1. Molecular phylogenetics
Lecture 8
Molecular phylogenetics

2. NB: Phylogenetic trees are hypotheses
The goal of phylogeny is simply to reconstruct the historical relationships between a group of taxa
NB: Phylogenetic trees are hypotheses
A tree may have very strong support, or it may have very little support - a large number of characters supporting a specific topology
Weak support for a topology may arise due to – many possible alternatives which cannot be excluded

3. NB Gene trees are not the same as species trees
species trees illustrate the evolutionary histories of a group of related species
- i.e., species trees record the details of speciation for the group
gene trees show the evolutionary relationships among DNA sequences for a locus
gene trees may not be the same as species trees for one main reason – the existence of ancestral polymorphism
if this ancestral polymorphism is lost in some taxa but not in others, then one sequence isolated in species A may be more closely related to one in species B than to any other conspecific sequence
the gene tree will thus be different from the true species tree
the best way to guarantee that this will not occur is to use information provided by multiple independent loci!

4. Terminology Trees may be Rooted and Unrooted
By an Outgroup – Which is a taxon assumed to have diverged before the taxa studied
Topology – refers to the branching pattern
You can have internal and external branches
Any type of data can be used to reconstruct phylogenetic trees
Historically morphological data was used
Molecular data sources are:
Allozymes, immunological distance, DNA-DNA hybridization, Restriction site data, Amino acid sequences, DNA sequence data

5. Characters Characters may be binary (i.e., presence or absence
of an isozyme allele) or multistate (i.e., ACGT)
characters may also be ordered or unordered
when characters are ordered a certain directionality is implied among changes

6. The important stuff
Two important assumptions about the characters used to build trees:
1. the characters are independent
2. the characters are homologous
a homologous character is one shared by two species because it was inherited from a common ancestor
homoplasy
character or trait is possessed by two species but was not possessed by all the ancestors intervening between them, it is said to exhibit
homoplasy can result from convergent or parallel evolution, or from evolutionary reversals.
reversals are very common at the DNA sequence level because there are only four nucleotide bases.
the molecular characters used must also minimize “homoplasy”.
- homoplasy occurs when two taxa possess a certain character but that character was not present in all ancestors of the two taxa.
- homoplasy can occur by convergent or parallel evolution, or by reversals.
- for molecular data, evolutionary reversals are the main source of homoplasy.
- for example, consider the following series of substitutions:

7. How do we construct trees?
There are four major types of phylogenetic methods:
1. Distance methods (e.g. UPGMA, NJ)
2. Maximum parsimony methods (MP)
3. Maximum likelihood methods (ML)
4. Bayesian tree-building methods (such as that used by the computer program MrBayes)
MP and ML are both called “cladistic” methods
All these methods can use an
Outgroup or Root

8. Distance Methods
The general strategy behind distance methods is to cluster taxa (or OTUs) so that the most similar ones are found close together in the tree
This strategy is called a phenetic approach
The best tree, according to this approach, is to minimize the total distance among all taxa
The branch lengths in phenograms carry important information
The closer two taxa resemble one another the higher they are positioned in the phenogram
phenograms may not represent the true phylogeny - in fact construction of the true phylogeny is not one of their goals.
- the branch lengths in phenograms carry information about the degree of similarity between any pair of taxa.
- an important assumption of UPGMA is that an equal rate of evolution occurs along all branches.
- although this assumption may be violated frequently, the UPGMA methods does quite well in simulation studies recovering true tree topographies.
- the principle behind NJ is to find neighbors sequentially that may minimize the total length of the tree.
- the total length of the tree is simply the sum of all branch lengths.
an important advantage of the NJ approach over UPGMA is that it allows for unequal rates of evolution along different branches
distance methods are fast and efficient but all suffer from the same problem.
- this problem is that they are all based on an estimate derived from the data – they do not use the data itself to produce the tree.
- because information is lost in coverting the data into a distance matrix, distance methods fail to use all of the information present in the data.

9. Maximum parsimony (MP)
according to the MP approach, the best tree minimizes the number of evolutionary steps (i.e., changes among characters)
this is the principle of parsimony - the least number of changes, required the better the tree
evolutionary change does not always obey laws of parsimony but it is a reasonable starting point
MP trees are based exclusively on synapomorphies
shared by two or more taxa that are derived from some ancestral state
essential to use one or more outgroups

10. Maximum Likelihood (ML)
given a certain model of base substitution and a specific tree, what is the probability of obtaining this set of DNA sequences?
this probability is estimated by a tree’s likelihood score
the best tree is that which has the highest likelihood, or probability of being produced
ML methods are computationally intensive and thus have not been easy to use until recently

11. How do you select the correct tree
Correlation between distance, MP, and ML topologies is found – Reconstruction is GOOD
Common approach is to use a statistical technique called bootstrapping
Bootstrapping procedure works by randomly re-sampling the nucleotide sequence data (with replacement), constructing a tree from this data and counting the number of times a particular branch is found out of say, 100, 500, or 1,000 replicate pseudosamples

12. So?
Trees based on genetic markers will accurately reflect evolutionary relationships only if the
rates of evolution are constant
markers are neutral
foundation population is monomorphic (or there are many independently inherited markers)
If starting population is polymorphic, fixation of different initial sequences in different lineages (termed lineage sorting) may lead to incorrect inferred phylogenies

13. Outbreeding depression
Outbreeding depression is the reduction in reproductive fitness resulting from crossing of populations
Occurs when: adaptation to a certain area occurred; crossing different sub-species

14. Diagnosing genetic problems
1. How large is the population (Ne)?
2. Has it experienced significant bottlenecks in the past?
3. Has it lost genetic diversity?
4. Is it suffering from inbreeding depression?
5. Is it genetically fragmented?
How do you recover a small population?
outbreed (if available), or
inbred but genetically differentiated from the population to which they are being introduced
DL - Eldridge et al – Black-footed Rock wallaby

15. Genetically viable populations
How large must populations be, to be genetically viable in the long term?
minimum viable population size (MVP)
the minimum size required to retain reproductive fitness and evolutionary potential over thousands of years

16. How large?
Three genetic components must be considered in answering this question:
Is the population size large enough to avoid inbreeding depression?
Is there sufficient genetic diversity for evolution to occur in response to environmental change?
Is the population large enough to avoid accumulating new deleterious mutations?