RESEARCH INTERESTS - DETAILS
My research interests are focused on the study of genetic variation within and between species. This essentially means three closely related activities: i) understanding how different processes affect levels and patterns of genetic variation by modelling the evolution of genetic lineages in populations and species and making predictions either theoretically or by simulation; ii) developing (and/or testing) statistical methods for estimating parameters and for quantitatively comparing alternative hypotheses; iii) producing molecular data in the laboratory and using the appropriate statistical techniques to reconstruct the evolutionary processes acting on a specific gene, a population, a species or a group of species.
I am very interested in, and I have been working on, all these three areas. I will briefly describe six research projects I am involved in currently.
1. The relevance of ancient DNA data for demographic and historical inferences: a simulation study
The relevance of ancient DNA data for the reconstruction of past demographic and divergence processes has been confirmed in many studies. However, ancient samples are difficult to find, and their molecular analysis is expensive and time consuming. It is therefore crucial to identify the characteristics of the sampling (number of ancient and modern speciments, their spatial and temporal distribution, etc.) under which ancient DNA yield a significant increase in the power of statistical methods for reconstructing population processes, in comparison to studies based on modern DNA data only. It is also very important to identify biases introduced when modern and ancient DNA data are jointly analysed using methods that assume the same age for all samples. For example, we recently found that classical neutrality tests detect a signature of demographic expansion in a population with constant population size when samples with different ages are jointly analysed (Mona et al., submitted). We are addressing these questions using intensive computer simulations based on coalescent theory.
2. Approximate Bayesian Computations in conservation genetics
Among several new statistical techniques, Approximate Bayesian Computation (ABC) is a very promising approach for analysing genetic data in species with complex histories. In this approach, summary statistics are used to compare observed data with data simulated for different values of the parameters of interests. The posterior distribution of parameters is obtained from simulations that produce the smallest difference between observed and simulated data. In principle, this approach can be used to estimate many parameters and compare several alternative models, since genetic data can be simulated under complex scenarios without major difficulties. We recently began to use this approach to study patterns of genetic variation in chamois populations, and found high posterior probability for a model which included unrecorded human-mediated translocations (reintroductions) Crestanello et al., 2009, Journal of Heredity, in press). We are now analysing all potential applications and problems of the ABC approach, especially in conservation genetics and molecular ecology. An invited review on this topic is in preparation for Molecular Ecology.
3. A genetic simulation tool supporting conservation strategies
A general tendency among policy makers and managers is to ignore the conservation of the most fundamental building blocks of adaptive evolution: the genetic differences within species. CONGRESS is a recently established consortium of 13 European Union research groups, with the mission to embed, enhance and broaden consideration of genetic biodiversity in conservation management in the EU and beyond. Within CONGRESS, my research unit will be in charge of producing a web package to be used for simulations to support intelligent project planning. Computer simulation underlies most recent developments in the analysis of the impact of complex demographic events on the patterns and levels of genetic variation within a species. Simulations of genetic variation specifically useful for conservation biologists and conservation managers will be carried out. In particular, a genetic variation simulator will be developed to address two types of problems commonly faced in practical conservation studies: 1) identifying key sampling requirements in a conservation genetics study, especially those which are relevant for deciding among alternative management plans; 2) predicting changes in genetic variation expected under various hypothetical conservation actions.
4. Genetic variation and divergence in wild boar and domestic pig breeds
The Eurasian wild boar is the wild ancestor of the domestic pig. They belong to the same species, Sus scrofa, hybridize with fertile offspring, and both have biological and economical value. We initiated a study of patterns of genetic variation in wild and domestic forms some years ago, in order to reconstruct the impact of demographic decline and subsequent expansion in some areas, reintroduction of allochtonous individuals, and hybridization with domestic forms. We were also interested in the domestication process (how many events? where?) and the evolution of genetic variation after the domestication (Vernesi et al., Molecular Ecology, 2003; Scandura et al., Molecular Ecology, 2008). We recently initiated a collaboration which involves typing of ancient samples (15.000 to1000 YBP) at the mtDNA control region, and both modern and ancient samples at a fragment of the MC1R gene (where some mutations are associated with coat colour), to examine the history of domestication and successive introgressions, and the selection processes acting on natural populations and domestic breeds before and after domestication events.
5. Genetic variation and conservation in the Herman’s tortoise (Testudo hermanni)
Genetic variation in this endangered species was analysed at several microsatellites (developed ad hoc, Forlani et al, 2005, Molecular Ecology Notes) and mtDNA markers in multiple populations, from Spain to Greece. Genetic structure and its origin were reconstructed. Habitat fragmentation and illegal introductions of allochtonous animals in some areas (with consequent hybridization) pose serious concerns for the conservation and management of this species. The implementation phase of the project is in preparation, which will involve (pending Ministry funding), the typing of several thousand individuals now maintained in captivity by local and governmental institutions. The genetic assignment of each individual to specific natural popoulations, and the detection of hybrids, will be used to select appropriate animals for reintroduction projects.
6. Genetic variation, translocations, and inter-specific hybridization in the chamois (Rupicapra spp)
We analyzed levels and patterns of genetic variation in the Alpine and the Pyrenean chamois (Mona et al., 2008, Molecular Ecology; Crestanello et al., 2009, Journal of Heredity, in press). In particular, we were interested in the taxonomy, the distribution of genetic variation among populations, and the genetic impact of over-hunting and past translocation events. We also compared neutral and MHC (Major Histocompatibility Complex) polymorphisms to better understand and distinguish the impact of natural selection on the geographic structure. During these studies, we found clear evidence of inter-specific hybridization occurring in some Alpine areas, where reintroduced chamois belonging to the Pyrenean species (R. pyrenaica) interbred with local Alpine chamois (R. rupicapra). This is a very interesting non-planned experiment. Two species, probably separated by more than one million years (based on the cytochrome b molecular clock), are mixing and producing fertile offspring. We plan to investigate in detail this process, which could represent a rare event of speciation reversal in a mammal. Our analysis will imply the genotyping of both neutral markers and coding regions, and we plan to measure fitness-related traits in the wild.
