Topics in Zoology: Integrative Taxonomy with an Emphasis on Squamata

ZOO 397806, Semester 1, March–August 2016
F, 2-6 pmEnyalius_bilineatus
Departamento de Zoologia, Universidade de Brasília

 

“The first step to wisdom is getting things by their right names.” – Chinese Proverb quoted by Edward O. Wilson in Naturalist.

Enyalius bilineatus; Photo credit: Guarino Colli.

Instructors and Office Hours:

  • Dr. Justin C. Bagley; E-mail: jcbagley (at) unb.br; Office Hours: Wednesdays from 12:30-2:30 pm, or appointment by e-mail.
  • Dr. Maria Florencia Breitman; E-mail: breitman (at) unb.br. Office Hours: Tuesdays from 1:00-2:40 pm, or appointment by e-mail.
  • Dr. Fabricius M. C. B. Domingos; E-mail: fabricius (at) unb.br. Office Hours: Thursdays from 4-6 pm, or appointment by e-mail.
  • Dr. Helga Wiederhacker; E-mail: helgawied (at) unb.br. Office Hours: Mondays from 4-6 pm, or appointment by e-mail.

Office Hours:   Instructors will hold their office hours prior to class, or by appointment (e-mail the instructors to set up a meeting in person or via Skype call), in the Coleção Herpetológica (CHUnB), initially for ~2 h/week, and later modified according to the needs of the students.

I. Course Description: Taxonomy is the field of biology concerned with discovering, naming, describing, and classifying organisms. Taxonomic classifications provide a means of communicating and storing information about species, which are the fundamental components of biodiversity. As such, taxonomy forms the basis of all studies in ecology, systematics, biogeography, and conservation biology. Taxonomy has a longstanding history dating back to the 17th and 18th Centuries, and the majority of alpha taxonomy work (species descriptions) have been conducted based on comparisons of morphological data gathered from specimens, including continuous measures and meristic counts of anatomical structures. However, alpha taxonomy has now evolved to incorporate a variety of data types, including molecular (genetic), ecological, behavioral, and physiological data from individuals of different species. This change towards an ‘Integrative Taxonomy’ has emerged in association with paradigm shifts in our concepts of the nature and classification of species. To-date, taxonomists have described an estimated 1.78 million species; however, the number of species probably in existence on Earth today is estimated to range from 5 to 30 million species! During this course, students will learn the principles and practices of Integrative Taxonomy, including how to integrate different sources of evidence to describe independent evolutionary lineages as new species. By collaborating with the instructors, students will develop a species description project involving gathering morphological data and combining those data with information from DNA sequences and ecology in an integrative taxonomy framework. This course will promote the use and value of scientific collections, and will also use approaches to teaching, course development, and research based in the spirit of the scientific method.

 A. Class Size: This course is designed for 15-20 undergraduate, postgraduate, and/or graduate students.

B. Course pre-requisites: We will teach a variety of the principal statistical methods used to delimit and test hypotheses of species limits, e.g. using simulations and multivariate statistics. We will also teach students how to integrate a variety of data types. As a result, it is recommended that students have good general background knowledge of biology and ecology, as well as basic statistics.

II. Course Fundamentals and Learning Objectives: 

reptileclade2A. Fundamentals: why study Integrative Taxonomy?  All biodiversity studies depend on the naming and classification of organisms. In light of the on-going biodiversity crisis and Sixth Extinction (Anthropocene) wrought primarily by increased human exploitation of natural resources, taxonomy is now more important than ever. A key challenge in biology has been and remains to be achieving taxonomic classifications that reflect phylogenetic relationships. However, an equally important goal of taxonomy is to rapidly and objectively detect or delimit, and describe, new species and place them within existing taxonomic classifications. Integrative Taxonomy provides a means of addressing both of these issues, and thus has important implications for 1) facilitating accurate biodiversity accounting, 2) developing conservation and management strategies, 3) predicting species responses to climate change, and 4) understanding factors responsible for the assembly and diversification of biotic communities (this is broad, e.g. including facilitating community phylogenetic or comparative evolutionary studies). 

