classifications 2 Flashcards
give an example of how a phylogeny has caused a shift in the naming of banksia and dyandra
hought to be two distinct groups
phylogeny shows dyandra to be in the banksia branch
put dyandras in the banksia genus
when a group is not monophyletic what two approaches are there to renaiming it
lumping - merge into the same genus
splitting - make more groups
describe bootsrap support give an example
take different combinations of the chacrteristics analysed
gives a slight change in the data sets
gives a percentage chance of the clade being repeated in every different run
two speceis of scenecio found within jacobea, jaccobea no longer monophyletic
either change name of scencio to jacobea - lumping
or change the name of the group around scencio to make a new genus - splitting
what is meant by the great plate anaomoly
way more cells in a microscope image than we can cultivate
give some culturability stats of some bacteria
seawater 0.001
soil 0.3
have cultivated 31 bacteria phyla out of around 100
what steps are reuired to name a bateria
send to two other labs with independant culture collections
phentypic charc
phylogenetic charac
there are - million rrna sequences from bacteria in lubraires — are described. at the current rate it will take over —– years to detect all the worlds microbes
4
12,000
1000
give the advantages and disadvantages of using the following techniques to charcterise and name microbes barcoding meta genomics meta transciriomics meta proteiomics stable isotope probing
barcoding - quick and lots of data is avlaible
- only speculation to the phenotype
metagenomics - full genetic potential
- does not tell use what it is actually doing relies on quallity of refernce data, moonlighting
meta transciprtomics
- as result of the environment
difficult because mrna decrades very fast. still need a refernce to the meta genome
- lots of rna is rrna which tells us nothing 95%
meta proteomics
- east to sequence and slow degradation
- hugeeee volumes of data, needs refernce data, hard to reverse translate
- look for funtional genes e.g. pmoA - methane oxidation
stable isotope probing
- dna or rna, can you for genomics
- long inubation times and causes cross breeding
descrbe how stable isotope probing works
- whats the problem
heavier isotopes added to respitatory substrate
- incorporated into the dna
- only organisms consuming methane will incoprate
needs long incubating time which can lead to cross feeding, where the organism respires CO2 back which then others can incoporate
what is the purpose of metadata
allows resampling
conditoins to support
method used
allows replication
give parts of the biochemistry used to chacterise a bacteria
respiratory quinones - type of isoprenoid chain
lipids and fatty acids - membrane is fundamental
- how archae were disocoverd
define enrichment and isolation
enrichment is creating several colonise in an agar plate from one sample
isolation is getting just one strain of bacteria
enrichment is creating several colonise in an agar plate from one sample
isolation is getting just one strain of bacteria
pcr amplificatoin models of nucleotide sub indels for allignment mutation rates orthologues vs paralogues vertical vs horizontal gene transfer
describe the knowledge needed about mutation rates in phylogenetic studies
supervariable - couldnt allign
super conserved no info
depends on taxonomic rank how conserved you want
describe orthologues vs paralogues
how do you solve this pattern
orthologue - displats homology due to speciation
paralogue - displaus homology due to duplication
the paralogue leads to errors
- primers anneal to both genes
- get wrong pattern
look at a few regions to see if you get the same pattern
