Biology 403-01 & 403-02, Evolution - Spring Semester, 2010 – access course information at Desire2Learn login if not already there.

Instructor (2^nd half of the Spring semester): Matt Lavin, 308 & 339 Plant Bioscience Building, preferred manner of communication: email

Office phone: 994-2032.

Lecture section 01: 304 Lewis 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 308 or 339 Plant Bioscience Building, or by appointment.

Text: Evolutionary Analysis, 4th ed., by Scott Freeman &Jon C. Herron (Prentice Hall). This text is on reserve at the front desk of Renne Library.

Goals during the 2^nd half of the course: The study of evolutionary history is the focus of the second half of this course. The goal is to be able to reconstruct phylogenetic relationships from gene frequency, nucleotide substitution, and morphological data. Data sets will be simplified for ease of hand-calculation and to emphasize the general concepts behind the methods. Reconstructed phylogenies will be quantitatively analyzed for informationbearing on epidemiology and adaptation. Human evolution will be understood in terms of phylogenetic evidence.

This course will not focus on 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. Because most scientific activity in evolutionary history is centered on the mechanisms of change among the living species, little of the fossil record will be covered. Contemporary methods of fossil analysis include the phylogenetic methods presented in this class, however.

SCHEDULEOFLECTURES (notes will be finalized the evening before the date listed)

15-19 March – Spring Break

22 March – key concepts: theory, phylogenetics, chaos, neutrality

24 March – recent population divergence (genetic drift, eugenics, inbreeding, and the short attention span of humans) – analysis of the human PV92 locus

26 March – recent population divergence – stochastic drift

29 March – recent population divergence – analysis of the Redfish Lake sockeye

31 March – recent population divergence – analysis of YNP grizzly bears

2 April – University Day (no classes)

5 April – recent population divergence – Ponderosa pine in Montana (data sets: 1. mtDNA, 2. cpDNA)

7 April – review

9 April – exam 3

12 April – old population divergence (mutation, substitution, speciation, and the law of large numbers) – the stochastic behavior of mutation

14 April – old population divergence – phylogenetic distance methods

16 April – old population divergence

19 April – old population divergence – cladistic methods

21 April – old population divergence – cladistic work problems

23 April – speciation

26 April – epidemiology

28 April – human nature

30 April – review

Thursday 6 May – Exam #4, section 02 at 8:00-9:50 AM

Friday 7 May – Exam #4, section 01 at 8:00-9:50 AM

GRADES will be derived from four exams. 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 test format and kinds of questions will be related to the questions provided for each chapter in the text, Evolutionary Analysis, 4^th edition.

Relevant web sites:

• 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.
• Science, Evolution, and Creationism (National Academy of Science).
• gaps in the fossil record by paleontologist Kevin Padian.

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)