Wolf

The process of organismal change and diversification through generational time from shared common ancestry.

Darwin: ‘Descent with modification’

Microevolution happens on a small scale (within a single population), while macroevolution happens on a scale that transcends the boundaries of a single species

Microevolution can result in complex structure.

• Evolution is not the only process generating seemingly complex forms (e.g. snowflakes)

• Ultimately genetic variation is the raw material for evolution (not only phenotype)

• Evolution is most readily visible in higher order taxa; yet, it unfolds through inheritance with modification of individuals at the population level.

• Evolution does not progress towards a goal, nor is it just random fluctuation.

• Evolution ≠ natural selection ≠ adaptation.

• Evolution did not just happen in the past. It is ongoing here and now.

Hierarchical organization of life. Assuming a historical process of branching and diverging best reflects biological reality of species and higher-order groups with ever decreasing similarity. It is superior to any other organizing system proposed so far.

• Homology. Similarity of structure despite differences in function is best explained by shared ancestry, not by best design.

• Embryological similarities. Homologous characters not needed at later life stages appear transitorily during embryological development. This can only be understood by shared ancestry.

• Vestigial characters. There are numerous examples of ancestral features that are degenerated and of no use to the remnant organism. Cave dwelling fish e.g. display eyes in every stage of degeneration.

• Convergence. Functionally similar features often evolved independently and differ profoundly in structure. This provides evidence for adaptation by natural selection and cannot be understood by the hypotheses of optimal design.

• Suboptimal design. Indeed, many structures show suboptimal design (e.g. blind spot in human eye) and can only be understood by historical constraint. Evolution simply has to work with the variation present at the time.

• Geographic distributions. The distributions of many taxa align well with what we know from the movement of plate tectonics and don’t make sense without assuming contiguous change from a common ancestor.

• Intermediate forms. The hypothesis of evolution proceeding by gradual small change is well supported by intermediate forms, both in living organisms (some snakes still have vestigial legs) and fossils (e.g. Archaeopterix).

• Fossils. Though incomplete, the fossil record in conjunction with radioactive dating clearly demonstrates that evolution is a long, historical process of change. Dinosaurs are simply not found in the same strata as humans.

• Molecular evidence. Common ancestry is seen in a large variety of molecular properties (codon usage, basic molecular machinery, organelles, etc.) and homologies displaying similar functionality across millions of years (if you insert a mouse ‘eye’ gene into drosophila it will start making an eye providing evidence for a shared bilaterian ancestor).

• Domestication

• Agriculuture

• biomedical implications

• sexual antagonisms and human disease

• personalized medicine

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Aristotele’s’ hierarchical organization of organismal life.

• Plato: world is a shadow of underlying essences in a metaphysical world

• Aristoteles: Scala Naturae

  • emphasizes experimentation and conceptualizes evo-devo (epigenesis vs. preformation)

  • species fixed, aligned in ladder of life (Scala Naturae).

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• Middle Age: Scala Naturae (modified into Great Chain of Being) profoundly influential.

  • Thomas Aquinas: natural theology; order and perfection in adaptation from divine design (still prevails in the mind of creationists).

  • Christianity introduced the concept that creation was recent. Bishop Ussher (1581-1656) : creation occurred 4004 BC (nightfall on 22nd october).

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• Linnaeus Systema Naturae (1735) - modern binomial system of biological nomenclature (species grouped in genera and orders). System thought to reflect God’s plan. Variation = imperfection.

  
  

• The fossil record (dinosaurs) ➡ speciation and extinction becomes a fact.

• Methods for dating rock strata (Cuvier) + marine fossils ➡ earth is older than

6000 years

• Uniformitarians (Charles Lyell, James Hutton)

• Long time + gradual change + same forces as today = geological change

• Highly influential to coeval Darwin.

• Theory of evolution by natural selection.

• Voyage on the Beagle: Could present processes also explain the ‘mystery of mysteries’, i.e. the origin of new, well adapted species from a single ancestor?