B. Learning goals: 

  1. Understand the complexity of the problem of developing a concept of species, and utilize the General Lineage Concept of species.
  2. Understand fundamental concepts of speciation, cladogenesis, and anagenesis.
  3. Understand the difference between the discovery and description (i.e. “formalization”) of species, as well as their value in the light of the ongoing biodiversity crisis.
  4. Understand the origins and bases of classical and integrative taxonomy.
  5. Learn to score and/or measure morphological variation in lizards deposited in the Coleção Herpetológica da Universidade de Brasília (CHUnB).
  6. Use appropriate statistics to quantify the differences between morphological variables across populations and species.
  7. Learn to use statistical tools to compare the values of morphological characters between closely related lineages of lizards.
  8. Understand the difference between diagnostic characters and characters that are not diagnostic.
  9. Use integrative taxonomy to describe species.
  10. Understand the different parts of an article on the description of a new species.
  11. Collaborate with other researchers to produce a species description for a new species.
  12. For students to think critically, be skeptical, and make arguments from their naturally differing points of view.

C. Learning outcomes: 

  1. The students will be able to define and contrast different species concepts.
  2. The students will be able to define and explain the General Lineage Concept of species.
  3. The students will be able to evaluate the specific status of lineages using the General Lineage Concept.
  4. The students will identify lineages that could be classified as candidate species but are not presently formally described.
  5. The students will discuss and argue on the necessity of describing new lineages.
  6. The students will be able to explain the origin of taxonomy and the necessity of classification.
  7. Students will be able to synthesize the theoretical bases of Integrative Taxonomy and compare them to those of classical taxonomy.
  8. Students will evaluate the relevance of different morphological characters for differentiating species.
  9. Students will carefully handle preserved material deposited in herpetological collections, without allowing specimens to be affected by dessication or damaged during handling.
  10. Students will be able to use different equipment and instruments to make qualitative and quantitative measurements to characterize variation in morphological characters of different lineages of lizards (deposited in CHUnB).
  11. Students will develop technical abilities in analyzing, interpreting, and synthesizing data.
  12. Students will be able to decide on the appropriate statistical analyses to be used, and which data need to be analyzed.
  13. Students will be able to use software programs and algorithms to statistically evaluate the variation of morphological characters between lineages.
  14. Students will be able to describe the principles and concepts of taxonomy using appropriate (professional) vocabulary.
  15. The students will be able to outline the different sections required in a valid description of species.
  16. Students will be able to analyze and present morphological data and integrate them with the results of molecular (DNA) and ecological studies.
  17. The students will expand upon their own knowledge, previous experiences, and intellectual abilities. They will do this by criticizing positions of colleagues that agree and disagree with them.
  18. Students will write summaries of the methods used and results obtained during their research project.
  19. Students will analyze and discuss the implications of their results and their relation to different aspects of the Brazilian biota (e.g. Cerrado diversity, biogeography, and ecology).
  20. Students will aid one another in mutual intellectual development.
  21. Students will be able to present critical arguments of concepts, ideas, and writing of others.

III. Course Procedures: 

A. The in-class dynamic: During the semester, we will have 15 obligatory class meetings each four hours in length. Each class will be divided into four 50-minute periods, or “blocks”, broken up by breaks that will be 10, 20 and 10 minutes in length, respectively. The last two blocks of each class (at least) will be reserved for taking (and analyzing) morphological data from specimens. During the breaks, the students should leave the classroom. 

The students will be divided into four groups that will participate by gathering different datasets for the research project (see details below); these groups will be randomly chosen, except we will ensure a balance of experienced and less experienced students, and that at least one graduate student is present in each group. During each class meeting, one group of students will be responsible for bringing the specimen material, gloves, etc. from CHUnB. These students will need to meet in CHUnB at ~1:40 pm to help one another separate and transport materials for the class to the classroom (with Fabricius’ help), and they should also help return/organize the material back to the collection after class has concluded.

Each class will have theoretical and practical components. The lessons were planned using the theoretical framework of Scientific Teaching, in which learning is based in the nature of scientific, including discovery, scientific questioning and skepticism, and experimentation. Each lesson will align clear and significant learning objectives with measurable learning outcomes based on the levels of learning proposed in Bloom’s Taxonomy. Also, all classes will be student-centered and will include activities and appropriate and continuous assessments.

