The Drew Lab at Columbia University

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Ichthyology

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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: Lais Araujo Coelho

Email: lac2208@columbia.edu

Meeting Time:          Wednesday 1-4

Location: Schermerhorn 1015

                       

Office Hours: Tuesday 3-4 or by appointment

Textbook:

Required: 

The Diversity of Fishes, 2nd 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

Primary Literature Reports

1 @ 100 points            100

Lecture Final

1 @ 100 points            100

Term Paper

1 @ 100 points            100

Discretionary / Participation Points   50

Total-600 points

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 Please note: This class is scheduled to meet the day before Thanksgiving, and most likely will have its final on December 23rd.

Week 1 September 9th Lec. 1: Intro to Ichthyology / A Brief History of Fish Taxonomy

Week 2 September 16th Lec. 2: Jawless Fishes/ Conservation of phylogenetic diversity Candy Phylogeny Lab Due

Week 3 September 23rd Lec. 3: Chondrichthyes / Shark finning and wildlife trade Shark tooth lab due

Week 4 September 30th Lec. 4: Advanced Jawed Fishes/ The Transition to Land: Sarcopterygii

Week 5 October 7th Lec. 5: Chondrostei/ Saving Sturgeon

Week 6 October 14th Lec. 6: Lower Teleosts (Elopaforms, Osteoglossomorpha etc.)

Week 7 October 21st Lec. 7: Trip to AMNH fish collections

Week 8 October 28th Midterm / Mating and sexual diversity

Week 9 November 4th Lec. 8: Protacanthopterygii / Global Fisheries

Week 10 November 11th Lec. 9: Neoteleostei / Adaptation to extreme environments

Week 11 November 18th Lec. 10: Scavenger Hunt at AMNH

Week 12 November 25th Lec. 11: Acanthomorpha 1

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

Week 14 December 9th Lec 13: Threats to fishes – Global climate change

Week 15 December 16th: Reading Week

Week 16 December 23rd: 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; Heimberg, Cowper-Sal, Sémon, Donoghue, & Peterson, 2010; Near 2009; Strecker, Olden, Whittier, & Paukert, 2011; Winter, Devictor, & Schweiger, 2013) 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) 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) 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) 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) 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)   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): HCF&B Chapter 25 (Donelson, Munday, McCormick, & Pitcher, 2012; Lönnstedt, McCormick, & Chivers, 2013; MacNeil et al., 2015; Motani & Wainwright, 2015; Simpson et al., 2011)

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),

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 Change, 2(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). Evolution, 69(1), 146-161.

Drew, A. (2011). The role of natural history institutions and bioinformatics in conservation biology. Conservation Biology, 25(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 One, 7(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 Ichthyology, 18, 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 Biology, 15, 113. doi:10.1186/s12862-015-0415-0

Heimberg, A. M., Cowper-Sal, R., Sémon, M., Donoghue, P. C., & Peterson, K. J. (2010). MicroRNAs reveal the interrelationships of hagfish, lampreys, and Gnathostomes and the nature of the ancestral vertebrate. PNAS, 107(45), 19379-19383.

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. PNAS, 108(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 One, 8(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 Reports, 3, 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. Nature, 406(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 Ecology, 12(11), 2963-2973.

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 One, 8(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 Reports, 5, 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 Evolution, 73, 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 Biology, 26(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 Evolution, 312(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 Evolution, 63(6), 826-41. doi:10.1007/s00239-005-0293-y

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 One, 3(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 Evolution, 13(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 Letters, 7(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 Applications, 21(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. Zootaxa, 3586, 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 & Evolution, 28(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 Science, 60(1), 23-36.

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 Science, 60(2), 285-299.

Vollmar, A., Macklin, J. A., & Ford, L. (2010). Natural history specimen digitization: Challenges and concerns. Biodiversity Informatics, 7(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 Biology, 14(12), 2796-2809.

Winker, K. (2004). Natural history museums in a postbiodiversity era. BioScience, 54(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 & Evolution, 28(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 Research, 153, 9-17.

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