PALEOGENOMICA
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- Versione italiana
- Academic year
- 2021/2022
- Teacher
- GLORIA MARIA GONZALEZ FORTES
- Credits
- 6
- Didactic period
- Secondo Semestre
- SSD
- BIO/18
Training objectives
- Paleogenomics, also known as genome-wide ancient DNA analysis, is a multidisciplinary and rapidly evolving field of research, involving genetics, archaeology and palaeontology. During the last decade, aDNA studies evolved from the analysis of shorth DNA fragments (mainly from mitochondrial sequences) to the reconstruction of complete genomes from millenary remains. The success of the field goes together with the development of cutting-edge technologies for DNA enrichment and sequencing, which allow the recovery of ancient DNA (aDNA) molecules from fossils. As more ancient genomes are being sequenced, we are able to directly investigate the genetics of past populations and extinct species, which is enormously changing our understanding of the evolutionary processes.
In the subject of Paleogenomics, the students will be introduced to the study of aDNA molecules, both at the level of laboratory processes and computational analysis. We will explore the nature of post mortem molecular damage that are characteristic of aDNA and the technological advances for the extraction and sequencing of these highly degraded molecules from fossil materials. They will learn about different optimization methods for the recovery of aDNA molecules, including specific modifications in the construction of Next Generation Sequencing (NGS) libraries, as well as a range of hybridization capture approaches for DNA enrichment. Once the students are familiar with the molecular aspects of aDNA, they will be introduced to the computational methods for the mapping of aDNA sequences and to different software to evaluate the quality and authenticity of the ancient sequences. Finally, they will be provided with theoretical and practical knowledge for the analysis of ancient DNA sequences in the context of forensics and population genetics. We will explore different methods for individual identification based on the reconstruction of monoparental markers, and the identification of phenotypic traits from genetic data. At population level, the students will be guided through a set of software and statistical tools for the characterization of the genetic backgrounds, patterns of admixture and demographic changes in ancient populations.
By the end of the course, the students will have developed a set of highly demanded skills for the analysis of genome sequences, both at the level of individual and population genetic analysis. The students will be able to understand scientific papers on the field and to integrate knowledge from different areas in order to interpret the genetic data in their archaeological and palaeontological context. Beyond the acquisition of theoretical and practical knowledge specific to the subject, Paleogenomics will allow students to apply prior knowledge from subjects of the first and second years (as for example in population genetics, biostatistics, conservation genetics), into a multidisciplinary, cutting-edge and expanding field of research, with a wide range of applications in the fields of forensic, anthropology and palaeontology. Prerequisites
- The student must have a solid based on genetics, as well as basic knowledge of biostatistics and bioinformatics. Ideally, but not mandatory, the students choosing this course, shall have completed the first year subjects of Population genetics and Evolution, and Bioinformatics and Biostatistics, also prior knowledge from the second year subject of Conservation Genetics would be useful.
Course programme
- This is a 52 hour course, 48h of theory and 12h of practical lessons. The teaching hours and contents are distributed as follow:
Part I. Concepts, Challenges and Technical advances (10 hours)
Ancient DNA: Achievements, potential and limits of this young research field.
Characteristics of ancient DNA. Post-mortem damage in DNA molecules.
Laboratory methods and technical improvements. An overview of classical and next-generation methods for the sequencing of ancient DNA molecules.
Setting up an ancient DNA laboratory.
Case study: Laboratory workflows in the pre- and post-petrous era. A focus on DNA extraction methods.
Rohland N et al. 2010. A rapid column-based ancient DNA extraction method for increased sample throughput. Mol Ecol Resour 10:677–683
Dabney et al. 2013. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. PNAS, 110(39): 15758-15763
Gamba et al 2014. Genome flux and stasis in a five millennium transect of European prehistory. Nature Communications 5: 5257
Part II. Genome-scale analysis of ancient DNA (12 hours of theory and 4 hours of practice).
Application of cutting-age technologies to the reconstruction of ancient DNA sequences. Capture vs shotgun sequencing strategies. A focus on the Human Origin array.
Computational processing of high-throughput ancient DNA sequencing data. Authentication and assessment of contamination in NGS data from ancient remains.
Case Study: Enrichment of endogenous ancient DNA by hybridization capture.
Gonzalez-Fortes et al 2016. Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears. Mol Ecol, 25(19):4907-18.
Lazaridis et al. 2014. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513: 409–413.
Practical lessons (4 hours):
Getting used to Unix. Understanding NGS data. Mapping to a reference genome. Checking for PCR duplication problems, contamination, etc. Variant calling. Filtering and handling VCFs. Mitochondrial haplogroup determination in humans and estimation of contamination from mitochondrial data.
Part III. Population and Evolutionary inferences from ancient DNA (14 hours of theory and 8 hours of practice).
Molecular anthropology in the era of paleogenomics. Defining ancestral components and inferring demographic history from ancient genome data. Integration of ancient and modern DNA data in population genetic analysis.
Archaic hominids and the role of admixture in human evolution. Detecting hybridization with D- and f- statistics.
Population Genomics of Animal Domestication: an ancient DNA perspective.
Learning from the past: can paleogenomics aid conservation and management decisions?
Case study I: Identification of the main demographic events in European prehistory: The Neolithic and Russian steppes genetic legacy.
Haak et al 2015. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature, 522: 207–211.
Case study II: Detecting admixture from archaic hominids.
Green et al 2010. A Draft Sequence of the Neandertal Genome. Science 328: 710-722
Hajdinjak et al. 2018. Reconstructing the genetic history of late Neanderthals. Nature 555: 652–656
Case study III: The role of admixture in ancient domestication processes.
Verdugo et al 2019. Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. Science 365: 173-176
Practical lessons (8 hours):
Characterization of the genetic structure from Principal component analysis (PCA) and Admixture. Formal test of admixture using f-statistics. Detecting gene flow with D-statistics.
Part IV. Prospects: The present and future of ancient biomolecule studies (4 hours). Environmental DNA. Ancient RNA. Ancient Epigenomics. Paleoproteomics. Didactic methods
- The course is organized in master classes complemented with practical lessons. The master classes will be used for the transfer of theoretical knowledge through oral presentations, supported on audio-visual resources (power point and video presentations). The students will be guided through the process of finding and understanding scientific bibliography related to the main concepts addressed in the theory lessons. The master lessons will be complemented with small research projects and practical training for the computational analysis of ancient DNA data.
Learning assessment procedures
- Written exam including 21 questions in the form of multiple-choice and short answer questions. Also, the students may be offered the possibility of taking an oral exam if the final number of the matriculated students allows so. In any case, the examination time will not excess one hour.
Reference texts
- Specific texts and material for the study will be provided by the teacher.
Ancient DNA, Methods and Protocols. Springer Protocols. Editors: Shapiro, B., Barlow, A., Heintzman, P.D., Hofreiter, M., Paijmans, J.L.A., Soares, A.E.R. (Eds.)
