Classes

Ichthyology

 

photo 2-1

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

Instructor:  Joshua Drew

1013 Schermerhorn Ext.

212 845-7807

email – [email protected]

Twitter: @Drew_Lab

 

Graduate TA: Emily Chou

Email: [email protected]

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

Location: Schermerhorn 1015

                       

Office Hours: Wednesday 10:30-11:30

Textbook (recommended)

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

Objectives: The purpose of the course is to understand how the ecology mnhnd 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 AmericanThe 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 6th Lec. 1: Intro to Ichthyology / A Brief History of Fish Taxonomy

Week 2 September 11th Lec. 2: Jawless Fishes/ Conservation of phylogenetic diversity Candy Phylogeny Lab Due on Sept. 27

Week 3 September 18th Lec. 3: Chondrichthyes / Shark finning and wildlife trade Shark tooth lab due on Sept. 20

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

Week 5 October 1st Lec. 5: Chondrostei/ Saving Sturgeon

Week 6 October 9th Lec. 6: Lower Teleosts (Elopaforms, Osteoglossomorpha etc.)

Week 7 October 16th Lec. 7: Caviar Dreams showing (Mon) Discussion (Wed)

Week 8 October 23rd Midterm / Mating and sexual diversity

Week 9 October 30th Lec. 8: Protacanthopterygii / Global Fisheries

Week 10 November 6th Lec. 9: Neoteleostei / Adaptation to extreme environments

Week 11 November 13th Lec. 10: Scavenger Hunt at AMNH

Week 12 November 27th Lec. 11: Acanthomorpha 1

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

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

Week 15 December 16th: Reading Week

Week 16 December 18thProjected 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; Erdmann 1999; King, Shubin, Coates, & Hale, 2011; Mccabe & Wright, 2000Recommended HCF&B Chapter 13

Week 5 (Chondrostei/ Saving Sturgeon): (Billard & Lecointre, 2001; Cooke et al., 2014; Erickson, North, Hightower, Webber, & Lauck, 2002; Roston 2017Recommended 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 Caviar Dreams

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 Series367, 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 Change4(3), 211-216.

Billard, R., & Lecointre, G. (2001). Biology and conservation of sturgeon and paddlefish. Reviews in Fish Biology and Fisheries10, 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 Biology154(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 Conservation144(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 One7(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 Science66(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 One8(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 Biogeography40(2),

Donelson, J. M., Munday, P. L., McCormick, M. I., & Pitcher, C. R. (2012). Rapid transgenerational acclimation of a tropical reef fish to climate change. Nature Climate Change2(1), 30-32.

Dornburg, A., Moore, J., Beaulieu, J. M., Eytan, R. I., & Near, T. J. (2015). The impact of shifts in marine biodiversity hotspots on patterns of range evolution: evidence from the Holocentridae (squirrelfishes and soldierfishes). Evolution69(1), 146-161.

Drew, A. (2011). The role of natural history institutions and bioinformatics in conservation biology. Conservation Biology25(6), 1250-1252. doi:10.1111/j.1523-1739.2011.01725.x

Dutel, H., Maisey, J. G., Schwimmer, D. R., Janvier, P., Herbin, M., & Clément, G. (2012). The giant cretaceous coelacanth (Actinistia, Sarcopterygii) Megalocoelacanthus dobiei Schwimmer, Stewart & Williams, 1994, and its bearing on Latimerioidei interrelationships. PloS One7(11), e49911. doi:10.1371/journal.pone.0049911

Erdmann, M. V. (1999). An account of the first living coelacanth known to scientists from Indonesian waters. Environmental Biology of Fishes, (September 1997), 439-443.

Erickson, D. L., North, J. A., Hightower, J. E., Webber, J., & Lauck, L. (2002). Movement and habitat use of green sturgeon Acipenser medirostris in the Rogue River, Oregon, USA. Journal of Applied Ichthyology18, 565-569.

