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Chapter 26: Phylogeny and the Tree of Life

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Phylogeny
The evolutionary history of a species or group of related species
Systematics
a scientific discipline focused on classifying organisms and determining their evolutionary relationships
Taxonomy
A scientific discipline concerned with naming and classifying the diverse forms of life.
Binomial
The two-part latinized name of a species, consisting of genus and specific epithet.
Genus
A taxonomic category above the species level, designated by the first word of a species two-part scientific name
Family
In classification, the taxonomic category above genus.
Order
In classification, the taxonomic category above family
Classes
In classification, the taxonomic category above order
Phyla
In classification, the taxonomic category above class
Kingdoms
a taxonomic category, the second broadest after domain
Domains
(1) A taxonomic category above the kingdom level. The three domains are Archaea, Bacteria, and Eukarya. (2) An independently folding part of a protein.
Taxon
a named taxonomic unit at any given level of classification
Phylogenetic Tree
a branching diagram that represents a hypothesis about the evolutionary history of a group of organisms
PhyloCode
System of classification of organisms based on evolutionary relationships: Only groups that include a common ancestor and all of its descendents are named.
Branch Points
the representation on a phylogenetic tree of the divergence of two or more taxa from a common ancestor. Most of these are shown as dichotomies, in which a branch representing the ancestral lineage splits into two branches, one for each of the two descendant taxa
Sister taxa
Groups of organisms that share an immediate common ancestor and hence are each other's closest relatives.
Rooted
Describing a phylogenetic tree that contains a branch point (typically, the one farthest to the left) representing the last common ancestor of all taxa in the tree.
Polytomy
In a phylogenetic tree, a branch point from which more than two descendant taxa emerge. This indicates that the evolutionary relationships among the descendant taxa are not yet clear.
Analogy
similarity between two species that is due to convergent evolution rather than to descent from a common ancestor with the same trait
Homoplasies
Similar (analogous) structure or molecular sequence that has evolved independently in two species.
Molecular Systematics
a scientific discipline that uses nucleic acids or other molecules in different species to infer evolutionary relationships
Cladistics
an approach to systematics in which common descent is the primary criterion used to classify organisms by placing them into groups called clades
Clades
a group of species that includes an ancestral species and all its descendants
Monophyletic
Pertaining to a group of taxa that consists of a common ancestor and all its descendants. A monophyletic taxon is equivalent to a clade.
Paraphyletic
Pertaining to a group of taxa that consists of a common ancestor and some, but not all, of its descendants.
Shared Ancestral Character
A character, shared by members of a particular clade, that originated in an ancestor that is not a member of that clade.
Shared Derived Character
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. An outgroup 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.
Ingroup
a species or group of species whose evolutionary relationships we seek to determine
Maximum Parsimony
A principle that states that when considering multiple explanations for an observation, one should first investigate the simplest explanation that is consistent with the facts.
Maximum likelihood
as applied to systematics, a principle 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
Phylogenetic Bracketing
An approach in which features shared by two groups of organisms are predicted (by parsimony) to be present in their common ancestor and all of its descendants.
Orthologous Genes
homologous genes that are found in different species because of speciation
Paralogous Genes
homologous genes that are found in the same genome due to gene duplication
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 appear to evolve at constant rates.
Neutral Theory
the hypothesis that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian natural selection
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.