• On the Origin of Species by Means of Natural Selection:

  • Heritable variation in the trait.

  • Over production (Malthus), but fixed resources leading to selection.

  • Variation in lifetime reproductive success linked to the trait.

• Evidence for Darwin’s thesis at the time

  • Fossil record and discovery of Archaeopterix (1861), missing link between birds and reptiles.

  • Observation of overproduction and struggle for life.

  • Artificial selection in domestic animals and plants.

• Laws of genetic inheritance

• hereditary principles based on controlled crosses of plants (mostly peas)

  • Law of segregation, Law of independent assortment, Law of dominance

• Mendel’s laws: evidence for the role of large, discontinuous mutations (‘sports’) in evolution; at odds with continuous variation.

• Sequencing of proteins (1952)

• Discovery of the structure of DNA (1953)

• Discovery of the genetic code (1962)

• Protein electrophoresis: more genetic variation than previously thought (Lewontin and Hubby 1966)

• Sequencing of DNA (1967)

• The Neutral Theory of Molecular Evolution (1968)

  • the great majority of evolutionary changes at the molecular level (...) are caused not by Darwinian selection, but by random drift of selectively neutral or nearly neutral variants”

• The ‘Nearly’ Neutral Theory of Molecular Evolution 2005

  • allowing for mutations with continuous fitness effects

• The classical view with Thomas H. Morgan and Herman Muller as its prominent proponents holds that a single (wild-type) form has highest fitness and all other variants are purged by selection. As a consequence genetic variation in natural populations should be very low.

• The balancing school on the contrary (Dobzhansky) assumes a creative role for selection stating that different alleles are maintained by balancing selection – providing ample raw material for adaptive evolution.

• The debated required empirical input —> protein electrophoresis Lewontin

  • showed that the amount of genetic variation was even higher than previously thought, even higher than proposed by the balance school

    
    

• mutation

• selection

• genetic drift

• recombination

• migration

on population

Mutation happens in individuals and generates polymorphism in populations.

• Mosaicism

  • can be due to somatic mutations

  • two or more populations of cells with different genotypes are present in a single individual.

• Evolutionary geneticists are usually interested in germ line mutations—> trans-generational processes (somatic: interesting for fate of individual)

• Somatic variation can also be due to epigenetic change (X-chromosome inactivation). ginger and black allele on X – white by other, independent gene.

• Haplotypes are combination of alleles that are inherited together from a single parent. Haplotypes can have many more alleles than single polymorphic loci. (in general AA,Ab, aB, ab)

• change of genetic architecture of trait (poly vs monogenic traits)

• The allelic effect of a gene on a given phenotypic trait is given by its dominance effect, which if often conceptualized by three discrete classes: alleles are said to be dominant, co-dominant or recessive.

• point mutation

  • The 3rd position (synonymous site) of a codon is more variable than the 1st and the 2nd (non-synonymous sites)

  • missense (change aa)

  • nonsense (stopcodon)

• frameshift mutations

  • indel of single base —> drastically different popypeptid product —> nonfunctional

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• Structural mutations

  • Insertions – Deletions:

    e.g. Chorea-Huntington’s disease transposable elements (jumoing genes) (> 40% of human genome retrotransposon)

  • Duplications generate paralogues (hemoglobin)

  • Inversions

    • reversal of DNA order. Inversions spanning the centromere are called pericentric, inversions restricted to one chromosomal arm are called paracentric. Both types often produce errors during meiosis.

  • Translocations

    • exchange of segments among non-homologous chromosomes.

  • Fission and Fusion

    • one chromosome becomes two or two become one.

