Topic 4a: taxonomy

Question 1

what is the origin of early life

Answer 1

rna - can be enzymatic on itself, single strand, template like dna
–first molecule able to act as enz to reprod self

Question 2

what is the main idea of endosymbiosis

Answer 2

-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

Question 3

what is genetic drift

Answer 3

changes in pop that have randomly happened
causes ev divergence
indep of selection
if bottle neck, get small pop that become founders

Question 4

what are mutations

Answer 4

random changes to dna
source of variation in orgs

Question 5

what is survival of fittest

Answer 5

mutations happen to act as advantage for some pops w changes in env and then thrive comp’d to unmut’d pops

Question 6

what is the LTEE

Answer 6

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

Question 7

what are homologues

Answer 7

if you have orgs in same gene family, that are related and have common ancestor
–gene that is related

Question 8

how do we get duplications in gene families (2 ways)

Answer 8

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

Question 9

what is vertical gene transfer

Answer 9

genome rep and cell division

Question 10

what are the 3 ways of horiz gene transfer

Answer 10

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)

Question 11

what is a taxonomical challenge

Answer 11

only described small amnt of species
phenotypic classification likely imposs

Question 12

what is a phenotypic classification

Answer 12

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

Question 13

what is phylogenetic classification

Answer 13

based on ev relationships

Question 13

what is genotypic classification

Answer 13

classify orgs based solely on their genome
bad: very arbitrary (basically based on pheno rels)

Question 13

what is taxonomy

Answer 13

grp orgs/classifying them and putting into grps
-classify, name, ID

Question 14

what are taxa

Answer 14

grps of orgs arranged by mutual similarity

Question 15

order of phylogeny

Answer 15

domain, phylum, class, order, family, genus, species, strain

Question 16

species

Answer 16

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)

Question 17

strain

Answer 17

descendants of single, pure cult

Question 18

biovar

Answer 18

strains that differe biochem

Question 19

morphovar

Answer 19

strains look dif

Question 20

serovar

Answer 20

strains are immunologically distinct

Question 21

pathovar

Answer 21

able to create disease

Question 22

candidate species

Answer 22

based on geentic info but never grown in pure cult
not italicized

Question 23

what are the subunits for ribosomes

Answer 23

proks/bact - 30S and 50S
-whole ribosome = 70S
–30S has 16S rRNA

euks - 60S, 40S; overall 80S
use 18S rRNA

Question 24

what are sequencing small subunit rRNA (SSU rRNA) and why use it (6 reasons)

Answer 24

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

Question 25

what is MLST

Answer 25

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)

Question 26

what is multigene phylogenetic analysis

Answer 26

gene seq analysis
challenge = hard to get info on species

Question 27

what is biochemical analysis

Answer 27

phenotypic analysis

examine composition of FA
FAME - fatty acid methyl ester

Question 28

what is ecological analysis

Answer 28

phenotypic
based on ability to colonize new env

Question 29

what is morphological analysis

Answer 29

phenotypic
based on struct feats

Question 30

what is physiological and metabolic analysis

Answer 30

phenotypic
relates to microbial activities
indirect genomic comparison

Question 31

what is a phylogenetic tree and what are the components

Answer 31

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)

Question 32

what is a cladogram

Answer 32

-only tells you ab rels
-no info on ev distance/number of changes

Question 33

what is an unrooted tree

Answer 33

phylog rel but no evolutionary path
unbiased
-all lines are dist’s

Question 34

what is a rooted tree and what is an outgrp

Answer 34

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

Question 35

how do you build a tree (pairwise alignments)

Answer 35

compare in pairs
start from most sim and work backwards
assume rate of mutation is consant

Question 36

how do you build a tree (UPGMA - cluster analysis)

Answer 36

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

Question 37

how to build a tree - neighbour joining

Answer 37

start in middle and push out ones most closely related
-still doing pairwise but dont assume constant rate of ev

Question 38

how do you assess accuracy of trees

Answer 38

bootstrapping - data columns randomized, realigned and reassembled into tree
–if tree constructed recurs in more than 70% of bootstrapped trees, tree = valid