Instructor:  Edward Saiff
Email:  esaiff@ramapo.edu
Phone:  201-684-7723

Texts:

• Coyne, J. and H. Allen Orr, 2004, Speciation, Sinauer.
  
• Schuh, R.,  2000, Biological Systematics, Cornell Univ. Press
• Wheeler, Q. & R. Meier, 2000, Species Concepts and Phylogenetic Theory, Columbia Univ. Press

Attendance and class participation 25%; midterm 25%; term paper 25%; final 25%.

Structure:

The course is taught as a graduate seminar with a combination of short lectures, in-class discussions of concepts and discussions of published scientific papers. Attendance is required and participation in discussion and other class activities contributes to the course grade that students earn.

Objectives:

Students will...

• learn the history of modern biological systematics
• understand and apply the terminology of systematics
• know the several definitions of the term, species
• understand the concept of speciation
• understand the principle of parsimony
• understand how to use homology and character analysis to establish phylogenies
• understand how to evaluate phylogenies
• know how to utilize systematics to establish evolutionary scenarios
• know how to utilize systematics to understand biodiversity issues
• know how to utilize systematics to understand conservation issues

1.     Can we find a species definition that works for organisms that are sexual, asexual and hybridizers?  Do we have to?
2.     When does an organism cease being a member of the species to which its ancestors belong?
3.     Do stem species survive speciation events?
4.     Assuming that we can accurately define species, how can we use that information?

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TRIP TO THE AMERICAN MUSEUM OF NATURAL HISTORY

September 13 – Course introduction; discussion of important terms and concepts; discussion of how the course should proceed. How can the course best serve the needs of the students? Assignment: Read the introductions of our three texts, look at the tables of contents and skim the chapters. Then, design a syllabus for the course (due September 20).  Comb literature for class to read in addition to the texts (list with abstracts due September 27).

September 20 – Continue discussion of important terms and concepts, discuss syllabi from the members of the class and design a syllabus and assignments for the rest of the course. Begin to make a list of important terms that we’ll need to define. Discuss introductions to the three textbooks. Assignment:  Continue September 13 assignment.

September 27 – Abstracts due.  Discuss Schuh chapter 1 - Introduction to Systematics, and Coyne and Orr chapters 1 - Species:  Reality and Concepts, 3 - Allopatric and Parapatric Speciation, and 4 - Sympatric Speciation.

October 4 – Continue to discuss abstracts and schedule dates for student presentations.  Continue discussion on Schuh chapter 1 and Coyne & Orr chapters 1, 3 & 4.  Skim Schuh chapters 2 & 3.  Read Schuh chapter 4 and Coyne & Orr chapter 5.

October 11 – Discuss chapters 5-11 in the Schuh text.

October 18 – Guest Speaker - Dr. Randall Schuh, American Museum of Natural History.

October 25 – Discuss the Wheeler/Meier text and the Appendix from Coyne & Orr.

November 1 – Midterm Exam due.  Discuss Coyne & Orr chapters 11 & 12.  Papers to read and discuss:

• Davison, A.,  M. Benko  & B. Harrach 2003 Genetic content and evolution of adenoviruses. J. Gen. Virol. 2003. 84: 2895 - 2908.
• Gábor M. Kovács, et al 2004. Analysis of the first complete genome sequence of an Old World monkey adenovirus reveals a lineage distinct from the six human adenovirus species J. Gen. Virol. 2004; 85: 2799 - 2807.
• Anderson, J. et al. 2001 A phylogenetic approach to following West Nile virus in Connecticut PNAS 98(23):12885-12889.

November 8 – Papers to read and discuss:

• Vilas-Boas, G. et al. 2002. Genetic Differentiation between Sympatric populations of Bacillus cereus and Bacillus thuringiensis. Applied & Environmental Microbiology 68(3): 1414-1424.
• Vossbrinck, C. et al 2004 Molecular phylogeny and evolution of mosquito parasitic Microsporidia (Microsporidia: Amblyosporidae). J. Eukaryot Microbiol. 51(1): 88-95.
• Kendrick, P. & P. Crane 1991. Water conducting cells in early fossil land plants: implications for the early evolution of Tracheophytes. Botanical Gazette 152(3): 335-356.
• Daehler, C. et al. 1997 Hybridization between smooth cordgrass (Spartina alterniflora: Poaceae) and native Calif. Cordgrass (S. foliosa) in San Francisco Bay, Calif. USA. Amer. J. of Botany 84(5): 607-611.
• Becker, P. 2000 Competition in the regeneration niche between conifers and angiosperms: Bond’s slow seeding hypothesis. Functional Ecology 14(4): 401-412.
• Ellstrand, N. & K. Schierenback 2000 Hybridization as a stimulus for the evolution of invasiveness in Plants. PNAS 97(13): 7043-7050.
• Hoberg, E. P. et al 2001 Out of Africa: origins of the Taenia tapeworms in humans. Proc. Royal Society, London B. 268: 781-787.
• Gonzalo, G. & R. Carles 1998 The position of arthropods in the animal kingdom: a search for a reliable outgroup for internal arthropod phylogeny. Molec. Phylogenetics and Evolution 9:481-488.
• Shaw, K. 2002. Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: What mtDNA reveals and conceals about modes of speciation in Hawaiian crickets. PNAS 99 (25): 16122-16127.
• Gooding, R.H. 1982 Classification of nine species and subspecies of tsetse flies (Diptera: Glossinidae: Glossina Weidemann) based on molecular genetics and breeding data.  Canadian Journal of Zoology, 60, 2727-2744.