Eytan, R. I., Evans, B. R., Dornburg, A., Lemmon, A. R., Lemmon, E. M., Wainwright, P. C., & Near, T. J. (2015). Are 100 enough? Inferring Acanthomorph teleost phylogeny using anchored hybrid enrichment. BMC Evolutionary Biology15, 113. doi:10.1186/s12862-015-0415-0

King, H. M., Shubin, N. H., Coates, M. I., & Hale, M. E. (2011). Behavioral evidence for the evolution of walking and bounding before terrestriality in Sarcopterygian fishes. PNAS108(52), 21146-51. doi:10.1073/pnas.1118669109

Lecointre, G., Améziane, N., Boisselier, M. C., Bonillo, C., Busson, F., Causse, R., . . . David, B. (2013). Is the species flock concept operational? The Antarctic shelf case. PloS One8(8), e68787. doi:10.1371/journal.pone.0068787

Lönnstedt, O. M., McCormick, M. I., & Chivers, D. P. (2013). Predator-induced changes in the growth of eyes and false eyespots. Scientific Reports3, 2259. doi:10.1038/srep02259

MacNeil, M. A., Graham, N. A., Cinner, J. E., Wilson, S. K., Williams, I. D., Maina, J., . . . McClanahan, T. R. (2015). Recovery potential of the world’s coral reef fishes. Nature. doi:10.1038/nature14358

McCabe, H., & Wright, J. (2000). Tangled tale of a lost, stolen and disputed coelacanth. Nature406(July), 2000-2000.

McCartney, M. A., Acevedo, J., Heredia, C., Rico, C., Quenoville, B., Bermingham, E., & Mcmillan, W. O. (2003). Genetic mosaic in a marine species flock. Molecular Ecology12(11), 2963-2973.

McCord, C. L., & Westneat, M. W. (2015). Phylogenetic relationships and the evolution of BMP4 in triggerfishes and filefishes (Balistoidea). Molecular Phylogenetics and Evolution. 94 397-409

McCoy, Victoria E., et al. “The ‘Tully monster’is a vertebrate.” Nature 532.7600 (2016): 496-499.

McMahan, C. D., Chakrabarty, P., Sparks, J. S., Smith, W. M., & Davis, M. P. (2013). Temporal patterns of diversification across global cichlid biodiversity (Acanthomorpha: Cichlidae). PloS One8(8), e71162. doi:10.1371/journal.pone.0071162

Motani, R., & Wainwright, P. (2015). How warm is too warm for the life cycle of Actinopterygian fishes? Scientific Reports5, article number 11597.

Muñoz-Ramírez, C. P., Unmack, P. J., Habit, E., Johnson, J. B., Cussac, V. E., & Victoriano, P. (2014). Phylogeography of the ancient catfish family Diplomystidae: Biogeographic, systematic, and conservation implications. Molecular Phylogenetics and Evolution73, 146-160.

Nadon, M. O., Baum, J. K., Williams, I. D., McPherson, J. M., Zgliczynski, B. J., Richards, B. L., . . . Brainard, R. E. (2012). Re-creating missing population baselines for pacific reef sharks. Conservation Biology26(3), 493-503. doi:10.1111/j.1523-1739.2012.01835.x

Near, T. J. (2009). Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and Gnathostomes. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution312(7), 749-761.

Near, T. J., Dornburg, A., Kuhn, K. L., Eastman, J. T., Pennington, J. N., Patarnello, T., . . . Jones, C. D. (2012a). Ancient climate change, antifreeze, and the evolutionary diversification of Antarctic fishes. PNAS 109(9), 3434-9. doi:10.1073/pnas.1115169109

Near, T. J., Eytan, R. I., Dornburg, A., Kuhn, K. L., Moore, J. A., Davis, M. P., . . . Smith, W. L. (2012b). Resolution of ray-finned fish phylogeny and timing of diversification. PNAS 109(34), 13698-703. doi:10.1073/pnas.1206625109

Saitoh, K., Sado, T., Mayden, R. L., Hanzawa, N., Nakamura, K., Nishida, M., & Miya, M. (2006). Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-level relationships of the world’s largest freshwater fish clade based on 59 whole mitogenome sequences. Journal of Molecular Evolution63(6), 826-41. doi:10.1007/s00239-005-0293-y

Sallan, Lauren, et al. “The ‘Tully Monster’is not a vertebrate: characters, convergence and taphonomy in Palaeozoic problematic animals.” Palaeontology60.2 (2017): 149-157.

