Biology 440

Due date for final paper: Monday December 3rd at 4:00 pm in my office (Rm. 4428 Biosciences) or my mailbox in the main Department of Biology office. Remember to afix your graded outline to you paper.


Tutorial Peer Evaluation Sheets | HERE |

Handout for Group Phylogenetics Exercise provided | HERE |

Guidelines for Critical Review outline | HERE |

Phylogenetics Project Peer Evaluation Sheets | HERE |

Marking Rubric for Critical Review | HERE |

Biology 440 Laboratory

Week starting … Activity
Mon. Sept. 10 Introduction, overview of lab goals, assignment to student groups, and assignment of papers for individual tutorials.
Mon. Sept. 17 Open Lab. Preparing for your individual presentations. Bring questions about your articles
Mon. Sept. 24 Student Individual Tutorials. Groups A, B and C.
Mon. Oct. 1 Student Individual Tutorials. Groups A, B and C.
Mon. Oct. 8 No labs. Please do meet to chat about your phylogenetic project possibilities.
Mon. Oct. 15 Student Individual Tutorials. Groups D, E, and F.
Mon. Oct. 22 Student Individual Tutorials. Groups D, E, and F.
Mon. Oct. 29 Phylogenetics practicum.
Mon. Nov. 5 Open lab for work on group phylogenetics projects.
Mon. Nov. 12 Oral presentation of group phylogenetic proposals (see below). All groups. Note that the outline for your critical review is due Monday October 29th at 4:00 pm
Mon. Nov. 19 Presentations for Phylogenetics Group Exercise. Groups A, B and C.
Mon. Nov. 26 Presentations for Phylogenetics Group Exercise. Groups D, E and F.

Individual Tutorial (worth 15% of your final grade): A key objective of this course is to illuminate major issues in speciation and macroevolution by exploring recent primary literature. We thus ask each student to read a peer-reviewed journal article (selected in the first lab period, with student names to be posted below) and present the major findings in a brief (15 minute + 5 minutes of questions) oral presentation. The subjects of these articles relate roughly to the order of topics presented in lecture. Note that you should read these articles thoroughly soon after you choose them so that you may come to the second week’s sessions armed with questions.

The presentations based on this article should include a clear summation of the context and importance of the research undertaken (i.e. how does it fit onto the broader framework of understanding biodiversity origins and overarching evolutionary patterns), a concise statement of the objectives and methods used to address them, and a succinct statement of the major findings of the paper. You will wish to read some of the antecedent papers cited by the authors, or other papers by the same authors to augment your insights. Remember to start broadly and NOT with “My paper is by …” or “The title of my paper is …” Time limits will be strictly enforced so that we do not run late (i.e. practice your presentation at least once before coming to class). Presentations should include approximately 15 PowerPoint slides.

A few pointers for the PowerPoint slides:

Click | HERE | to access a pdf version of the TUTORIAL MARKING SHEETS required for each presentation.

Tutorial Schedule

We provide some ideas for emphases in your presentation in parentheses after the article title but these are simply suggestions that you need not (and should not) slavishly adhere to. As we imply above, you are encouraged to 1. add to or enrich these themes, and 2. read other related articles to facilitate your understanding and presentation. Below in the second and third columns, I will paste your names after we have decided. Click on the links to go to the relevant journal web sites.

Week starting … Monday aft Wednesday aft Journal Article
Mon. Sept. 24 1. TBA



2. Emma Douglas



3. Michelle Cohen



4. Hayden Wainwright



5. Hana Thompson



6. Mansuba Rana




2. Liying Xu



3. Yona Traubici



4. Liam Joiner




5. Emma Sinclair



6. TBA

1. Haggerty & Hinsdale. 2017. Distinct biogeographical patterns of marine bacterial taxonomy and functional genes. Global Ecology and Biogeography 26: 177-190. [importance of taxonomy evaluation of biogeographic hypotheses]

2. Cicconardi, Fanciulli & Emerson. 2013. Collembola, the biological species concept and the underestimation of global species richness. Molecular Ecology 22: 5382-5396. [cryptic diversity, quantification of species richness]

3. McKay & Zink. 2015. Sisyphean evolution in Darwin’s finches. Biological Reviews 90: 689-698. [conflict among species concepts versus traditional taxonomy, re-evaluation of a class example of adaptive radiation]

4. Boucher, Zimmermann & Conti. 2016. Allopatric speciation with little niche divergence is common among alpine Primulaceae. Journal of Biogeography 43: 591-602. [evidence for allopatric speciation, consequences for phenotypic divergence]

5. Spurgin et al. 2014. Genetic and phenotypic divergence in an island bird: isolation by distance, by colonization or by adaptation? Molecular Ecology 23: 1028-1039. [the role of founder effects in speciation]

6. Bono & Markow. 2009. Post-zygotic isolation in cactophilic Drosophila: larval viability and adult life-history traits of D-mojavensis/D-arizonae hybrids. Journal of Evolutionary Biology. 22: 1387-1395. [evidence for reinforcement in speciation]

