignment Group 2: Documentary Analysis Presentation / Writing:

We will be assessing environmental documentaries as an exercise. Each Monday, one pair of students will present on a documentary they have watched that dealt with some aspect of coastal and estuarine ecology. The pair must provide the title of the documentary at least one week in advance so that the class as a whole can watch the video before the presentation on Monday (choosing videos that are available online, or on Netflix, Amazon Prime, etc. will help facilitate the class’ viewing and discussion). Each pair will present the documentary to the class, explaining 1) the positive qualities of the documentary (ex. strategies they used to engage the audience, truthfulness of their message, etc.), 2) where it needed improvement, and 3) if any biases were introduced by the directors. Each student in the pair should think about these points independently: this will allow you to discuss differences in opinions, bringing multiple views to strengthen your presentation. Presentations will be capped at 10 minutes (strictly enforced).

In addition to presenting your chosen documentary, each student is additionally required to write a reflection on one video chosen by another pair. This assignment, which should be approximately 1500 words, should be a critical viewing of a video presentation. For this assignment choose at least two documentaries and compare and contrast their presentation styles, the hypotheses put forward (if any) and what evidence is used to support the main points. Importantly, use what you have learned in class to assess the quality, biases and kinds of science presented within the documentary. What was included, and as critically, what was omitted? Why do you think these choices were made? Lastly, did it change your views?

For those who are not familiar with critical viewing the following resources may be of some help

http://www.medialit.org/reading-room/critical-viewing-and-critical-thinking-skills

http://www.corndancer.com/fritze/invntdknwldg/invknw_critique.html

Assignment Group 3: Class readings.

We will have on average two peer-reviewed articles to read per class. We will have a class discussion on all of the weeks papers on Wednesdays which will be facilitated by the same team which lead the documentary discussion on that Monday. The goal of these discussions will be to draw themes across the papers and to talk about new directions in ichthyology. The discussion team will be responsible for asking questions of their peers, and nurturing discussions. Please feel free to see me about the weeks readings if you have questions.

For each lecture exam you will be responsible for all reading material and all lecture materials. The final exam is comprehensive, but will be weighted for material after the mid-semester exam. If you have a conflict with exams contact me as soon as possible and arrangements will be made to take the exam prior to the scheduled date. There are no make-ups for missing an exam unless you have a valid preapproved excuse or medical emergency etc. Participation/Discretionary Points may be given to students who willingly participate in class discussions and field trips. No other extra credit points will be available.

There will be three written assignments dealing with the descriptions of fishes, as well as a more intensive term paper. There will also be a presentation assignment. More details about these assignments will be given in class. Plagiarism will not be tolerated and will result in a 0 grade for that assignment and disciplinary action from the university.

Title IX makes it clear that violence and harassment based on sex and gender are Civil Rights offenses subject to the same kinds of accountability and the same kinds of support applied to offenses against other protected categories such as race, national origin, etc. If you or someone you know has been harassed or assaulted, you can find the appropriate resources at http://sexualrespect.columbia.edu. We also provide accommodations for students with documented disabilities; please check with https://health.columbia.edu/disability-services to ensure I get notified if this is applicable. Lastly, I want to maintain a respectful atmosphere where students are free to discuss topics in a safe and collegial atmosphere. We will be covering some potentially contentious topics in class, discussion is encouraged, disrespect is not.

CLASS SCHEDULE

Week 1 September 6^th Lec. 1: Intro to Ichthyology / A Brief History of Fish Taxonomy

Week 2 September 11^th Lec. 2: Jawless Fishes/ Conservation of phylogenetic diversity Candy Phylogeny Lab Due

Week 3 September 18^th Lec. 3: Chondrichthyes / Shark finning and wildlife trade Shark tooth lab due

Week 4 September 25^th Lec. 4: Advanced Jawed Fishes/ The Transition to Land: Sarcopterygii NO CLASS ON MONDAY SEPTEMBER 25th

Week 5 October 9^th Lec. 5: Chondrostei/ Saving Sturgeon

Week 6 October 18^th Lec. 6: Lower Teleosts (Elopaforms, Osteoglossomorpha etc.)

Week 7 October 23^rd Lec. 7: Trip to AMNH fish collections

Week 8 October 30^th Midterm / Mating and sexual diversity

Week 9 November 6^th Lec. 8: Protacanthopterygii / Global Fisheries

Week 10 November 13^th Lec. 9: Neoteleostei / Adaptation to extreme environments

Week 11 November 20^th Lec. 10: Scavenger Hunt at AMNH

Week 12 November 27^th Lec. 11: Acanthomorpha 1

Week 13 December 4^th Lec. 12: Acanthoporpha 2 / Speciation and species flocks

Week 14 December 11^th Lec 13: Threats to fishes – Global climate change

Week 15 December 16^th: Reading Week

Week 16 December 18^th: Projected Final

Readings with the exception of week 1, readings should be done ahead of class:

Week 1: N/A

Week 2 (Jawless Fishes / Conservation of phylogenetic diversity): (Baker, Sardella,Rummer, Sackville, & Brauner, 2015; McCoy et al 2016; Near 2009; Sallan et al. 2017; Winter, Devictor, & Schweiger, 2013) Recommended HCF&B Chapter 13

