Topic 4a: taxonomy Flashcards
what is the origin of early life
rna - can be enzymatic on itself, single strand, template like dna
–first molecule able to act as enz to reprod self
what is the main idea of endosymbiosis
-by lynn margulis
-organelles in euk have hallmark chars of arch and bact meaning that organelles were once indep orgs that came together to create euks
what is genetic drift
changes in pop that have randomly happened
causes ev divergence
indep of selection
if bottle neck, get small pop that become founders
what are mutations
random changes to dna
source of variation in orgs
what is survival of fittest
mutations happen to act as advantage for some pops w changes in env and then thrive comp’d to unmut’d pops
what is the LTEE
long term evolution exp
took 12 “ e coli pops and watched how evolved (some were able to aerobically grow on citrate)
fitness of org inc’d
what are homologues
if you have orgs in same gene family, that are related and have common ancestor
–gene that is related
how do we get duplications in gene families (2 ways)
paralogue - get new function (1 does old, 1 does new, allowing for change)
orthologue - have speciation (divergence bw 2 orgs that create 2 species); same function
what is vertical gene transfer
genome rep and cell division
what are the 3 ways of horiz gene transfer
unidirectional, asym, not constrained by species boundary
dna can be transferred from one species to another:
1. transformation (from env)
2. transduction (from viruses)
3. conjunction (cell to cell)
what is a taxonomical challenge
only described small amnt of species
phenotypic classification likely imposs
what is a phenotypic classification
what it looks like
-could use g pos/neg
bad:
-lim’d to cell shapes
-doesnt reflect ev relationships
-no wt assigned to phenotypic features
what is phylogenetic classification
based on ev relationships
what is genotypic classification
classify orgs based solely on their genome
bad: very arbitrary (basically based on pheno rels)
what is taxonomy
grp orgs/classifying them and putting into grps
-classify, name, ID
what are taxa
grps of orgs arranged by mutual similarity
order of phylogeny
domain, phylum, class, order, family, genus, species, strain
species
collection of strains that share stable properties which differ from those of other strains
–traits distinct from others and grp traits are shared
usu monophyletic (e/t in that grp share recent common ancestor)
strain
descendants of single, pure cult
biovar
strains that differe biochem
morphovar
strains look dif
serovar
strains are immunologically distinct
pathovar
able to create disease
candidate species
based on geentic info but never grown in pure cult
not italicized
what are the subunits for ribosomes
proks/bact - 30S and 50S
-whole ribosome = 70S
–30S has 16S rRNA
euks - 60S, 40S; overall 80S
use 18S rRNA
what are sequencing small subunit rRNA (SSU rRNA) and why use it (6 reasons)
16S rRNA
used as phylogen tool to class
can use database
can create genetic tree
universally distributed
functionally constant
highly conserved
long enough
req’f for survival
no horiz gene transfer
what is MLST
gene seq analysis
multilocus seq typing
-look at lots of dif genes that are housekeeping genes (always going to be there doing reg jobs), which lets us look at more than rrna (looks at several dif genes/rrna and comp evolutionary rels)
what is multigene phylogenetic analysis
gene seq analysis
challenge = hard to get info on species
what is biochemical analysis
phenotypic analysis
examine composition of FA
FAME - fatty acid methyl ester
what is ecological analysis
phenotypic
based on ability to colonize new env
what is morphological analysis
phenotypic
based on struct feats
what is physiological and metabolic analysis
phenotypic
relates to microbial activities
indirect genomic comparison
what is a phylogenetic tree and what are the components
graphical display of evol rels
sequenced orgs on tips of branches = OTUs (operational taxonomic units); the taxa
branching = denotes divergence
nodes = pts of divergence; allows for rotation
dist bw orgs (length conveys number of changes)
must align seq’s (use mix of random and matched positions to create comparisons)
what is a cladogram
-only tells you ab rels
-no info on ev distance/number of changes
what is an unrooted tree
phylog rel but no evolutionary path
unbiased
-all lines are dist’s
what is a rooted tree and what is an outgrp
incorps node to rep a common ancestor and shows ev progression from ancestor
biased
-only horiz lines are dist’s
has outgrp - species/taxa more dif than others and has sep ancestor; related
how do you build a tree (pairwise alignments)
compare in pairs
start from most sim and work backwards
assume rate of mutation is consant
how do you build a tree (UPGMA - cluster analysis)
start w most closely related (have the most similar seqs), which create small grp which is then used to compare as grp to other seq’s
assume constant rate of ev change
–doesnt work when rate of mut is not constant
how to build a tree - neighbour joining
start in middle and push out ones most closely related
-still doing pairwise but dont assume constant rate of ev
how do you assess accuracy of trees
bootstrapping - data columns randomized, realigned and reassembled into tree
–if tree constructed recurs in more than 70% of bootstrapped trees, tree = valid
