Entomology 601

Fall 2015

Papers for Friday Discussions

Week 1, Friday September 4
Can we describe all species on earth?

Discussion Leader: Jim Woolley

Paper: Wheeler et al. (2012), Mapping the biosphere: exploring species to understand the origin, organization and sustainability of biodiversity. Systematics and Biodiversity 10(1): 1-10.

For a very different point of view on this question, see: Costello, M. J., R. M. May and N. E. Stork (2013). "Can we name earth's species before they go extinct?" Science 339: 413-416.

Week 2, Friday Sept. 11
Species vs. subspecies: implications for biodiversity and conservation

Discussion Leaders: Richelle Marquess, Bryant  McDowell, Cody Gale

Paper: Zachos et al. (2013), Species inflation and taxonomic artefacts - a critical comment on recent trends in mammalian classification. Mammalian Biology 78:1-6.

Week 3, Friday September 18
Role of morphology in contemporary systematic biology

Discussion Leaders: Hee Kim, Karen Poh

Paper: Deans, Yoder and Balhoff. (2012) Time to change how we describe biodiversity. Trends in Ecology and Evolution 27(2): 78-84.

For an updated treatment of this topic, see: Deans et al. (2015) Finding our way through phenotypes.  PLOS Biology 13(1):e1002033.

Week 4, Friday Sept. 25
Homology and molecular biology

Discussion Leaders: Erin Maxson, Andrew Davitt, Iliana Mock

Paper: Mindell, D.P. and A. Meyer. (2001) Homology evolving. Trends in Ecology and Evolution 16(8):434-440.

Week 5, Friday Oct. 2
Future of molecular systematics

Discussion Leaders: Tyler Raszick, Jocelyn Holt

Paper:  McCormarck, J.E. et al. (2013). Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution 66:526-538.

Week 6, Friday Oct. 9
DNA "bar-coding"

Discussion Leaders: Mckensie Daugherty, Michael Vestal, Trevor Steele

Paper: DeSalle, R. et al. (2005). The unholy trinity: taxonomy, species delimitation and DNA bar-coding. Phil. Trans. R. Soc. B 360: 1905-1916.

Week 7, Friday Oct. 16
Character optimization and study of trait evolution

Discussion Leaders: Ashley Tessnow, Cragen King

Paper: Hardy, C.R. (2006).    Reconstructing ancestral ecologies: challenges and possible solutions.  Diversity and Distributions 12: 7-19.

Week 8, Friday Oct. 23
Concatenation of data vs. separate analysis

Discussion Leaders: Brittany Moody, Violet Ndeda, Danielle Restuccia

Paper:  Degnan J.H. and N.A. Rosenberg (2009). Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology and Evolution 24(6):332-340

For a very different point of view, see: Gatesy, J. and M.S. Springer (2014).  Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum.  Molecular Phylogenetics and Evolution 80: 231-266.

Week 9, Friday Oct. 30

Bootstrap resampling and clade support 

Discussion Leaders: Reza Manshouri, Xing Zhao

Paper: Soltis and Soltis (2000), Applying the bootstrap in phylogeny reconstruction. Statistical Science 18(2):256-267

Week 10, Friday Nov. 6
"Bar-coding" revisited: will it yield monophyletic taxa?

Discussion Leaders: Mackenzie Tietjen, Alexis Trubenbach, Polly Harding

Paper: Yassin et al. (2010).  The genus Drosophila as a model for testing tree- and character-based methods of species identification using DNA barcoding.  Molecular Phylogenetics and Evolution 57: 509-517

Week 11, Friday Nov. 13
Host-Associated Differentiation

Discussion Leaders: Kristina Chyn, Ivy Chen

Paper: Stireman III, J.O. et al. (2006) Cascading host-associated genetic differentiation in parasitoids of phytophagous insects. Proc. Royal Society B 273:523-530.

Week 12, Friday Nov. 20
Species concepts

Discussion Leaders: Timothy Garrett, Mark Janowiecki

Paper: Helbig, A.J. et al. (2002). Guidelines for assigning species rank. Ibis 144: 518-525.

Week 14, Friday Dec. 4
The future of taxonomic publication

Discussion Leaders:  Brittny Jones, Chelsea Holcomb

Paper: Blagoderov, V. et al. (2010) Streamlining taxonomic publication: a working example with Scratchpads and Zookeys. ZooKeys 50: 17-28.