Phylogenetics

Question 1

Who coined the term Phylogeny?

Answer 1

Ernst Haeckel

Question 2

What percentage of species on Earth have already gone extinct?

Answer 2

More than 99%

Question 3

Anagenesis

Answer 3

Change within a lineage - evolution of a new species without branching

Question 4

Cladogenesis

Answer 4

Splitting of lineages - one species branching into two descendent species
Thought to be the main form of speciation for sexually reproducing organisms

Question 5

Hybrid speciation

Answer 5

Merging of lineages - the hybridisation of two or more distinct taxa that contributes to the formation of a new species

Question 6

What does the biological species concept define species as?

Answer 6

Groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups

Question 7

3 mechanisms of reproductive isolation

Answer 7

1. Premating - eg behaviour
2. Post-mating prezygotic - gamete incompatibility
3. Postzygotic - hybrid inviability or sterility

Question 8

Are the 3 mechanisms of reproductive isolation reversible?

Answer 8

Premating - reversible
Post-mating prezygotic - can be reversible
Postzygotic - typically irreversible

Question 9

Bateson-Dobzhansky-Muller Model

Answer 9

A simple model for the evolution of genetic incompatibilities that decrease hybrid viability or fertility

Question 10

4 major aims of phylogenetics

Answer 10

1. Reconstruct correct evolutionary relationship
2. Estimate the times of divergence
3. Describe the sequence of evolutionary changes
4. Locate the geographic origins

Question 11

Operational taxomic units (OTUs)

Answer 11

The actual nodes being studied

Question 12

Monophyletic clade

Answer 12

A taxonomic group in which all of the taxa are derived from a common ancestor not shared by other taxa (a natural clade)

Question 13

Paraphyletic clade

Answer 13

A taxonomic group whose most recent common ancestor is shared by another taxa

Question 14

Two ways to root an unrooted tree

Answer 14

1. Midpoint rooting
   2.Outgroup rooting

Question 15

Midpoint rooting

Answer 15

Calculate all of the tip-to-tip distances and select the longest. Place the root exactly half way between these two longest distances

Question 16

Outgroup rooting

Answer 16

The root must be on the branch leading to the outgroup

Question 17

4 methods of tree reconstruction

Answer 17

1. Distance-based
2. Maximum parsimony
3. Maximum likelihood
4. Bayesian

Question 18

Distance based method

Answer 18

. use distance data based of level of dissimilarity between two OTUs
. construct a distance matrix to cluster samples in a bottom up manner identifying pairs of sequences that are most similar
. UPGMA - unweighted pair group with arithemtic means
. Neighbour-joining

Question 19

Maximum parsimony

Answer 19

. Identify trees with fewest number of evolutionary changes
.

Question 20

What method is used for above 20OTUs?

Answer 20

Heuristic method - no guarantee the most parsimonious tree will be found

Question 21

Maximum likelihood

Answer 21

evaluates the probability that the chosen evolutionary model will have generated the observed sequences

Question 22

Bayesian Phylogenetics

Answer 22

Estimates the probability of a tree, given the data and model of evolution

Question 23

Assessing tree reliability

Answer 23

Bootstrapping - assigns measures of accuracy to estimates using random sampling with replacement

Question 24

autopomorphies

Answer 24

distinct trait unique to a given taxon

Question 25

homoplasies

Answer 25

trait shared across clades that don’t share an ancester

Question 26

Sympleisomorphy

Answer 26

A shared ancestral character state

Question 27

The three domains of life

Answer 27

1. Archaea
2. Bacteria
3. Eukaryotes

Question 28

Did LUCA have a nucleus

Answer 28

Unlikely, as the root of life is in bacteria or archaea