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DRPS : Course Catalogue : School of Biological Sciences : Evolutionary Biology

Undergraduate Course: Human Evolutionary Genomics (EVBI10010)

Course Outline
SchoolSchool of Biological Sciences CollegeCollege of Science and Engineering
Credit level (Normal year taken)SCQF Level 10 (Year 4 Undergraduate) AvailabilityNot available to visiting students
SCQF Credits10 ECTS Credits5
SummaryThe extension of next-generation DNA sequencing from extant organisms to fossils has been spearheaded by the desire to understand human origins. This course will cover the methods by which this knowledge is gained, what has been learnt with respect to the last 100,000 years of human history and the population genetics that is critical to our understanding of the underlying processes.
Course description The extension of next-generation DNA sequencing to geologically fossils has been spearheaded by the desire to understand human origins. This course covers the methods by which this knowledge is gained, what has been learnt with respect to the last 100,000 years of human history and the population genetics that is critical to our understanding of the underlying processes.
The course will focus on modern humans, Neanderthals and Denisovans, the exit from Africa and its evolutionary consequences. Introgression among these will be considered in detail, its present-day outcome and the role both positive and negative selection has played in determining that. The course will also consider more recent events, including the major population movements that have been revealed by palaeogenomics to have been associated with the Neolithic revolution and the spread of the Indo-European languages, and evidence for parallel events within Africa.
Students will be aware at the conclusion of this course that Africa is the origin of modern humans and the African human population shows far more genetic diversity than that found among non-African populations. They will understand the nature of species mixing that affects all non-African populations as they show introgression of Neanderthal DNA, and for Melanesian populations of Denisovan DNA as well. The students will acquire understanding of population genetics, particularly of human mutation rates, linkage disequilibrium and selection which will allow them to evaluate the evidence for these events. They will acquire skills in analysis of data from such settings from practicals using real data and in critical evaluation of the literature in assessed coursework.
Topics to be covered:
The palaeontological background of hominin evolution over the last 2 million years
Molecular population genetics revision - reviewing fundamental concepts in population genetics of particular relevance to human molecular evolution and variation
Mutation rate in humans - contrasting estimates of the mutation rate in humans, based on between-species molecular divergence and genome sequencing of relatives. The human deleterious mutation rate and the mutation load paradox.
Problems and technical solutions in palaeogenomics: DNA degradation & contamination; ultra-short reads & CT modification
Variation in nucleotide diversity across the human genome - why genetic linkage reduces the efficiency of natural selection and how linkage to sites under selection reduces diversity.
Palaeogenomics - Neanderthals, Denisovans and modern humans up to 20kyrBP: divergence and diversity in recent hominins
Archaic introgression from Neandertals and Denisovans into Eurasians; lack of evidence for introgression from mt trees; ABBA/BABA test and admixture graphs; archaic introgression in Africa
The mechanistics of recombination in humans; hotspots and coldspots and their evolution (comparing Great Apes); sex bias in recombination.
Recombination as a clock: Modelling recombination along the genome; inferring the out of Africa bottleneck from single diploid genomes. Homozygosity tracts and inbreeding in Altai Neandertals and Denisova. Introduction to chromosome painting. The fate of introgressed tracts under neutrality; comparison of Neanderthal tracts in modern and ancient H.sapiens genomes.
Introgression and its legacy: Adaptive archaic introgression in Humans (e.g. Denisova high altitude haplotype, MC1R, Toll-like receptors). Maladaptive archaic introgression: autoimmune disorders; perhaps a little bit on complex traits linked to archaic introgression
What made modern humans - long-term selection acting on the lineage leading to modern humans - MK-like analysis of selection on the hominin lineage, and historic sweep analyses of the AMH lineage
Post-glacial palaeogenomics: The hunter-gatherers and the Neolithic revolution. Population diversity in the Bronze age.
Global mass migration - its long history revealed in 5 continents
Recent positive selection - recent selection on the human genome, including soft, recent, and local sweeps at loci involved in appearance, immunity, and the (sometimes self-imposed) environment
Basis of genetic disease - potential epistatic costs of past positive or balancing selection ('mismatches with modernity') and the potential to identify loci through GWAS given the DFE

The course will be delivered through lectures, with a small number of tutorials on specialist topics and will be assessed by a single piece of in-course assessment counting for 20% and an exam counting 80% of the total marks for the course.
Entry Requirements (not applicable to Visiting Students)
Pre-requisites Students MUST have passed: Evolutionary and Ecological Genetics 3 (BILG09004)
Prohibited Combinations Other requirements None
Course Delivery Information
Academic year 2020/21, Not available to visiting students (SS1) Quota:  None
Course Start Semester 1
Timetable Timetable
Learning and Teaching activities (Further Info) Total Hours: 100 ( Lecture Hours 19, Seminar/Tutorial Hours 4, Revision Session Hours 1, Programme Level Learning and Teaching Hours 2, Directed Learning and Independent Learning Hours 74 )
Assessment (Further Info) Written Exam 0 %, Coursework 100 %, Practical Exam 0 %
Additional Information (Assessment) 100% In-Course Assesment
Feedback Not entered
No Exam Information
Learning Outcomes
On completion of this course, the student will be able to:
  1. Know the recent evolutionary history of the hominin group as revealed by studies of ancient macromolecules and the fossils they came from.
  2. Understand the population genetic basis for interpreting ancient genomes, and be able to evaluate the evidence for the events revealed
  3. Understand how the complex pattern of relationships among the genomes of recent hominins indicates hybridisation events involving archaic forms and selection on the introgressed genes
  4. Be familiar with the genetic evidence for successive population replacements in Europe
  5. Acquire skills in analysis of data from such settings and in critical evaluation of the literature
Reading List
Additional Information
Graduate Attributes and Skills Not entered
Course organiserProf Andrew Leigh-Brown
Tel: (0131 6)50 5523
Course secretaryMiss Rachel Law
Tel: (0131 6)51 3689
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