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What are phylogenetics

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


In phylogenetics how do we group species

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


What are phylogenetic trees based on

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


What are cladistics

– classification based on shared derived characteristics.


Why are neutral mutations important in making phylogenetic trees

- 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


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

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


What is synapomorphy

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


What do phylogenetic methods seek to do

(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.


What affects the accuracy of phylogenetic trees

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)?


What are shared derived mutations called

homologous = co-occurring (present in common ancestor)


What are non shared derived mutations called

homoplastic = randomly occurring (not present in common ancestor)


how do we know what is a true shared derived mutation

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


Are phylogenectic trees absolute answers or hypotheses

always hypothesessss


Explain the branch and bound algorithm

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


What does bootstrap resampling do

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.


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

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


When did homo sapiens evolve

200,000 years ago


When did the human lineage diverge the chimp lineage

6 million years ago


What 2 questions could fossils not answer about hominins

When did hominins lose their body hair?
When did hominins begin to wear clothes?


What are lice

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


What kind of lice do humans have

The head, pubic and body llice


What 3 potential mechanisms lead to humans acquiring 3 lice

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


Which hypothesis explained the origin of head lice



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

Human head and chimp lice lineages diverged at the
same time that hominins and ancestral chimps diverged.


How would you test the head lice co-speciation hypothesis

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


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

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


Hypothesis for the origin of body lice

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


How would you test the third niche hypothesis

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


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

100,000 years ago


How did human body arised

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.