Phylogenetics Flashcards
Who coined the term Phylogeny?
Ernst Haeckel
What percentage of species on Earth have already gone extinct?
More than 99%
Anagenesis
Change within a lineage - evolution of a new species without branching
Cladogenesis
Splitting of lineages - one species branching into two descendent species
Thought to be the main form of speciation for sexually reproducing organisms
Hybrid speciation
Merging of lineages - the hybridisation of two or more distinct taxa that contributes to the formation of a new species
What does the biological species concept define species as?
Groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups
3 mechanisms of reproductive isolation
- Premating - eg behaviour
- Post-mating prezygotic - gamete incompatibility
- Postzygotic - hybrid inviability or sterility
Are the 3 mechanisms of reproductive isolation reversible?
Premating - reversible
Post-mating prezygotic - can be reversible
Postzygotic - typically irreversible
Bateson-Dobzhansky-Muller Model
A simple model for the evolution of genetic incompatibilities that decrease hybrid viability or fertility
4 major aims of phylogenetics
- Reconstruct correct evolutionary relationship
- Estimate the times of divergence
- Describe the sequence of evolutionary changes
- Locate the geographic origins
Operational taxomic units (OTUs)
The actual nodes being studied
Monophyletic clade
A taxonomic group in which all of the taxa are derived from a common ancestor not shared by other taxa (a natural clade)
Paraphyletic clade
A taxonomic group whose most recent common ancestor is shared by another taxa
Two ways to root an unrooted tree
- Midpoint rooting
2.Outgroup rooting
Midpoint rooting
Calculate all of the tip-to-tip distances and select the longest. Place the root exactly half way between these two longest distances
Outgroup rooting
The root must be on the branch leading to the outgroup
4 methods of tree reconstruction
- Distance-based
- Maximum parsimony
- Maximum likelihood
- Bayesian
Distance based method
. use distance data based of level of dissimilarity between two OTUs
. construct a distance matrix to cluster samples in a bottom up manner identifying pairs of sequences that are most similar
. UPGMA - unweighted pair group with arithemtic means
. Neighbour-joining
Maximum parsimony
. Identify trees with fewest number of evolutionary changes
.
What method is used for above 20OTUs?
Heuristic method - no guarantee the most parsimonious tree will be found
Maximum likelihood
evaluates the probability that the chosen evolutionary model will have generated the observed sequences
Bayesian Phylogenetics
Estimates the probability of a tree, given the data and model of evolution
Assessing tree reliability
Bootstrapping - assigns measures of accuracy to estimates using random sampling with replacement
autopomorphies
distinct trait unique to a given taxon
homoplasies
trait shared across clades that don’t share an ancester
Sympleisomorphy
A shared ancestral character state
The three domains of life
- Archaea
- Bacteria
- Eukaryotes
Did LUCA have a nucleus
Unlikely, as the root of life is in bacteria or archaea
