Fall 2012 Advanced Topics Course

The Advanced Topics in Ecology and Evolutionary Biology Course kicks off tomorrow at 9:40. The instructors for this semester will be Justin Ramsey, Dave Lambert and Rich Glor. Below is a schedule of the instructors and associated topics.

Aug 30: Ramsey – Field Biology
Sept 4, 6: Ramsey – Field Biology
Sept 11, 13: Ramsey – Field Biology
Sept 18, 20: Lambert – Animal Diversity
Sept 25, 27: Lambert – Animal Diversity
Oct 2, 4: Lambert – Evodevo
Oct 9, 11: Lambert – Evodevo
Oct 16, 18: Lambert -Evodevo
Oct 23, 25: Glor – Phylogenetic Inference
Oct 30, Nov 1: Glor – Phylogenetic Inference
Nov 6, 8: Glor – Phylogenetic Comparative Methods
Nov 13, 15: Glor – Phylogenetic Comparative Methods
Nov 20: Glor – Vertebrate Evolution and Diversity
Nov 27, 29: Ramsey – Population and Community Ecology
Dec 4, 6: Ramsey – Population and Community Ecology
Dec 11: Ramsey – Plant Evolution and Diversity

Journal Club, Sept. 4th: Species Concepts and Species Delimitation

Before beginning our discussion of speciation, we must first address some fundamental questions about species and speciation, including: Are they species real? What are species? and How do we diagnose and delimit species? We’re going to largely skirt the first of these questions by accepting the notion that species are real, at least in the sense that they correspond with actual discontinuities in nature rather than being entirely subjective constructs of our human minds.

Our discussion of how to define and delimit species begins with a classic paper by the German-born ornithologist Ernst Mayr. No biologist has had a stronger impact on modern views of species than Mayr; indeed, the biological species concept (BSC) that continues to dominate our thinking about species and speciation is often traced back to Mayr’s 1942 classic Animal Species and Evolution. Like most good ideas in science, however, the BSC did not appear from whole cloth in a single contribution. Instead, Mayr’s formulation of the BSC was inspired by earlier views expressed by Dobzhansky, Wright, Rensch, Remane, and others. Our first reading this week is a Mayr paper that preceded Animal Species and Evolution in which Mayr outlines the foundations for his own nascent perspective on species and speciation (Mayr 1940). In his paper in The American Naturalist on “Speciation Phenomena in Birds” Mayr sought to formulate a new definition for species that avoided perceived conceptual and practical shortcomings of the definitions offered by his predecessors.  He was particularly interested in formulated a concept that was both evolutionarily meaningful and could be applied in nature to groups such as birds.  Although this paper does not use the term “biological species concept,” it establishes the core features of the modern BSC. It is also clear that Mayr, even in contributions that are now more than 70 years old, had a fairly nuanced view of the major challenges that would face the BSC in the years to follow.

Botanists have always been among the strongest critics of the BSC, often arguing that this concept simply does not apply in groups such as plants where hybridization between phenotypically distinct forms and asexual reproduction are common phenomena. Our second two readings involve an exchange between Mayr and a critic over application of the BSC to plants. In his 1992 report in The American Journal of Botany, Mayr directly addresses critics of the BSC by arguing that the vast majority of plant species in a regional fauna can be diagnosed as biological species.  In addition to addressing a range of conceptual critiques of the biological species concept, Mayr applies the BSC to a well-studied plant community in Concord Massachusetts.  Although Mayr identifies a number of instances where species delimitation via the BSC is challenged by, for example, apomixis, hybridization, or cryptic morphological differentiation, he ultimately concludes that the vast majority of the species in this flora conform with the expectations of “good species” under the BSC.

In a response to Mayr’s paper Whittemore (1993) argues that Mayr’s approach is flawed, perhaps most importantly because the criteria that Mayr uses to diagnose and delimit species are not necessarily directly tied to Mayr’s conceptual view of what species actually are.  In other words, Whittemore argues that Mayr is not actually delimiting species using the same criteria that he uses to define what species are.  Whittemore is a botanist whose own work has focused specifically on a plant genus (Quercus) whose frequent hybridization has proven particularly problematic for taxonomists (Burger 1975, Whittemore and Schaal 1991).  Although Whittemore does not offer an explicit or easily characterized alternative to Mayr’s approach, he makes it clear in several places that one of his main concerns stems from the possibility that the integrity of species may be maintained in nature in spite of fairly extensive hybridization and introgression (e.g., p. 579, 581 in Whittemore 1993), and ultimately argues that species may be “maintained by factors other than total reproductive isolation.”

This exchange between Mayr and Whittemore occurred at a time when the formulation of competing species concepts was somewhat of a cottage industry, culminating in a number of lengthy articles and book length volumes that catalogued and debated dozens of alternative species concepts (Mayden 1997, Wheeler and Meier 2000). What seems to have been lost in this polarizing debate was the fact that most biologists broadly agreed about the expected properties of species, and differed primarily in how they went about diagnosing them. Although he was certainly not the first to recognize this problem, Kevin De Queiroz, a herpetologist at the Smithsonian, has provided the most influential solution to this problem. In a series of papers dating back to the late 1990s, de Queiroz outlines his General Lineage Concept of species, and suggests that “[a]ll modern species definitions either explicitly or implicitly equate species with segments of population level evolutionary lineages.” Under the GLC, most of the previously proposed species concepts are recognized as non-mutually exclusive criteria that one might use to delimit population level evolutionary lineages. Although often overlooked by workers interested primarily in laboratory model organisms, the GLC has been highly influential among practicing systematists and taxonomists. Our final reading is one of de Queiroz’s earliest papers on the GLC and comes from the Endless Forms: Species and Speciation volume edited by Howard and Berlocher (Note: the PDF for this reading is relatively low quality, but should be readable as long as you don’t zoom in too much).

