Phylogenetic Trees

What is a phylogeny?

The history of evolution of a species or group especially in references to lines of descent and relationships among groups of organisms

What is Tokogeny

• nonhierarchical network of relationships among individuals organisms within species based on reproductive connections

• For asexual organisms: only vertical lineages with simple tree like structure

Why is phylogeny not a pedigree?

It is about speciation events and has branching patterns

What‘s a phylogenetic tree good for?

• way to visualise evolutionary pathways

• Organises biological knowledge

• Identifies common characteristics and can help us predict for related species

• Visualise trait change over time and look at patterns

Anagenesis

• Single slow line of evolution of a single species without branching or splitting over time

• Over time it will lead to divergence of species

Monophysitism group

• part of a rooted tree that can be separated from the rest of the tree by cutting a single branch

• Represents a group of related lineages united by descent from a common ancestor

Phenetics

Define species as groups of organisms that share greater similarity than with organisms outside the group

• very subjective

• Random

• Evolutionary origins not taken into account

Cladistic Classification

• Taxa grouped of basis of shared derived characteristics not preset in their derived ancestors

• assumed to indicate common ancestry

• Therefore called informative characters

Cladogram

• group so that taxa with historically more recent ancestors form groups nested within groups of taxa with more distant ancestors

Dendogram

Clustering tree

Phylogenetic tree

Evolutionary history

Cladogram

Topology but the branch lengths don‘t matter

Phylogram

Topology but branch lengths are drawn proportional to the amount of change attributed to each branch

Additive phylogen

• distance between each pair of nodes is sum of connected branch path

Ultrametric Tree

• rooted tree where units of branch lengths accumulate evenly on all branches

• All contemporaneous terminal nodes are equidistant from the root node

• Scale bar

Why do branch lengths require a scale?

For interpretation

Units are number of substitutions er site or number of character changes

Which axis is meaningful in a phylogram?

Y axis

What is present at the terminal nodes?

• depends on unit of analysis

  • Individuals

  • Species

  • Sets of related species

  • Individual genes

Operational Taxonomic Unit

• taxonomic level of sampling selected by the user to be used in a study such as individuals, populations, species, genera, or bacteria strains

Completely unresolved tree

Star tree

Partially resolved tree

More than two proceeding branches, multifurcating

Fully resolved tree

Strictly bifurcating

Types of polynomials

• polypodies: represent uncertainty (soft polypodies)

• True polytonal: represent origin of 3 or more lineages from ancestral lineages

Network trees

• lack of knowledge or complex evolutionary relationships in a tree

  • Network at ambiguous nodes

  • Network showing recombination or GT

  • Can add in different lines to show more development and information

3 methods for rooting

• outgroop

• Molecular clock assumption

• Paralogue rooting

Outgroup rooting

• requiring prior knowledge of what is an outgroup (relating to an ingroup)

• Place root at ancestral node of the outgroup, ingroup

• Best to have 2 or 3 outgroup taxa to form a Clade

Clock rooting

• root at point in tree with equal amounts of change to all terminal nodes

• Computationally challenging

Midpoint rooting

• simple appropriation is midpoint rooting

  • Find two taxa with the largest patriotic distance

  • Place root midway between those tow taxa

  • Still assumes there is a standard molecular clock

Paralogue footings

• Construct a tree using sequences of two Paralogue genes from different organism

• Assume the most parsimonious gene duplication event to root tree

SDI

Speciation duplication inference - assuming the mot parsimonious gene duplication event to root tree