Overview: Evolution Biology and Population Genetics

The levels of variability

* Phenotypic variation
* Chromosomal polymorphism
* Variation at the molecular level

Phenotypic variation

Variability in phenotypes that exists in a population (Example: height, weight, and body shape, hair, eye color, and the ability to roll your tongue) Divided into quantitative and qualitative traits.

Chromosomal polymorphism

A condition where one species contains members with varying chromosome counts and shapes

Variation at the molecular level

Includes enzyme polymorphism and variation at the DNA level. Allows organisms to respond to a wide range of environmental stimuli.

Enzyme polymorphism

The presence of two or more variant forms of a specific DNA sequence that occurs among different individuals or populations. Alleles are differentiated by the size of the molecules

Variation at the DNA level

Involves mini and micro satellites, and DNA sequencing. Describes the variation in the DNA sequence of genomes.

DNA sequencing

Sequenced using mtDNA, Nuclear DNA - SNP, Reduced-representation sequencing (RRS)

mtDNA

Maternal inheritance (DNA inherited only from the mother, not from the parents). DNA changes result from mutations. All individuals are related to each other maternally.

Nuclear DNA - SNP

The DNA of individuals are compared, specifically with SNP (Single Nucleotide Polymorphism), found at a specific position

Reduced-representation sequencing (RRS)

A genomics technique that sequences a locus of the genome using restriction enzymes to cut DNA into smaller fragments. It is used in to identify genetic variation within and between populations.

The ideal/ Mendelian population

Has…

* Infinite population size
* Random mating
* No mutation
* No selection (same environmental effect on all phenotypes)
* No migration
* In Hardy-Weinburg equilibrium

Different strategies to avoid mating between kin

Recognition of kin, Promiscuity, Migration

Recognition of kin

Example: Mouse (Mus musculus)

* Recognize kin based on the smell of their urine
* If the urine smells the same, they won’t mate

Promiscuity

Example: Fairy wren (Malurus elegans)

* Birds mate with those other than their partner
* 70% of offspring is not from the attendant male

Migration

Example: Pied babbler (Turdoides bicolor)

* Lives in groups, young birds leave the group

Continent- Island model

One population is much larger, so it can be assumed that population y (larger) to x (smaller) would be larger

Continent island model: Asymmetric gene flow

Due to this, the small population becomes more and more similar to the large population. Resulting in a loss of genetic identity for the small population.

Introgression

* The result of the continent-island model coupled with hybridization The asymmetric gene flow and hybridization cause the smaller taxa to lose its genetic identity.
* a gene transfer process between two species, typically as a result of hybridisation and backcrossing

Examples of introgression

* Mallard duck (Anas platyrhynchos) → Mottled duck (Anas fulvigula)
* Domestic cat (Felis catus) → Wild cat (Felis silvestris)
* Song of the common chaffinch (Fringilla coelebs)

Island models

Wright’s island model, Isolation by distance, Stepping stone model

Wright’s island model

* Involves 2 populations with diff genetic content but similar pop. size.
* The migration rate is very similar, causing symmetric gene flow.
* The allele frequency change will have around equal impact.

Wright’s island model 2

Isolation by distance model

Genetic difference increases with distance

Isolation by distance example

* Brook trout (Salvenius fontonalis), having limited dispersion → Atlantic salmon (Salmo salar), having high dispersion
* Eurasian otter (Lutra lutra)

Stepping stone model

* Individuals can only migrate between neighboring populations.
* Has two types: One-dimensional model, and two dimensional model.
* Results in Geographic cline: A gradual change in the genetic or phenotypic composition of the populations
* Example: House sparrow (Passer domesticus)

Stepping stone model: One-dimensional model

The arrangement of the populations is linear

Stepping stone model: Two-dimensional model

The populations are arranged like a net (between neighboring populations)

Types of speciation

Allopatric, Parapatric, Sympatric

Allopatric speciation

The first step is the geographical separation of populations

Parapatric speciation

Selection in different directions affecting neighboring populations

Sympatric speciation

All forms of species formation that do not have geographical isolation in the initial stages

Erasmus Darwin

* Supported the background to Darwin’s theory of evolution
* Wrote Zoonomia: Species are descended from a common ancestor
* Raised the idea of natural selection

