Lectures

Andy Knoll

Lecture 1 - The Deep History of Life

The fossil record of animals goes back some 600 million years, but the Earth is much older than that -- some 4567 million years, in fact. Phylogenies suggest that the deep history of life on Earth is microbial. In this lecture, we will explore how fossils, preserved biomolecules and a chemical record of environmental history inform our understanding of the first 85 percent of life’s history.

Required Reading

1. Knoll, A.H. (2012) Systems paleobiology. Geological Society of America Bulletin, in press

Lecture 2 - Fossils, Physiology and Evolution on a Dynamic Planet

Fossils provide a narrative history of life, and chemical signatures in sedimentary rocks document a dynamic environmental history marked by both transient perturbations and long term state changes. In this lecture, I will argue that physiology provides the conceptual bridge between Earth’s records of biological evolution and environmental change.

Required Reading

2. Knoll, A.H. (2009) The coevolution of life and environments. Rendiconti Lincei 20: 301-306.

3. Knoll, A.H. (2011) The multiple origins of complex multicellularity. Annual Review of Earth and Planetary Sciences 39: 217–239.

 

Alexander Kellner

Lecture 1 - TBA

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Required Reading

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Lecture 2 - TBA

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Required Reading

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Susana Magallon

Lecture 1 - Fossils in phylogenies, and their role in calibrating molecular clocks.

The relevance of fossils in informing about past evolutionary processes is fully realized when considered in an explicitly phylogenetic context. This lecture will review available methods to explicitly include fossils in phylogenetic hypotheses, and will subsequently consider the nature of the fossil record, and what it implies regarding its potential to calibrate molecular clocks. Several recently available methods to identify placement of fossils on trees for calibration purposes will be discussed.

Required Reading

1. Wiens, J.J. 2009. Paleontology, genomics, and combined-data phylogenetics: can molecular data improve phylogeny estimation for fossil taxa? Syst. Biol. 58:87-99.

2. Pyron, R.A. 2009. A likelihood method for assessing molecular divergence time estimates and the placement of fossil calibrations. Syst. Biol.

Lecture 2 - Insights estimating the age of flowering plants: molecular clocks, long branches, gene effects, and the fossil record.

Angiosperms (flowering plants) are the preponderant structural and energetic components of modern terrestrial ecosystems. Although molecular clocks and fossil evidence congruently identify that angiosperms diversified much later than any other major group of plants, there are profound incongruences in the respectively estimated dates, with molecular estimates preceding fossil estimates by 60 Ma. This lecture will examine potential sources of error in these estimates, including the effect of genes with different substitution rates, and the use of fossil constraints.

Required Reading

3. Magallón, S. 2010. Using fossils to break long branches in molecular dating: a comparison of relaxed clocks applied to the origin of angiosperms. Syst. Biol. 59:384-399.

4. Brandley, M.C., et al., 2011. Accommodating heterogeneous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plesiodon (Eumeces) lizards. Syst. Biol. 60:3-15.

 

Nancy Moran

Lecture 1 - Symbiosis as a source of innovation and complexity in host evolution

There is increasing recognition that symbiosis is ubiquitous in animal and plant hosts and that host and symbiont show varying levels of intimacy. This lecture will explore the evidence that associations with bacterial symbionts are evolutionarily ancient and will illustrate how this complicates host biology. I will focus on how genomic data can be used to reconstruct the roles of symbionts in host biology.

Required Reading

1. McCutcheon, J. P., and N. A. Moran. 2012. Extreme genome reduction in symbiotic bacteria. Nature Reviews Microbiology 10: 13-26.

Lecture 2 - Genome dynamics in bacterial symbionts and consequences for host evolution

Symbiotic bacteria have provided case studies of genome evolution, illustrating the consequences of genetic drift for maintenance of genes and genome architecture. This lecture will consider how the population structure of bacterial symbionts, particularly the extent to which they arestrictly asexual and vertically transmitted, affects their evolution and, in turn, that of their hosts.

Required Reading

2. Burke, G. R., and N. A. Moran. 2011. Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids. Genome Biology and Evolution 3:195-208.

3. Oliver, K. M., P. H. Degnan, M. S. Hunter, and N. A. Moran. 2009. Bacteriophage encode factors required for protection in a symbiotic mutualism. Science 325:992-994.

 

Howard Ochmann

Lecture 1 - The evolution of bacterial genomes

What have we learned from the sequences of nearly 3000 bacterial genomes? This lecture will trace the history of bacterial genomics and describe the factors that shape the structure, contents and organization of bacterial genomes. As the number of complete genome sequences accumulate, the application of a comparative approach can help distinguish those features of bacterial genomes that are adaptive from those that arose through non-adaptive processes.

Required Reading

Reading 1

Reading 2

Lecture 2 - The origin and evolution of new bacterial genes.

What is the basis of the ecological, physiological and metabolic diversity displayed by bacteria? Unlike eukaryotes, in which major innovations arise mainly through the duplication of existing genes and through changes in the patterns of gene regulation, many (perhaps most) new traits in bacteria originate through gene acquisition. This lecture will describe the processes by which bacteria acquire new genes, how it is possible to recognize events of lateral gene transfer, and how gene transfer has caused changes in bacterial lifestyles, particularly its role in the evolution of bacterial pathogens.

Required Reading

Reading 1

Reading 2

 

Mark Martindale

Lecture 1 - Can development tell us anything about evolution?

 

Lecture 2 - The evolution of novel metazoan body plans and cell types.

 

Required Reading

1. Mark Q. Martindale and Andreas Hejnol (2009) A Developmental Perspective: Changes in the Position of the Blastopore during Bilaterian Evolution. Developmental Cell.

