First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
MOLECULAR BIOLOGY
Course unit
COMPUTATIONAL ANTHROPOLOGY
SCP8085072, A.A. 2019/20

Information concerning the students who enrolled in A.Y. 2018/19

Information on the course unit
Degree course Second cycle degree in
MOLECULAR BIOLOGY
SC2445, Degree course structure A.Y. 2018/19, A.Y. 2019/20
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Degree course track MOLECULAR BIOLOGY [005PD]
Number of ECTS credits allocated 6.0
Type of assessment Mark
Course unit English denomination COMPUTATIONAL ANTHROPOLOGY
Website of the academic structure http://biologiamolecolare.scienze.unipd.it/2019/laurea_magistrale_molecularbiology
Department of reference Department of Biology
Mandatory attendance
Language of instruction English
Branch PADOVA
Single Course unit The Course unit can be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Lecturers
Teacher in charge LUCA PAGANI BIO/08

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Educational activities in elective or integrative disciplines BIO/08 Anthropology 6.0

Course unit organization
Period First semester
Year 2nd Year
Teaching method frontal

Type of hours Credits Teaching
hours
Hours of
Individual study
Shifts
Practice 3.0 48 27.0 No turn
Lecture 3.0 24 51.0 No turn

Calendar
Start of activities 30/09/2019
End of activities 18/01/2020
Show course schedule 2019/20 Reg.2018 course timetable

Syllabus
Prerequisites: Prior knowledge needed for the classes in Computational Anthropology is that normally provided for students at the final class of the first degree in Molecular Biology. Particularly, the basic understanding of Genetics, Statistics, Phylogeny, and Evolutionary Biology in their fundamental principles and processes, is required. Students must also be familiar with the Unix/Shell environment. No prior knowledge is requested about specific contents in Population Genetics and Genomics, however scientific contents of the "Anthropology" course may be of great help during this course.
Target skills and knowledge: Contents and skills to be acquired at the end of the classes in Computational Anthropology belong mainly to four areas:
1) basic notions on genetic admixture dynamics and on methods to infer them, applied to the fields of personal genomics and ancestry analyses;
2) practical skills: PCA, Admixture, Ancestry Deconvolution;
3) population differentiation analyses (Fst) and search for statistical outlier markers as putative indicators of natural selection events;
4) ability to partly reproduce results and analyses of the most recent scientific papers (for which data is available) on ancient DNA and human-archaic hybridizations;
Examination methods: Examination will be based on a practical exercise of approximately 3 hours, to be carried out in the computer room. The exercise will include the main topics of the course and will be comparable to what already experienced during the hands on lectures. Final evaluation will be based upon the obtained results and will follow a discussion with the teacher about the information and procedures carried out to solve the exercise.
Assessment criteria: Evaluation criteria are:
- Argumentative skills;
- Acquired knowledge in the field of Molecular Anthropology;
- Bioinformatic skills applied to the case studies
Course unit contents: The course aims at blending basic knowledge within the fields of Molecular Anthropology and Human Population Genetics with practical (bioinformatic) skills, transferable to the expanding occupational sectors of Personal Genomics and Ancestry analyses.
The following topics will be explored from a theoretical and a practical/applicative angle:
1) Genetic admixture and local ancestry;
2) Ancestry deconvolution and ancestry-specific analyses;
3) Population differentiation among human groups, both at a genome-wide and at a locus-specific level;
4) Effect on the genome of natural selection events;
5) Introgression events between Homo sapiens and Archaic humans;


These general objectives are addressed through critical discussion of case-studies taken from primary scientific literature on Molecular Anthropology, and through extensive hands on exercise in a computer lab.
Planned learning activities and teaching methods: The course is structured in 12 frontal lectures of 2 hours each (24 frontal hours, 3 CFU) and in 12 hands on lectures of 4 hours each (48 lab hours, 3 CFU).
Frontal lectures will introduce topics and basic theory through recent scientific results.
The introduced topics will be further addressed from a practical angle, in a Unix environment, during the lab hours under the constant supervision of the teacher. Hands on work will compile, step by step, the toolkit needed to carry out ancestry analyses, which will form the starting point for the final (practical) exam.
Additional notes about suggested reading: The available materials are:
- 1) Slides for each lesson, made available to students by e-learning a few days after the lesson; PPT presentations allow students to follow the thread of the discussion;
- 2) Textbooks for a general introduction to the subject;
- 3) Recent scientific papers and reviews;
- 4) Further texts (optional) suggested during the classes.
Textbooks (and optional supplementary readings)
  • Mark Jobling, Chris Tyler-Smith, Edward Hollox, Matthew Hurles, Toomas Kivisild, Human Evolutionary Genetics, Second Edition. --: Garland Science, 2013. Cerca nel catalogo

Innovative teaching methods: Teaching and learning strategies
  • Laboratory
  • Problem based learning
  • Case study
  • Working in group
  • Problem solving
  • Work-integrated learning
  • Active quizzes for Concept Verification Tests and class discussions
  • Loading of files and pages (web pages, Moodle, ...)
  • Students peer review

Innovative teaching methods: Software or applications used
  • Moodle (files, quizzes, workshops, ...)
  • Kahoot

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