Chapter 26: Phylogeny Flashcards
Horizontal gene transfer
The transfer of genes from one genome to another through mechanisms such as transposable elements, plasmid exchange, viral activity, and perhaps fusions of different organisms.
Taxonomy
A scientific discipline concerned with naming and classifying the diverse forms of life.
Parallelism (homoplasy)
An instance of two taxa sharing a derived trait while lacking an immediately recent ancestor ommon to them both.
Paraphyletic group
An invalid clade where at least one taxon is missing.
Clade
A group of taxa that includes an ancestor and all of its descendants.
Transition
DNA substitution mutation wherein purines are interchanged with purines and pyrimadines with pyrimadines.
Homology
An instance of a trait being present in both an ancestor and its descendants.
Phylogeny
The evolutionary history of a species or a group of related species.
Sister taxa
Two taxa that share an immediate common ancestor.
Polyphyletic group
An invalid clade where the common ancestor is missing.
Neutral theory
The theory that most evolutionary change in genes and proteins has no effect on fitness and is not enfluenced by natural selection.
Polytomy
An instance of unresolved phylogeny wherein a branch point diverges into more than two taxa.
Transversion
DNA substitution mutation wherein purines are interchanged with pyrimadines.
Maximum likelihood
A principle applied to DNA sequence data that states that when considering multiple phylogenetic hypotheses, one should take into account the hypothesis that reflects the most likely sequence of evolutionary events, given certain rules about how DNA changes over time.
Orthologous gene
Homologous genes that are found in different species because of speciation.
Synapomorphy
An instance of a shared derived character that is an evolutionary novelty unique to a particular clade.
Outgroup
A species or group of species from an evolutionary lineage that is known to have diverged before the lineage that contains the group of species being studied; this group is selected so that its members are closely related to the group of species being studied, but not as closely related as any study-group members are to each other.
Character matrix
A matrix that maps traits against taxa. This matrix is often binary, indicating the presence or absence of a trait.
Nested taxonomy
The system of supergroups and subgroups applied to standard taxonomy.
Phylogenetic tree
A branched mapping of hypothetical evolutionary relationships.
Plesiomorphy
An instance of a shared character that originated in an ancestral taxon.
Paralogous gene
Homologous genes that are found in the same genome as a result of gene duplication.
Cladistics
The system of grouping organisms by common descent.
Basal taxon
The null taxon that diverged at the beginning of a particular phylogenetic tree, branching off at the last common ancestor.
Reversal (homoplasy)
An instance of a trait shared between an ancestor and one of its distant descendants that is not present in intermediate descendants.
Maximum parsimony
The principle that states that when considering multiple explanations for an observation, one should first investigate the simplest explanation that is consistent with the facts.
Molecular clock
A method for estimating the time required for a given amount of evolutionary change, based on the observation that some regions of genomes evolve at constant rates.
Branch point
The intersection of two branches on a phylogenetic tree, indicating where two taxa have diverged from their common ancestor.
Polymerase chain reaction
A technique for amplifying DNA in vitro by incubating it with specific primers, a heat-resistant DNA polymerase, and nucleotides.
Taxon
A taxonomic unit at any given level of classification.
Monophyletic group
A valid clade, i.e. a group that includes an ancestor and all of its descendants.
Gene family
A group of related genes within an organism’s genome.
Ingroup
A species or group of species whose evolutionary relationships are being examined in a given analysis.
Systematics
A scientific discipline focused on classifying organisms and determining their evolutionary relationships.
Rooted tree
A phylogenetic tree that includes a single ancestral branch at one end to indicate the last common ancestor of all taxa on the tree.