Week 3 (Chondrichthyes / Shark finning and wildlife trade): (Nadon et al., 2012; Sandin et al. 2008, Trebilco et al. 2013, Wilson et al. 2008) Recommended HCF&B Chapter 12

Week 4 Advanced Jawed Fishes/ The Transition to Land: Sarcopterygii): (Cavin & Kemp, 2011; Dutel et al., 2012; Erdmann 1999; King, Shubin, Coates, & Hale, 2011; Mccabe & Wright, 2000) Recommended HCF&B Chapter 13

Week 5 (Chondrostei/ Saving Sturgeon): (Billard & Lecointre, 2001; Collins, Rogers, Smith, & Moser, 2000; Cooke et al., 2014; Erickson, North, Hightower, Webber, & Lauck, 2002) Recommended HCF&B Chapter 13

Week 6 (Lower Teleosts (Elopaforms, Osteoglossomorpha etc.): (Barange et al., 2014; Cowman & Bellwood, 2012; Eytan et al., 2015; Near et al., 2012b) Recommended HCF&B Chapter 14

Week 7 Trip to AMNH: (Costello et al., 2013; Drew 2011; Shaffer, Fisher, & Davidson, 1998; Vollmar, Macklin, & Ford, 2010; Winker 2004)

Week 8: Study for Midterm

Week 9 (Acanthopterygii / Elopomorpha): HCF&B Chapter 14, 19 (Tsukamoto & Okiyama, 1997; Woodcock & Walther, 2014)

Week 10 (Neoteleostei / Global Fisheries / Adaptation to extreme environments): (Chakrabarty, Davis, & Sparks, 2012; Near et al., 2012a; Tobler et al., 2011; Vega-Cendejas & de Santillana, 2004) Recommended HCF&B Chapter 18

Week 11 (AMNH Scavenger hunt) no readings

Week 12 (Acanthomorpha): (Albins & Hixon, 2008; Varela et al., 2013; Dornburg et al., 2015; McCord and Westneat 2015)

Week 13 (Percoidea / Speciation and Species Flocks) (Burford & Bernardi, 2008; Lecointre et al., 2013; McCartney et al., 2003; McMahan, et al, 2013)

Week 14 (Threats to fishes – Global climate change): (Donelson, Munday, McCormick, & Pitcher, 2012; Lönnstedt, McCormick, & Chivers, 2013; MacNeil et al., 2015; Motani & Wainwright, 2015; Simpson et al., 2011) Recommended HCF&B Chapter 25

Readings:

Albins, M., & Hixon, M. (2008). Invasive indo-pacific lionfish Pterois volitans reduce recruitment of atlantic coral-reef fishes. Marine Ecology Progress Series, 367, 233-238. doi:10.3354/meps07620

Baker, D. W., Sardella, B., Rummer, J. L., Sackville, M., & Brauner, C. J. (2015). Hagfish: Champions of CO2 tolerance question the origins of vertebrate gill function. Scientific Reports, 5, 11182. doi:10.1038/srep11182

Barange, M., Merino, G., Blanchard, J. L., Scholtens, J., Harle, J., Allison, E. H., . . . Jennings, S. (2014). Impacts of climate change on marine ecosystem production in societies dependent on fisheries. Nature Climate Change, 4(3), 211-216.

Billard, R., & Lecointre, G. (2001). Biology and conservation of sturgeon and paddlefish. Reviews in Fish Biology and Fisheries, 10, 355-392.

Burford, M. O., & Bernardi, G. (2008). Incipient speciation within a subgenus of rockfish (Sebastosomus) provides evidence of recent radiations within an ancient species flock. Marine Biology, 154(4), 701-717. doi:10.1007/s00227-008-0963-6

Cavin, L., & Kemp, A. (2011). The impact of fossils on the evolutionary distinctiveness and conservation status of the Australian lungfish. Biological Conservation, 144(12), 3140-3142.

Chakrabarty, P., Davis, M. P., & Sparks, J. S. (2012). The first record of a trans-oceanic sister-group relationship between obligate vertebrate troglobites. PloS One, 7(8), e44083. doi:10.1371/journal.pone.0044083

Collins, M. R., Rogers, G., Smith, T. I. J., & Moser, M. L. (2000). Primary factors affecting sturgeon populations in the southeastern United States; fishing mortality and degradation of essential habitats. Bulletin of Marine Science, 66(3), 917-928.

Cooke, S. J., Hogan, Z. S., Butcher, P. A., Stokesbury, M. J., Raghavan, R., Gallagher, A. J., . . . Danylchuk, A. J. (2014). Angling for endangered fish: Conservation problem or conservation action? Fish and Fisheries.

Costello, M. J., Bouchet, P., Boxshall, G., Fauchald, K., Gordon, D., Hoeksema, B. W., . . . Appeltans, W. (2013). Global coordination and standardization in marine biodiversity through the world register of marine species (worms) and related databases. PloS One, 8(1), e51629. doi:10.1371/journal.pone.0051629

Cowman, P. F., & Bellwood, D. R. (2012). The historical biogeography of coral reef fishes: Global patterns of origination and dispersal. Journal of Biogeography, 40(2),