Module 2A: Microbial Phylogeny and Systematics Flashcards
jusq pirteng hangaka na ba. tabang (121 cards)
1
Q
the classification through identification
and nomenclature of microbes, both “prokaryote” and
eukaryote, has been in a mess – we were stuck with it for
traditional reasons.
A
Systematics
2
Q
We know ____% of prokaryotes
A
<1%
3
Q
Estimates of actual prokaryotic species
A
100,000 to 10,000,000
4
Q
the classification through identification
and nomenclature of microbes, both “prokaryote” and
eukaryote that has been a mess.
A
Traditional Taxonomy
5
Q
- based on evolutionary
relatedness - thus, organisms in same “genus” (a collection of
“species”) would have similar properties in a fundamental sense.
A
Natural Taxonomy
6
Q
- has long been possible
- Large
organisms have many easily distinguished features (e.g., bodyplans and developmental processes, that can be used to describe
hierarchies of relatedness).
A
Natural taxonomy of macrobes
7
Q
- usually have few distinguishing properties that relate
them.
A
Microbes
8
Q
Has not been possible
A
Hierarchical Taxonomy
9
Q
- Isolate ~1% of the total bacteria in marine ecosystems.
- Severely underestimating diversity and community structure
A
Traditional culturing technique
10
Q
groups organisms
together based on similar
phenotypic
characteristics
A
Phenetic System
11
Q
Microbial organism able to grow in pure cultura and Clones isolated from environment
A
Less than 1% Crossover between these groups
12
Q
select for copiotrophic bacteria
A
Nutrient rich culture media
13
Q
Copiotrophic
A
Needy
14
Q
Nutrient-rich culture media select for copiotrophic (needy) bacteria
A
MO’s able to grow in pure culture
15
Q
Traditional culturing techniques isolate ~1% of the total bacteria in marine ecosystem, severely underestimating diversity and community structure
A
Clones isolated from environment
16
Q
constitute a taxonomy, but
do not provide
relationships (except as
might be inferred
subjectively).
A
Classical physiological
descriptions of microbes
17
Q
Methods such as: (4)
- establish relationships but only if close.
- are not
sufficiently general to be
broadly applicable.
A
- G+C ratios,
- FAME,
- DNA-DNA
hybridization, or - REP PCR
18
Q
All these methods require
________ of
organisms for
characterization, but we
can’t cultivate much of
what is out there.
A
pure-cultivation
19
Q
Recent advances in _______ have changed Microbial taxonomy
A
molecular phylogeny
20
Q
a relatively quantitative way to view
biodiversity, in the context of
A
phylogenetic maps or
evolutionary trees.
21
Q
- used for large-scale
structure - (e.g. rRNA)
A
Slowly evolving molecules
22
Q
molecules used for fine-structure.
A
“fast- clock”
23
Q
- remain solidly rooted in the tradition
of Linnaeus - (e.g. “species”)
A
literature language and formal
nomenclature
24
Q
Compares organisms based on evolutionary relationshios
A
Phyletic system
25
- More in-depth methods may establish relationships, but only f organisms are closely related.
- Not applicable on broad evolutionary ladscapes
Phenetic System
26
Methods under Phenetic system
%GC (G+C rations
DNA:DNA Hybridization
FAME
Ribotyping
27
FAME
Fatty acid methyl ester analysis
28
Methods under Phyletic system
rRNA sequence comparison
Multilocus sequence typing (MLST)
29
MLST
Multilocus sequence typing
30
This polyphasic approach to taxonomy uses three kinds of
methods
phenotypic, genotypic, and phylogenetic.
31
___________ (particularly bacterial
taxonomy) has evolved into a field that utilizes a
combination of methods for the identification and
description of new species.
Microbial taxonomy
32
examines the morphological, metabolic,
physiological, and chemical characteristics of the cell.
Phenotypic analysis
33
- considers characteristics of the genome.
- These two kinds of analysis categorize organisms based on
similarities.
Genotypic analysis
34
___________ provide a record of past evolutionary events and can be used to
build phylogenetic trees.
Molecular sequences
35
are diagrams used to depict evolutionary history.
phylogenetic trees
36
Mutations in the genetic material of all cells (DNA) can accumulate over time and lead to
natural variations that allow evolution.
37
can be used to infer evolutionary
relationships.
can be used to infer evolutionary
relationships.
38
The difference in ___________ between the DNA of any two organisms will be a
function of the number of mutations that have accumulated since they shared a common
ancestor.
nucleotide sequence
39
NOT culture-based.
rRNA methods
40
are
excellent descriptors of microbial taxa based on phylogeny.
Ribosomal RNAs (rRNAs) and its respective genes (rDNA)
41
Certain molecules are
molecular chronometers
42
Certain molecules are “molecular chronometers”: differences __________________ are a function of their
evolutionary distance.
in
nt or aa sequences of homologous molecules
43
- universally distributed among all living organisms (essential for
even the most primitive cells)
- functionally homologous
- lack horizontal gene transfer that could confound phylogenetic
analysis
Molecular chronometers
44
Can’t accumulate many mutations in such an important macromolecule
… so, evolutionary
distance between rRNAs reflects evolutionary distance between organisms. Molecular
chronometers let us look deep into the evolutionary past.
