Group Alvarez
Comparative Phylogeography of Biotic Interactions

Coevolution has been invoked to explain the incredible diversity of life on Earth. Coevolution appeared to have shaped this diversity in several ways as for example the apparition of eucaryots (intracellular coevolution), the maintenance of complex environments (as the case of the fig and the fig-wasps and its nutritional role in forests), or the ecosystemic services that interactions provide in terms of protection (e.g. coral reefs) or food (fruit and nutriment production).

Studying interactions allows us understanding the forces that molded their apparition, their development and their final establishment and survival. It also provides tools for the understanding of the complexity of communities in order to best protect them.

While coevolution can happen in a relaxed (generalistic) or a close (specialized) manner, studying specific and obligate interactions is an optimal way to understand the dynamics of interbiotic relationships, since the level of complexity –in terms of number of interacting organisms– is reduced and variables are thus easier to understand.

Suggested references
Malmstrom, C. (2010) Ecologists study the interactions of organisms and their environment. Nature Education Knowledge. 1(8):9.
Weiblen, GD. (2002) How to be a fig wasp. Annu. Rev. Entomol. 47, 299-330.

Comparative phylogeography seeks to discover common historical patterns in the elements of biotas, in relation with topographical or ecological factors. By comparing the phylogeographic structures of sympatric species, one can infer whether the current assemblage of species has been historically stable, as evidenced by the relative frequency of geographically congruent reciprocally monophyletic groups. Alternatively, if species distributions are ephemeral over evolutionary time, a mixture of phylogeographic structures is expected.

Timing of vicariance or dispersal events can be estimated by applying a molecular clock to species phylogenies. However, by doing so, differences in effective population sizes, mutational rates and mutational rate heterogeneity are not taken into account. As a consequence, evolutionary events that arose at different times can be difficult to distinguish from one another and might be interpreted as a single event. The second corollary is that this variation can also cause a simultaneous event to appear to have occurred at multiple times. To reduce such uncertainty, it is necessary to use coalescence-based methods from the field of statistical phylogeograph, which account for the stochastic nature of the evolutionary process while allowing tests of simultaneous diversifications. These methods can also incorporate biologically realistic scenarios such as different effective population sizes, expanding populations and various levels of gene flow, making them potent tools. These scenarios can also be drawn from inferences of past distributions yielded using ecological niche modelling approaches.

Suggested references
Carstens, BC. Richards, CL. (2007) Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution. 61, 1439-1454.

Knowles, L. L. 2004 The burgeoning field of statistical phylogeography. J. Evol. Biol. 17, 1-10.

Rosenberg, N. A. & Nordborg, M. 2002 Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3, 380-390.

Zink, R. M. 2002 Methods in comparative phylogeography, and their application to studying evolution in the North American Aridlands. Integr. Comp. Biol. 42, 953-959.

The theory of coevolution has been first proposed when studying plants and insects. This is not just by chance. These two groups frequently develop coevolutionary processes for the last 400 million years. Plant and insects are also the two most specious living groups on Earth (eg, at least 400'000 species of herbivorous insects have been described up to date).

Plant-insect interactions appear thus ideal to test and investigate (co)evolutionary topics, since they present the advantages of being numerous, but also of having been happening for a long time.

Suggested references
Jolivet, P. (1998) Interrelationship between insects and plants. CRC Press, Boca Raton, FL.

Proctor, M. (1996) The natural history of pollination. Timber Press, Portland, OR.

Studying the history of lineages in non-model species basically relies on the rough combination of classic sequencing/genotyping technologies with ecological and geographical data. Here, we develop a methodological framework to implement outputs from the recently developed ultra-high-throughput-sequencing technologies (UHTS) into the field of statistical phylogeography. Our study will allow disentangling historical and selective processes that arose in specifically interacting species of plants and insects.

Since the late 1980s, the combination of classic molecular biology, ecology and geography has allowed researchers to address the phylogeography (or biogeographic history) of thousands of species around the world. In the recent few years, with the advent of the pyrosequencing revolution, molecular biologists have increased the resolution and power of sequencing technologies by several levels of magnitude. These new technologies have, however, not been included yet into main stream phylogeographic studies. In this project, we aim at integrating outputs from these promising methods into a more thorough analytical approach of phylogeography. We will consider coalescence and multi-genic analyses to explore the biogeographic history of several species of interest one step further. Following a previous SNSF project (3100A0-116778), we will focus on two mutualistic interactions involving plants and insects (ie, the globeflower & its pollinating flies and the yellow loosestrife & its pollinating bees). Thanks to the increased power of UHTS technologies and while this study takes place in the framework of comparative phylogeography, we will be able to address historical and selective patterns that arose from coevolutionary processes between tightly linked species of plants and insects.

Objectives
By integrating new sequencing technologies into the classical framework of phylogeography, this project aims going deeper into the resolution of single-species historical biogeographies. The objective is to develop a fully probabilistic approach in comparative phylogeography. By considering coalescence and multiple genes sequencing, we will go one step further into the understanding of historical and selective processes that shaped genetic lineages of interacting species of plants and insects.

Signification
Whereas recently developed pyrosequencing methods are widely used in genomic sciences, "natural sciences" oriented fields are still relying on thirty-years old sequencing technologies. Integrating pyrosequencing technologies into phylogeographical studies of non-model species is crucial to address the history of lineages with more accuracy.

Suggested references
Emerson, KJ., Merz, CR., Catchen, JM., Hohenlohe, PA., Cresko, WA., Bradshaw, WE., Holzapfel, CM. (2010) Resolving postglacial phylogeography using high-throughput sequencing. Proc. Natl. Acad. Sci. U.S.A. 107, 16196-16200.

Tautz, D., Ellegren, H., Weigel, D. (2010) Next generation molecular ecology. Mol. Ecol. 19, 1-3.