Genome 570

• News
• Description from the UW Course Catalog
• Syllabus of lectures
• The Course Text
• Some data sets you can download and use
• Who is this guy who is teaching the course, anyway?
• What are some other related courses?
• What are some Internet resources on evolutionary biology?
• Where can I get a copy of PHYLIP?
• What other phylogeny programs are available?

• If you are told you need an entry code from us, graduate students can get one from the Brian Giebel in the Genome Sciences office, K328B Health Sciences, and they don't need to see me. Undergraduates and others should see me.
• Homework #1 is now assigned. Here is a PDF of the assignment. Get to it -- a fair amount of getting programs and running them.
• Homework #2 is now assigned. Here is a PDF of the assignment.
• Note that we are currently (April 10) two lectures ahead of our lecture schedule. We will need the extra time.
• The syllabus has been revised so that it will more accdurately reflect which subjects will be on which days. So it is once again accurate, at least for current lectures.
• Ken Karol's topic for May 5 has a different title. Also, as I will not be here May 5, I am extending the homework deadline to May 8.
• Homework #3 is now assigned. Here is a PDF of the assignment.
• Grades are now assigned. The exam total, course total, and grade are written on the front of the exams. These will be available in Health Sciences K328B from Brian Giebel after late Monday morning. Here is a PDF of a histogram of course totals, with indication of how these relate to grades.
• If you got a low score on exam question #6 (the coalescent one), you have lots of company. Only two students came close to getting it correct, and neither of those got it exactly correct (10 points was a typical score for that question). Here is a PDF of an explanation of the steps in computing the correct answer.

The course text is my book, Inferring Phylogenies, published by Sinauer Associates. I believe that the University Book Store has copies. It can also be ordered from Sinauer Associates or from Amazon. The first printing of the book has many typos. A web page listing the typos is available. Many of these were corrected in the second printing. If there is a box on the back cover with reviews of the book, that is the second edition.

Almost all the data sets used in the book can be downloaded from its data sets web site.

These additional data sets are so that we can discuss common examples when people try out various programs. They are in PHYLIP formats, but these can often be read by other programs such as PAUP and MacClade. These data sets can be downloaded by ftp by clicking on the appropriate words. If clicking on them happens to display the file rather than open a window that asks you where to put the file, you may be able to get your browser to save it by using a "Save As" function (on Netscape that's in the Files menu).

• A 15-species, 40-character discrete-characters (0/1) data set of fossil elephants by Pascal Tassy and Pierre Darlu. From a paper in Geobios 19: 587-600 1986. Click here to download.
• A 16-species, 1992-site DNA data set from the paper by Clint Turbeville and others:
  Turbeville. J. McC., Schulz, J .R. and R. A. Raff. 1994. Deuterostome phylogeny and the sister group of the chordates: evidence from molecules and morphology. Molecular Biology and Evolution 11: 648-655.
  Alignment is by them. These are chordates, protochordates, echinoderms, thisachordates, and thatachordates. Heavy-duty industrial-strength data. These sequences are in interleaved format. Click here to download.
• A 76-species protein sequence data set for Transcription Elongation Factor Alpha (EFTU-alpha), alignment by the Protein Information Resource of the National Biomedical Research Foundation. Click here to download. Some species are represented more than once, and some by fragments.

Biology 354 Foundations in Evolution and Systematics

The main evolution course at the University, taught twice yearly (Winter and Spring). Text is the 3rd edition of Freeman and Herron's "Evolutionary Mechanisms". This year course was taught by Toby Bradshaw in the Winter quarter, and is being taught by Peter Ward and Ray Huey in the Spring Quarter.

Genome 453 (Evolutionary Genetics)

This is an undergraduate-level course on evolution and genetics. Given every Autumn, it overlaps somewhat with Biology 354 but covers the genetic aspects of evolution with less emphasis on ecology and paleontology than the first, less emphasis on molecular evolution than the second. It should be understood that this is basically an undergraduate course.

