Phylogenetics Flashcards
Phylogeny
Depicting the evolution of a lineage into branches
Tips
the terminal end of an evolutionary tree, representing species, molecules, or populations being compared
Branches
a lineage evolving through time that connects successive speciation or other branching events
Nodes
a point in a phylogeny where a lineage splits (a speciation event or other branching event, such as the formation of subspecies)
internal nodes - a node that occurs within a phylogeny and represents ancestral populations or species
Monophyletic
describes a group of organisms that form a clade
Clade
a single “branch” in the tree of life; each clade represents an organism and all of its descendants
Paraphyletic
describes a group of organisms that share a common ancestor, although the group does not include all the descendants of that common ancestor
Outgroup
a group of organisms (for example, a species) that is outside of the monophyletic group being considered. In phylogenetic studies, outgroups can be used to infer the ancestral states of characters
Taxon (taxa)
a group of organisms that a taxonomist judges to be a cohesive taxonomic unit, such as a species or order
Most recent common ancestor (MRCA)
the most recent individual from which all the organisms of the set are descended
Character
a heritable aspect of organisms that can be compared across taxa
character state (ancestral state, derived state)
mutually exclusive features among taxa of a single paralog-equivalent assemblage that exhibit orthologous relationships to each other
Synapomorphy
a derived form of a trait that is shared by a group of related species (that is, one that evolved in the immediate common ancestor of the group and was inherited by all of its descendants)
Homoplasy
describes a character state similarity not due to shared descent (for example, produced by convergent evolution or evolutionary reversal
Convergent evolution
the independent origin of similar traits in separate evolutionary lineages
Evolutionary reversal (= character reversal)
the reversion of a derived character state to a form resembling its ancestral state
Vestigial
the retention, during the process of evolution, of genetically determined structures or attributes that have lost some or all of the ancestral function in a given species
Symplesiomorph
An ancestral character state (i.e., a plesiomorphy) shared by two or more lineages in a particular clade
Homoplasy
When similar characteristics are not due to common ancestry, but instead arise by convergent evolution or evolutionary reversals (Homoplasy is common because there is only four possible character states)
Reversal
ana ancestral trait that reappears in a lineage
Slowly evolving characters
(include DNA sequences) can show the relationships between distantly related taxa
Rapidly evolving characters
(including DNA sequence) can reveal relationships between closely related taxa
How can DNA sequences be used to build phylogenetic trees?
- First align the DNA sequences from the species being examined so that the positions match eg. gene 1 is aligned with gene 1
- This is the character matrix. This matrix is no different than any other character matrix we’ve looked at, but instead of morphological traits, we have variation ata nucleotide position in the gene
Neutral theory of molecular evolution
there are special types of DNA mutations that are not necessary favored or disfavored by natural selection
Synonymous mutations
typically occur at a normal rate and behave like a clock
Cladogram
shows branching order or topology only, the branch lengths do not mean anything
Phylogram
a type of cladogram with branch lengths that reflect the amount of evolutionary change. Often this is derived from the number of mutations in DNA sequences
Chronogram
a type of cladogram with branch lengths that are calibrated to real time; nodes indicate estimated ages of ancestors
Symplesiomorphy
a shared ancestral character or trait
Paraphyletic group
one that includes an ancestor and some, but not all, of its descendants
Two ways to build trees
Morphological data
Molecular data