Mon. Oct. 1 1. TBA



2. TBA



3. James MacKay



4. Kassia Regnier



5. Jonathan Ulanick


6. Emily Grishaber

1. Mina Macdonald



2. TBA



3. Jenna Brennan



4. Carson Tomalty



5. Bronte Mcphedron



6. Kiana Smith

1. Peccoud et al. 2009. A continuum of genetic divergence from sympatric host races to species in the pea aphid complex. Proceedings of the National Academy of Sciences of the United States of America. 106: 7495-7500. [sympatric speciation, host specialization, diminution of gene flow]

2. Novikova et al. 2017. Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica. Molecular Biology and Evolution 34: 957-968. [Can polyploid speciation result instantaneously from a single, selfing individual?]

3 Hermansen et al. 2011. Hybrid speciation in sparrows I: phenotypic intermediacy, genetic admixture and barriers to gene flow. Molecular Ecology 20: 3812-3822. [evidence for hybrid speciation in birds]

4. Brawand et al. 2014. The genomic substrate for adaptive radiation in African cichlid fish. Nature 513: 375-81.  [genomic bases of adaptation & adaptive radiation]

5.Schweizer, Hertwig & Seehausen. 2014. Diversity versus disparity and the role of ecological opportunity in a continental bird radiation. Journal of Biogeography. 41: 1301-1312. [adaptive radiations on continents – the role of ecological opportunity?]

6. Blackburn. 2015. Evolution of viviparity in squamate reptiles: Reversibility reconsidered. J. Exp. Biol. 324: 473-486. [evolutionary reversibility & convergent evolution]

Mon. Oct. 15 1. Adam Binhammer



2. TBA


3. Katie Madonia


4. TBA



5. Cooper Mosel



6. Farah Sadoon



1. Nesar Safajou



2. Sam Sears



3. Aliana Hellmuth



4. Jena Li



5. Dean Haydon



6. TBA



1. Joy & Crespi. 2012. Island phytophagy: explaining the remarkable diversity of plant feeding insects. Proceedings of the Royal Society of London Series B. 279: 3250-3255. [island biogeography theory, speciation in phytophagous insects, lineage age as a correlate of diversity]

2. Khadjeh et al. 2012. Divergent role of the Hox gene Antennapedia in spiders is responsible for the convergent evolution of abdominal limb repression. Proceedings of the National Academy of Sciences of the United States of America. 109: 4921-4926. [how are HOX genes possibly implicated in convergent evolution? at what level, genetic or morphological, might we define convergent evolution?]

3. Rosenblum, Roempler, Schoeneberg & Hoekstra. 2010. Molecular and functional basis of phenotypic convergence in white lizards at White Sands. Proceedings of the National Academy of Sciences of the United States of America, 107: 2113-2117. [molecular basis of convergence]

4. Wills. 2007. Fossil ghost ranges are most common in some of the oldest and some of the youngest strata. Proceedings Royal Society. Biological Sciences. 274: .2421-2427. [completeness of the fossil record,  the meaning of gaps, spurious evolutionary trees]

5. Doolittle & Bapteste. 2007. Pattern pluralism and the Tree of Life hypothesis. Proceedings of the National Academy of Sciences of the United States of America, 104: 2043-2049. [tree of life? pattern pluralism, alternative views of the history of life on Earth]

6. Crampton & Gale. 2005. A plastic boomerang: speciation and intraspecific evolution in the Cretaceous bivalve Actinoceramus. Paleobiology, 31: 559-577. [Is macroevolution simply the result of microevolutionary processes scaled up? How does this fit into the paradigm of punctuated equilibrium?]

Mon. Oct. 22 1. Sean Vanderluit



2. Emma Redfearn



3. Scott Schrempf



4. Cassandra Pereira



5. TBA



6. Phoebe Graham


1. Cassandre Pyne



2. Lucia Park



3. Michaele Corbisiero



4. Kristen Panetta



5. TBA



6. TBA


1. Powell & MacGregor. 2011. A geographic test of species selection using planktonic foraminifera during the Cretaceous/Paleogene mass extinction. Paleobiology 37: 426-437. [species selection?]

2. Eastman & Storfer. 2011. Correlations of life-history and distributional-range variation with salamander diversification rates: Evidence for species selection. Systematic Biology. 60: 503-518. [species selection; geographic ranges as species’ characters]

3. Sibert & Norris. 2015. New Age of Fishes initiated by the Cretaceous-Paleogene mass extinction. Proceedings of the National Academy of Sciences USA 112: 8537-8542. [What role might extinction play in paving the way for new diversity?]

