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7.2 Evolutionary Trees
We refer to phylogenies in many different ways, and all of these terms appear in the
literature. The terms phylogeny, phylogenetic tree, and evolutionary tree can be
used interchangeably. We also use the term tree of life to refer to the tree of life (the
evolutionary tree for all of life) or to the phylogeny of a really large group (or lineage) of organisms, such as the plant tree of life or the vertebrate tree of life.
7.2.1 How to Read Phylogenies
The idea that species descend from a common ancestor is at the very core of the
theory of evolution. Evolutionary trees represent the branching structure of life and
describe how species are related to each other similarly to how a genealogical tree
recounts how people are related. A branch on a phylogenetic tree is a species; when
it speciates, two (typically) descendant species arise. The two lineages coming from
the same ancestor are known as sisters. These lineages can continue to branch, leading to more descendants. An ancestor and all its descendants are known as a clade:
since these descendants all came from the same species, they share many inherited
traits. Relatedness among organisms is encoded in the phylogeny’s structure—its
topology—which defines a series of lineages that are hierarchically nested. The
branch lengths also usually convey information, such as the time since divergence,
amount of molecular similarity, or number of generations (Fig. 7.1). Dated fossil
information can be used to calibrate the age of some of the nodes in a phylogeny.
This is one means by which branch lengths can be made to represent time fairly
accurately. Typically, the spacing between tip nodes (the y-axis in Fig. 7.1a, b, and
d) has no meaning, but it can sometimes be used to display information about the
trait values of a species (Fig. 7.1c). Because no one has been taking notes of how
lineages split over the last 4 billion years, phylogenetic trees must be estimated by
analyzing current species data, generally DNA sequences, using models of evolution. This means that phylogenies are statistical inferences that have uncertainty
about their topology and their branch lengths (Fig. 7.1d).
7.2.2 Why Care About Phylogenetic Accuracy?
An accurate phylogeny is key for understanding life. A phylogeny in which dandelions were more closely related to ferns than to roses would tell us a very different
story about the evolution of flowering plants than would the true phylogeny, in
which all flowering plants belong to a single lineage. In other words, the accuracy
of the estimated tree topology—the structure of the relationships between species—
matters to how we understand trait evolution. Accurately inferring divergence times
J. E. Meireles et al.
7.2 Evolutionary Trees
We refer to phylogenies in many different ways, and all of these terms appear in the
literature. The terms phylogeny, phylogenetic tree, and evolutionary tree can be
used interchangeably. We also use the term tree of life to refer to the tree of life (the
evolutionary tree for all of life) or to the phylogeny of a really large group (or lineage) of organisms, such as the plant tree of life or the vertebrate tree of life.
7.2.1 How to Read Phylogenies
The idea that species descend from a common ancestor is at the very core of the
theory of evolution. Evolutionary trees represent the branching structure of life and
describe how species are related to each other similarly to how a genealogical tree
recounts how people are related. A branch on a phylogenetic tree is a species; when
it speciates, two (typically) descendant species arise. The two lineages coming from
the same ancestor are known as sisters. These lineages can continue to branch, leading to more descendants. An ancestor and all its descendants are known as a clade:
since these descendants all came from the same species, they share many inherited
traits. Relatedness among organisms is encoded in the phylogeny’s structure—its
topology—which defines a series of lineages that are hierarchically nested. The
branch lengths also usually convey information, such as the time since divergence,
amount of molecular similarity, or number of generations (Fig. 7.1). Dated fossil
information can be used to calibrate the age of some of the nodes in a phylogeny.
This is one means by which branch lengths can be made to represent time fairly
accurately. Typically, the spacing between tip nodes (the y-axis in Fig. 7.1a, b, and
d) has no meaning, but it can sometimes be used to display information about the
trait values of a species (Fig. 7.1c). Because no one has been taking notes of how
lineages split over the last 4 billion years, phylogenetic trees must be estimated by
analyzing current species data, generally DNA sequences, using models of evolution. This means that phylogenies are statistical inferences that have uncertainty
about their topology and their branch lengths (Fig. 7.1d).
7.2.2 Why Care About Phylogenetic Accuracy?
An accurate phylogeny is key for understanding life. A phylogeny in which dandelions were more closely related to ferns than to roses would tell us a very different
story about the evolution of flowering plants than would the true phylogeny, in
which all flowering plants belong to a single lineage. In other words, the accuracy
of the estimated tree topology—the structure of the relationships between species—
matters to how we understand trait evolution. Accurately inferring divergence times
J. E. Meireles et al.