AMNH-RGGS Elective Course

Course Title: The Tree of Life and Invertebrate Zoology

Proposer/Lead Instructor Name: Rob DeSalle (RD; Professor RGGS and Curator AMNH)

 

Other Course Instructor(s): Bernd Schierwater (BS; Professor TIHO, Hannover Germany and Research Associate, AMNH); Heike Hadrys (HH; Professor TIHO, Hannover Germany and Research Associate, AMNH).

 

Course Description: The course will take a modern and multidisciplinary approach to the study of Invertebrate Zoology, integrating classical anatomy, modern genomics and evo-devo. The course will cover all of the major invertebrate animal phyla (excluding protists) and use phylogenetic matrices to organize the anatomical and sequence information for each of the greater than 30 phyla we will focus on.

 

Duration in weeks: 4

 

Number of lectures/seminars/meetings per week: 2

Lecture/seminar/meeting length per session (min.):

2.0 hours each lecture (total = 16 lecture hours in the classroom lecture)

Number of labs per week: 1

Lab length per session (min.):

4 hrs each lab (total = 16 hours in the classroom lab)

            Anticipated commitment to class projects:

                       Total 60 hours

 

Credits:  2:

 

Location: RGGS Laboratory 5th floor RGGS facility                                                   

Prerequisites: College Biology

                                                                                    

Learning Objectives:

  • The primary objective is to increase the student’s knowledge of the diversity of invertebrates using the greater than 30 phyla of animal invertebrates as a guide
  • The student will become familiar with the phyla that are commonly encountered, and be able to understand the anatomical characters that are used to diagnose these phyla.
  • The student will utilize phylogenetic matrices comprised of both anatomical and molecular characters to understand the evidence available for the organization of invertebrates.
  • The student will gain an integrated understanding of invertebrate phylogeny and biology.

Bibliography:

Textbook: Invertebrate Zoology: A Functional Evolutionary Approach [Hardcover]

Edward E. Ruppert, Richard S. Fox and Robert D. Barnes

Class notes: each student will receive detailed notes on anatomical analysis of each phylum. These notes come from teaching notes from DeSalle and Schierwater.

 

Assigned papers: Examples of assigned papers are:

Werren JH, Baldo L, Clark ME: Wolbachia: master manipulators of invertebrate biology. Nature Reviews Microbiology 2008, 6(10):741-751.

  1. Sarda, J. Zeng, B.G. Hunt, S.V. Yi, 2012. The evolution of invertebrate gene body methylation Mol. Biol. Evol., 29 (2012), pp. 1907–1916.
  • J. Swalla, A.B. Smith, 2008. Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives. Philos. Trans. R. Soc. Lond. B Biol. Sci., 363 (2008), pp. 1557–1568.

Rota-Stabelli O., Kayal E., Gleeson D., Daub J., Boore J., Pisani D., Blantor M., Lavrov D. V. 2010 Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda. Genom. Biol. Evol. 2, 425–440. (doi:10.1093/gbe/evq030)

Erwin, D. H., Laflamme, M., Tweedt, S. M., Sperling, E. A., Pisani, D., and Peterson, K. J.

(2011). The Cambrian conundrum: Early divergence and later ecological success in the

early history of animals. Science 334, 1091–1097.

Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, et al. (2009) Phylogenomics revives traditional views on deep animal relationships. Curr Biol 19: 706–712. doi: 10.1016/j.cub.2009.02.052.

Wörheide G, Dohrmann M, Erpenbeck D, Larroux C, Maldonado M, et al. (2012) Deep phylogeny and evolution of sponges (Phylum Porifera). Adv Mar Biol 61: 1–78.

A more comprehensive list of assigned papers will be compiled prior to the execution of the course.

Grading/Evaluations Basis: The class grade will be based on attendance and on performance on the individual projects assigned to them (see below).

Final Exam/Project Description: Each student will be assigned at least five phyla for the duration of the course. The projects will involve compiling and curating character matrices using both anatomy and molecules for each of the five phyla assigned to them. As well, each student will compile a bibliography of relevant phylogenetic literature for each phyla assigned and complete the assignment with a written assessment of analysis of their compiled matrices with the literature. These written assessments should be no longer than 1500 words per phyla.