45
Useful features of molecular chronometers
- regions of sequence conservation so DNA can be aligned
- sequence change should reflect evolutionary change in organism as a
whole
46
Examples of molecular chronometers
- rRNA,
- ATPase,
- RecA,
- DNA polymerase, etc.
47
In Molecular chronometeres, ________ is the most widely used.
rRNA
48
A huge database of rRNA sequences exists. For example, the
____________ contains a large collection of
such sequences, now numbering over 100,000.
Ribosomal Database Project (RDP)
49
contains a large collection of
such sequences, now numbering over 100,000.
Ribosomal Database Project (RDP)
50
Sequences used for molecular phylogeny
1. DNA
2. RNA
51
Typically extracted from a culture (pure) for organisms that can
be grown in the laboratory.
DNA
52
The DNA isolated is also called
genomic DNA
or gDNA.
53
genomic DNA can be sequenced directly or used for
PCR amplification
54
PCR amplification =
______________
genome sequencing
55
a standard tool employed in
analyses of microbial phylogeny
genome sequencing
56
the basis of much of microbial phylogeny
sequence analysis of small subunit (SSU) ribosomal RNA
(rRNA) genes
57
sequence analysis of small subunit (SSU) ribosomal RNA
(rRNA) genes is the basis of much of microbial phylogeny
RNA
58
are highly conserved, present in all cellular
organisms, and easily sequenced and analyzed
SSU rRNA genes
59
REMEMBER:
- Procaryotes =
- Eucaryotes =
- Procaryotes = 16S rRNA
- Eucaryotes = 18S rRNA
60
similar in secondary
structure (folding) but has
numerous differences in primary
structure (sequence)
16S rRNA from
Archaea
61
The molecule
is composed of _________ and
_______ regions (V1–V9)
conserved, variable
62
'Folding'
Secondary structure
63
Sequence
Secondary structure
64
The rRNA gene can have
different levels of
phylogenetic specificity
65
- to
target discrete species,
genera, phyla, or domains,
- there are even
“universal” primers that will
amplify the SSU rRNA gene
from any organism.
Importance of different levels of phylogenetic specificity
66
amplify the SSU rRNA gene
from any organism.
“universal” primers
67
Why ribosomal RNAs?
• Found among all living organisms (for 3.8 of the last 4.5 billion years).
• Integral part of protein synthesis machinery (and therefore highly
conserved among organisms).
• Cell component analyses provide culture-independent means of
investigating questions in microbial ecology (lack of morphology).
• rRNAs offer a type of sequence information that makes them excellent
descriptors of an organism's evolutionary history.
• No detectable horizontal gene transfer, especially important for the
prokaryotes.
• Large and growing database; RDP contains ~100K SSU rRNAs. (more
about RDP in Module 4)
68
Can be obtained at any taxon level
Signature sequences
69
- Identified Archea, a separate branch of life from eubacteria
- Demonstrated that differences in rRNA sequences usefully reflect evolutionary relaationships
Carl Woese and George Fox (1977)
70
2 types of prokaryotic cells
Archea and Bacteria
71
PCR amplification of
the 16s rRNA gene
Following DNA isolation:
1. primers complementary to
the ends of the 16S rRNA are used to PCR-amplify the
16S rRNA gene from the genomic DNA of five different
unknown bacterial strains
2. The products are run
on an agarose gel
3. The bands of amplified DNA are
approximately 1465 nucleotides in length.
4. Positions
of DNA kilobase size markers are indicated at the left.
Excision from the gel and purification of these PCR
products is followed by sequencing
5. analysis to
identify the bacteria
72
Tinamad version sa PCR amplification of
the 16s rRNA gene
1. Isolate DNA
2. Amplify 16S gene by PCR
3. Products are run on an agarose gel
4. Sequence
5. Align sequences; generate tree
73
Sequence Alignment Principle
1. Phylogeny can be inferred only from genes that have
homology or genes that have been inherited from a
common ancestor
2. Similarity and homology are NOT interchangeable
3. Phylogenetic analyses typically focus on analysis of
orthologous genes that have similar function.
4. Phylogenetic analyses estimate evolutionary changes from the number
of sequence differences across a set of homologous nucleotide
positions.
5. Alignment of DNA sequences
74
✓ genes that have been inherited from a common ancestor
✓ homology is a binary trait; sequences are either
homologous or they are not
Phylogeny can be inferred only from genes that have
homology or genes that have been inherited from a
common ancestor
75
✓Similarity is a continuous trait defined as a percentage of nucleotide
positions shared between any two sequences
✓Sequence similarity is used to infer homology, but a similarity value
can be calculated between any two sequences regardless of their
function or evolutionary relationship
Similarity and homology are NOT interchangeable
76
have the same function and originate from a single
ancestral gene in a common ancestor
orthologs
77
have evolved to have different functions as a result of
gene duplication
paralogs
78
- is done to add gaps to molecular sequences in order to
establish positional homology.
