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Biology 4289b
Biosystematics and Phylogenetics |
Instructor: André LachanceRoom 2036 Biology and Geology Building |
Lectures
Tuesday, Wednesday, and Friday 9:30 - Physics and Astronomy 106
Practicals
Tuesday and Friday 10:30 - North Campus Building 105
We shall start lectures and tutorials in full force Friday, January 6, 9:30-11:30
For further information on the importance of attending classes during the first week of term, please refer to Tom Wayman's excellent poem.
Midterm in class February 17
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Assignments
1. Find a relatively recent research article dealing the description of a species or the taxonomy of a group of species.
Make sure that the authors used sequence information as part of their data.
Using the NCBI Taxonomy
and BLAST
sites, select a set of 5 species on the basis
of the following criteria:
A set of homologous sequences should be
available for all species.
The species should be significantly related.
Here are some hints on how to proceed.
Presentation
of 2-3 min introducing your
species, their general biological interest, and a brief summary of the
article that you found.
The following specialized journals publish this sort of article - there are more!
Antonie van Leeuwenhoek Journal of Microbiology
Blumea - Biodiversity, Evolution and Biogeography of Plants
European Journal of Phycology (algae)
European Journal of Protistology
Herpetologia (reptiles and amphibians)
International Journal of Systematic and Evolutionary Microbiology
Proceedings of the Biological Society of Washington
Systematic and Applied Microbiology
The Journal of Eukaryotic Microbiology
Taxonomic papers also appear in more general journals:
2. Draw a list of your species (Excel)
with a few (3-5) characters, the relevant states or values,
and an analysis of these characters in terms of
data
types.
Construct a dichotomous, monothetic
identification key to your species.
Presentation of 3-5 min outlining some of
the salient features of
your character table and demonstrating some aspects
of
your key.
3. Discuss how authors of a relevant research
article have applied various species concepts.
Perform an etymological analysis of some
of the names.
Presentation of 3-5 min.
4. Align a set of homologous sequences one of the tools provided in Mega6.
Ensure that the data contain at least some parsimony-informative sites.
Trim the fringe and save as a 'mas' file;
export to phylogeny.
Construct a tree of any kind, but with scaled branches.
Format and export the tree to PowerPoint.
Map selected phenotypic characters of
your species onto the tree,
identifying examples of synapomorphies,
homoplasies, or symplesiomorphies.
Presentation of 10 min.
By
the end of the course, you should be familiar with all the
concepts listed here
By
the end of the course, you should have memorized the names
and order
of
all eons and eras, all periods of
the Paleozoic and Mesozoic, and all epochs of the Cenozoic
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