 

Statement on Academic Integrity: Each graduate student bears the responsibility to observe traditional canons of scholarly discourse, scientific research, and academic honesty. Plagiarism, cheating, and fraud in research will not be tolerated. Accordingly it is expected that students work individually unless specifically instructed to work in groups. The full Academic Integrity policy is in the student handbook.

 

 

Student Evaluation: Each student is required to complete an anonymous course evaluation at the end of the term. The course evaluation is a tool for faculty and administrators to improve the student learning experience.

Lecture #

Date

Topic

Hours

                       

1

MON

3/21/16

9am-11am

Invertebrates and Systematics; How We Examine Invertebrates (RD)

2

 

 

 

 

 

                       

2

WED

3/23/16

9am-11:30am

Protostomia-Ecdysozoa (HH)

2.5

 

 

 

 

 

                       

3

FRI

3/25/16

9am-11:30am

Arthropoda, Pterygota, Odonates (HH)

2.5

 

 

 

 

 

                       

4

MON

3/28/16

9am-11am

Protostomia-Lophotrochozoa (BS)

2

 

 

 

 

 

                       

5

WED

3/30/16

9am-11:30am

Flatworms; Deuterostomia (BS)

2.5

 

 

 

 

 

                       

6

FRI

4/1/16

9am-11:30am

Base of Metazoa: Placozoa, Porifera, Cnidaria (all classes), Ctenophora (BS)

2.5

 

 

 

 

 

                       

7

MON

4/4/16

9am-11:30am

EVO DEVO and IZ (RD)

2.5

 

 

 

 

 

                       

8

WED

4/6/16

9am-11:30am

Synthesis and Summary (RD)

2.5

 

 

 

 

 

           

Total = 19 hours

         
                       
                       
                         

 

Lab #

Date

Time

Topic

Hours

                       

1

MON

3/21/16

1:15pm-5:15pm

Basic Classification and Invertebrate Morphology - Cell Types; How to score characters in invertebrate zoology; phylogenetic methods (RD)

4

         
                   

2

FRI

3/25/16

1pm-5pm

In lab identification of Ecdysozoa (HH)

4

         
                       

3

MON

4/4/16

1:15pm-5:15pm

In lab identification of Lower Metazoa (BS)

4

         
                       

4

MON

4/11/16

1:15pm-5:15pm

In lab identification of Lophotrochozoa and

Deuterstomes without backbones (BS)

4

         

                                                                                                         Total lab hours = 16

 

Appendix 1. A detailed synopsis of course proposal

The Tree of Life and Invertebrate Zoology

 

Course Instructors: Rob DeSalle (Curator, AMNH), Hieke Hadrys (Research Associate, AMNH) and Bernd Schierwater (Research Associate, AMNH)

 

The course will be an intense month long minicourse, that will be for 2 credits. We have divided the course into four sections, corresponding to the four weeks the course will run. There will be one lecture and one lab per week. Each lecture will be three hours long and each lab will be three hours long (for a total of 24 in class or in lab hours). This uniqueness of the course will lie in its use of morphological and molecular characters to interpret the major groups of invertebrates on the planet. At the end of week two of the course, each student will choose a well defined monophyletic phylum or a well defined group of phyla and compile a phylogenetic matrix for the taxa in their chosen group. They will then rigidly analyze their matrices and extensively compare these to the published record on their chosen group. We hope that this exercise will lead to meaningful treatments of several invertebrate groups that will add to our knowledge of invertebrate zoology.

DeSalle, Hadrys and Schierwater will share lectures and lab duties and both will attend all lectures and lab exercises. DeSalle will focus on the molecular evidence while Schierwater will focus on the morphological evidence for each group.

The lectures will consist of a mixture of slide shows and computer exercises. The labs will consist of examining specimens and identifying characters of interest. We envision no requirements for the course except for perhaps basic systematics and phylogenetic analysis.

Textbook: Invertebrate Zoology: A Functional Evolutionary Approach [Hardcover]

Edward E. Ruppert, Richard S. Fox and Robert D. Barnes

Section I. The Basics of Invertebrate Systematics

Lectures 1 and 2. Invertebrates and Systematics

Our discussion of systematics will include detailing how morphology and molecules have been used to accomplish systematics and construct a tree of life. Since the thrust of the text is to explain diversity within the context of systematics, we will also discuss the various methods used to construct phylogenetic trees in this chapter. While we do not expect to fully discuss systematic analysis in this lecture, we will present some detail because subsequent lectures will require a strong basis in how phylogenies are constructed.   In this context we will discuss the dichotomy of molecules versus morphology and the concept, methods and pitfalls of data concatenation. The specific nuances of phylogenetic analysis that accompany large numbers of taxa and genome scale data sets will also be. Some very basic exercises will accompany the lecture to show how programs are used to create phylogenies.

