Syllabus
PART I.
1 - THREE KEYWORDS IN GENETICS
The concepts of gene, locus and allele, despite being so fundamental in the modern science of Genetics, are surprisingly fuzzy
Suggested reading: Pesole G. What is a gene? An updated operational definition. Gene. 2008;417:1-4
2 - WHAT IS POPULATION GENETICS?
The goal of a complete theory of population genetics is to describe the evolutionary change of populations as a process where changes in the phenotypic space maps to changes in the genotypic space, and then back to the phenotypic space of the next generation. This is, in general, a formidable challenge. In extremely simplified cases, this task has been accomplished with reasonable confidence of having approximated reality fairly well
3 - THE MANY FACETS OF POPULATION GENETICS
For most part of the history of Genetics, population genetics was almost only a theoretical science; starting from the late 70ies, a huge amount of experimental data on genetic variation in natural populations became available, and the main goal of population genetics shifted towards describing and interpreting this variation; with the advent of high-throughput DNA analysis, population genetics has found applications in a variety of different fields, including evolutionary genetics, ecological genetics, demographic genetics, genetic epidemiology, conservation genetics, quantitative genetics, forensic genetics
Further readings:
CastanoSanchez_SNPDiscoveryRainbowTrout_BMCGenomics_2009.pdf
Jorde_DemographicGeneticsBrownTrout_Genetics_1996.pdf
Schilthuizen_RapidHabitatRelatedEvolutionSnail_Heredity_2013.pdf
Vidal_EcologicalGeneticsFreshwaterFish_AnimBiodivConserv_2011.pdf
4 - THE SPECIES PROBLEM
Is the species a true biological entity, a superorganism that has its own individuality, or is it an arbitrary concept, used only for the sake of convenience?
5 - VARIATION WITHIN SPECIES
With the concepts of subspecies,
populations, races, and breeds we try to grasp the complexity of
the variation observed within species. Populations have a clear-cut definition, and are the smallest units
of evolution.
6 - MENDELIAN VS QUANTITATIVE VARIATION
In nature, Mendelian inheritance of phenotypic traits is a rare occurrence, meaning that most of the variation among individuals that is the basis of evolutionary change is not due to variation of single genes
7 - GENETIC POLYMORPHISMS
Genetic polymorphism is the occurrence in the same population of two or more alleles at one locus, each with appreciable frequency. Variation at the DNA level is enormous in any natural population, but what is its phenotypic/evolutionary meaning?
Leffer_RevisitingGeneticDiversityWithinSpecies_PLOSBio_2012.pdf
8 - GENOTYPE AND ALLELE FREQUENCIES
Estimates of genotypic and allelic frequencies, and test for Hardy-Weinberg equilibrium are the first steps for any population genetics study
PART II.
9 - MEASURING GENETIC VARIATION
Among several indexes used to quantify the level of genetic variation in populations, the expected heterozygosity plays a pivotal role
Bouga_AllozymwVariabilityHoneyBee_BiochGenet_2005.pdf
10 - MIXED POPULATIONS
Mixing populations with different allele frequencies has the surprising effect of generating an excess of homozygotes compared to Hardy-Weinberg expectations
11 - INBREEDING
What does it mean to eliminate genetic variation from genomes? The case of the inbred strains of mice
12 - HIERARCHICAL POPULATION STRUCTURE
Natural populations are often hierarchically structured. The original notation of Wright's F-statistics is still widely used to describe population structure, though several other computational methods have been proposed in the course of the years
Wilson_PopulationStructureArticCharr_MolEcol_2004.pdf
13 - GENETIC DISTANCES
A genetic distance is a measure of how much any two population have differentiated from each other in terms of allele frequency; it is also a measure of how much any two DNA sequences, however evolutionary distant, differ from each other
14 - ELEMENTS OF SYSTEMATICS
Similarities versus relatedness: the evolution of a taxonomic theory of living things
15 - PHYLOGENETIC TREES
Dendrograms may show visually the relative similarities of any collection of objects (including DNA sequences); phylogenetic trees intend to depict the real genealogical history of the taxa (usually species) represented at the tip of the branches
16 - COALESCENCE AND GENE GENEALOGIES
All extant homologous DNA tracts, sampled from whatever set of organisms, however diverse they can be, "coalesce" to a single DNA molecule present in the genome of a certain individual lived in the past. Each piece of extant DNA tells its specific and particular genealogical story
PART III.
17 - GENETIC DRIFT
The effect of genetic drift, or the random change of allele frequency due to gamete sampling, is to increase the differentiation among populations, and at the same time to decrease the genetic variation in each population. This effect is cumulative over generations, and cannot be ignored in any population genetics analysis
18 - EFFECTIVE POPULATION SIZE
The size of a population that really matter in determining the dynamics of genetic variation is not the census size, since many individuals of real populations do not reproduce; the effective size is a non-observable quantity that can be estimated and is the main parameter determining the amount and distribution of genetic variation in populations
19 - MUTATIONS
The mutation rate is the probability that a copy of an allele changes to some other allelic form in one generation (or one DNA replication); the mutation substitution rate is the number of mutants reaching fixation per unit time in a given lineage.
20 - SELECTION
Selection has the trivial effect of reducing the genetic variation underlying the selected characters. However, as allele frequencies of the loci subjected to selection becomes lower and lower, selection becomes less efficient in changing allele frequency. In addition, some form of selection may lead to stable polymorphisms.
