Lesson 2 - Microbial Phylogeny and Systematics Flashcards
1
Q
is the study of the diversity of
organisms and their relationships. It links phylogeny with taxonomy
A
systematics
2
Q
the science in
which organisms are characterized, named,
and classified according to defined
criteria”
A
taxonomy
3
Q
taxonomic ranks of known prokaryotic species
A
domain
phyla
classes
order
families
genera
species
4
Q
estimates of actual prokaryotic species:
A
7029
(100,000 to 10,000,000)
5
Q
numbers of known prokaryotic species in each taxonomic rank: bacteria
A
domain - 1
phyla - 25
classes - 34
orders- 78
families- 230
genera - 1227
species - 6740
6
Q
numbers of known prokaryotic species in each taxonomic rank: archaea
A
domain - 1
phyla - 4^a
classes - 9
order - 13
families -23
genera -79
species -289
7
Q
numbers of known prokaryotic species in each taxonomic rank: total (archaea+ bac.)
A
domain - 2
phyla - 29
classes - 43
order - 91
families -243
genera -1306
species - 7029
8
Q
has been in a mess – we were stuck with it for
traditional reasons.
A
Traditional taxonomy or the classification through identification
and nomenclature of microbes, both “prokaryote” and
eukaryote
9
Q
would be based on evolutionary
relatedness
A
“natural” taxonomy
10
Q
would have similar properties in a fundamental sense
A
organisms in same “genus”
11
Q
a collection of
“species”
A
genus
12
Q
has long been possible:
A
natural taxonomy of macrobes
13
Q
have many easily distinguished features
A
Large organisms
14
Q
example that Large
organisms have many easily distinguished features
A
body
plans and developmental processes, that can be used to describe
hierarchies of relatedness
15
Q
usually have few distinguishing properties that relate
them
A
microbes
16
Q
has not been possible in microbes
A
hierarchical taxonomy
17
Q
why hierarchical taxonomy has not been possible in microbes
A
microbes usually have few distinguishing properties that relate
them
18
Q
groups organisms
together based on similar
phenotypic
characteristics
A
phenetic system
19
Q
what technique was to clones isolated from environment
A
traditional culturing
20
Q
how many perrcent crossover bet. micrrorganism able to grow in pure cultures and clones isolated from environment?
A
less than %
21
Q
what does less than 1& crossover between these 2 groups indicate?
A
less than 1% of environmental microbes can actually be grown in the lab using standard culture techniques
22
Q
nutrient-rich culture media select for what kind of bacteria
A
copiotrophic (needy) bacteria
23
Q
isolate ~1 % of the total bacteria in marine ecosystem, severely underestimating diversity and community structure
A
traditional culturing techniques
24
Q
constitute a taxonomy but
do not provide relationships (except as might be inferred
subjectively)
A
Classical physiological
descriptions of microbes
25
methods that establish relationships, but only
if close, i.e., they are not
sufficiently general to be
broadly applicable
G+C ratios, FAME, DNA-DNA
hybridization, or REP PCR
26
All these methods require
pure-cultivation of
organisms
27
what is pure-cultivation of
organisms for
characterization, but we
can't cultivate much of
what is out there.
28
changed the problem of unculturability
Recent advances in molecular phylogeny h
29
With molecular phylogeny, we have now relatively quantitative way to view
biodiversity, in the context of
phylogenetic maps or
evolutionary trees
30
used for large-scale
structure
Slowly evolving molecules
31
Slowly evolving molecules example
rRNA
32
molecules used for fine-structure.
"fast- clock"
33
remain solidly rooted in the tradition
of Linnaeus at this time.
The literature language (e.g. "species") and formal
nomenclature
34
methods for microbial taxonomy and determination of evolutionary relationship
1. phenetic system
2. phyletic system
35
- more in-depth methods may establish relationships, but only if organisms are closely related
- not applicable on broad evolutionary landscapes
phenetic system
36
methods in phenetic system
% GC (G+ C ratios)
DNA:DNA hybridization
Fatty acid methyl ester analysis (FAME)
ribotyping
37
compare organism based on evolutionary relationship
phyletic system
38
methods in phyletic sysetm
rRNA seq. comparison
Multilocus sequence typing (MLST)
39
has evolved into a field that utilizes a
combination of methods for the identification and
description of new species.