Written work prepared by students must be based on the student’s ow ideas, presented in sentences and paragraphs written in university-level Brazilian Portuguese. When appropriate, students will reference the ideas and work of others, but this material should be complementary to the work of students (and not replace the students’ work). Where used, the material of others must be clearly identified and accompanied by appropriate in-text citations and bibliography.

B. Behavior and notes on PowerPoints: Our classroom will be an environment free from discrimination of any kind, and we will place a premium on respect for students, teachers, and other living organisms at all times. Students and instructors alike must comply with rules for the use of the laboratory, and everyone in the classroom must be mutually responsible for safety and ensuring that the course rules and laboratory rules are being followed. Because we are mature learners, all cell phones should be turned off throughout class time. Regarding course content, notes based on the text of PowerPoint slides and multimedia material used during lectures will be made fully available to students and can be used as notes or starter material for study guides. Our slides do not cover all of the material that we discuss in class. Our PowerPoint slides do not include all of the material that you will be tested on. Also, some concepts will not be presented using PowerPoint (but will be in the readings or written on the board), and this is where college note-taking skills come in handy (or, if lacking, must be developed).

 

IV. Course Requirements:  

A. Class attendance and participation policy: We encourage students to attend and participate in every class meeting, as we consider this in their best interest for a variety of reasons. In particular, the classes are planned with activities that facilitate student learning, and we will score student participation during discussions and lab blocks during each class and these scores will contribute to students’ final grades in the course. It is important to emphasize that students that attend class generally perform better and receive higher grades than those that do not; and, in particular, students who attend classes with a scientific teaching format using active learning techniques tend to perform 1.5 times better than those who attend traditional lecture classes. Each student’s participation, involvement, studying habits, and curiosity are reflected their final grades. We hope that our students understand the material, rather than simply memorizing, although there will be a certain amount of specific and technical concepts and terminology that students must commit to memory. Studies show that everyone present in a university science class, including the students and the instructors, benefits from discussion and participation during class. Thus, we encourage our students to participate and ask all of their intriguing questions about biology and taxonomy, because all questions are good questions. The only bad questions are those that are never asked! So, we hope students will always share their curiosity with the whole class!

In accordance with the rules of the Universidade de Brasília, students must attend at least 75% of class meetings in each course, and an attendance of less than 75% of class periods will result in failure of the course. As a result, students must attend classes and are only allowed to have one unjustified absence during the semester (and three absences total); a subsequent absence above 75% will result in a failing final grade. It is obligatory for all students to be present during each exam (Exam I, Exam II, and the Oral Presentation); however, students will be allowed to re-take exams they miss if the student can provide suitable justification for their absence using the appropriate documents (e.g. signed medical doctor’s statement or hospital records). As the final two blocks of each class will be used to work on the class research project, students who are not able to attend because they have another course or OK’d field outing to attend during the period of the last two blocks (between 4-6 pm) must arrange extra times with the instructors to make up their hours lost measuring specimens while absent from class. Four Saturdays, including the dates of April 2nd, April 16th, April 30th, and May 7th shall be reserved for meetings in the classroom devoted solely to measuring morphological characters for the project. The instructors will decide when to hold Saturday class sessions, and while we may not meet on all of these dates, student attendance will be compulsory for all Saturday sessions decided on by the instructors.

Students are also encouraged to use all resources available to them, and one important way of doing this is to attend the instructors’ office hours. During office hours, we are going to be in our office in CHUnB, and we hope that the students come to divulge any doubts, seek clarifications on the material or assignments, and/or exchange ideas about the class and the research project. Students should also use office hours to seek instructor help in “catching up” on course content if they should miss any class meeting.

