Reconstructing and Using Phylogenies

Reconstructing and Using Phylogenies
16 Reconstructing and Using Phylogenies

Concept 16.1 All of Life Is Connected through Its Evolutionary History
All of life is related through a common ancestor: Phylogeny—the evolutionary history of these relationships Phylogenetic tree—a diagrammatic reconstruction of that history commonly used to depict the evolutionary history of species, populations, and genes. Also called a cladogram

A lineage is a series of ancestor and descendant populations, shown as a line drawn on a time axis:

When a single lineage divides into two, it is depicted as a split or node: For example: this could happen due to a geographic barrier

Each descendant population gives rise to a new lineage, which continues to evolve:

A phylogenetic tree may portray the evolutionary history of: All life forms Major evolutionary groups Small groups of closely related species Individuals Populations Genes

The common ancestor of all the organisms in the tree forms the root of the tree.

Vertical distances between branches don’t have any meaning, and the vertical order of lineages is arbitrary.

Taxon—any group of species that we designate with a name Examples: humans, primates, mammals, vertebrates etc. Clade—taxon that consists of all the evolutionary descendants of a common ancestor Identify a clade by picking any point on the tree and tracing all the descendant lineages.

Clades Represent All the Descendants of a Common Ancestor
Figure 16.1 Clades Represent All the Descendants of a Common Ancestor

Sister species: Two species that are each other’s closest relatives Sister clades: Any two clades that are each other’s closest relatives

Before the 1980s, phylogenetic trees were used mostly in evolutionary biology, and in systematics—the study and classification of biodiversity. Today trees are widely used in molecular biology, biomedicine, physiology, behavior, ecology, and virtually all other fields of biology.

Evolutionary relationships among species form the basis for biological classification. As new species are discovered, phylogenetic analyses are reviewed and revised. The tree of life’s evolutionary framework allows us to make predictions about the behavior, ecology, physiology, genetics, and morphology of species.

Homologous features: Shared by two or more species Inherited from a common ancestor They can be any heritable traits, including DNA sequences, protein structures, anatomical structures, and behavior patterns.

Each character of an organism evolves from one condition (the ancestral trait) to another condition (the derived trait). Shared derived traits provide evidence of the common ancestry of a group and are called synapomorphies. The vertebral column is a synapomorphy of the vertebrates. The ancestral trait was an undivided supporting rod.

Similar traits can develop in unrelated groups: Convergent evolution—when superficially similar traits may evolve independently in different lineages

In an evolutionary reversal, a character may revert from a derived state back to an ancestral state. These two types of traits are called homoplastic traits, or homoplasies.

Figure 16.2 The Bones Are Homologous, the Wings Are Not

A trait may be ancestral or derived, depending on the point of reference. Example: Feathers are an ancestral trait for modern birds. But in a phylogeny of all living vertebrates, they are a derived trait found only in birds.

Concept 16.2 Phylogeny Can Be Reconstructed from Traits of Organisms
Ingroup—the group of organisms of primary interest Outgroup—species or group known to be closely related to, but phylogenetically outside, the group of interest

Could you make a phylogenic tree from this information?
Table Eight Vertebrates and the Presence or Absence of Some Shared Derived Traits Could you make a phylogenic tree from this information?

Figure 16.3 Inferring a Phylogenetic Tree

Parsimony principle—the preferred explanation of observed data is the simplest explanation In phylogenies, this entails minimizing the number of evolutionary changes that need to be assumed over all characters in all groups. The best hypothesis is one that requires the fewest homoplasies. WEB ACTIVITY 16.1 Constructing a Phylogenetic Tree INTERACTIVE TUTORIAL 16.1 Phylogeny and Molecular Evolution APPLY THE CONCEPT Phylogeny can be reconstructed from traits of organisms

Evolutionary relationships can be revealed through studies of:
16.2 Evolutionary relationships can be revealed through studies of: Morphology (presence, size, shape of body parts) Development (larvae, embryos) Behavior Molecular Data (nuclear DNA, mitochondrial DNA)

Figure 16.4 The Chordate Connection (Part 1)

Sea Squirt

Phylogenetic trees can be tested with computer simulations and by experiments on living organisms. These studies have confirmed the accuracy of phylogenetic methods and have been used to refine those methods and extend them to new applications. ANIMATED TUTORIAL 16.1 Using Phylogenetic Analysis to Reconstruct Evolutionary History

Figure 16.5 The Accuracy of Phylogenetic Analysis (Part 1)

Figure 16.5 The Accuracy of Phylogenetic Analysis (Part 2)

Concept 16.4 Phylogeny Is the Basis of Biological Classification
The biological classification system was started by Swedish biologist Carolus Linnaeus in the 1700s. Binomial nomenclature gives every species a unique name consisting of two parts: the genus to which it belongs, and the species name. Example: Homo sapiens Linnaeus (Linnaeus is the person who first proposed the name)

Species and genera are further grouped into a hierarchical system of higher categories such as family—the taxon above genus. Examples: The family Hominidae contains humans, plus our recent fossil relatives, plus our closest living relatives, the chimpanzees and gorillas. Rosaceae is the family that includes the genus Rosa (roses) and its relatives.

Families are grouped into orders Orders into classes Classes into phyla (singular phylum) Phyla into kingdoms

Linnaeus recognized the hierarchy of life, but he developed his system before evolutionary thought had become widespread. Today, biological classifications express the evolutionary relationships of organisms. APPLY THE CONCEPT Phylogeny is the basis of biological classification

But detailed phylogenetic information is not always available. Taxa are monophyletic—they contain an ancestor and all descendants of that ancestor, and no other organisms (=clade). APPLY THE CONCEPT Phylogeny is the basis of biological classification

Polyphyletic—a group that does not include its common ancestor Paraphyletic—a group that does not include all the descendants of a common ancestor

Figure 16.11 Monophyletic, Polyphyletic, and Paraphyletic Groups

Codes of biological nomenclature: Biologists around the world follow rules for the use of scientific names, to facilitate communication and dialogue. There may be many common names for one organism, or the same common name may refer to several species. But there is only one correct scientific name.

Figure 16.12 Same Common Name, Not the Same Species
All known As Indian paintbrush

Reconstructing and Using Phylogenies

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