Biology 4289b

Biosystematics and Phylogenetics

Biology 9289b

 

Instructor: André Lachance

Room 2036 Biology and Geology Building

 


Schedule for 2015

 

Lectures

Tuesday, Wednesday, and Friday 9:30 - University Community Centre (UCC) 53

 

Practicals

Tuesday and Friday 10:30 - Somerville House 1310

Lectures and practicals start January 6.  For further information on the importance of attending classes during the first week of term, please refer to Tom Wayman's excellent poem.

 

 

Course outline for 2015

 

Legal stuff:

Accommodations

Scholastic offenses

 

Stress - distress

Consult UWO Health and Wellness website

 


Assignments

 

1. 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.

Presentation of 2-3 min introducing your species and their general biological interest.

New: Help in finding information

 

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 various species concepts as they may apply to your selected species.

Focus on one or two concepts.

Include an etymological analysis of some of the names.

Presentation of 3-5 min.

   

4. Retrieve a set of homologous sequences for your chosen species and save them as a multiple FASTA file (or otherwise).

Align them with one of the tools provided in Mega6; trim the fringe; 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.

 


Concepts

By the end of this course, you should be familiar with all the concepts listed here

 

The 4289b Tree of Life

 

The Geological Timescale

By the end of this 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

 

Here is today


Links

Biosystematics & Phylogenetics in the News

Archaea and the origin of Eukarya (April 2015)
New World Monkeys (December 2013)

People

Concepts

Software, etc.

Hennig

Linnaeus

Borge

Herpetology, Ornithology, and Phylogenetics

 

Genealogical concordance

 

Hemiplasy


Phylogeny of Plants

 

Phylogenomics

 

The Origin of Land Plants

 

Biosystematics

 

Phylogenetics


 

DNA Forensics

 

Canada

 

USA - FBI - CODIS


A bit of Latin grammar


Aristotle's Great Chain of Being

drawn  by Didacus Valades, Rhetorica Christiana (1579)


Population thinking versus typology: the importance of multiple isolates in microbial species descriptions

 

Multiple strains in yeast species descriptions


Understanding the protostome/deuterostome split

 

Deuterostomy came first


Ape stuff

 

Taxon structure

 

Ape chromosomes

 

Ape mtDNA alignment and trees


DNA chemical structure


Likelihood

BLAST


Install Chromas Lite


Download a raw electropherogram to edit with Chromas

This is a sequence from my lab.  See if you can edit it with Chromas and then BLAST it to see if it matches anything.

 

More electropherograms


PCR

How primer sequences are artefacts


An-online dot-plot program at Colorado State

(Draws the forward plot only.  To detect inverted sequences, you will need first to obtain the reverse complement of one of the two sequences.)


Dot matrix spreadsheet


Mega5


An RFLP gel


The big Texas tree


The breakup of Pangea

From Rodinia to present


Earth's history


Major differences

Trees

The Tree of Life


One-Zoom Tree of Life

 

DiscoverLife

The Timetree of Life

Old trees

Maximum likelihood for idiots

Gene tree vs species tree

Hemoglobin, paralogs and orthologs

 

Tree exercises

Books

References

Theophrastus

 

Linnaeus

Lecture notes

UWO bookstore, $11


Reference used in class

The Ancestor's Tale

Richard Dawkins


Complete text online

 

A phylogram

Hennig 1965 

 

C.H. Smith's Early Classics 

 

Mayr's species concept 

 

Gregory: Evolutionary Trees 

 

Archibald: Pre-Darwinian Trees


Evolution of homeobox genes 

 

A new mammalian phylogeny 

 

An irreverent look at evolution and biodiversity


Image gallery

 

Eubacteria

Archaea
Basal eukaryotes

Glaucophytes - Rhodophytes
Plants

Amoebozoa
Fungi

Mesomycetozoans

Choanoflagellates
Placozoans
Acoelomorphs - Protostomes

Ambulacrarians

Urochordates - Cephalochordates

Agnathes - Chondrichthyans

Fish

Marsupials

Afrotheres

Books on systematics at Sinauer

 

Books on systematics at Roberts

 


Nomenclatural Codes - Full text online

 

International Code of Nomenclature for algae, fungi, and plants (Melbourne Code)

 

The International Code of Nomenclature of Bacteria

 

International Code of Zoological Nomenclature

Reserve list - Taylor Library

As per your requests

Biology 3466b Website   ●   Biology 9214 Website   ●   André Lachance's UWO-Biology Website   ●   Yeast Newsletter Website

Updated 140814