BIOB 420-01 & 420-02, Evolution - Spring Semester, 2013 - the link to this website is posted in the Desire2Learn system.

Instructor (2^nd half of the Spring semester): Matt Lavin, 308 & 339 Plant Bioscience Building, or 408 Lewis Hall - best way to communicate is by email

Office phone: 994-2032 (for leaving a message).

Lecture section 01: 105 Reid Hall on Monday, Wednesday, and Friday, 9:00-9:50AM

Lecture section 02: 304 Lewis Hall on Monday, Wednesday, and Friday, 1:10-2:00 PM

Office Hours. Mondays 10 AM - 12:30 PM in 339 Plant Bioscience Building or by appointment.

Text: none. Some examples will be derived from Evolutionary Analysis, 4th ed., by Scott Freeman & Jon C. Herron (Prentice Hall), a copy of which will be placed on reserve in Renne Library.

Learning outcomes. Students will be able to: 1) use basic methods of inferring the history of biological evolution, including the reconstruction phylogenetic relationships from genetic and morphological data using distance and cladistics methods on data sets that are simplified for ease of hand-calculation; 2) using these methods, answer questions that are related to population management, forensics, epidemiology, and adaptation; 3) analyze allele frequency data on population samples in order to study recent historical events; 4) analyze nucleotide sequence, DNA structural, and morphological data on individual samples in order to study older historical events; 5) describe why merely accepting the truth of evolutionary theory is not so much the issue as is valuing the principles of reasoning and educated discourse that now make belief in evolution obligatory (quoting Sam Harris). This course will not focus on biochemical theories that address the ultimate origins of life. If interested, a good starting point includes chapters 17 and 18 in Evolutionary Analysis, 4^th edition.

SCHEDULE OF LECTURES: section 01 and 02 are identical. Problem sets and notes will be finalized the evening before the date listed.

11-15 March - Spring Break

18 March - introduction - the scientific study of history and neutral genetic variation

20 March – introduction continued

22 March - recent population divergence (human PV92 locus worksheet without or with answers - review & UPGMA construction - also Dolan DNA presentation of the PV92 locus)

25 March - recent population divergence - review of scientific study of history; analysis of the Redfish Lake sockeye (without and with answers)

26 March - recent population divergence - Redfish Lake sockeye (continued)

29 March - University Day (no classes)

1 April - recent population divergence - analysis of YNP grizzly bears (without and with answers)

3 April - recent population divergence - Ponderosa pine in Montana - worksheets: without answers: mtDNA & cpDNA; with answers: mtDNA & cpDNA

5 April - review

8 April - The 2013 exam without and with answers.

10 April -the scientific study of history (review)

12 April - phylogenetics and morphological data (without and with answers)

15 April - mutation, drift, and substitution: phylogenetic distance methods

17 April - mutation and drift in a colonizing versus late-successional species

19 April - mutation and drift, introduction to cladistics

22 April - review of cladistics, study problems without and with answers

24 April - monophyly and phylogenetic species concept

26 April - review (2013 exam 4 without and with answers)

Wednesday 1 May - Exam #4, bring a calculator and pencils, section 02 at 8:00-9:50 AM in 304 Lewis Hall

Thursday 2 May - Exam #4, bring a calculator and pencils, section 01 at 4:00-5:50 PM in 105 Reid Hall

GRADES will be derived from four exams (two from the 1^st half and two from the 2^nd half of the course). The dates of the last two exams in this final half of the course are given above. Each of the four exams will count one fourth of your grade. The exams will involve mostly problem solving questions. See the above links to exams from 2012).

Web sites from which examples, data, and tools for analysis are utilized:

• Stephan Jay Gould unofficial website
• Science, Evolution, and Creationism (National Academy of Science).
• Dolan DNA Learning Center provides bioservers and information sources for the study of allelic variation and mtDNA sequences in human populations.
• Data used during this course will include: - PV92 data, mtDNA data (5' variation, 3' variation - African-Asian 5' variation), mtDNA phylogeny
• AlleleA1, Phylostrat, ForensicEA, and other software programs are available at a web site by Jon C. Herron, one of the authors of the textbook of this course.
• ThetaSim, and other software programs are available at a web site by Paul O. Lewis at the University of Connecticut.
• POPULUS. This program covers many topics in evolution and ecology.

MSU Departments of Ecology, LRES (Kevin O'Neill - 1^st half - section 001) and Plant Sciences (Adam Richman- 1st half - section 02,and Matt Lavin)