Lecture 20. Molecular Phylogenetics Flashcards
What can evolution be represented as ?
A branching process
What is the most recent common ancestor (MRCA) ?
The recent individual from which a set of biological entities descend
What is anagenesis ?
Evolution of a new species without branching
What is cladogenesis ?
An evolutionary splitting of one species into two descendent species
What is extinction ?
The evolutionary termination of a biological entity
What is a phylogenetic tree ?
A branching diagram showing the theorised relationships between different biological entities with respect to their evolutionary history
What is a phylogeny ?
A guess based on observed data
What are the major aims of phylogenetics ?
- To reconstruct the correct evolutionary relationships between biological entities
- To estimate the times of divergence between them
- To describe the sequence of evolutionary changes along the lineage
- To locate the geographic origins of ancestral lineages
What are nodes ?
Represent taxonomic units - DNA sequences, genes, proteins, individuals, populations, species
What are branches ?
Define the relationships between nodes in terms of descent and ancestry
What are operation taxonomical units ?
The terminal nodes of the tree. They represent the actual data under study
What are two operational taxonomic units separated by a single node called ?
Neighbours
What are two operational taxonomic units separated by a single node called ?
Neighbours
What is a hypothetical taxonomic unit ?
The internal nodes represent inferred ancestral units. We have no actual data for these
What is a mulitfurcating node ?
More than two immediate descendants
What is another name for a multifurcating node ?
Polytomous
What is a bifurcating node ?
Only two immediate descendants
What is another name for a bifurcating node ?
Dichotomous
What is the root ?
The earliest node and anchors the tree in time
What is an unrooted tree ?
A tree without a root node
What does an unrooted tree specify ?
The degree of relatedness between taxonomic units, but does not define the direction of the evolutionary path
What is topology ?
The branching pattern of the tree
What is the topology of unrooted and rooted trees not affected by ?
Rotating branches around the internal nodes
What is outgroup rooting ?
Uses external rooting to be more distantly related to everyone else
What is an unscaled tree ?
The branch lengths are not proportional to the number of evolutionary changes which are indicated on the branches
What is a cladogram ?
An unscaled tree
What is a scaled tree ?
The branch lengths are proportional to the number of evolutionary changes
What is a phylogram ?
A scaled tree
What is cladistics ?
Biological classification based on shared descent
What is a clade ?
A group of taxa composed of a common ancestor and all its descendants
What is monophyletic ?
A taxonomic group in which all of the taxa are derived from a common ancestor and not shared by other taxa
What type of clade is a monophyletic ?
A natural clade
What is paraphyletic ?
A taxonomic group whose most recent common ancestor is shared by another taxa
What type of clade is a paraphyletic ?
Not a true clade
What is a polyphyletic ?
A grouping of taxa each more closely related to other taxa not in the grouping than they are to each other
What type of clade is polyphyletic ?
Not a true clade
What are the three steps in drawing a phylogeny ?
- Identify homologous sequences
- Align sequences and identify variant sites
- Calculate tree
What are the methods of calculating a tree ?
- Distance based
- Maximum parsimony
- Maximum likelihood
- Bayesian
How do you calculate the tree using the distance method ?
- Calculate a measure f molecular distance between pairs of operational taxonomic units and enter the value into a distance matrix
- Sequentially cluster samples in a bottom up manner identifying pairs that are most similar first and placing them in a clade together
- Calculate new average distances between this clade an other operational taxonomic units
What is the calculating the tree method for maximum parsimony aim to achieve ?
Identify the trees that require the fewest number of evolutionary changes
How do you calculate the tree using the maximum parsimony method ?
- Identify character states for each variant site for all operational taxonomic units
- Scroll through the trees and find the one that require the fewest number of character state changes
What is phylogeography ?
Describes the geographical distribution of operational taxonomic units and attempting to make inferences about the geographic location of hypothetical taxonomic units
