Phylogenetics

Question 1

what is phylogenetics

Answer 1

evolutionary history of species through the construction of trees/phylogenies

Question 2

what is phylogenetic inference

Answer 2

the process behind the construction of a tree

Question 3

what is taxonomy

Answer 3

the process of biological classification of organisms based on shared characteristics

Question 4

what is the order of taxonomic ranks

Answer 4

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

Question 5

what do branch lengths indicate

Answer 5

genetic change - longer = more change/divergence

Question 6

what do nodes represent

Answer 6

sequences or hypothetical sequences at various points in evolutionary history

Question 7

what do branches represent

Answer 7

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

Question 8

what is tree topology

Answer 8

the structure of branches, leaves and nodes in the tree

Question 9

what is a cladogram

Answer 9

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

Question 10

what is an ultrametric diagram

Answer 10

branch lengths represent the evolutionary time between the corresponding species

Question 11

what is a phylogram

Answer 11

branch lengths are proportional to the amount of divergence

Question 12

what are orthologous genes

Answer 12

same function different species

Question 13

what are paralogous genes

Answer 13

genes evolved different functions

Question 14

what is a phylogenetic marker

Answer 14

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

Question 15

what are the best markers to infer species phylogenies

Answer 15

single copy housekeeping and orthologous genes

Question 16

what is an outgroup

Answer 16

distantly related organism that serves as a reference group

Question 17

what is an ingroup

Answer 17

the organism under investigation

Question 18

what are the two methods of rooting a tree

Answer 18

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

Question 19

what are the 2 tree file formats

Answer 19

Newick and Nexus

Question 20

what is newick format

Answer 20

standard format - brackets and commas

Question 21

what are the two main approaches in tree building

Answer 21

distance based methods and character based methods

Question 22

what are the two distance based methods

Answer 22

Neighbour joining and UPGMA

Question 23

what are the two character based methods

Answer 23

maximum parsimony and maximum likelihood

Question 24

what is a distance matrix

Answer 24

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

Question 25

what does a distance matrix express

Answer 25

dissimilarities between objects - different phenotypic characteristics and substitutions

Question 26

what is UPGMA

Answer 26

Simplest method - assumes evolutionary rate is the same for all

Question 27

what is neighbour joining suited for

Answer 27

datasets comprising lineages with largely varying rates of evolution

Question 28

what are the advantages of neighbor joining

Answer 28

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

Question 29

what are the disadvantages to neighbour joining

Answer 29

returns only one possible tree depends on model of evolution used

Question 30

what is maximum parsimony

Answer 30

minimises the total number of evolutionary steps required

Question 31

advantages to maximum parsimony

Answer 31

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

Question 32

what are the disadvantages of maximum parsimony

Answer 32

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

Question 33

advantages of maximum likelihood

Answer 33

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

Question 34

advantages of maximum likelihood

Answer 34

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

Question 35

disadvantages of maximum likelihood

Answer 35

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

Question 36

short comings of sequence alignment

Answer 36

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

Question 37

what are problems associated with assessing tree reliability

Answer 37

long branch attraction and lateral gene transfer

Question 38

what is multi locus sequence typing

Answer 38

strain typing system that focuses on conserved housekeeping genes