Charles Lyell

* Supported the background to Darwin’s theory of evolution
* Supported uniformitarianism
* Provided geological and fossil evidence of Darwin’s theory

Thomas Malthus

* Supported the background to Darwin’s theory of evolution
* Wrote An essay on the Principle of Population: Human population increase exponentially: nature compensates with wars, famines, diseases

The basis of Darwin’s Theory of Evolution

1. The Diversity of species
2. The idea of natural selection

Darwin’s Theory of Evolution

1. __Limited resources__ → Check the increasing potential of populations
2. Individuals of a population __vary in__ their __phenotypic traits__, much of the variability is heritable → Affects individual survival, reproduction → __Affects fitness__
3. __Natural selection__ → Individuals are more suited to the environment will survive on and pass their more favorable traits
4. Natural selection causes the population to __evolve gradually__ → adapt to the environment → evolutionary change accumulates in different lineages → __speciation__

Phenotypic variation

* Variability in phenotypes that exists in a population. (Ex: height, weight, and body shape, hair, eye color, and the ability to roll your tongue)
* Quantative and Qualitative traits
* Vp = Vg + Ve + Vge

Phenotypic variance= genotypic+ environmental+interaction

Genotypic/genetic variation

* The final phenotypes of heterozygous offspring (Example: AA, Aa, aa)
* Vg = Va + Vd + Vi
* Interactions between genes

Cladogram

A diagram showing a hypothetical relationship between groups of organisms (Branch length is not important)

Chronogram

Branch lengths are proportional to time

Monophyletic group

Phylogenetically equivalent sister groups derived directly from a common ancestor

Paraphyletic group

A grouping in which the members of a group can be traced back to a common ancestor, but the group does not include all descendants of the common ancestor

Polyphyletic group

An artificially created taxon (supraspecific category) whose members, although similar, cannot be traced back to a common ancestor, but have evolved from different ancestral forms through convergent or parallel evolution.

Character states

The concepts used in phylogenetic character analysis are always relational, expressing the direction (polarity) of character change.

Homology, Homoplasy, Plesiomorphy, Simplesiomorphy, Apomorphy, Autapomorphy, Synapomorphy

Homology

The basic structural (or functional) similarities between taxa that existed in their straight or distant ancestors, so that they have not changed substantially in their lineage, but have been modified adaptively at most (Ex: Five-toad limbs, insect antennae, plant leaves)

Homoplasy

Morphological features showing similarity but not common origin (Ex: animal eyes, wings)

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Reversion

A type of homoplasy. If the secondary similarity is created by a return to a previous state of character.

Parallelism

A type of homoplasy. If the similarity is the result of independent parallel evolution from a more or less similar initial state. (Ex: Four chambered-heart in birds and mammals)

Convergence

A type of homoplasy. If the similarity is the result of a development from a different prior condition to a similar one, usually as a result of a transition to a similar lifestyle.

Plesiomorphy

Relatively ancient, primitive or ancestral character state. (Ex: Legs of reptiles)

Symplesiomorphy

A shared plesiomorphic character state. Ancestral character shared by all members of a clade which does not make this the clade different from other clades (Ex: backbone)

Apomorphy

Modified character state that comes from the previous (plesiomorphic) character state. (Ex: leglessness in reptiles)

Autapomorphy

A trait carried exclusively by a given taxon (species or any rank of unit above species), usually result of a specialization change. (Ex: marsupium of marsupials

Synapomorphy

The common derivative trait of two or more groups. These groups had/ have a common ancestor that already had this character. When it was formed, this character was autapomorphic.

**Coevolution**

Development of two species (or supra-species taxa) ininteraction with each other.

