Bacterial Phylogeny Flashcards
What shifted the viewpoint that life could be classified in 5 kingdoms of life to the belief that there are 3 primary lines of descent (Eukaryotes, Bacteria, and Archaea)?
The concept that the determination of molecular sequences can be used to relate organisms.
Wose used ribosomal RNA as a molecular chronometer to trace the evolutionary decent of organism
Evolutionary Distance
The extent of sequence change between organism
Read as the distance between two lines on a phylogenetic tree
Molecular Chronometer
Nucleic acid sequences that are used to measure the evolutionary relatedness between organisms based on diffrences within the particular sequence
Can have a highly evolving gene - such as metavolic genes that allow one to asess short term scales of events
Slowly evolving genes, which provide a function that is resistant to change allow a deeper look at the phylogenetic tree
Why are metabolic genes not used as a molecular chronometer?
Used to look at short term events
These genes evolve quickly due to interactions with the environment, and the organisms need to change to deal with limiting factors
Because they rapidly chang, these versions of the phylogenetic tree do not concur with the rRNA version
What is the goal of evolutionary biology?
Look at the totality of life
Understand relationships between organisms
Explain the mechaistic diversity
Look at the interrelatedness of life
What has to happen for evolution to occur?
Mutation
Reproductive fitness
What allows an organism to survive?
When ans organism moves to a new environment and the thresholf for reproductive fitness changes its ability to survive, genetic changes that allow the organism to survive in an adaptive manner
The genetic changes are passed onto the progeny
Changes can be genetic, due to ecological environments, or gene transfer events that are inherited due to sucessful reproduction
What is the best way to define evolutionary relatedness?
DNA sequencing
Changes occur at the DNA level, and manifest as physiological changes
By looking at the difference in sequences between organisms, one can quantify evolutionary relatedness
What were the key experiments of the Wose/Pace papers?
Created a catalog od SSU rRNA sequences and quantifies the relatedness in regards to RNA divergence between all organisms of life
Wose selected oligonucleotide sequences from the SSU rRNA by digesting the RNA with a ribonuclease cleaving at G residues and sequenced using Sangers method.
Sanger Method
A 32P labeled RNA was digested with base specific RNases, and sequences of the oligonucleotifes were determined by digestion with other nucleases
Fragments were analyized and overlapped
Sequence could be ingeered from the oligonucleotide contents of overlaping fragments
Why was the ssu rRNA used?
Needed to use a gene that is in every organism for deep phylogenetic research
The gene also must contain some diversity, but not so much that it is unrecognizable
Looked at a slowly evolving gene that provides a function to the organism that is highly resistant to change
rRNA was in a resonably mature version of itself and does not undergo high levels of evolution because the transcriptional machinery does not tolerate high levels of change
What molecular chronometer would be used to look at the short term scale of events?
Genes that interact directly with the environment, which evolve quickly to survive changing conditions
Receptors
Metabolic genes
Virulence factors
What is the technical problem with Woses tree?
Wose was only able to look at a small subset of species due to the inability to culture an organism
However, all main conclusion of Woses tree remained fundamentally correct.
Woses’ Claims:
- 3 domains of life (Bacteria, Eukarya, and Archaea)
- Endosymbiosis occured to form organells
- Taxonomy is not an appropriate way of classification
- The last common ancestor was a thermophillic lithotroph
How did scientists deal with the inability to culture organisms?
Scientists issolated genes from the environment using PCR amplification
Designed primers that are specific to the highly conserved regions of rRNA, and amplified rRNA genes of all types of organisms present in an environmental sample
Linear Descent
Geneological descent is the passing of genes to progeny through sexual reproduction
Gene is passed from mother to daughter
Adaptive traits are passed through geneological descent
Results in a phylogenetic tree with a clear descendant
