Molecular evolution

Introns

Non-coding sequence area of a gene

Exons

Protein coding sequence of a gene

Intervenir space

A stretch if DNA sequence located between genes. This contains functional elements and junk DNA

Redundancy in the genetic code

Not all changes in DNA sequence result in change to the amino acid sequence

Nucleotide substitution

Replication mistakes (affects single base pair)

Replication mistakes

Indel’s (insertion-deletions) smaller than a gene

Miotic and meiotic mistakes

Aberrant crossovers, unreduced gametes, + results in whole chromosomes to whole genome duplication

Retrotransposition

Single genes. RNA intermediate

The process by which genetic elements are copied and unserved until new locations in a genome

Transposable elements

Pieces of DNA that replicate and insert themselves in new places (Selfish DNA)

Single nucleotide changes

Non-synonymous, synonymous, and non-coding

Non-synonymous

Changes in amino acid, and may be adaptive, deleterious, or neutral

Synonymous

Does not change the amino acid/protein sequence, and usually considered neutral

Non-coding

Usually does not affect anything so it’s neutral

Indel

Insertion deletions that can be any number of base pairs.

Non-frame shift

Multiples of 3 maintain the open reading frame. Could be adaptive, deleterious, or neutral

Frame shift

Anything other than multiple of 3 base pairs changes the reading frame. This causes all amino acids to change and usually truncation of the protein. Deleterious

Types on indels

Non-frame shifts and frame shifts

Homologous genes

A gene inherited in two species from a common ancestor

Two types of homologous genes

Orthologus and paralogus genes

Orthologus genes

The same gene in different species or individuals. To compare gene sequences, they must be this

Paralogus genes

Genes that are copies of each other in the same or different species

Whole genome duplication

Most common in plants (polyploidy) and results in fertilisation by unreduced gametes. Occurs in strawberries, cotton, brassica, and wheat

Whole genome duplication in vertebrates

Hox genes

Hox genes

Highly conservative genes but have 4 duplicate sets. These are responsible for embryonic patterning from flies to humans

sub-functionalisation

Pattern functions of original gene, such as special, temporal, functional, and/or partition

Pseudogenization

Gene loss. Could happen to a new or original copy of a gene. Most common fate of new duplicates

Neo-functionalisation

These evolve into new functions

Eukaryotes hace a large discrepancy between this

Genome size and gene number

Reasons for eukaryotic size discrepancy

Psyduogenes, introns, and transposable elements

Percentage of the human genome that codes for functional proteins

Less than 2% (>2%)

Horizontal gene transfer

An acquisition of new genetic variation. Genes are passed from one organism to another untreated organism

Horizontal gene transfer example

HIV inserts its RNA genome into human DNA through reverse transcription. The virus carries an enzyme which converts its RNA to DNA and integrates it into the host’s genome. This allows hijacking into human cells, forcing them to produce new viral material while altering the host’s genetic material

Ka

Non-synonymous substitutions per site

Ks

Synonymous substitutions per site

Ratio of Ka and Ks

Changes per site gives ab indication of whether natural selection is acting and which type

Ka/Ks Formula

Measures the rate of protein evolution relative to the neutral rate

Ka/Ks>1

Positive adaptive selection faster than neutral. More amino acid changes

Ka/Ks<1

Purifying selection, slower than neutral with fewer amino acid changes

Ka/Ks=1

Neutral evolution. Amino acid changes occurring at same rate

Breeder’s equation

R = h²S

R- response to selection; h²- heritability; S - selection differential

Migration

Measure patterns of neutral variations among populations. Large differences in frequencies among populations means low migration rates. Usually, genome wide effect

Natural selection

Reduction in polymorphism only for the gene under selection. This effects specific genes “regional effect”

Random genetic drift

Genome wide reduction in polymorphism