Mots-Clés

Bioinformatics, evolution, markers, phylogeny, paleoproteomics, ZooMS

Description

Scientific backgroung: In recent years, the analysis of ancient biological samples has changed our understanding of the evolution of life on Earth, renewing the approaches previously used in paleontology based on the study of fossils or carbon-14 dating. At the forefront of new molecular techniques is paleogenomics (sequencing of ancient DNA), although DNA degrades relatively quickly. More recently, paleoproteomics via ZooArchaeology by mass spectrometry (ZooMS) offers a possibility to identify morphologically ambiguous or unidentifiable bone fragments from bone assemblages. Identification of bones with ZooMS results from the sequencing of a target protein, such as collagen, which is abundant in bone fragments. The collagen present in the samples is digested and the mass of the peptides obtained by spectrometry gives indirect information on the amino acid sequence of the protein studied.  To exploit this data, the community works with so-called marker peptides, which serve as a sort of molecular barcode for taxonomic assignment.

Research objectives: The goal of the thesis is to  formalise and  automate  ZooMS analyses in order to obtain robust and reproducible assignments, even on a large scale. This raises multiple questions:

• How to infer marker peptides at different taxonomic levels?
• How to measure the phylogenetic signal contained in the target protein and its peptides?
• How to use marker peptides for taxonomic assignment of mass spectra?
• How to reconstruct ancestral protein sequences from spectra and contemporary sequences to enrich contemporary data sets?

To address these topics, we want to develop innovative methods combining sequence algorithmic approaches and probabilistic frameworks using protein sequence evolution models to reconstruct phylogenetic trees and ancestral sequences. The expected results are twofold: to develop a toolbox for data analysis, and to propose a methodological framework for the informed use of marker peptides in ZooMS.

Partnership : The thesis will take place at University of Lille. It will be supervised by Hélène Touzet (DR CNRS, bioinformatics, bonsai team at CRIStAL) and Céline Poux  (associate professor, evolution, Evo-eco-paleo) in close collaboration with Fabrice Bray (MSAP) in charge of the ZooMS platform in Lille and Patrick Auguste (palaeontologist, EEP).