B. Readings and texts:
As we progress through the course, students will have regularly assigned readings. PDF files of readings will be made available on the UnB Moodle website (part of the Aprender web) and should be downloaded and read prior to the lectures or Discussion sessions specified on the Syllabus (available here and on Moodle). Here is a list of some of the articles that have been selected for course readings:
Dayrat, B. 2005. Towards integrative taxonomy. Biological Journal of the Linnean Society, 85:407–415.
De Queiroz, K. 2007. Species Concepts and Species Delimitation. Systematic Biology, 56:879–886.
Padial, J.M., Miralles, A., Da Riva, I., Vences, M. 2010. The integrative future of taxonomy. Frontiers in Zoology, 7:16.
Pante, E., Schoelinck, C., Puillandre, N. 2015. From Integrative Taxonomy to Species Description: One Step Beyond. Systematic Biology, 64(1):152–160.

Recommended text: Winston, J.E. (1999) Describing Species: Practical Taxonomic Procedure for Biologists. Columbia University Press, New York. One copy is available from the instructor.  Buy it on Amazon.  

C. Research project: Students will work in groups (see below) to develop part of the morphological database used for a collaborative research project validating and describing a new/candidate species of lizard. Here, the students will apply the practical and theoretical knowledge they learned during the course. For this project, students will be responsible for measuring the morphological characters that are assigned them on all specimens included in the study. The same measurer or “observer” will collect measurements of the same variables for all specimens, so there can be no exchange of variables between students. The students will handle specimen material and laboratory equipment in a responsible and careful manner while working on the research project. Students will record the data for their variables for each specimen using pencil and paper, and all data will subsequently be digitized/input into an Excel spreadsheet containing the morphological database.

The students will be divided into four groups and each group will be facilitated by one instructor. The group facilitator will help students stay “on the right path” throughout their group learning experiences. The central goal of the facilitator will be to assist students and student groups to achieve goals on an appropriate timeframe; however, the facilitator will not be a part of the group, micromanage the group, or organize tasks in the group. The facilitator is not a leader. Each member of the group, regardless of their academic training or experience level, is responsible for the project and for maintaining dynamic interactions and organization of the group.

It is important that we finish measuring morphological on or before the date of May 7, 2016. After this date, each group will analyze its results qualitatively and quantitatively by organizing their data and selecting appropriate statistical tools for the analysis. Each group will need to interpret and compare their results with those of previously published studies. After the project is completed, results will be presented in written and oral format. The write up of results must include the following sections in a Microsoft Word document (or other similar format compatible with Word): Title, Names of the Authors, Summary (max. 200 words), Introduction, Materials and Methods, Results, Discussion and References (including bibliographic details for all references cited in the main text). Students will submit their papers for a first round of revision on June 10, 2016. After 5 days, the students will receive the suggestions/corrections of their papers. The final revisions of each paper will be due, in Word format, on July 1, 2016, without exception, and the oral presentations will be conducted starting the same date. Oral presentations should be accompanied by PowerPoint slides and may not exceed 30 minutes. Each oral presentation will be evaluated by student colleagues, instructors and other invited professors. The oral and written presentation of student work will be formally assessed and will form part of the final grades of students (details below).

We expect that the students will work together with the respective instructor-facilitator, and with other instructors as needed, throughout the course. Also, we remind students that the instructors will be performing other tasks during class and outside of class, and thus we may not be available at the last moment. Therefore, it is expected that the students work in an organized way valuing group cohesiveness and respecting the time of others.

 

V. Grading

A. Grading criteria: Student grades will be assigned based on performance on:

Written Paper (Research Project)

30% [deadline for first submission, and final submission]

Oral Presentation (Research Project)

15% [final class period]

Exam 1

15%

Exam 2

15%

Participation Grade

10%

Homework and In-class Activities

15%

VI. Academic Honesty/Plagiarism Statement: Each student in this course is expected to abide by the Universidade de Brasília policies for academic integrity. Any work submitted by a student in this course for academic credit will be the student’s own work. For this course, collaboration is allowed in all non-graded aspects of the course; this course is, in fact, a collaborative effort among us all; however, no collaboration is allowed on graded assignments.

Plagiarism, the use of others’ words or ideas without proper attribution, is an impediment to your education and to the educational mission of the university. Work that has been plagiarized must receive a failing grade.  However, there is a difference between unintentionally plagiarized work, which must be corrected in order to be considered for a passing grade, and intentional plagiarism, which will require a disciplinary action on the part of the university. Because plagiarism is not always a “black and white” issue, it is recommended that students speak to their instructor if they have questions about avoiding plagiarism. External resources on plagiarism include http://www.plagiarism.org.