Sandin, S. A., Smith, J. E., DeMartini, E. E., Dinsdale, E. A., Donner, S. D., Friedlander, A. M., . . . Obura, D. (2008). Baselines and degradation of coral reefs in the northern Line Islands. PloS One3(2), e1548.

Shaffer, H. B., Fisher, R. N., & Davidson, C. (1998). The role of natural history collections in documenting species declines. Trends in Ecology and Evolution13(1), 27-30.

Simpson, S. D., Munday, P. L., Wittenrich, M. L., Manassa, R., Dixson, D. L., Gagliano, M., & Yan, H. Y. (2011). Ocean acidification erodes crucial auditory behaviour in a marine fish. Biology Letters7(6), 917-20. doi:10.1098/rsbl.2011.0293

Strecker, A. L., Olden, J. D., Whittier, J. B., & Paukert, C. P. (2011). Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity. Ecological Applications21(8), 3002-3013.

Sulaiman, Z. H., & Mayden, R. L. (2012). Cypriniformes of Borneo (Actinopterygii, Otophysi): An extraordinary fauna for integrated studies on diversity, systematics, evolution, ecology, and conservation. Zootaxa3586, 359-376.

Tobler, M., Palacios, M., Chapman, L. J., Mitrofanov, I., Bierbach, D., Plath, M., . . . Mateos, M. (2011). Evolution in extreme environments: Replicated phenotypic differentiation in livebearing fish inhabiting sulfidic springs. Evolution, 65(8), 2213-28. doi:10.1111/j.1558-5646.2011.01298.x

Trebilco, R., Baum, J. K., Salomon, A. K., & Dulvy, N. K. (2013). Ecosystem ecology: Size-based constraints on the pyramids of life. Trends in Ecology & Evolution28(7), 423-31. doi:10.1016/j.tree.2013.03.008

Tsukamoto, Y., & Okiyama, M. (1997). Metamorphosis of the pacific tarpon, Megalops cyprinoides (Elopiformes, Megalopidae) with remarks on development patterns in the Elopomorpha. Bulletin of Marine Science60(1), 23-36.

Varela, A. I., Ritchie, P. A., & Smith, P. J. (2013). Global genetic population structure in the commercially exploited deep-sea teleost orange roughy (Hoplostethus atlanticus) based on microsatellite DNA analyses. Fisheries Research140, 83-90.

Vega-Cendejas, M. E., & de Santillana, M. H. (2004). Fish community structure and dynamics in a coastal hypersaline lagoon: Rio Lagartos, Yucatan, Mexico. Estuarine, Coastal and Shelf Science60(2), 285-299.

Vollmar, A., Macklin, J. A., & Ford, L. (2010). Natural history specimen digitization: Challenges and concerns. Biodiversity Informatics7(2), 93 – 112.

Wilson, S. K., Fisher, R., Pratchett, M. S., Graham, N. A. J., Dulvy, N. K., Turner, R. A., . . . Rushton, S. P. (2008). Exploitation and habitat degradation as agents of change within coral reef fish communities. Global Change Biology14(12), 2796-2809.

Winker, K. (2004). Natural history museums in a postbiodiversity era. BioScience54(5), 455-459. doi:10.1641/0006-3568(2004)054

Winter, M., Devictor, V., & Schweiger, O. (2013). Phylogenetic diversity and nature conservation: Where are we? Trends in Ecology & Evolution28(4), 199-204 doi:10.1016/j.tree.2012.10.015

Woodcock, S. H., & Walther, B. D. (2014). Trace elements and stable isotopes in Atlantic tarpon scales reveal movements across estuarine gradients. Fisheries Research153, 9-17.

 

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