Lab 1. How to Examine Invertebrates

This lab will detail and outline how we will proceed with the 36 invertebrate phyla that we intend to cover in the course. Specifically we will detail for each phylum the following

- number of known species, size range, habitat range         

- diagnostics and autapomorphies

- terminology

- Morphology and Anatomy

- Reproduction

- Physiology

- Ecology (including economic importance)

- Genetics

- phylogenetic position

molecular vs. traditional interpretations

- taxonomy and systematics (down to the order level)

molecular vs. traditional interpretations

  • open taxonomic and systematic questions

For each phylum we will also create a matrix of anatomical chatacters as well as a DNA sequence matrix that the student can manipulate with phylogenetic analysis programs. This lab will detail to the student how such matrices are produced and how they are analyzed. These matrices will allow the student to explore the evolution of characters within each of the phyla we will examine in the rest of the course, so we will spend some time showing the student how such analyses proceed.

Section II.   Invertebrates and the Base of the Tree of Life

Lectures 3 and 4. Higher Classification- Lower Metazoa and Diploblasts

This lecture will discuss the basics of higher classification to describe the placement of invertebrates in the tree of life. Specifically we will discuss the 3 domain system of classifying cellular life (Archaea, Bacteria, Eukarya). To discuss Eukarya we will separate these organisms into the various higher level Regna – Metazoa (monophyletic), Plantae (monophyletic), Fungi (monophyletic) and Protista (not monophyletic. Once this classification has been delivered we will delve into the Metazoa and use the following scheme to proceed with the lecture.

Regnum Metazoa

            Division Diploblastic Animals

                       Introduction Para-/Eumetazoa

                      Cnidaria, Porifera, Ctenophora. Placozoa

            Division Bilateria (Triploblastic Animals)

                       Introduction Proto-/Deuterostomia

                       Introduction Ecdyso-/Lophotrochozoa

Lab 2. Lower Metazoa and Diploblasts

Each lecture will be comprised of a discussion the elements listed above we will list only subject Phyla for the lab units to follow.

Porifera

Placozoa

Cnidaria

Ctenophora

Choanoflagellata:

 

Section III.  Major divisions of higher invertebrates

Lectures 5 and 6 Protostomes –Ecdysozoa

The phylogenetic placement of invertebrate taxa of Protostomes has been examined at length by many authors. In this introductory lecture, we will describe the evidence for monophyly of protostomes, discuss the developmental biology of this large group and discuss the division of the group in to its two major lineages Lophotrochozoa and Ecdysozoa as well as several enigmatic taxa that are difficult to place in this context.

Lab 3. Protostomes - Ecdysozoa

Arthropoda, Onychophora and Tardigrades

Maxillopoda

Nematoda

Minor Ecdysozoan Phyla (Kinorhyncha, Nematomorpha, Priapulida and Loricifera)

Unplaced Protostome Phyla (Rotifera, Chaetognatha, Platyhelminthes,

Cycliophora, Gnathostomulida, Gastrotricha)

Section IV. Lophotrochozoa - Deuterostomes and Summary

Lectures 7 and 8. We will conclude the lecture part of the course with a detailed discussion of Deuterstomes and delve into such topics and Dorsal ventral inversion, development of the nervous system and phylogenetic relationships. In this lecture we will also take the opportunity to briefly summarize the pervious 26 chapters and to posit some interesting subjects that we feel will become important for the further and future study of Invertebrate Zoology. The students will also use part of this lecture period to present the results of their projects.

 

Lab 4. Lophotrochozoa and Deuterostomes Without Backbones

Sipuncula

Mollusca and Polyplacophora.

Annelida

Bryozoa,

Brachiopoda and Phoronida

Minor Lophotrochozoan Phyla (Entoprocta, Nemertea)

Echinodermata, Xenoturbellida, Hemichordata, Pterobranchia, Acoelomorpha

A Brief and Concise treatment of Vertebrata

The students will also use part of this lab period to summarize their projects.

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