November 15 – Papers to read and discuss:

• Van Dover, C. L. et al. 2002. Evolution and biogeography of deep-sea vent and seep invertebrates. Science 295 (5558): 1253-1257.
• Lombard, R. E. & D. Wake 1986. Tongue Evolution in the Lungless Salamanders, Family Plethodontidae IV. Phylogeny of Plethodontid Salamanders and the Evolution of Feeding Dynamics Systematic Zoology 35(4): 532-551.
• Vences, M., J. Kosuch, R. Boistel, C. F. B. Haddad, E. La Marca, S. Lötters & M. Veith (2003): Convergent evolution of aposematic coloration in Neotropical poison frogs: a molecular phylogenetic perspective. – Organisms Diversity and Evolution 3: 215-226.
• Schaefer, H.-C., M. Vences & M. Veith (2002): Molecular phylogeny of Malagasy poison frogs, genus Mantella (Anura: Mantellidae): homoplastic evolution of colour pattern in aposematic amphibians. – Organisms Diversity and Evolution 2: 97-105.
• Vences, M., J. Kosuch, S. Lötters, A. Widmer, J. Köhler, K.-H. Jungfer & M. Veith (2000): Phylogeny and classification of poison frogs (Amphibia: Dendrobatidae), based on mitochondrial 16S and 12S ribosomal RNA gene sequences. – Molecular Phylogenetics and Evolution 15: 34-40.
• Beheregaray, L. et al 2004 Giant tortoises are not so slow: Rapid diversification and
• biogeographic consensus in the Galapagos.  PNAS 101 (17): 6514-6519.
• Malhotra, A. & R. Thorpe 2000 A phylogeny of Trimeresurus group of pit vipers: new evidence from a mitochondrial gene tree. Molec. Phylogenetics and Evol. 16:199-211.
• Sanders, K. et al 2004 Ecological diversification in a group of Indomalayan Pitvipers (Trimeresurus): Convergence in taxonomic important traits has implications for species identification. J. Evol. Biol. 17: 721-731.
• Alfaro, M. & S. Arnold 2001 Molecular systematics and evolution of Regina and Thamnophline snakes. Molec. Phylogenetics. & Evol. 21:408-423.
• Queiroz, A. et al. 2002 Phylogenetic relationships of  N. American garter snakes (Thamnophis) based on four mitochondrial genes: How much DNA is enough? Molec. Phylogenetics & Evol. 22:315-329.

November 22 – Papers to read and discuss:

• Grant, P. & R. Grant. 1996. Speciation and Hybridization in Island Birds. Phil. Trans.: Biol. Sci. 351: 765-772.
• Coyne, J. & T. Price 2000. Little evidence for Sympatric Speciation in Island Birds. Evolution 54(6): 2166-2171.
• Grant, PR. 1968  Bill size, Body size and the ecological adaptations of bird species to competitive situations on islands. Systematic Zoology, Vol 17, No 3 (Sept. 1968) 319-333.
• Avise, J. C. & D. Walker 1998. Pleistocene Phylogeographic Effects on Avian Populations and the Speciation Process.  Proc. Roy. Soc.. Lond. B. 265: 457-463.
• Baker, A. J. et all 1995. Flightless Brown Kiwis of New Zealand Possess Extremely Subdivided Population Structure and Cryptic Species Like Small Mammals. PNAS 92: 8254-8258.
• Cann, R. L. 2001. Genetic clues to dispersal in human populations: Retracing the past from the present. Science 291(5509): 1742-1748.

November 29 – Term Paper Presentations

December 6 – Term Paper DUE - Term Paper Presentations

December 13 – Final Exam