Biology 390 Evolution
Instructor: Alex Kondrashov (firstname.lastname@example.org)
Кондрашов А.С. "История одного открытия" Наука и Жизнь, N6 2005.
Программа курса по эволюционной биологии для аспирантов университета Мичигана
(на ББС будет в сокращенном варианте и по-русски)
Syllabus (detailed) :
I. PAST EVOLUTION
Surprisingly, we know a lot about past evolution of life. This knowledge is based on indirect data, provided by modern organisms, and on direct data, provided by fossils. A number of generalizations can be derived from facts about past evolution. In some cases, we directly observe substantial ongoing evolution.
1. What is evolutionary biology?
Fundamental concepts: evolution, common ancestry, phase space, determinism, space of genotypes, levels of organization, phenotype, trait, fitness, adaptation, mutation, variability, population, selection, allele replacement, fitness landscape, similarity, relatedness, compatibility, connectedness, species, form of life, Microevolution, Macroevolution, complexity, optimality, evolvability, designability, stochasticity, predictability, reproducibility, random drift.
2. Evidence for past evolution of life - reasoning
Can we have, and do we need, any evidence for past evolution? Indirect and direct evidence. Great evidence which we do not have. Evidence we do have: suboptimality, homology (similarity not forced by function), unforced hierarchy, unforced spatial distributions, continuous variability, theory-based evidence.
3. Evidence for past evolution of life - examples
A small sample from countless indirect evidence for evolution: pseudogenes, gene duplications, comparisons of genomes of very different organisms, universal genetic code, morphological homology, cospeciation, species flocks, ring species, correspondence between patterns in mutation and in molecular evolution, etc.
4. Reconstructing the course of past evolution
Representation of evolution by phylogenetic trees. Reconstructions of such trees assuming evolutionary clock or exclusively divergent evolution. Testing the validity of reconstructions. Obstacles: variable rates of evolution, homoplasy. Phylogenies which are not tree-like (symbioses, lateral gene transfers).
5. History of the Earth
A necessarily superficial review of Earth sciences: structure of modern Earth, age and origin of the Earth, changes in the Earth orbit, sedimentation, rock cycle, stratigraphy, geochronology (radioactive isotopes, switches of magnetic poles, traces of cosmic rays), plate tectonics, paleogeography, paleoenvironments (stable isotopes, changing atmosphere).
6. History of life on Earth
A standard review of what is known about the evolution of past life from 3,500 million years ago (first unambiguous fossils of cyanobacteria) to the present: early prokaryotes, stromatolites, first eukaryotes, origins of multicellularity, mass extinctions, Ediacaran fauna, Paleozoic, Mesozoic, and Cenozoic life.
7. Recent history of the Homo sapiens lineage
A review of what happened to our lineage (and to its extinct offshoots, robust Australopithecus and Neanderthals) since it diverged from the ancestors of chimpanzees ~5 million years ago: early fossils, Australopithecus afarensis, hominisation, Homo erectus, first dispersal out of Africa, Homo sapiens and second dispersal out of Africa.
8. Generalizations derived from the history of life - diversity
Numerous facts about past evolution can be distilled into several generalizations. Some of them are concerned with the origin and dynamics of the diversity of life: structure of diversity at a particular moment, evolution of individual lineages, birth and death of lineages, and evolution of multiple lineages.
9. Generalizations derived from the history of life - structure and function
Other evolutionary generalizations are concerned with the evolution of structure and function of living beings. These generalizations remain the main source of our very limited understanding of the evolution of complex phenotypes.
10. Evolution while you are watching
Observations of ongoing evolution provide a natural bridge between studies of past evolution and attempts to understand Microevolution. Substantial evolution has been observed in the course of domestication, in controlled populations, in some natural populations, and in many crucial pathogens.
II. UNDERSTANDING MICROEVOLUTION
Microevolution, changes at the scale of within-population variability, is the best-understood facet of evolution. A well-developed theory of Microevolution is available, and there are a lot of useful data.
11. What is a population and how it can be studied?
Selection-based and mating-based definitions of population. Distributions, their parameters, and statistical estimates. Confidence limits. Five factors of Microevolution. Classification of modes of selection, based on fitness landscapes.
Molecular mechanisms of spontaneous mutation and molecular nature of small-scale and large-scale mutations. Mutation rates at the level of nucleotides and of genomes. Mutation and phenotypes. Mutation and fitness. Mutational equilibrium.
Fitness and its components. Genetic load, fitness variance, selection differential. Variability of fitness in natural populations. Dynamics of an allele replacement. Fisher's fundamental theorem of natural selection. Estimates of selection.
14. Sex. Population structure. Random drift.
Amphimictic life cycles in nature. Ancient apomicts. Hardy-Weinberg ratios. Dynamics of linkage disequilibrium. Non-random mating. Spatial and temporal structures of populations. Sampling and Fisher-Wright model of a finite population. Effective population size. The rate of selectively neutral evolution.
15. Theory of Microevolution - predicting genetic changes
Selection (positive) which promotes changes vs. selection (negative and balancing) which prevents changes. Survival of a new, advantageous allele. Multiple, simultaneous allele replacements. Polymorphism due to deleterious mutations and to Mendelian segregation. Evolution under very weak selection. Phenotypical approaches to evolution.
