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Bioinformatics > Phylogenetics > Flashcards

Phylogenetics Flashcards

1
Q

what is phylogenetics

A

evolutionary history of species through the construction of trees/phylogenies

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2
Q

what is phylogenetic inference

A

the process behind the construction of a tree

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3
Q

what is taxonomy

A

the process of biological classification of organisms based on shared characteristics

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4
Q

what is the order of taxonomic ranks

A

domain, kingdom, phylum, class, order, family, genus, species

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5
Q

what do branch lengths indicate

A

genetic change - longer = more change/divergence

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6
Q

what do nodes represent

A

sequences or hypothetical sequences at various points in evolutionary history

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7
Q

what do branches represent

A

the path of transmission of genetic information from one generation to the next

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8
Q

what is tree topology

A

the structure of branches, leaves and nodes in the tree

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9
Q

what is a cladogram

A

not based on sequence alignment
represent general taxa relatedness not phylogenetic relationships

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10
Q

what is an ultrametric diagram

A

branch lengths represent the evolutionary time between the corresponding species

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11
Q

what is a phylogram

A

branch lengths are proportional to the amount of divergence

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12
Q

what are orthologous genes

A

same function different species

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13
Q

what are paralogous genes

A

genes evolved different functions

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14
Q

what is a phylogenetic marker

A

a representative gene providing phylogenetic info about the relatedness among taxa - present in all organisms

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15
Q

what are the best markers to infer species phylogenies

A

single copy housekeeping and orthologous genes

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16
Q

what is an outgroup

A

distantly related organism that serves as a reference group

17
Q

what is an ingroup

A

the organism under investigation

18
Q

what are the two methods of rooting a tree

A

rooting by outgroup - fall outside the ingroup
rooting by midpoint distance - midway point between two most distant taxa

19
Q

what are the 2 tree file formats

A

Newick and Nexus

20
Q

what is newick format

A

standard format - brackets and commas

21
Q

what are the two main approaches in tree building

A

distance based methods and character based methods

22
Q

what are the two distance based methods

A

Neighbour joining and UPGMA

23
Q

what are the two character based methods

A

maximum parsimony and maximum likelihood

24
Q

what is a distance matrix

A

a square table containing distances between pairs of elements in a dataset

25
Q

what does a distance matrix express

A

dissimilarities between objects - different phenotypic characteristics and substitutions

26
Q

what is UPGMA

A

Simplest method - assumes evolutionary rate is the same for all

27
Q

what is neighbour joining suited for

A

datasets comprising lineages with largely varying rates of evolution

28
Q

what are the advantages of neighbor joining

A

fast and suited for large datasets
allow lineages with largely different branch lenths

29
Q

what are the disadvantages to neighbour joining

A

returns only one possible tree
depends on model of evolution used

30
Q

what is maximum parsimony

A

minimises the total number of evolutionary steps required

31
Q

advantages to maximum parsimony

A

simple, logical
used on molecular and non molecular data
provides tree hypothesis of character evolution

32
Q

what are the disadvantages of maximum parsimony

A

not statistically consistent
provides reliable results only if data is not affected by homoplasy

33
Q

advantages of maximum likelihood

A

consistent and reliable
used on molecular and non molecular data
provides tree and hypothesis of character evolution

34
Q

advantages of maximum likelihood

A

consistent and reliable
used on molecular and non molecular data
provides tree and hypothesis of character evolution

35
Q

disadvantages of maximum likelihood

A

not simple and intuitive
computationally expensive
reliable results only if data is not affected by homoplasy

36
Q

short comings of sequence alignment

A

heuristic methods are only an estimate
optimal alignment is not always homologous
alignments require human intervention
hierarchically aligning pairs generates biases

37
Q

what are problems associated with assessing tree reliability

A

long branch attraction and lateral gene transfer

38
Q

what is multi locus sequence typing

A

strain typing system that focuses on conserved housekeeping genes

Bioinformatics (4 decks)

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