MICROBIAL TAXONOMY (part. bacterial taxonomy)
40
what has microbial taxonomy (particularly bacterial tax.) has evolved into
evolved into a field that utilizes a
combination of methods for the identification and
description of new species.
41
uses three kinds of
methods—phenotypic, genotypic, and phylogenetic.
polyphasic approach to taxonomy
42
3 methods used to polyphasic approach to taxonomy
phenotypic, genotypic, and phylogenetic.
43
genotypic, chemotaxonomic and phenotypic methods for determining taxonomic position of microbes
polyphasic approach
44
examines the morphological, metabolic,
physiological, and chemical characteristics of the cell.
phenotypic analysis
45
what does phenotypic analysis examine
morphological, metabolic,
physiological, and chemical characteristics of the cell
46
analysis considers characteristics of the genome.
genotypic
47
phrnotypic and genotyphic analysis categorize organisms based on
what
similarities
48
2 kinds of analysis in molecular phylogeny
phenotypic and genotypic analysis
49
both phenotypic and genotypic analysis are complemented by what
phylogenetic analysis
50
what is phylogenetic analysis
seeks to place organisms within an
evolutionary framework using molecular sequence data.
51
provide a record of past evolutionary events and can be used to
build phylogenetic trees, which are diagrams used to depict evolutionary history
molecular sequence
52
moleculaar seq. provide a record of ___ and can be used to build ___
record - past evolutionary relationships
build - phylogenetic tree
53
what is phylogenetic tree
diagrams used to depict evolutionary history
54
can accumulate over time and lead to
natural variations that allow evolution.
Mutations in the genetic material of all cells (DNA)
55
mutations leads to what
natural variations that allow evolution.
56
will be a
function of the number of mutations that have accumulated since they shared a common
ancestor.
The difference in nucleotide sequence between the DNA of any two organisms
57
can be used to infer evolutionary
relationships.
differences in DNA sequences
58
ompares organisms based on evolutionary
relatedness
phyletic system
59
not culture-based
rRNA methods
60
excellent descriptors of microbial taxa based on phylogeny
Ribosomal RNAs (rRNAs) and its respective genes (rDNA)
61
Ribosomal RNAs (rRNAs) and its respective genes (rDNA) are
excellent descriptors of microbial taxa based on what
phylogeny
62
certain molecules are ehwat
molecular chronometers
63
why certain molecules are molecular chronometers
differences in
nt or aa sequences of homologous molecules are a function of their
evolutionary distance
64
molecular chronometers are:
universally distributed among all living organisms (essential for
even the most primitive cells)
-functionally homologous
-lack horizontal gene transfer that could confound phylogenetic
analysis
65
molecular chronometers cannot accumulate what
many mutations in such important macromolecule
66
reflects evolutionary distance between organisms.
evolutionary
distance between rRNA
67
let us look deep into the evolutionary past
Molecular
chronometers
68
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
69
Examples of molecular chronometers:
rRNA, ATPase, RecA, DNA polymerase, etc.
rRNA is the most widely used
70
A huge database of this sequences exists
rRNA seq.
71
contains a large collection of
such sequences, now numbering over 100,000
Ribosomal Database Project (RDP)
72
- Typically, DNA is extracted from a culture (pure) for organisms that can be grown in the laboratory. The DNA isolated is also called genomic DNA or gDNA.
