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Systematics > Introduction to Phylogenetic Analysis > Flashcards

Introduction to Phylogenetic Analysis Flashcards

1
Q

the evolution of a genetically related group of organisms

A

phylogeny

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2
Q

a study of relationships between collection of “things” (genes, proteins, organs..) that are derived from a common ancestor.

A

phylogeny

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3
Q

the science of classification of organisms.

A

taxonomy

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4
Q

purpose of phylogenetic tree

A
  • 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.
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5
Q

similar sequences, ____ and this means ___

A

common ancestor; similar function

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6
Q

From a ____ sequence, ____ are diverged. Each of these two sequences start to accumulate ____ . The number of these mutations are used in ____.

A

common ancestor; two DNA sequences; nucleotide substitutions; molecular evolution analysis

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7
Q

How we calculate the Degree of Divergence

A

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%.

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8
Q

When 2 sequences found in 2 organisms are
very similar, we assume that they have derived
from ___

A

one ancestor

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9
Q

The progressive multiple alignment of a group of
sequences, first aligns the ___. Then it adds the ___.

A

most similar pair; more distant pairs

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10
Q

Most phylogenetic methods assume that each
position in a sequence can ___ from the other positions

A

change independently

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11
Q

Gaps in alignments represent mutations in
sequences such as:

A

insertion, deletion, genetic rearrangments

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12
Q

Gaps are treated in various ways by thephylogenetic methods. Most of them ___.

A

ignore gaps

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13
Q

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.

A

sequences similarity scores; alignment itself

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14
Q

The similarity scores based on scoring matrices (with gaps scores) are used by
the ___

A

DISTANCE methods

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15
Q

what is a phylogenetic tree?

A

An illustration of the evolutionary relationships among a group of organisms.

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16
Q

another name for a phylogenetic tree.

A

dendrogram

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17
Q

A tree is composed of ___ and ___. One branch connects any two adjacent nodes. ___represent the taxonomic units. (____)

A

nodes and branches; Nodes; sequences

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18
Q

very similar sequences will be neighbors on the outer branches and will be connected by a ____

A

common internal branch

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19
Q

types of trees

A

trees and networks

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20
Q

type of tree that has only one path between
any pair of nodes

A

tree

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21
Q

a type of tree with more than one path between any pair of
nodes

A

network

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22
Q

Represent the taxa (sequences)

A

Leaves = Outer branches

23
Q

Represent the relationships among the taxa (sequences)

A

Nodes = 1 2 3

24
Q

The length of the branch represent the # of changes that occurred in the __ prior to the next level of separation

A

sequence (branch)

25
Q
  • are branches that end with a tip
  • more evident diversions
A

external branches

26
Q
  • are branches that do not end with a tip.
  • more ancient diversions
A

internal branches

27
Q

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).

A

node

28
Q

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).

A

BRANCH; 2 NODES; BRANCH; NODE

29
Q

In a phylogenetic tree, note that The ____ from the separation of the 2 sequences is not known. The phylogenetic analysis can only estimate the ___

A

amount of evolutionary time that passed; # of changes that occurred from the time of separation

30
Q

After the ___, one taxon (sequence) can undergo more mutations then the other taxon

A

branching event

31
Q

the branching pattern of a tree

A

topology of a tree

32
Q

What represents the data (e.g sequences) under comparison (A,B,C,D,E), and is also known as OTUs, (—-).

A

terminal nodes; Operational Taxonomic Units

33
Q

What represents inferred ancestral units (usually without empirical data), also known as HTUs, (—-).

A

Internal nodes; Hypothetical Taxonomic Units

34
Q

Different kinds of trees can be used to depict different aspects of evolutionary history. What are those?

A
  1. cladogram
  2. additive trees
  3. ultrametric trees
35
Q

A kind of tree that simply shows relative recency of common ancestry

A

cladogram

36
Q

a cladogram with branch lengths, also called phylograms and metric trees

A

additive tree

37
Q

(dendograms) special kind of additive tree in which the tips of the trees are all equidistant from the root

A

ultrametric tree

38
Q

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

A

The Molecular Clock Hypothesis

39
Q

What hypothesis is most suitable for
closely related species?

A

The Molecular Clock Hypothesis

40
Q

rooted tree = –
unrooted tree = –

A

cladogram; phenogram

41
Q
  • 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.
A

Rooted Tree = Cladogram

42
Q
  • 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.
A

Unrooted Tree = Phenogram

43
Q

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.

A

much higher; smaller

44
Q

genes related by speciation events. Meaning same genes in different species.

A

orthologs

45
Q

genes related by duplication events. Meaning duplicated genes in the same species.

A

paralogs

46
Q

The rate of mutation is assumed to be the same in both coding and non-coding regions. However, there is a difference in the ___ .

A

substitution rate

47
Q

___ have more substitution than coding regions.

____ are much more conserved since they “need” to conserve their function.

A

Non-coding DNA regions; Proteins

48
Q

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 —.

A

protiens; building the trees

49
Q

Are treated differently by different alignment programs and should play no part in building trees.

A

gaps

50
Q

Alignment of a coding region should be compared with the alignment of their ____, to be sure about the placement of gaps.

A

protein sequences

51
Q

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

A

Low complexity regions

52
Q

If you delete low complexity regions, you need to
consider the effect of the ___ on the branch lengths of the whole tree.

A

deletions

53
Q

Sequences that are being compared belong together (—-).

A

orthologs

54
Q

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.

A

outgroup; outgroup

Systematics (15 decks)

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