VII. Accommodations for students with disabilities: In compliance with UnB policy and equal access laws, if you have any disability that may impair your ability to successfully complete this course, please let the instructors know and they will send you to the correct university department to assist you. Academic accommodations are granted for all students who have qualified disabilities. Services are coordinated with the student and instructor by the Accessibility Services Department, and I must have a letter from their office to give you accommodations. We ask that students to please make requests for academic accommodations within the first two weeks of class, if possible.

VIII.  Diversity Statement
We understand that our members represent a rich variety of backgrounds and perspectives. We and the Department of Zoologia are committed to providing an atmosphere for learning that respects diversity. While working together to build this community we ask all members to:

  • share their unique experiences, values and beliefs,
  • be open to the views of others,
  • honor the uniqueness of their colleagues,
  • appreciate the opportunity that we have to learn from each other in this community,
  • value each other’s opinions and communicate in a respectful manner,
  • keep confidential discussions that the community has of a personal (or professional) nature,
  • use this opportunity together to discuss ways in which we can create an inclusive environment in this course and across the UnB community.

IX. Class Schedule: 

We will do everything we can to stay on the following schedule throughout the course:

Date

Class Topic

Reading

3/11/2016

Welcome to Topics in Zoology!

3/18/2016

Practical and Discussion

3/25/2016

Holiday – NO CLASS

4/1/2016

What is a Species?

4/2/2016

Possible Saturday session (to catch up with measurements)

4/8/2016

Practical and Discussion

4/15/2016

Why Should We Describe Species?

4/16/2016

Possible Saturday session (to catch up with measurements)

4/22/2016

Classical Taxonomy to Integrative Taxonomy: A Historical Perspective

4/29/2016

EXAM 1

4/30/2016

Possible Saturday session (to catch up with measurements)

5/6/2016

We Have the Data, Now What? Cleaning Data – Watch Out!

5/7/2016

Possible Saturday session (to catch up with measurements)

5/13/2016

Why and How Should We Use Statistics to Describe Species?

5/20/2016

Super Statistics! Intro. to Multivariate Statistics

5/27/2016

Holiday – NO CLASS

6/3/2016

Integrating Morphology, Ecology, and Genetics in Taxonomy (Research Project Pre-submission deadline)

6/10/2016

Structure of a Scientific Paper + EXAM 2

6/17/2016

Nomen calatus (Taxonomic Nomenclature)

6/24/2016

Oral Presentations (Final Research Project paper submission deadline)

We will do everything we can to have an awesome experience in this class!

XI. Additional Resources and Readings on Integrative Taxonomy 

[LIST HERE]

 

XII. Student Research Project Group Assignments

GROUP 1:
Anandha de Almeida Silva
Gabriela Carvalho Santos
Isabella Monteiro Gomes da Silva
Tayná Ferrari
Vitor Hugo Gomes Lacerda Cavalcante
Facilitator: Helga
Dates responsible for specimen/lab material: 4/15, 5/6, (5/7)*, 6/3, 6/24

GROUP 2:
Ângela Vilela Camargo Talarico
Gabriela Ferreira Rodrigues
Ingrid Pinheiro Paschoaletto
Tarcisio Lyra dos Santos Abreu
Thiago Marques de Lima
Facilitator: Justin
Dates responsible for specimen/lab material: (4/2)*, 4/8, 4/29, 5/20

GROUP 3:
Ana Cecilia Holler Del Prette
Anderson Kennedy Soares de Lima
André Costa Pereira
Gabriel Caputo de Carvalho
Facilitator: Flor
Dates responsible for specimen/lab material: 4/1, (4/16)*, 4/22, 6/17

GROUP 4:
Carlos José da Silva Morais
Caroline Azevedo Matias
Izabella Paim de Melo Costa da Silva
João Álvaro Lima Pantoja Leite
Facilitator: Fabricius
Dates responsible for specimen/lab material: 3/18, (4/30)*, 5/13, 6/10, 7/1

*Possible Saturday session Sábado, in case we need to work extra days to complete morphological data generation.