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SYSTEMATICS FINALS > LECTURE 4: CONSISTENCY AND RETENTION INDEX > Flashcards

LECTURE 4: CONSISTENCY AND RETENTION INDEX Flashcards

1
Q

are the indexes or matrix used to assess the homoplasy in a data set and how we use the tree explains the observed data

A

Consistency and Retention Index

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2
Q

it relies in morphological data obtained by measuring and grantifying the phenotypic properties of a representative organisms

A

Traditional phylogenetics

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3
Q

it is the evolutionary history of a group of organisms

A

Phylogeny

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4
Q

it is often represented by a phylogenetic tree

A

phylogeny

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5
Q

it is a branching diagram that shows how organisms are related

A

Phylogenetic tree

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6
Q

the study of phylogeny

A

phylogenetics

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7
Q

it is strictly based on genetic material revealed through DNA and RNA sequencing

A

Phylogenetics

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8
Q

it is useful fields like biology, medicine, and forensic sciences

A

phylogenetics

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9
Q

it can be used to track the differences in viral genes and determine the relatedness of the 2 sample organisms

A

phylogenetic analysis

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10
Q

it is for screening closely related species that may have the same useful traits

A

phylogenetic analysis

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10
Q

3 types of phylogenetics

A

traditional phylogenetics
computational phylogenetics
molecular phylogenetics

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11
Q

it is the application of computational algorithms, methods and programs to phylogenetic analyses

A

computational analyses

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12
Q

uses nucleotide sequences encoding genes or amino acids sequencing/sequences encoding proteins as the basis for classification

A

molecular phylogenetics

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13
Q

it represents a hypotheses about teh evolutionary ancestry of a set of genes, species, or other taxa

A

phylogenetic tree

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14
Q

what techniques have been used to explore the family tree of hominid species and the relationships between specific genes shared by many types or organisms

A

traditional, molecular, and computational phylogenetics

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15
Q

they requires explicit decisions about which physical characteristics to measure and how to use them to encode distinct states corresponding to the input taxa

A

morphological studies

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16
Q

it takes into account homology and shaped derived characters

A

morphological studies

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17
Q

2 types of phylogenetic trees

A

rooted tree
unrooted tree

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18
Q

a directed graph that explicitly identifies a most recent common ancestor

A

rooted tree

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19
Q

it requires inclusion of atleast 1 outgroup to the sequences of interest

A

rooted tree

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20
Q

constructed by grouping taxa from a matrix in which polarity i not indicated

A

unrooted tree

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21
Q

has no hypthetical ancestor or outgroup

A

unrooted tree

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22
Q

in this tree, due to no polarity and outgroup the characters connot be ascertained

