Introduction to Phylogenetic Analysis Flashcards
the evolution of a genetically related group of organisms
phylogeny
a study of relationships between collection of “things” (genes, proteins, organs..) that are derived from a common ancestor.
phylogeny
the science of classification of organisms.
taxonomy
purpose of phylogenetic tree
- Find evolutionary ties between organisms. (Analyze changes occurring in different organisms during evolution).
- Find (understand) relationships between an ancestral sequence and its descendants. (Evolution of a family of sequences)
- Estimate the time of divergence between a group of organisms that share a common ancestor.
similar sequences, ____ and this means ___
common ancestor; similar function
From a ____ sequence, ____ are diverged. Each of these two sequences start to accumulate ____ . The number of these mutations are used in ____.
common ancestor; two DNA sequences; nucleotide substitutions; molecular evolution analysis
How we calculate the Degree of Divergence
If two sequences of length N differ from
each other at n sites, then their degree of
divergence is:
n/N or n/N*100%.
When 2 sequences found in 2 organisms are
very similar, we assume that they have derived
from ___
one ancestor
The progressive multiple alignment of a group of
sequences, first aligns the ___. Then it adds the ___.
most similar pair; more distant pairs
Most phylogenetic methods assume that each
position in a sequence can ___ from the other positions
change independently
Gaps in alignments represent mutations in
sequences such as:
insertion, deletion, genetic rearrangments
Gaps are treated in various ways by thephylogenetic methods. Most of them ___.
ignore gaps
Another approach to treat gaps is by using ____ as the base for the phylogenetic analysis, instead of using the ___, and trying to decide what happened at each position.
sequences similarity scores; alignment itself
The similarity scores based on scoring matrices (with gaps scores) are used by
the ___
DISTANCE methods
what is a phylogenetic tree?
An illustration of the evolutionary relationships among a group of organisms.
another name for a phylogenetic tree.
dendrogram
A tree is composed of ___ and ___. One branch connects any two adjacent nodes. ___represent the taxonomic units. (____)
nodes and branches; Nodes; sequences
very similar sequences will be neighbors on the outer branches and will be connected by a ____
common internal branch
types of trees
trees and networks
type of tree that has only one path between
any pair of nodes
tree
a type of tree with more than one path between any pair of
nodes
network
Represent the taxa (sequences)
Leaves = Outer branches
Represent the relationships among the taxa (sequences)
Nodes = 1 2 3
The length of the branch represent the # of changes that occurred in the __ prior to the next level of separation
sequence (branch)
- are branches that end with a tip
- more evident diversions
external branches
- are branches that do not end with a tip.
- more ancient diversions
internal branches
In a phylogenetic tree, Each ___ represents a speciation event in evolution. Beyond this point, any sequence changes that occurred are specific for each branch (specie).
node
In a phylogenetic tree, The – connects – of the tree. The length of each – between one – to the next, represents the # of changes that occurred until the next separation (speciation).
BRANCH; 2 NODES; BRANCH; NODE
In a phylogenetic tree, note that The ____ from the separation of the 2 sequences is not known. The phylogenetic analysis can only estimate the ___
amount of evolutionary time that passed; # of changes that occurred from the time of separation
After the ___, one taxon (sequence) can undergo more mutations then the other taxon
branching event
the branching pattern of a tree
topology of a tree
What represents the data (e.g sequences) under comparison (A,B,C,D,E), and is also known as OTUs, (—-).
terminal nodes; Operational Taxonomic Units
What represents inferred ancestral units (usually without empirical data), also known as HTUs, (—-).
Internal nodes; Hypothetical Taxonomic Units
Different kinds of trees can be used to depict different aspects of evolutionary history. What are those?
- cladogram
- additive trees
- ultrametric trees
A kind of tree that simply shows relative recency of common ancestry
cladogram
a cladogram with branch lengths, also called phylograms and metric trees
additive tree
(dendograms) special kind of additive tree in which the tips of the trees are all equidistant from the root
ultrametric tree
what hypothesis is this? All the mutations occur at the same rate in all the tree branches. The rate of the mutations is the same for all positions along the sequence
The Molecular Clock Hypothesis
What hypothesis is most suitable for
closely related species?
The Molecular Clock Hypothesis
rooted tree = –
unrooted tree = –
cladogram; phenogram
- A phylogenetic tree that all the “objects” on it
share a known common ancestor (the root). - There exists a particular root node
- The paths from the root to the nodes correspond to evolutionary time.
Rooted Tree = Cladogram
- A phylogenetic tree where all the “objects” on it are related descendants - but there is
not enough information to specify the common
ancestor (root). - The path between nodes of the tree do not specify an evolutionary time.
Unrooted Tree = Phenogram
The number of tree topologies of rooted tree is ___ than that of the unrooted tree for the same umber of OTUs.
Therefore, the error of the unrooted tree topology is ____ than that of the rooted tree.
much higher; smaller
genes related by speciation events. Meaning same genes in different species.
orthologs
genes related by duplication events. Meaning duplicated genes in the same species.
paralogs
The rate of mutation is assumed to be the same in both coding and non-coding regions. However, there is a difference in the ___ .
substitution rate
___ have more substitution than coding regions.
____ are much more conserved since they “need” to conserve their function.
Non-coding DNA regions; Proteins
it is better to use sequences that mutate slowly. This is —-. However, if the genes are very small, or they mutate slowly, we can use them for —.
protiens; building the trees
Are treated differently by different alignment programs and should play no part in building trees.
gaps
Alignment of a coding region should be compared with the alignment of their ____, to be sure about the placement of gaps.
protein sequences
effect the multiple alignment because they create
random bias for various regions of the alignment
- should be removed from the alignment before building the tree
Low complexity regions
If you delete low complexity regions, you need to
consider the effect of the ___ on the branch lengths of the whole tree.
deletions
Sequences that are being compared belong together (—-).
orthologs
If no ancestral sequence is available you may use an “___” as a reference to measure distances. In such a case, for an —- you need to choose a close relative to the group being compared.
outgroup; outgroup