2. Yale J. Passamaneck Nina Furchheim, Andreas Hejnol, Mark Q Martindale, Carsten Lüter (2011) Ciliary photoreceptors in the cerebral eyes of a protostome larva. EvoDevo 2:6.

 

Michael Alfaro

Lecture 1 - New tools for macroevolutionary studies on large trees

As we resolve ever-larger sections of the Tree of Life there is an increasing need for comparative methods that are well-suited to the analysis of large phylogenetic data sets. I will present new comparative methods that solve some common problems presented by large trees and data sets including: how can we scan for rate shifts on very large trees, how can we integrate taxonomic data with incompletely resolved phylogenies, and how can we use fossils to improve models of trait evolution? These methods will be available as part of the GEIGER 2.0 package in R.

 

Lecture 2 - What are the engines of fish biodiversity?

Ray-finned fishes represent the largest radiation of vertebrates and contain several lineages which exhibit startling degrees of morphological and ecological diversity and species richness. I will explore the role of macroevolutionary phenomena such as colonization of reef and other novel habitats, trophic innovation, adaptive radiation and convergent evolution in shaping diversity patterns in several major lineages of marine fishes. I will also present evidence of correlated rates of speciation and morphological evolution across the fish tree of life that is consistent with the idea that evolvability has played a major role in generating the diversity of the modern fauna.

 

Required reading:

Slater, G. J., L. J. Harmon, and M. E. Alfaro. 2012. Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution in press.

Eastman, J. M., M. E. Alfaro, P. Joyce, A. L. Hipp, and L. J. Harmon. 2011. A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution 65

 

Gunter Wagner

Lecture 1- Transposable elements as engines of gene regulatory network evolution

Cis-regulatory elements are critical for transcriptional regulation and thus changes to CREs are a key feature of the evolution of gene regulatory networks as well as the evolution of development. A well documented mode of CRE evolution is by nucleotide substitutions that either create or destroy a transcription factor binding site. However, major innovations require massive re-organizations of the gene regulatory network and nucleotide substitutions are inadequate to effect changes of large scale. In recent years it became clear that transposable elements can be major contributors to gene regulatory changes. In this module I will discuss the role of transposable elements as drivers of gene regulatory network evolution.

Required Reading

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Lecture 2 - The role and mechanisms of transcription factor evolution

Besides CRE evolution it is now clear that changes to transcription factors make a major contribution to gene regulatory evolution. I will review the facts that initially led people to think that transcription factor evolution is not important, and then show the evidence for the role of transcription factor evolution. Then I will discuss the two major remaining questions 1) how do transcription factors change and affect gene regulation? 2) what is the biological role of transcription factor evolution.

Required Reading

TBA

 

Tiago Quental

Lecture 1 - The role of speciation and extinction on biodiversity dynamics.

In this lecture we will discuss the role of speciation and extinction on the origin, maintenance and elimination of biodiversity. We will also illustrate how the fossil record, molecular phylogenies and computer simulation can be integrated to investigate the dynamics of diversification, and the potential factors that might affect speciation and extinction rates.

Required Reading

1. Bambach RK, Knoll AH, Wang SC (2004) Origination, extinction, and mass depletions of marine diversity. Paleobiology, 30:522-542

2. Quental TB, Marshall CR (2010) Diversity dynamics: molecular phylogenies need the fossil record. Trends in Ecology and Evolution 25:434-441.

 

Marcello Simões

Lecture 1 - Evolutionary paleoecology of the Bivalve Mollusks in Epeiric Sea Systems: Permian and Miocene Examples from South America.

Why molluscan faunas are considered good model groups for the study of evolution in Paleobiology? Gastropods and bivalve mollusks are among the dominant groups thriving in long-lived lakes and shallow epicontinental seas. These particular, isolated geological settings are considered to be aquatic islands of diversity and endemicity over cratonic areas (continental interior). Their molluscan faunas are almost completely isolated from freshwater and fully marine faunas. Huge lake/sea systems were common during the Late Paleozoic, and well-preserved sedimentary sequences are available in Brazil. In these successions, the exceptional fossil preservation (Fossil Lagerstätten) of bivalve shells indicates that in many clades, extensive radiations in unrelated lineages have occurred. These resulted in relatively high species numbers and a puzzling array of morphologies (high morphological disparity). Since these faunas evolved in situ within the lake/sea setting, they offer us key case study examples in evolutionary ecology. Here we will show and discuss the taphonomy, and evolutionary ecology of Permian bivalve mollusks that evolved in a large lake/sea system, namely the Paraná Basin and compare it with the evolution of Miocene bivalves in the long-lived Pebas Lake, from Amazon.

Required Reading

1. Allison PA, Bottjer DJ (2011) Taphonomy: bias and process through time. Topics in Geobiology 32.

2. Wesselingh FP (2007) Long-lived lake molluscs as Island Faunas: a bivalve perspective. In: Biogeography, time and place: distributions, barriers and Islands.

 

Antonio Carlos Marques

Lecture 1 - Evolutionary reasoning applied to conservation biology

In its core, conservation biology deals with the conservancy of evolutionary patterns and processes, both historical and ecological. Therefore, the understanding of the outcomes of evolution, or biodiversity itself, from genes to ecosystems or areas of endemism, is mandatory for conservation purposes. The the goal of this lecture is to present different time and biological scales in marine examples dealing with several interdependent and entangled areas of research ultimately related to conservation.

Required Reading

1. Soulé ME (1985) What is conservation biology? Bioscience 35:727-734

 

André V. L. Freitas

Lecture - TBA

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Required Reading

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