With debate about species concepts (at least temporarily) on the back-burner, systematists have developed a diverse range of new tools for delimitation of species in nature and are broadly applying these methods to a range of taxa (reviewed in Sites and Marshal 2003, 2004).

More details on readings are below the fold. Continue reading

Fall 2012 Journal Club: Speciation

Daven and I are leading a journal club on speciation this semester.  Our goal is to introduce core topics through classic papers.  This journal club will be a bit more structured than is typical because we are selecting some of our favorite papers a priori, focusing on those that we think will generate lots of discussion.  An outline of the topics we intend to cover is below.  Each week we will have three or four required readings.  Please be sure to get an early jump on these readings so that you come to journal club prepared for discussion.  In most cases, we’ll also distribute a set of supplemental or review readings that those of you who are leading the journal club or are particularly unfamiliar with the topic should consider reading.  Our topic for next Tuesday will be species concepts and species delimitation, with more details to follow in another post shortly.

Week 1 (Sept. 4th): The reality of species: concepts, definitions, and reality – Glor
Week 2 (Sept. 11th): Geographic speciation and allopatry – Landeen/Glor
Week 3 (Sept. 18th): Speciation with gene flow I: hybrid zones and speciation – Ahmed/Glor
Week 4 (Sept. 25th): Speciation with gene flow II: divergence population genetics – Geneva/Presgraves
Week 5 (Oct. 2nd): Natural and sexual selection I: reinforcement – Johnson/Glor
Week 6 (Oct. 9th): Natural and sexual selection II: sexual selection and speciation – Binshuang/Glor
Week 7 (Oct. 16th): Natural and sexual selection III: divergent natural selection/ecological speciation – Longjun/Glor
Week 8 (Oct. 23rd): Genetics of speciation I: Dobzhansky-Muller incompatibilities – Brand/Presgraves
Week 9 (Oct. 30th): Genetics of speciation II: Haldane’s rule – Brand/Presgraves
Week 10 (Nov. 6th): Genetics of speciation III: Chromosomal speciation – Longjun/Presgraves
Week 11 (Nov. 13th): Genetics of speciation IV: Genomics of speciation – Binshuang/Glor
Week 12 (Nov. 20th): Genetics of speciation V: Selfish genetic elements and speciation – Chengcheng/Presgraves
Week 13 (Nov. 27th): Speciation and macroevolution – Johnson/Glor
Week 14 (Dec. 4th): The future of speciation research – Chengcheng/Glor/Presgraves

The Presgraves and Jaenike Labs: Women in Science!

This week the women of the Presgraves and Jaenike Labs lead an outreach program at a Rochester Museum of Science mini camp. The focus of this camp was Women in Science where girls were able to learn about female role models in the science community.

We lead a workshop about courtship behavior using Drosophila and Nasonia as our model species. We all enjoyed interacting with the girls at the camp, and of course watching the males court the females!

If you’re interested in leading you’re own outreach program about courtship, please contact us- we’d be happy to share the materials and PowerPoint we used!

-Amanda L., Cara, Emily, Sarah, Amanda S., Tammy

News from the Werren Lab

Munni ready for Rochester summer

Three new members are welcomed to the Werren lab and Biology Department.  Mrinalini (Munni) arrived in April from Bangor University, Wales. She is researching the function and evolution of parasitoid venoms. Aisha Siebert is an MD/PhD candidate at UR who is investigating function and medical implications of parasitoid venoms. Matthias Williams is a new technician, also working on venoms.

Aisha

Dylan Sacks, an undergraduate scholar studying wing size evolution, has received an EDEN (Evo-Devo-Eco Network) Undergraduate Summer Internship to continue his work on positional cloning of a male specific wing size quantitative trait locus (QTL) causing wing size differences among Nasonia species.

Dylan

Congratulations to David Loehlin (Biology PhD 2011)! He received the Outstanding Dissertation Award from the University of Rochester School of Arts and Sciences for his work on the genetics of wing size and growth evolution.

Dave, being Dave

Spring bloom in the desert

About this time of year in Rochester, we are still early in the spring. However, in the Sonoran Desert spring bloom is almost over. One of the last plant species to bloom in the spring is the saguaro cactus, Carnegiea gigantea. Rob Laport and Bob Minckley were in Tucson and surrounding areas from 25 April to 7 May doing field work and giving presentations at a conference (madreanconference.org/) that meets every 8 years to discuss science and management issues of the Sky Island region (=northwestern Chihuahuan and northeastern Sonoran Deserts).

During the visit, we took this picture. Saguaros flowers produce tremendous amounts of pollen and nectar at night that attract bats. What is left over is cleaned up the following morning by bees and white-winged doves (Zenaida asiatica). The bees in the picture are honey bees (Apis mellifera).

Karyotypes of Two Species of Malagasy Ground Geckos

Over the last couple of years I’ve collaborated with Tony Gamble on a survey of karyotypes in geckos.  Tony is studying the evolution of sex determining mechanisms and geckos are an ideal model clade for such an endeavor because they have evolved every mechanism known in vertebrates.

An adult male of the undescribed Paroedura species in our study cleans his eye. Gekkonid geckos lack moveable eyelids and so clean their eyes with their tongues.

Around the time this collaboration started I “discovered” an undescribed gecko from the Malagasy genus Paroedura on a reptile dealer’s list.  I sent all of the specimens to Tony for karyotyping, and the results from this study were published in this month’s African Journal of Herpetology.

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