UH Summer 2006 Journal Club

Journal Club Meets Thursdays at 1:30 in the Zoology Conference Room

Any room changes are noted after meeting dates

If enough people are interested I thought this summer we could read and discuss John Avise's new book Evolutionary Pathways in Nature: A Phylogenetic Approach. 

Here is a PDF of the Table of Contents.

It is fairly short, only 7 chapters over 218 pages. We could meet once a week and discuss 1 or two chapters, depending on length and content. We could also supplement the book with readings from the current literature where desirable.

The book is available from all the normal online retailers beginning sometime the first week of June if we are lucky

Cambridge University Press  -  Amazon  -  Barnes & Noble

If you are not already on the mailing list and want to be included please send me (Ken Hayes) an email.


While we are awaiting the arrival of the book we can begin reading journal papers.


June 8 - (Meet in Edm 260) Fyler, C. A. et al. 2005 Historical biogeography and phylogeny of monachine seals (Pinnipedia: Phocidae) based on mitochondrial and nuclear DNA data. J. Biogeography 32:1267-1279. (PDF)


Supplemental reading: This is a paper the does a good job of discussing data partitioning and analyses. 

Brandley, M. et al. 2005. Partitioned Bayesian analysis, partition choice, and the phylogenetic relationships of scinicid lizards. Syst. Biol. 54:373-390. (PDF)

June 15 - Jarvi, S. et al. 2004. Natural selection of the major histocompatibility complex (Mhc) in Hawaiian honeycreepers (Drepanidinae). Molecular Ecology 13:2157-2168. (PDF)

Supplemental reading: The bird paper we talked about from Nature and the Fish Mhc paper that Paul discussed, and a TREE paper the Matt pointed out. Also, not necessarily related, but brought today, speciation by hybridization in butterflies.

Filardi, C. E. and R. G. Moyle. 2005 Single origin of a pan-Pacific bird group and upstream colonization of Australasia. Nature 438:216-219. (PDF)


Cohen, S. 2002. Strong positive selection and habitat-specific amino acid substitution patterns in Mhc from estuarine fish under intense pollution stress. Mol. Biol. Evol. 19:1870-1880. (PDF)


Mavarez, J. et al. 2006. Speciation by hybridization in Heliconius butterflies. Nature 441:868-871. (PDF)


Acevedo-Whitehouse, K. and A. Cunningham. 2006. Is MHC enough for understanding wildlife immunogenetics? TREE In Press. (PDF)

June 22 - Appendix: a primer on phylogenetic character mapping and Chapters 1 & 2

Supplemental reading: These are a couple of papers that were mentioned during our discussion

Service, R. 2006 The race for the $1000 Genome. Science 311:1544-1546. (PDF)

Daeschler, E.B. et al. 2006. A Devonian tetrapod-like fish and the evolution of the tetrapod body plan. Nature 440:757-763. (PDF)

Pennsi, E. 2006. Fossil shows and early fish (almost) out of water. Science 312:33 (PDF)

Ahlber, P. E. and J. A. Clack. 2006. A firm step from water to land. Nature 440:747-749. (PDF)

And a few on shell coiling for those interested. The Urdy & Chirat paper addresses issues with the Collins & Cipriani (2003) interpretations discussed in Chapter 2.

Davison, A. et al. 2005. Speciation and gene flow between snails of opposite chirality. PLOS Biology 3:1559-1571. (PDF)

Schilithuizen, M. and A. Davison. 2005. The convoluted evolution of snail chirality. Naturwissenschaften 92:504-514. (PDF)

Urdy, S. and R. Chirat. 2006. Snail shell coiling (re-)evolution and the evo-devo revolution. J. Zool Syst. & Evol. Res. 44:1-7. (PDF)

June 29 - Chapter 3, Body Colorations. Also the two recent papers discussing coloration and evolution. If the second one looks familiar that's because it was brought up at the June 15 meeting. It may seem like a lot to read, but the two additional papers are fairly short.

Lahti, D. 2005. Evolution of bird eggs in the absence of cuckoo parasitism. PNAS 102:18057-18062 (PDF)

Mavarez, J. et al. 2006. Speciation by hybridization in Heliconius butterflies. Nature 441:868-871. (PDF)

Even more reading:

Bridge, E. S. et al. 2005. A phylogenetic framework for the terns (Sternini) inferred from mtDNA sequences: implications for taxonomy and plumage evolution. Mol. Phyl. & Evol. 35:259-469. (PDF)

July 6 - Chapter 4, Sexual features and reproductive lifestyles

Supplemental reading: Papers mentioned this week

Mank, J. E. and J. C. Avise. 2006. Comparative phylogenetic analysis of male alternative reproductive tactics in ray-finned fishes. Evolution 60:1311-1316. (PDF)

Sato, J. J. et al. 2006. Evidence from nuclear DNA sequences sheds light on the phylogenetic relationships of Pinnipedia: Single origin with affinity to Musteloidea. (PDF)

July 13 - No meeting

July 20 - Chapter 5: More behaviors and ecologies, and Chapter 6: Cellular physiological, and genetic traits.

July 27 - No meeting, Hawaii Conservation Conference

August 4 - Chapter 7, Geographical distributions.