• Ploidy Changes (trisomie 21 – aneuploidy): change of number of chr

• Karyotype changes

not connected

mutation is random

μ is a central population genetic parameter determining

• Divergence (mutation as molecular clock)

• Diversity

• random ..> poisson distribution

Measuring the mutation rate

• Pedigree based (count mutations)

• Experimental based

• Comparative genetics

Mutation rates differ

• among genomic regions among organisms

current estimate in humans of about 0.3-1 10-9 mutations site-1 year -1 – 0.7-2 10-8 mutations site-1 generation -1or assuming a generation time of 20 years.

• There are 29.52 million differences in 2.4 Gb (109 bases) orthologous sequence (1.2%) shared between human and chimpanzee

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• more new mutations are transmitted through sperm then through eggs (male-biased mutation rate).

  • —>in males (XY) X- chromosome is exposed to fewer mutations than the autosomes, in female heterogametic species (females: WZ) it has the opposite effect

  • genes on autosomes spend an equal amount of their time in males and females—>net mutation rate is the average of the male and female mutation rates

  • In humans and other male heterogametic species, X-linked genes spend only one-third of their time in males and two- thirds of their time in females. If spermatogenesis is more mutagenic than oogenesis, the X chromosome is thus subjected to a lower mutation rate than the autosomes or the Y chromosome. The reverse is true for Z-linked genes in taxa with female heterogamety.

Mutation:

1) a process that produces a novel allele differing from existing version(s) (or the wild type)

2) the allele that results from a mutational process

Mutant: organism or cell who has received a mutation; often also: whose changed phenotype is attributed to a mutation

study effects of plain inheritance

assumption

• no slection

• no mutation

• no genetic drift

• no recombination

• no migration

• infinitely large population

• random mating (panmictic)

• non-overlapping generations

• hermaphroditic (i.e. no differences among males and females, each contributes

  gametes at equal proportion)

Hardy-Weinberg genotype frequencies as a function of allele frequencies at a locus with two alleles. Heterozygotes are the most common genotype in the population if the allele frequencies are between 1/3 and 2/3

once HWE is reached, also the genotype freq. do not change anymore

1. Assortativemating

• Individuals may be more likely to mate with individuals from the same, or similar, genotype. This is called assortative mating. The opposite situation is called negative assortative mating or dis-assorative mating.

2. Inbreeding

3. Populationstructure

• When deriving the HWE we assumed one large panmictic population. Inadvertently pooling individuals from two populations pop1 and pop2 can lead to strong deviations from HWE.

4. Selection

• Considering that phenotypes are eventually determined by the underlying genotype, it is not difficult to see that selection can cause deviations from HWE

• deviations from HWE can only be detected after selection has been acting

5. (MutationandGeneticDrift)

• small population size (genetic drift) + matuation only small effect on HWE (randomn devaitions, accumulate over time)

• random draws

• Wright-Fisher model assumes a haploid population without sexes, in which each individual reproduces without the need of finding a mate

• dynamics in a diploid, randomly mating population are almost identical to the dynamics of the haploid model

• Gene copies are transmitted from generation t to generation t+1, by random sampling independently and with equal probability.

• null mdoel in population genetics

• Random genetic drift in an experimental setup of 107 Drosophila populations. (see Futuyma 2005).

• Allele frequency changed, variance increased, overall diversity (4 allozymes) lost

• 1) Allele frequencies changed within populations

  2) Variation in allele frequency increased across populations


  3) Heterozygosity and the genetic variation within populations declined

• any allele must eventually be lost or fixed.

• no selection —> probability of transmission is the same for all gene copies.

• The time it takes for allele A to fix depends on the population size and its initial frequency p0.

the average number of generations it takes an allele to fix (excluding its loss) is given by

• genetic diverity gets lost

• Mean allele frequency stays the same

• Variance in allele frequency decreases

• Effects strongest in small populations

• due to the sampling process. As a result, allele frequencies will fluctuate, and eventually one of the two alleles will get fixed, the other will be lost

• Genetic drift, also known as allelic drift or the Wright effect,[1] is the change in the frequency of an existing gene variant (allele) in a population due to random chance

Illustration of genetic drift by random sampling of gene copies (marbles) with two allelic states (red, blue) across discrete generations t, t+1, ..., t+4.

