Phylogenetic Data Analysis Flashcards
Define topology
Relative branching order in a phylogenetic tree
What is a bifurcating node?
A node that only has two immediate descendents
What is another name for a node that is bifurcating?
Dichotomous
What is a multifurcating node?
If it has more than two immediate descendent lineages
What is another name for a multifurcating node?
Polytomous
True or false, in a cladogram branch lengths have no meaning?
True
Define tree balance
A measure of the degree of symmetry of a rooted phylogenetic tree. It serves as an indication of the pattern of speciation events in the group of taxa under study
Or
The degree to which sister groups contain the same number of tips
What is a clade?
A group of organisms that includes a single ancestor and all of its descendents
List three problems with phylogenetic tree construction
1) Hybridisation and gene flow
2) Gene tree versus species tree
3) How do you define a species
What is the Newick format?
It is a standard format to write phylogenetic trees in text.
The pattern of the parentheses indicated topology.
Each pair of parentheses enclose all members of a monophyletic group
Always ends in a semicolon
Define genetics
Functional effect of specific genes, as well as their evolution and mutations
Define genomics
Large stretches of DNA (coding and non-coding
the branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes.
What is a polymorphic site?
A gene is said to be polymorphic if more than one allele occupies that gene’s locus within a population
What is a parsimony-informative site?
It contains at least two types of nucleotides (or amino acids), and at least two of them occur with a minimum frequency of two
When was the human genome project completed?
2003 (it cost $2.7 billion and took 13 years)
How long does it take to sequence a human genome today?
It takes 2 days and costs under $10,000
What is NGS
Next Generation Sequencing
What is a tree?
To be considered a tree the diagram has to be directed (time moves in one direction along each branch) and acyclic (the lineages that diverge never subsequently meet)
What is the root of a tree?
A special node that marks the point where time enters the diagram
What are sister groups/taxa?
Two descendants of a single node
What is phylogenetic inference?
The reconstruction of phylogenetic trees
What is an unrooted tree?
A tree without a root and, thus, without a specified time axis
What is a cladogram?
A tree diagram that communicates the topology but not the branch lengths. It provides all the information needed to determine the degree of evolutionary relatedness between taxa
What is a gene tree?
The history of a set of homologous recombinational genes
Define merging
A way of simplifying a tree by representing a clade with a single terminal
Define phylogenetics
The field of study concerned with inferring the evolutionary relationships of living and extinct taxa
What is a phylogram?
A tree in which branch lengths are drawn proportional to the amount of change attributed to the branch
Explain what is meant by ‘polymorphic’
Having two or more states within a single population o taxon
Define pruning
The process of removing terminals/clades from a phylogenetic tree without changing the implied relationships of the remaining terminals