4. Peters. 2008. Environmental determinants of extinction selectivity in the fossil record. Nature 454:626-629. [extinction selectivity, causes of mass extinction, biological interactions, environmental sieves]

5. Bapst et al. 2012. Graptoloid diversity and disparity became decoupled during the Ordovician mass extinction. Proceedings of the National Academy of Sciences of the United States of America. 109: 3428-3433. [dynamics and causes of recovery after mass extinction]

6. dos Reis et al. 2015. Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales. Current Biology 25: 2939-2950. [origins of major animal lineages, molecular clock, Cambrian explosion]


Phylogenetics Group Exercise (worth 25% of your final grade):

In the first lab period we divided you into groups of 3-5 students for purposes of this group phylogenetics project.

Group Monday afternoon
(Katie Birchard)
Wednesday afternoon
(JieYuen Ong)
  • Michelle Cohen
  • TBA
  • TBA
  • Emily Grishaber
  • TBA
  • TBA
  • Liying Xu
  • Emma Sinclair
  • Jenna Brennan
  • Liam Joiner
  • Hayden Wainwright
  • Hana Thompson
  • Mansuba Rana
  • Kristen Panetta
  • Lucia Park
  • Jena Li
  • Dean Haydon
  • Emma Redfearn
  • Katie Madonia
  • Farah Sadoon
  • Cassandra Pereira
  • Scott Schrempf
  • Sean Vanderluit
  • Not applicable
  • Not applicable
  • Not applicable

Overview. Easily obtained molecular data, an ever-expanding tool chest of phylogentic methods and software, and readily-accessible, high-performance personal computers and now the advent of cloud computing have revolutionized our ability to evaluate the evolutionary affinities of groups of taxa. The purpose of this exercise is to introduce some of the basic issues of molecular phylogenetics, provide practical (albeit brief) experience in phylogeny estimation, and to illustrate how phylogenetics can be used to address specific hypotheses. In consultation with me and your TA, Danielle, I would like each group to propose a hypothesis (e.g. biogeographical, adaptive, gene duplication) for a select group of organisms (e.g. HIV, ranid frogs, ratite birds) for which suitable DNA sequence exists (i.e. evolving at an appropriate rate and available in Genbank or other reliable source). Obviously if sequences exist in Genbank then there is a good chance that they have been used in a publication; however, I wish for each group to derive an evolutionary tree from first principles.

During labs in the week starting November 6th, you will as a group present your hypothesis and ideas for analysis in class. This is to be a constructive session of discussions on how you may best go about addressing your hypothesis. (Worth 5%)

Each research group will select approximately 40-50 homologous sequences (with at least one outgroup taxon) and copy each of them into a text file in FASTA format. We will then create a DNA alignment using the program CLUSTALX or other alignment program We will save this in a Phylip or nexus format text file which can then be ported into other programs for phylogenetic analysis (e.g. MrBayes, BEAST). Not to worry – I will provide more information and guidance in the lab and we will walk through some of the basic phylogenetic analyses together (i.e. we will sit down with your file at a series of scheduled meetings and work through some of these analyses). Presentations illustrating your findings will be 20 minutes (max.) in length with about 5-10 minutes of questions to follow. Preparatory work, phyloegentic analyses, and presentations should be apportioned equally among all group members (how you do this is up to you).

Schedule for Findings from the Phylogenetics Computer Lab:

Week starting … November 19 Groups A, B & C
Week starting … November 26 Groups D, E & F

Handout for Group Phylogenetics Exercise provided | HERE |

Term paper (outline worth 10%; term paper worth 30%): This will be critical review of a major topic in speciation and macroevolution that is to be chosen in consultation with me or your TAs. Begin with a paragraph broadly stating what the major issues or controversies are and how they relate to speciation or macroevolution, and then in subsequent paragraphs focus more on the specifics of your chosen topic. At the end of the Introduction clearly state the objectives of your review. For the remainder of the review explore your subject, its theoretical underpinnings, and the empirical data that support or refute your views. Use subtitles to help organize your review. Use Trends in Ecology and Evolution as your template (including for format of references). Your paper should be 10-12 pages double-spaced 12 pt. font (not including references and figures). The Literature Cited section should include at least 10-15 research articles from the primary literature.

We would like you to provide an outline of your term paper (2 pages pt. form, divided into the sections that you will use in your paper). This is due on Monday October 30th by 4:00 pm and is worth 10% of your final grade.

Due date for final paper (30% of your final grade): Monday December 3rd at 4:00 pm in my office (Rm. 4428 Biosciences). Late reports lose 5 marks (out of a total of 25) for each 24 hours (or part thereof) they are overdue. Any concerns regarding this due date must be addressed to Dr. Lougheed, not your TA, BEFORE THE PAPER IS DUE.

A note on plagiarism: Plagiarism means “… to steal from the writings or ideas of another” (Chambers Dictionary. Larousse 1996). This definition does not capture all of the subtlety of the term. Obviously plagairism encompasses directly copying from other sources (and including fellow students’ papers) without due acknowledgement (and quotation marks or other suitable demarcation) but it also includes using an idea or opinion, reproducing a figure or a table (even when altered), citing statistics without giving appropriate credit. Even paraphrasing without suitable recognition of the source or author is considered plagiarism. Consequences of plagiarism can be substantial – see the Arts & Science calendar.