Genome 562 (Population Genetics)

Now given every other year, this is the graduate theoretical evolutionary genetics course that I give. Lots of equations, though mostly at a low mathematical level. No pictures of cute furry animals. Next time it's given will be Spring, 2007. Text: my own extensive lecture notes, downloaded as PDF's for free or sold inexpensively (no royalty is paid to me).

There are many:

Electronic journals

There is of course, the professional literature in evolutionary biology. Some of these journals (links given below) are available in electronic versions for UW people. Here are some:

• Molecular Biology and Evolution
• Systematic Biology
  • 1998-present
  • 1992-1997
  • 1952-1991 as Systematic Zoology
• Evolution
  • 2000-present
  • 1947-2002
• Journal of Molecular Evolution (1996-present)
• Molecular Phylogenetics and Evolution (1993-present)
• Paleobiology
  • 2000-present
  • 1975-2001
• Journal of Evolutionary Biology

Newsgroups

Some brief descriptions of some of the major ones covering evolution. These groups have many participants who are novices to evolutionary biology. I have provided links to the groups through Google, but UW students can read them using UW's newsreading facilities too. Unfortunately, Usenet newsgroups are dying out, with people shifting to Yahoo groups and blogs. These have not yet achieved the level of general discussion that the Usenet groups have, so the number of Internet resources for serious discussion of evolutionary biology has actually decreased.

sci.bio.systematics

Discussion of systematics, including phylogeny and classification. Most postings are serious discussions by researchers. Some percentage of them are semantic issues or legalistic discussions of taxon names. There has sometimes been an endless thread about cladistic versus evolutionary-systematic approaches to classification. Lately there is almost no traffic.

bionet.molbio.evolution

Discussion among researchers about molecular evolution. Low volume, high quality. Co-moderated by Jerry Learn of our Micro Department. Very inactive lately.

sci.bio.paleontology

Tends to be filled with postings by fossil enthusiasts and tends to be dinosaur-centered. Some creation/evolution debating too.

sci.bio.evolution

Moderated by Josh Hayes, formerly of our own Center for Quantitative Sciences, who should get some sort of award for putting up with a lot of nonsense. I think it was intended as a forum for discussion among researchers, but has tended to be filled with postings by others about whether humans are still evolving (answer: yes, but it's extremely slow compared to cultural change) and whether laughter is selectively advantageous. There is often an endless controversy of everybody against a couple of people who think they've proven that Hamilton's formula for kin selection is wrong (they haven't). Not intended for evolution/creation debates: Josh screens these out.

talk.origins

The arena for endless debate between creationists and others, with frequent digressions into theology. Extremely high noise to signal ratio. When a decisive point is made, the opponent changes the subject or just refuses to respond.

Web Pages

• The amazing Tree of Life , a phylogeny of all life, in the making. A professional data base system of systematics, in effect.
• TreeBASE, a database of evolutionary trees (phylogenies) from the scientific literature. Weighted towards flowering plants, and badly suffers being only sporadically updated.
• My own PHYLIP free package of computer programs for inferring phylogenies. Includes some web pages on all possible phylogeny programs and how to get them.
• The University of California Museum of Paleontology pages, which include a substantial evolution and phylogeny section. This is a sort of "virtual museum".
• Our own Burke Museum has a Vertebrate Paleontology Page that leads on to many images of vertebrate fossils.
• Evonet.org, an NSF-funded resource for evolutionary biology run by Patrick Phillips at the University of Oregon. Mostly a list of other web pages, with a directory of evolutionary biologists as well. Not reliably updated. A new version is due out soon, "in 2001" [!]
• The Population Biology, Evolution & Biomath Educational Index posted by Carlos Lara-Moreno in 1998 (and not much updated since). Links to population genetics courses, software, etc.
• Want some DNA or protein sequences? How about getting them from the international database? Try the Web pages of the databases at the NCBI, the National Center for Biotechnology Information of the National Library of Medicine, in Bethesda, Maryland. Not for the faint-hearted.
• The talk.origins Evolution FAQs (Frequently Asked Questions).
• The Harvard Biopages evolution page, with lots of links to other evolution resources.