• Heterozygosity matters for individual and population fitness

• Cosanguineous mating increase homozygosity

Nc vs Ne

Nc census population size

Neeffective population size(size of an ideal population that experiences genetic drift at the rate of the population in question)

• single events that drastically reduce population size N to small values are called bottlenecks. (example Bottleneck in Northern elephant seals)

• Bottlenecks reduce genetic diversity

• Ne matters for conservation

• most mutations are selectively neutral

• some are under strong purifying selection

• very few are under strong positive selection

genetic polymorphism only represent neutral variants

The rate of fixation for neutrally evolving sites is equal to the mutation rate

The emphasis in coalescent thinking is to view populations backwards in time, using the divergence observable in a population to estimate the time to a most recent common ancestor (MRCA); this ancestor is the point where gene genealogies come together, or `coalesce', in a single biological organism.

Figure 1: Example for random reproduction according the Wright-Fisher model in a population of size N = 10. In the left example two samples (n = 2) share a common ancestor, or coalesce, in generation j = 14. The example on the right shows the coalescent in case of three samples (n = 3).

• A species is a group of organisms that can create new individuals that are fertile, and thus, can produce even more offspring. Therefore, two organisms that cannot reproduce and create fertile offspring are different species.

• Allopatric speciation and sympatric speciation are the two major mechanisms by which new species form.

• Allopatric speciation occurs when a population of organisms becomes separated or isolated from their main group.

• This type of speciation happens in a population without geographic isolation. The main mechanisms resulting in sympatric speciation involve changes in the chromosomes of the organism

• FST is the proportion of the total genetic variance contained in a subpopulation (the S subscript) relative to the total genetic variance (the T subscript). Values can range from 0 to 1. High FST implies a considerable degree of differentiation among populations.

• the Wahlund effect

  • the sub- populations contain fewer heterozygous individuals than expected given by the pooled allele frequency

  • In large populations which contain sub-populations there are fewer homozygotes than in the average for the set of subdivided populations. This is a general, and mathematically automatic, result. The increased frequency of homozygotes in subdivided populations is called the Wahlund effect.

• inbreeding coefficients

  • The coefficient of inbreeding of an individual is the probability that two alleles at any locus in an individual are identical by descent from the common ancestor(s) of the two parents

  • The probability that two alleles at a given locus are identical by descent (durch Abstammung)

• Adaptation improves an individual’s fitness in its environment , e.g. mimesis.

• Allele frequency changes

• dominant /recessive allele advantageous

• Advantageous allele will always increase in frequency

• Selection speeds up change in allele frequency, the faster the larger the fitness differences

• Change is fastest at intermediate frequencies

• selection maintaining variation

(A)Three forms of directional selection in which P is favored over Q. (B) Selection on diploids in which the heterozygotes have the advantage. (C) Selection on diploids in which the heterozygotes are less fit.

• beta-hemoglobin locus in some African and Mediterranean populations

• One allele at the locus which differes by one amino acid substitution from normal haemoglobin (A) encodes sickle-cell haemoglobin (S).

• At low oxygen concentrations sickle-cell haemoglobin form elongate crystals, and is less efficient in transporting oxygen.

• In homozygous state, SS, the sickle allele causes distortion of the red blood cells causing severe anemia and damage to blood capillaries

• Heterozygotes AS only suffer slight anemia.

• Homozygotes AA produce oxygen best and show no signs of anemia.

• At first sight this sounds like a clear case of directional selection, where the A allele would be favoured.

• However, in regions exposed to malaria, selection pressures change. Here, normal AA homozygotes suffer higher mortality by malaria than AS heterozygotes, where red blood cells are broken down faster. This provides worse conditions for the malaria parasite Plasmodium falciparum to develop in the red blood cells.