Biology: A Global Approach
Chapter 22 Phylogenetic Reconstruction 2
Concept 22.1 Phylogenies show evolutionary relationships 2
Binomial Nomenclature 2
Hierarchical Classification 2
Linking Classification and Phylogeny 2
What We Can and Cannot Learn from Phylogenetic Trees 3
Applying Phylogenies 3
Concept 22.2 Phylogenies are inferred from morphological and molecular data 3
Morphological and Molecular Homologies 3
Sorting Homology from Analogy 3
Evaluating Molecular Homologies 4
Concept 22.3 Shared characters are used to construct phylogenetic trees 4
Cladistics 4
Phylogenetic Trees with Proportional Branch Lengths 5
Maximum Parsimony and Maximum Likelihood 5
Phylogenetic Trees as Hypotheses 5
Concept 22.4 An organism’s evolutionary history is documented in its genome 5
Gene Duplications and Gene Families 6
Genome Evolution 6
Concept 22.5 Molecular clocks help track evolutionary time 6
Molecular Clocks 6
Concept 22.6 Our understanding of the tree of life continues to change based on new
data 7
From Two Kingdoms to Three Domains 7
The Important Role of Horizontal Gene Transfer 7
1
, Chapter 22 Phylogenetic Reconstruction
Concept 22.1 Phylogenies show evolutionary relationships
Phylogeny is the evolutionary history of a species or group of species. Biologists reconstruct
phylogenies using systematics, a discipline focused on classifying organisms and
determining their evolutionary relationships.
Binomial Nomenclature
To avoid ambiguity when communicating about their research, biologists refer to organisms
by Latin scientific names. The two-part format of the scientific name, commonly called a
binomial. The first part of a binomial is the name of the genus to which the species belongs.
The second part, called the specific epithet, is unique for each species within the genus.
Hierarchical Classification
In addition to naming species, Linnaeus also grouped them into a hierarchy of increasingly
inclusive categories. The first grouping is built into the
binomial: Species that appear to be closely related are
grouped into the same genus. The classification system
named after Linnaeus, the Linnaean system, places
related genera in the same family, families into orders,
orders into classes, classes into phyla, phyla into
kingdoms and kingdoms into domains.
The named group at any level of the hierarchy is called a
taxon.
Linking Classification and Phylogeny
The evolutionary history of a group of organisms can be represented in a branching diagram
called a phylogenetic tree. The branching pattern often matches how systematists have
classified groups of organisms nested within more inclusive groups. Sometimes systematists
have placed a species within a genus to which it is not most closely related. One reason for
such a mistake might be that over the course of evolution, a species has lost a key feature
shared by its close relatives. Another issue is that while Linnaean system may distinguish
groups, it tells us nothing about these groups’ evolutionary relationships to one another.
Such difficulties in aligning Linnaean classification with phylogeny have led many
systematists to propose that classification be based entirely on evolutionary relationships. In
such systems, names are assigned only yo groups that include a common ancestor and all
of its descendants.
2
Chapter 22 Phylogenetic Reconstruction 2
Concept 22.1 Phylogenies show evolutionary relationships 2
Binomial Nomenclature 2
Hierarchical Classification 2
Linking Classification and Phylogeny 2
What We Can and Cannot Learn from Phylogenetic Trees 3
Applying Phylogenies 3
Concept 22.2 Phylogenies are inferred from morphological and molecular data 3
Morphological and Molecular Homologies 3
Sorting Homology from Analogy 3
Evaluating Molecular Homologies 4
Concept 22.3 Shared characters are used to construct phylogenetic trees 4
Cladistics 4
Phylogenetic Trees with Proportional Branch Lengths 5
Maximum Parsimony and Maximum Likelihood 5
Phylogenetic Trees as Hypotheses 5
Concept 22.4 An organism’s evolutionary history is documented in its genome 5
Gene Duplications and Gene Families 6
Genome Evolution 6
Concept 22.5 Molecular clocks help track evolutionary time 6
Molecular Clocks 6
Concept 22.6 Our understanding of the tree of life continues to change based on new
data 7
From Two Kingdoms to Three Domains 7
The Important Role of Horizontal Gene Transfer 7
1
, Chapter 22 Phylogenetic Reconstruction
Concept 22.1 Phylogenies show evolutionary relationships
Phylogeny is the evolutionary history of a species or group of species. Biologists reconstruct
phylogenies using systematics, a discipline focused on classifying organisms and
determining their evolutionary relationships.
Binomial Nomenclature
To avoid ambiguity when communicating about their research, biologists refer to organisms
by Latin scientific names. The two-part format of the scientific name, commonly called a
binomial. The first part of a binomial is the name of the genus to which the species belongs.
The second part, called the specific epithet, is unique for each species within the genus.
Hierarchical Classification
In addition to naming species, Linnaeus also grouped them into a hierarchy of increasingly
inclusive categories. The first grouping is built into the
binomial: Species that appear to be closely related are
grouped into the same genus. The classification system
named after Linnaeus, the Linnaean system, places
related genera in the same family, families into orders,
orders into classes, classes into phyla, phyla into
kingdoms and kingdoms into domains.
The named group at any level of the hierarchy is called a
taxon.
Linking Classification and Phylogeny
The evolutionary history of a group of organisms can be represented in a branching diagram
called a phylogenetic tree. The branching pattern often matches how systematists have
classified groups of organisms nested within more inclusive groups. Sometimes systematists
have placed a species within a genus to which it is not most closely related. One reason for
such a mistake might be that over the course of evolution, a species has lost a key feature
shared by its close relatives. Another issue is that while Linnaean system may distinguish
groups, it tells us nothing about these groups’ evolutionary relationships to one another.
Such difficulties in aligning Linnaean classification with phylogeny have led many
systematists to propose that classification be based entirely on evolutionary relationships. In
such systems, names are assigned only yo groups that include a common ancestor and all
of its descendants.
2
