Classifying Organisms

Systematics is the scientific study of the diversity of organisms and their evolutionary relationships.
Taxonomy is the branch of systematics devoted to naming, describing, and classifying organisms.
Classification is the process of arranging organisms into groups based on similarities that reflect evolutionary relationships.
Scientific names allow biologists from different countries with different languages to communicate about organisms.
Biologists in distant locations must know with certainty that they are studying the same (or different) organisms.
Classifications help biologists organize their knowledge.
In the binomial system of nomenclature, the basic unit of classification is the species.
The name of each species has two parts: the genus name followed by the specific epithet.
The hierarchical system of classification includes domain, kingdom, phylum, class, order, family, genus, and species.
Each formal grouping at any given level is a taxon.

Determining the Major Branches in the Tree of Life

The three-domain classification system assigns organisms to domains Archaea, Bacteria, or Eukarya.
The domain classification is based on molecular data.
Domain Eukarya includes the fungi, plants, animals, and protists.
Some systematists recognize the kingdoms Archaea, Bacteria,
Fungi, Plantae, and Animalia.
Several “supergroups” composed of mainly unicellular, mainly aquatic eukaryotic organisms were formerly classified as kingdom protista.
Members of Archaea and Bacteria are prokaryotes.
The fungi, which include molds, yeasts, and mushrooms, absorb nutrients produced by other organisms.
Kingdoms plantae and Animalia both consist of multicellular eukaryotes.
As new data are interpreted, organisms assigned to these kingdoms often must be reclassified.
In a cladogram each branch represents a clade, a group of organisms with a common ancestor.
Each node, or branching point, represents the splitting of two or more new groups from a common ancestor.
The node represents the most recent common ancestor of the clade represented by the branches.
The root represents the most recent common ancestor of all the clades shown in the tree.
We can determine the relationships among taxa by tracing along the branches back to the nodes.
The cladogram indicates which taxa shared a recent common ancestor and how recently they shared that ancestor compared to other groups.

Reconstructing Evolutionary History

Systematists seek to determine evolutionary relationships, or phylogeny, based on shared characteristics.
Homology, the presence in two or more species of a trait derived from a common ancestor, implies evolution from a common ancestor.
Some seemingly homologous characters are acquired independently by convergent evolution, independent evolution of similar structures in distantly related organisms, or by reversal, reversion of a trait to its ancestral state.
The term homoplasy refers to superficially similar characters that are not homologous.
Shared ancestral characters suggest a distant common ancestor.
Shared derived characters (synapomorphies) indicate a more recent common ancestor and can be used as evidence for constructing cladograms.
Molecular systematics depends on molecular structure to clarify phylogeny.
Comparisons of nucleotide sequences in DNA and RNA, and of amino acid sequences in proteins, provide important information about how closely organisms are related.
A monophyletic group, or clade, includes all the descendants of the most recent common ancestor.
A paraphyletic group consists of a common ancestor and some of, but not all, its descendants.
A polyphyletic group consists of organisms that evolved from different recent ancestors.

Constructing Phylogenetic Trees

Modern systematists agree that taxa must be monophyletic.
Each monophyletic group consists of a common ancestor and all its descendants.
Phylogenetic systematists (cladists) use shared derived characters to determine relationships among groups of organisms.
Contemporary systematists classify reptiles and birds in a single clade.
Cladists use shared derived characters to reconstruct evolutionary relationships and diagram these relationships in cladograms.
They use outgroup analysis to determine which characters in a given group of taxa are ancestral and which are derived.
An outgroup is a taxon that diverged earlier than any of the other taxa being investigated.
Systematists choose the simplest explanation to interpret the data—the principle of parsimony.

Applying Phylogenetic Information

Understanding how species are related can help scientists answer questions and solve problems in other disciplines.
For example, phylogenetic information has helped us better understand the origin and transmission of HIV.