A

unrooted tree

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23
Q

unrooted tree, due to no polarity and outgroup the characters connot be ——-

A

ascertained

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24
has no evolutionary hypothesis are implicit in an -------
unrooted tree
25
they cannot be recognized because relative ancestry is not indicated
monophyletic groups
26
3 methods for constructing cladograms
1. identification of characters and configurations 2. character coding 3. determination of the best cladograms
27
it refers to observable feature or attribute of an organisms
character
28
it involves the determination of characters
character coding
29
it involves determining whether or a relation between ancestors and descendants exists
character coding
30
its characters be listed in the form of presence or absence of 1 character
character coding
31
it is expressing different character states of one character indicating its presence or absence
binary variables
32
2 types of binary variables
- line layout linear - line layout cellular
33
he suggested a 5 step methodology for constructing a cladogram and year
Lipscomb 1998
34
5 steps of lipscomb in constructing cladograms
- selection of taxa - selection of characters - analysis of characters to reconstruct the relationship among the taxa - translation of tree into a formal classification system - use of the tree to test various hypothesis about environment of group
35
analysis of characters to reconstruct the relationship among the taxa includes 3 substeps
- includes analyzing the presence/absence of character - coding will be used - morphometric measurements
36
translation if tree into classification system takes into account ------- and ----
homology and shared derived characters
37
what is the type of tree and principle that is used to determine the tree
most parsimonious tree
38
it begins with the selection of taxa which may include living and or fossil organisms
taxon selection
39
taxon selection includes ------- and -----
ingroup and OTUs
40
what does OTUs mean
operational taxonomic units
41
they are previously classified members of the study group and may be species, infraspecies, or taxa
operational taxonomic units
42
they may also be in populations
operational taxonomic units
43
operational taxonomic units may also be populations if ---- and ---- to be on their own evolutionary track
distinctive and presumed
44
it is one of the major methods of reconstructing phylogenetic relationships
maximum parsimony
45
it is because there are generally many possible trees for any given data set
maximum parsimony
46
states that of the numerous possible cladograms for a given group of operational taxonomic units
Principle of parsimony
47
the tree exhibiting the fewest number of steps and changes shows the most ------
parsimony
48
it is the method of reconstructing phylogenetic relationship
maximum parsimony
49
it is the principle that has the fewest number of evolutionary steps
principle pf parsimony
50
it is created to have more in-depth analysis in terms of phylogenetics analyses of tree
indices
51
2 types of indices/index
consistency index retention index
52
it is the most commonly reported values for trees
consistency index
53
an index which measures the relative amount of homoplasy in a cladogram
consistency index
54
it reverses the level of difficulty in fitting a given data set to a given tree
consistency index
55
it is also known as CI
consistency index
56
it is calculated as the numbers of steps expected given the number of character states in the data, divided by the actual member of steps by 100
consistency index
57
the further from 1 and closer to 0 indicates more ------
homoplasious characters
58
having a high consistency index values results to ------
little or no homplasy
59
what is the highest possible value of consistency index
1.0
60
low values of consistency index shows considerable -------
homoplasy
61
for consistency indices, if there is no need to multiply by 100 you can interpret the data as ---------- or -----------
"if closer to 100" or "closer to 1"
62
formula of consistency index
total character staes changes expected given the data set DIVIDED by the actual numer of steps on the tree MULTIPLIED BY 100
63
the number of steps you expect should be equal to your ---------
number of characters
64
the number of steps you expect should be equal to your number of characters if there is no
homoplasy/analogy
65
it is the ratio of the minimum amount of changes/steps
consistency index
66
it might show (m) and the amount of change is done show on a tree
consistency index
67
the M in consistency index means
total number of character changes expected
68
the abbreviation that means the total number of character changes expected
M
69
the abbreviation that means the actual number of changes that occur in the tree
S
70
the S in consistency index formula means
actual number of changes that occur in the tree
71
it takes into account the presence of homoplasious characters
consistency index
72
consistency index is perfect if it equals to --- when multiplies by 100
1 or 100
73
it is when a character is present in all taxa from the start but absent in only 1 taxa
reversal
74
it is denoted by putting a negative sign
reversal
75
can be denoted like this 0 -----> 1 -------> 0
reversal
76
reversals can be denoted like;
0 -----> 1 -------> 0
77
reversal of character in a taxa is designated as -----
0
78
----- is high or leaning towards ----
1
79
1 is high or -----
leaning towards 1
80
if the index is 1 or is perfect there is no ----- at all
homoplasy
81
it equals to the number of characters
tree length
82
tree length equals to the -----
number of characters
83
helps show if there are any homplasious characters, littke homoplasy or no homplasy at all
Consistency index
84
may not show the bigger pictures as there are some instances when 2 datas may have the same value but different specific taxa
consistency index
85
limitation of consistency
2 datas may have the same value but different specific taxa
86
it is to counter the limitations of CI
Retention index
87
it measures the fraction of apparent synapomorphy to actual synapomorphy
retention index
88
introduced the rescaled consistency index
Farris 1989
89
first introduced the rescaled consistency index in '86
Farris Hennig
90
the product of the orginal consistency index of Kliuge and Farris
rescaled consistency index
91
the product of the original consistency index and the retention index
rescaled cosistency index
92
who developed retention index
Farris in 1989b
93
measures the proportion of synapomorphy expected frpm a data that in retained are synapomorphy on a tree
retention index
94
a measure of the proportion of similarities on a tree
retention index
95
to calculate retention index find first the ff:
s -value m-value g-value
96
was introduced by Farris (1988)
retention index
97
retention index formula
(G-S)/(G-M)
98
S and M in the retention index formula means ---
for consistency index
99
the G in the retention index means
maximal number of steps for the character on any cladogram
100
it means the maximal number of steps for the character on any cladogram in the retention index formula
G
101
it is the difference maximum number of steps on tree and number of state changes on the tree DIVIDED by the difference of teh maximum number of steps on tree and number of state changes in the data MULTIPLIED BY 100
Retention Index
102
in the retention index, the maximum number number of steps on the tree is the total number of ------
taxa with state 1 or state 0, summed over all the characters
103
the closer the retention index is to 1 the -------
the better the tree is considered
104
it takes into accpunt maximum steps
retention index
105
in the --------------- index the 2 data values resulted in similar value
consistency index
106
in the ------- index the 2 data sets resulted in similar value
Retention index
107
in this index the 2 data sets result in different values
retention index
108
the closer the RI is to ------ teh better the tree is considered to be
1

SYSTEMATICS FINALS (11 decks)

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