Mutualistic coevolution

* + / +
* Partners mutually increase each other’s fitness. If the connection lasts long enough, it can lead to cospeciation.
* Examples:
* Attini Ant- Lepiotaceae fungus mutualism: Ants care for fungi, parts of fungi fed to babies
* Figs - Fig wasps
* Yukka - yucca moths
* Specific pollination
* Darwin’s orchid (Angraecum sesquipedale) - Morgan’s sphinx moth (Xanthopan morgani praedicta) (flowers are specific to pollinators)

Antagonistic coevolution

* - / +
* Partners reduce each other’s fitness. (Ex: Parasitism, plants/phytophages, predators/prey)
* Examples:
* Sap sucking
* *Tetraopes* beetles – milkweeds (*Asclepias*): Beetles contain toxic carotenoids
* Common garter snake (Thamnophis sirtalis) – rough-skinned newr (Taricha granulosa): Predator/prey
* Common cuckoo (*Cuculus canorus*): Parasite

Genetic drift: Changes in allele frequency

The random fluctuations in the frequency of alleles in a population due to chance events. It can lead to changes in the genetic makeup of a population over time, and can be particularly important in small populations.

Genetic sampling Error

Unlike populations in Hardy-Weinburg Equilibrium, real populations have…

* Finite population sizes
* Random effects
* Resulting in an error of genetic sampling (not representing original allele distribution)

Random walk

Random changes in allele frequency through several generations

Bottleneck Effect

The population will have a given individual number and a given genetic variability. A catastrophe will cause a decrease in numbers leading to a decrease of genetic variability. This is also a random effect.

* Ex: Cheetah, Northern elephant seal

Founder Effect

A new habitat becomes available, and individuals that move there experience lower amounts of genetic variation (allele loss)

* Grey Fox → Channel Island Fox
* Amish population

Genetic distances

* A way to measure genetic differentiation
* Several ways to calculate this, based on allele frequency data between pairs of populations

Fixation Index

* A way to measure genetic differentiation

The fixation index (Fst) is a measure of population differentiation due to genetic structure. Fst values range from 0 to 1, with higher values indicating greater genetic differentiation between populations.

The Effect of Mutation on Fitness

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Types of mutations

Gene mutation (substitution), Gene duplication, Chromosome mutation, Genome mutation

Gene mutation (substitution)

A permanent alteration in the DNA sequence that makes up a gene. Substitution is a type of gene mutation where one nucleotide is replaced by another. Substitutions can be missenense (-, due to proline), silent (0, due to serine), or nonsense (null, due to stops), or frameshift (0, due to valine)

Gene Duplication

A gene is duplicated to produce two or more copies of the same gene. This can occur through various mechanisms such as unequal crossing over, retrotransposition, and chromosomal duplication.

Chromosome mutation

Any change in the structure or number of chromosomes in an organism's cells.

* Inversion- when a segment breaks off and reattaches within the same chromosome, but in reverse orientation
* Translocation- When a piece of one chromosome breaks off and attaches to another.
* Chromosome fusion- When telo- and acrocentric chromosomes fuse by their centromeres

Genome mutation

A change in the DNA sequence of an organism's genome.

Niche-selection

When a habitat is heterogeneous with different patches and individuals living in several patches. The individuals migrate among habitat patches, decreasing genetic differences

Selection coefficient (s)

The intensity of selection acting against the genotype (s + w = 1)

1. Precambrian

* Oldest: 3.5 billion years ago
* Just prokaryotes – Archaea colonies (Endosymbiont theory)

2. Cambrian

* 10 million years ago
* Marine animals w/ solid skeleton appeared
* Arhtropoda, Brachiopoda, Mollusca, Echinodermata, Agnatha

3. Ordovician

* Ozone layer
* First terrestrial organisms: spores and sporangia of plants related to recent liverworts

4. Silurian

Small vascular plants, their sporangia sat on short, leafless, dichotomically branched stems, had no real roots

5. Devonian

* First terrestrial arthropods

6. Carboniferous

* Extensive forests on land: tree-sized ferns, ground pines,horse-tails → carbon-age coal deposits
* Amphibians

7. Permean

* Amphibians have been pushed back into wet habitats,reptiles have spread
* First mammalian reptiles

8. Mesozoic

(Triassic, Jurassic, Cretaceous)

* Species considered as the first mammal
* Marsupials,placental at the end of the Cretaceous

9. Cenozoic

* Diversification: angiosperms, insects, birds
* Adaptive radiation: snakes, mammals, teleost fish

10. Tertiary

* Antarctica has moved to the South Pole, glaciated →breaking evolutionary relationships (e.g. marsupials)

11. Quaternary

* Glacial periods
* Megafaunal extinction