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Chapter 23: Understanding Diversity: Systematics

Classifying Organisms

Systematics is the scientific study of the diversity of organisms and their evolutionary relationships.
Taxonomy is the branch of systematics devoted to naming, describing, and classifying organisms.
Classification is the process of arranging organisms into groups based on similarities that reflect evolutionary relationships.
Scientific names allow biologists from different countries with different languages to communicate about organisms.
Biologists in distant locations must know with certainty that they are studying the same (or different) organisms.
Classifications help biologists organize their knowledge.
In the binomial system of nomenclature, the basic unit of classification is the species.
The name of each species has two parts: the genus name followed by the specific epithet.
The hierarchical system of classification includes domain, kingdom, phylum, class, order, family, genus, and species.
Each formal grouping at any given level is a taxon.

Determining the Major Branches in the Tree of Life

The three-domain classification system assigns organisms to domains Archaea, Bacteria, or Eukarya.
The domain classification is based on molecular data.
Domain Eukarya includes the fungi, plants, animals, and protists.
Some systematists recognize the kingdoms Archaea, Bacteria,
Fungi, Plantae, and Animalia.
Several “supergroups” composed of mainly unicellular, mainly aquatic eukaryotic organisms were formerly classified as kingdom protista.
Members of Archaea and Bacteria are prokaryotes.
The fungi, which include molds, yeasts, and mushrooms, absorb nutrients produced by other organisms.
Kingdoms plantae and Animalia both consist of multicellular eukaryotes.
As new data are interpreted, organisms assigned to these kingdoms often must be reclassified.
In a cladogram each branch represents a clade, a group of organisms with a common ancestor.
Each node, or branching point, represents the splitting of two or more new groups from a common ancestor.
The node represents the most recent common ancestor of the clade represented by the branches.
The root represents the most recent common ancestor of all the clades shown in the tree.
We can determine the relationships among taxa by tracing along the branches back to the nodes.
The cladogram indicates which taxa shared a recent common ancestor and how recently they shared that ancestor compared to other groups.

Reconstructing Evolutionary History

Systematists seek to determine evolutionary relationships, or phylogeny, based on shared characteristics.
Homology, the presence in two or more species of a trait derived from a common ancestor, implies evolution from a common ancestor.
Some seemingly homologous characters are acquired independently by convergent evolution, independent evolution of similar structures in distantly related organisms, or by reversal, reversion of a trait to its ancestral state.
The term homoplasy refers to superficially similar characters that are not homologous.
Shared ancestral characters suggest a distant common ancestor.
Shared derived characters (synapomorphies) indicate a more recent common ancestor and can be used as evidence for constructing cladograms.
Molecular systematics depends on molecular structure to clarify phylogeny.
Comparisons of nucleotide sequences in DNA and RNA, and of amino acid sequences in proteins, provide important information about how closely organisms are related.
A monophyletic group, or clade, includes all the descendants of the most recent common ancestor.
A paraphyletic group consists of a common ancestor and some of, but not all, its descendants.
A polyphyletic group consists of organisms that evolved from different recent ancestors.

Constructing Phylogenetic Trees

Modern systematists agree that taxa must be monophyletic.
Each monophyletic group consists of a common ancestor and all its descendants.
Phylogenetic systematists (cladists) use shared derived characters to determine relationships among groups of organisms.
Contemporary systematists classify reptiles and birds in a single clade.
Cladists use shared derived characters to reconstruct evolutionary relationships and diagram these relationships in cladograms.
They use outgroup analysis to determine which characters in a given group of taxa are ancestral and which are derived.
An outgroup is a taxon that diverged earlier than any of the other taxa being investigated.
Systematists choose the simplest explanation to interpret the data—the principle of parsimony.

Applying Phylogenetic Information

Understanding how species are related can help scientists answer questions and solve problems in other disciplines.
For example, phylogenetic information has helped us better understand the origin and transmission of HIV.