- genomic DNA can be sequenced directly or used for PCR amplification. = genome sequencing. genome sequencing a standard tool employed in
analyses of microbial phylogeny
DNA
73
DNA is extracted from what
from a culture (pure) for organisms that can
be grown in the laboratory
74
The DNA isolated is also called
genomic DNA or gDNA
75
can be sequenced directly or used for PCR amplification
GENOMIC DNA
76
a standard tool employed in
analyses of microbial phylogeny
GENOME SEQUENCING
77
- sequence analysis of small subunit (SSU) ribosomal RNA
(rRNA) genes is the basis of much of microbial phylogeny
- SSU rRNA genes are highly conserved, present in all cellular
organisms, and easily sequenced and analyzed
RNA
78
is the basis of much of microbial phylogeny
sequence analysis of small subunit (SSU) ribosomal RNA
(rRNA) genes
79
highly conserved, present in all cellular
organisms, and easily sequenced and analyze
SSU rRNA
80
Primary and secondary structure
of 16S rRNA from Escherichia coli
(Bacteria).
The 16S rRNA from
Archaea is similar in secondary
structure (folding) but has
numerous differences in primary
structure (sequence). The molecule
is composed of conserved and
variable regions (V1–V9). The
approximate positions of the
variable regions are indicated in
color
81
can have
different levels of
phylogenetic specificity to
target discrete species,
genera, phyla, or domains,
rRNA gene
82
will
amplify the SSU rRNA gene
from any organism
"universal" primers
83
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)
84
- identified archaea (Greek: "ancient ones"), a separate branch of life from eubacteria
- demonstrated that differences in rRNA seq. usually reflectsevolutionary relationship
carl woese and george fox (1977)
85
2 types of prokaryotic cell
archaea and bacteria
86
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), and the products are run
on an agarose gel (3). The bands of amplified DNA are
approximately 1465 nucleotides in length (3). 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 (4) and analysis to
identify the bacteria (5).
87
can be inferred
30
only from genes that have
homology or genes that have been inherited from a
common ancestor
phylogeny
88
a binary trait
homology
89
are NOT interchangeable
similarity and homology
90
continuous trait defined as a percentage of nucleotide
positions shared between any two sequences
similarity
91
used to infer homology, but a similarity value
can be calculated between any two sequences regardless of their
function or evolutionary relationshi
seq. similarity
92
Phylogenetic analyses typically focus on analysis of
orthologous genes
that have similar function.
93
have the same function and originate from a single
ancestral gene in a common ancestors
orthologs
94
have evolved to have different functions as a result of
gene duplication
paralogs
95
❑Phylogenetic analyses estimate evolutionary changes from the
number
of sequence differences across a set of homologous nucleotide
positions
96
Some mutations introduce what
nucleotide insertions or deletions
97
nucleotide insertions or deletions lead to what
differences in sequence length, and making it necessary to align nucleotide
positions prior to phylogenetic analysis of gene sequences
98
is done to add gaps to molecular sequences in order to
establish positional homology, i.e., to be sure that each position in the
sequence was inherited from a common ancestor of all organisms under
consideration
sequence alignment
99
Alignment of DNA sequences
(a) Sequences for a hypothetical region of a gene are shown for three species before alignment and after alignment. A sequence alignment should display homologous positions in vertical columns. Sequence alignment is achieved by adding gaps,
indicated by hyphens, to maximize local sequence similarity between the species in the alignment.
(b) The distance matrices show the number of sequence differences that would be inferred for each species pair both before and after
alignment.
100
A sequence
alignment should display
homologous
positions in vertical columns
101
how is sequence alignment achieved
by adding gaps
102
the gaps in sequence aligbhment is indicated by
hyphen
103
what is sequence alignment for
to maximize local
sequence similarity between the species in
the alignment.
104
show the number of
sequence differences that would be inferred
for each species pair both before and after
alignment
distance matrices
105
a
diagram that depicts the
evolutionary history of an
organism and bears some
resemblance to a family tree
phylogenetic tree
106
Phylogenetic trees allow us
to make what
hypotheses about
an organism’s characteristics
since organisms that share a
recent ancestor are likely to
share characteristics
107
Phylogenetic trees are also
of great use in
taxonomy and
species identification.