- to be sure that each position in the
sequence was inherited from a common ancestor of all organisms under
consideration
Sequence alignment
79
Steps in alignment of DNA sequences:
1. Sequences for a hypothetical region of a
gene are shown for (n) species before
alignment and after alignment.
2. A sequence
alignment should display homologous
positions in vertical columns
3. Sequence
alignment is achieved by adding gaps,
indicated by hyphens, to maximize local
sequence similarity between the species in
the alignment.
4. The distance matrices show the number of
sequence differences that would be inferred
for each species pair both before and after
alignment.
80
is a
diagram that depicts the
evolutionary history of an
organism and bears some
resemblance to a family tree
Phylogenetic tree
81
The tips of the branches
species (or strain)
82
the nodes
ancestors
83
Ancestral relationships are revealed by the
branching order in
rooted trees
84
Phylogenetic trees allow us
to make hypotheses about
an organism’s characteristics
since organisms that share a
_________ are likely to
share characteristics.
recent ancestor
85
Phylogenetic trees are also
of great use in
taxonomy and
species identification.
86
A phylogenetic tree is
composed of nodes and
branches
87
represent ancestor species
internal nodes
88
represent extant, known species
external nodes
89
represents evolutionary distance between species
branch lengths
90
show the position of the ancestor of all
organisms being examined.
Rooted trees
91
depict the relative relationships among
the organisms under study but do not provide evidence of
the most ancestral node in the tree.
Unrooted trees
92
The nodes represent a past stage of evolution where an
____________ into two new lineages.
ancestor diverged
93
The branch
length represents the _________ that have
occurred along that branch
number of changes
94
In a phylogenetic tree, only the position of _________ and _________ are informative
nodes and
branch lengths
95
rotation around nodes
has
no effect on the tree’s topology
96
Phylogenetic analysis uses __________________ in an
attempt to identify the one correct tree that accurately
represents the evolutionary history of a set of sequences.
molecular sequence data
97
The structure of a phylogenetic tree is inferred by
applying either an _______ or some _________
criteria.
algorithm, set of optimality
98
is a programmed series of steps
designed to construct a single tree.
algorithm
99
Algorithms used to build phylogenetic trees
- unweighted pair group method with arithmetic mean
(UPGMA)
- the neighbor-joining method.
100
Methods that employ optimality criteria include
parsimony, maximum likelihood, and Bayesian analyses
101
calculated on the basis of evolutionary models that
describe how molecular sequences change over time
Optimality scores
102
steps in composing or constructing a phylogenetic tree:
1. Align sequences
2. Calculate distance matrix using the number of sequence differences
3. Construct the tree by adding nodes to join lineages that have the fewest differences
103
Limitations of Phylogenetic Trees
1. difficult to choose the true tree based on available sequence data if several
different trees fit the data equally well.
2. Homoplasy, or convergent evolution, occurs when organisms share a trait
that was not inherited from a common ancestor.
3. prevalence of horizontal gene transfer also creates complications
for evolutionary history of microorganisms.
104
a statistical method
in which information is resampled at random, is an approach used to deal
with uncertainty in phylogenetic trees.
Bootstrapping
105
indicate the percentage of the time that a given
node in a phylogenetic tree is supported by the sequence data.
Bootstrap values
106
Bootstrap values indicate the that ______________ given
node in a phylogenetic tree is supported by the sequence data.
percentage of the time
107
indicate that a node in the tree is likely to be
correct
High bootstrap value
108
indicate that the placement of a
node cannot be accurately determined given the available data.
low bootstrap values
109
- occurs when organisms share a trait
that was not inherited from a common ancestor.
- also occurs in sequences
- when similar sequence positions result from recurrent mutation
rather than inheritance from a common ancestor
Homoplasy, or convergent evolution
110
as a result of homoplasy, the reconstruction of accurate
phylogenetic trees gets more
difficult when sequence
divergence between organisms is very high.
111
prevalence of horizontal gene transfer also creates complications
for
evolutionary history of microorganisms.
112
genes encoding SSU rRNAs appear to be transferred
horizontally at ______________,
very low frequencies
113
and rRNA gene
phylogenies agree _______ with those prepared from other
genes that encode genetic informational functions.
largely
114
__________ depicts evolutionary history of a gene, while
______________ depicts evolutionary history of a cell
gene
phylogeny, organismal phylogeny
115
are generally considered to
provide an accurate record of organismal phylogeny
SSU rRNA gene sequences
116
prevalence of _____________ also creates complications
for evolutionary history of microorganisms.
horizontal gene transfer
117
- Genes are transferred horizontally between distantly related microorganisms
- cause to have a different evolutionary history from the rest
of the genome
Horizontal gene transfer
118
the science of classifying organisms based on shared characteristics.
Taxonomy
119
the study of evolutionary relationships among organisms.
Phylogeny
120
Difference between Taxonomy and Phylogeny
Taxonomy = classification
Phylogeny = evolutionary history
121
How does HGT complicate evolutionary history and phylogenetic studies of microorganism?
HGT complicates evolutionary history and phylogenetic studies by introducing genes from unrelated organisms, making it difficult to trace accurate lineage and construct true evolutionary trees.
