Lectures 10-12

Question 1

What are phylogenetics

Answer 1

– the way in which we classify our organisms according to their similarities
and differences.

Question 2

In phylogenetics how do we group species

Answer 2

We group species using trees (phylogenies) which tell us about the evolutionary history
of species.

Question 3

What are phylogenetic trees based on

Answer 3

s based on characters, or traits such as anatomical and physiological
characteristics, behaviours, or genetic sequences.

Question 4

What are cladistics

Answer 4

– classification based on shared derived characteristics.

Question 5

Why are neutral mutations important in making phylogenetic trees

Answer 5

• species inherit the neutral mutations of their ancestors
• neutral mutations accumulate within a species through time
• species that share a common ancestor, also share the neutral mutations derived from that ancestor
  So they can used to reveal common ancestry

Question 6

When using neutral mutations to reveal common ancestry what do we assume

Answer 6

mutation rates are similar among species
drift also affects species
similarly
species that are more related will share more similar sequences.

Question 7

What is synapomorphy

Answer 7

possession by two or more organisms of a characteristic inherited exclusively from their common ancestor.

Question 8

What do phylogenetic methods seek to do

Answer 8

(1) obtain the tree most consistent with the data under a given set of assumptions,
(2) assess the strength of the tree from the data, and
(3) use this to hypothesise the history of the species.

Question 9

What affects the accuracy of phylogenetic trees

Answer 9

are the sequences evolving the way we assume?
how well is the sequence linked to the species (is the gene tree
the same as the species tree)?

Question 10

What are shared derived mutations called

Answer 10

homologous = co-occurring (present in common ancestor)

Question 11

What are non shared derived mutations called

Answer 11

homoplastic = randomly occurring (not present in common ancestor)

Question 12

how do we know what is a true shared derived mutation

Answer 12

We use e multiple positions and look at groupings - Shared derived mutations will be much more numerous and will be more
consistent

Question 13

Are phylogenectic trees absolute answers or hypotheses

Answer 13

always hypothesessss

Question 14

Explain the branch and bound algorithm

Answer 14

Imagine we had 5 spps and we want to make a tree
We take them and we group them randomly and find out that requires 156 mutations.
So we now want to try and do better than 156 mutations.
Build trees adding taxa randomly until either
1. the bound is exceeded: abort searching that path
2. all taxa are added at a new lower bound and the process is repeated

Question 15

What does bootstrap resampling do

Answer 15

It assess the robustness of the most parsimonious tree by sampling with replacement from the empirical sequence data and makes a tree that summarizes this for all the most frequently
occurring branches.

Question 16

Why is it good to assess the robustness of the most parsimonious tree

Answer 16

The most parsimonious tree may not be significantly different from the next most parsimonious tree

Question 17

When did homo sapiens evolve

Answer 17

200,000 years ago

Question 18

When did the human lineage diverge the chimp lineage

Answer 18

6 million years ago

Question 19

What 2 questions could fossils not answer about hominins

Answer 19

When did hominins lose their body hair?

When did hominins begin to wear clothes?

Question 20

What are lice

Answer 20

Lice are highly specialized blood-sucking parasites that live on a single host species.

Question 21

What kind of lice do humans have

Answer 21

The head, pubic and body llice

Question 22

What 3 potential mechanisms lead to humans acquiring 3 lice

Answer 22

1 - co-speciation of lice with the speciation of hominin
Hominin and lice lineages will look the same

2 - host switching,
lice evolved on one host and jumped on to hominin

3 - duplication and speciation on a single host
lice speciates but the hominin does not

Question 23

Which hypothesis explained the origin of head lice

Answer 23

Co-speciation

Question 24

What is the co-speciation hypothesis for the origin of head lice

Answer 24

Human head and chimp lice lineages diverged at the

same time that hominins and ancestral chimps diverged.

Question 25

How would you test the head lice co-speciation hypothesis

Answer 25

Compare DNA of human head lice to DNA of chimp lice at one nuclear and
one mitochondrial gene to estimate when they last shared a common
ancestor. If it is correct the divergence time for lice should be the same as the humans

Question 26

Evidence to support the co-speciation hypothesis of head lice origin

Answer 26

A DNA comparison suggests the most recent common ancestor of chimp lice and human head
lice lived ~6 million years ago. This was when humans diverged from chimps

Question 27

Hypothesis for the origin of body lice

Answer 27

The third niche hypothesis - human body lice arose because humans
started to wear clothing.

Question 28

How would you test the third niche hypothesis

Answer 28

Estimate when body lice arose, by identifying the
most recent common ancestor of all human head
and body lice.

Question 29

When was the last common ancestor of human head lice and human body lice

Answer 29

100,000 years ago

Question 30

How did human body arised

Answer 30

Human body lice arose from human head lice on Homo sapiens around when a new niche was formed when humans began to where clothes 72,000 years ago.

Question 31

When did humans acquire the pubic louse

Answer 31

~3-4 million years ago.

Question 32

How did pubic lice colonise humans

Answer 32

Potentially picked up from from early gorilla by sleeping in nests and preying on them

Question 33

When was the most recent common ancestor between human and pubic lice

Answer 33

12 million years ago which means head and pubic lice did not diverge on a hominin when we began to lose body hair. New niche hypothesis is wrong

Question 34

What is mutualism

Answer 34

when two organisms of different species exist in a relationship in which each individual benefits from the activity of the other.
A type of symbiosis

Question 35

What are the three types of mutualism

Answer 35

Trophic
Defensive
Dispersal

Question 36

What is a trophic mutualism, give example

Answer 36

usually involve partners specialised for obtaining energy and nutrients.

Rhizobium and plant roots that form nitrogen fixing rootnodules

Question 37

What is a defensive mutualism

Answer 37

involves species that receive food or shelter from their partners in return for a defensive function e.g ants and ant plants

Question 38

What are dispersal mutualisms

Answer 38

Involve animals that transport either:
– pollen in return for a nectar reward
– seed in return for a fruit reward