108
❑A phylogenetic tree is
composed of
nodes and branches
109
represent ancestor sp.
internal nodes
110
represent extant, known sp.
external nodes
111
represent evolutionary distance between species
branch lengths
112
show the position of the ancestor of all
organisms being examined
rooted trees
113
depict the relative relationships among
the organisms under study but do not provide evidence of
the most ancestral node in the tree.
unrooted trees
114
represent a past stage of evolution where an
ancestor diverged into two new lineages
nodes
115
represents the number of changes that have
occurred along that branch.
branch length
116
In a phylogenetic tree, only their position are informative;
position of nodes and the
branch lengths
117
has
no effect on the tree’s topology
rotation around nodes
118
used by phylogenetic analysis in an
attempt to identify the one correct tree that accurately
represents the evolutionary history of a set of sequences
molecular sequence data
119
The structure of a phylogenetic tree is inferred by
applying either an
algorithm or some set of optimality
criteria.
120
m is a programmed series of steps
designed to construct a single tree.
algorithm
121
Algorithms used to build phylogenetic trees include the
unweighted pair group method with arithmetic mean
(UPGMA) and the neighbor-joining method.
122
Methods that employ optimality criteria include
parsimony, maximum likelihood, and Bayesian analyses
123
parsimony, maximum likelihood, and Bayesian analyses evaluate what
many possible trees
124
waht do parsimony, maximum likelihood, and Bayesian analyses select?
the one
tree that has the best optimality score, that is, they select
the tree that best fits the sequence data given a discrete
model of molecular evolution.
125
how are optimality scores calculated
on the basis of evolutionary models that
describe how molecular sequences change over time
126
building phylogenetic trees
1. we can count the number of differences between each pair of sequences to build a
distance matrix
2. This distance matrix can
be used to build a tree
3. where the cumulative lengths of the horizontal
branches between
any two species in the tree are proportional
to the number of nucleotide differences
between these species
127
Limitations of Phylogenetic Tree
1. difficult to choose the true tree based on available sequence data if several different trees fit the data equally well
2. Homoplasy
3. prevalence of horizontal gene transfer also creates complications
for evolutionary history of microorganisms.
128
a statistical method
in which information is resampled at random, is an approach used to deal
with uncertainty in phylogenetic trees.
bootstrapping
129
indicate the percentage of the time that a given
node in a phylogenetic tree is supported by the sequence data.
bootstrap values
130
ndicate that a node in the tree is likely to be
correct
High bootstrap values i
131
indicate that the placement of a
node cannot be accurately determined given the available data
low bootstrap values i
132
or convergent evolution, occurs when organisms share a trait
that was not inherited from a common ancestor. This occurs in sequences also.
homoplasy
133
homoplasy is when similar sequence positions result from what
recurrent mutation
rather than inheritance from a common ancestor
134
result of homoplasy
reconstruction of accurate
phylogenetic trees gets more difficult when sequence
divergence between organisms is very high.
135
appear to be transferred
horizontally at very low frequencies
genes encoding SSU rRNAs
136
agree largely with those prepared from other
genes that encode genetic informational functions.
rRNA gene
phylogenies
137
where do rRNA gene
phylogenies agree largely
with those prepared from other
genes that encode genetic informational functions
138
SSU rRNA gene sequences are generally considered to
provide what
accurate record of organismal phylogen
139
depicts evolutionary history of a gene
gene phylogeny
140
depicts evolutionary history of a cell
organismal phylogeny
141
contain genes that have been acquired
by horizontal gene transfer at some point in their evolutionary
history
many microbial genome
142
many microbial genome contain gene that have been what
acquired
by horizontal gene transfer at some point in their evolutionary
history
143
horizontal gene transfer will cause what
cause gene to have a different evolutionary history from the rest
of the genome
144
horizontal gene transfer
(a) Genes are transferred horizontally between distantly related microorganisms. Colors are used to match microorganisms with their genomes.
(b) As a result of the horizontal transfer events in part a, different phylogenetic trees for gene 1, gene 2, and gene 3 are obtained. Only the gene tree for gene 1, which was not transferred, remains congruent with
the organismal phylogeny.