16. Theory of Microevolution - inferring parameters
Methods of measuring mutation rate. Methods of detecting positive selection: high rates of evolution, MacDonald-Kreitman test, clumps of replacements. Methods of detecting negative and balancing selection. Measuring migration.
17. Variability in natural populations
Individual alleles: SNPs, small indel polymorphisms, large-scale polymorphisms. Frequency distributions. Linkage disequilibria between alleles. Heritabilities and evolvabilities of phenotypic traits. Variability of population-level traits.
18. Selection in natural populations
Opportunity and overall strength of selection. Inbreeding and outbreeding depressions. Selection at the levels of genotypes and phenotypes. Variance in fitness and genetic load. Positive selection. Consequences of relaxed selection.
19. Microevolutionary foundations of Macroevolution
Selection on allele replacements. Constraints on the course of Macroevolution. Constraints on the rate of Macroevolution. Uniqueness of evolutionary trajectories. Role of inadaptive evolution. Contamination of the genome by mildly deleterious mutation. Microevolution of extinction.
20. Species and speciation
Epistasis, incompatibility, and species. Genetics and ecology of Dobzhansky-Muller incompatibilities. Phyletic and allopatric speciation. Orr's snowball effect. Sympatric speciation through disruptive and incompatibility selection. Parapatric speciation and hybrid zones. Importance of different mechanisms of speciation.
III. UNDERSTANDING MACROEVOLUTION
The ultimate goal of evolutionary biology is to understand Macroevolution, i. e. profound changes of living beings. This goal is currently very far from being achieved. Still, we understand something about Macroevolution at the levels of sequences and of populations and ecosystems. In contrast, Macroevolution of functioning molecules, cells, and multicellular organisms remains largely obscure.
21. Macroevolution of sequences - theory
Evolutionary distance between sequences. Homology of nucleotide sites and sequences alignment. Homology of genes. Evolution of gene order within genomes. Mutation and selection at the level of whole genomes. Advanced approaches to phylogenetic reconstructions.
22. Macroevolution of sequences - data
Genome duplications. Multigene families. Transposable elements. Genome size and junk DNA. Degeneration of organelle genomes and sex chromosomes. Origin of new functional sites on DNA and RNA. Evolution of alternative splicing and origin of new genes. Sequence-level manifestations of evolution at higher levels.
23. Macroevolution of functioning objects - theory
What a theory of Macroevolution of complex, functional objects should explain? Complex phase spaces and fitness landscapes. Modularity and robustness. Designability of complex phenotypes.
24. Macroevolution of functioning objects - molecules, cells, organisms
Functional segments of DNA - origin and evolution. Compensatory evolution within RNA molecules. Biochemical pathways, enzyme regulation, and networks of interacting genes. Origins of complex adaptations. Phenotypic plasticity.
25. Origin of life
RNA world. Hypercycle. Genetic code, proteins, and DNA. Cell membrane and metabolism.
26. Macroevolution of populations and ecosystems
Evolution of sex, recombination, and mutation rate. Sexual selection and origin of exaggerated signals. Evolution of ageing and longevity. Evolutionary conflicts. Life histories: evolution of clutch size, dormancy, and migration. Evolution of interactive behavior and altruism. Coevolution and Red Queen dynamics.
27. Evolutionary biology of modern humans
Imperfect human traits. Human variability of sequences and of phenotypes. Conditionally beneficial and unconditionally deleterious variability. Ongoing adaptive evolution. Changes in human populations in the foreseeable future.
28. Implications of evolutionary biology outside natural sciences
Origin of language. Evolutionary psychology. Evolution of life and contemporary societies. Attempts to derive morality and meaning of life from evolution.
A successful student will learn how to answer the following questions :
1) Why a crazy idea that humans and pine trees evolved from a common ancestor is universally accepted by biologists?
2) How life evolved on Earth during the last 3.5 billion years? How could life possibly originate from non-living matter (nobody knows exactly how this happened)?
3) How our ancestors evolved from apes?
4) What general patterns occurred repeatedly in the course of past evolution?
5) What do we see when evolution happens in front of us?
6) What is population and what factors affect its evolution?
7) What can we infer theoretically about evolution of populations?
8) How variable are natural populations, and what is known about selection in them?
9) How can new species evolve?
10) How do genomes evolve?
11) How do functioning molecules, cells, and organisms evolve (in fact, this issue is still rather poorly understood)?
12) Why organisms reproduce sexually, why we age, and why peacocks grow their tails (in fact, there are several hypotheses on each of these issues)?
13) How ecosystems are affected by evolution of their constituent populations?
14) Why evolutionary origin of modern humans is important?
More specifically, to get a good grade a student will need to know the following :
1) Why suboptimality, homology, unforced hierarchy, unforced spatial distributions, and wide continuous variability, observed in modern organisms, constitute indirect evidence for evolution of their ancestors? What are scenario-based and theory-based indirect evidence for evolution?
2) At least 3 examples of indirect evidence for evolution of each kind.