12/2 - Artificial Selection

plants provide critical benefits to humans

-provide fuel, fiber, building materials, and medicine
-produce oxygen
-prevent erosion
-buffer climate impacts

domestication

process of changing wild organisms for human use

an array of locations

plants were domesticated at

artificial selection

changes the traits of domesticated species

crop domestication can select for a variety of traits

1. simultaneous ripening of seeds on the plant
2. increased seed size
3. no seed dormancy
4. synchronous flowering
5. gigantism
6. loss of toxic or unpleasant compounds
7. loss of herbivore defenses
(but cannot be at the expense of reproduction)

artificial selection

direct manipulation by humans of the genetic composition of a population by allowing only individuals with desirable traits to reproduce

mendel

used artificial selection to understand genetics

Darwin

observed pigeon breeding to understand phenotypic changes over time

Darwin's explanations of artificial selection

1. methodical selection: modification of a breed according to some predetermined standard
2. unconscious selection: preserving the most valued individuals and destroying the less valued individuals, without the thought of altering the breed

critique of darwin's explanation of artificial selection (ex. of operationalism)

we shouldn't define selection types based on the intent, but rather on what is observed

four modes of selection

1. directional
2. stabilizing
3. disruptive
4. balancing

directional selection

favors one extreme phenotype, causing the avg phenotype in the population to change in one direction

stabilizing selection

favors phenotypes near the middle of the range of phenotypic variation, maintaining average phenotype

disruptive selection

favors extreme phenotypes at both ends of the range of phenotypic variation

balancing selection

no single phenotype favored in all populations of a species at all times

ex of directional selection in artificial crop breeding

bigger tomato

ex of stabilizing selection in artificial crop breeding

exact shade of red

ex of disruptive selection in artificial crop breeding

selecting multiple color varieties

ex of balancing selection in artificial crop breeding

both drought and flood tolerance

dog breeds

ex of artificial selection

dN/dS ratio

the ratio of nonsynonymous to synonymous nucleotide substitution rates on the protein-coding section of a given gene

synonymous mutations

do not change the amino acid sequence. can be used as a background "molecular clock"

nonsynonymous mutations

actually change the amino acid sequence

how do we determine if this gene is under selection

dN/dS>1 - natural selection is promoting protein changes
dN/dS<1 - natural selection is suppressing protein changes
dN/dS=1 no selection is occurring

two complications

1. more than one gene may be under selection for a particular phenotype
2. maybe the gene sequence itself doesn't change, but protein expression changes (more or less of the protein is produced)

gene

segment of DNA

genome

entire DNA sequence

transcript

single strand of RNA that is produced from DNA during transcription

transcriptome

all RNA sequences currently expressed in a cell

japanese quail artificial selection experiment

1. generate big-egg lines and small-egg lines (top and bottom 25% for 7 generations)
2. take a cell and sequence the transcriptome (all RNA sequences currently expressed_ (RNA-Seq)
3. identify which genes have different levels of RNA expression between the two lines
4. conduct a Gene Ontology analysis to see what those differentially expressed genes do

gene ontology (GO) anlysis

cross-referencing your gene expression dataset to an annotation database to find patterns of biological function

enrichment

over-representation of certain biological functions in a gene expression dataset.

japanese quail artifical selection experiment results

GO analysis found functional categories relates to egg formation and immune function

a perspective on artificial selection

populations reach carrying capacity due to limited resources

Thomas Malthus

wrote "An Essay on the Principle of Population," which describes a "struggle for existence" in the human population

evolution and natural selection

humans are undergoing

reduce

advances in medicine __________ the influence of natural selection on human population genetics

are not

humans __________ undergoing articificial selection

eugenics

scientifically inaccurate theory that humans can be improved through selective breeding

virginia sterilization act of 1924

legalized sterilization of individuals "afflicted w/ hereditary forms of insanity that are recurrent, idiocy, imbecility, feeble-mindedness or epilepsy"

1930s

popularity of the american eugenics society peaked in the