Chap 26 Phylogeny and The Tree of Life

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The scientific name for humans is Homo sapiens (kingdom Animalia).
The genus is Homo, while the specific epithet is sapiens.

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Scientific names. The combination genus Panthera and specific epithet epithet pardus uniquely identifies the leopard (Panthera pardus). The genus indicates its relationship to other big cats: lion (Panthera leo), tiger (Panthera tigris), and jaguar (Panthera onca). The domestic cat (Felis silvestris) is in a different genus (Felis) of the cat family, Felidae.

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The scientific name of an organism uses a binomial nomenclature composed of its genus and specific epithet. Thus genus Panthera and specific epithet pardus uniquely identifies the leopard (Panthera pardus), and humans are Homo sapiens. The cat family, Felidae, is a sister taxon with other families in the order Carnivora, which is a branch of class Mammalia.

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A character table can show shared derived characters inherited among organisms. A 0 indicates a character is absent; a 1 indicates that it is present. The shared derived characters can be arranged to track descent from a common ancestor.

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Monophyletic. Group I (species A, B, C) is a monophyletic group, or clade, made up of an ancestral species (X) and all of its descendant species.

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Paraphyletic. Group II is paraphyletic: it consists of an ancestor (X) and some (D, E, F), but not all (excludes G), of that ancestor’s descendants.

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Polyphyletic. Group III is polyphyletic: it lacks a common ancestor of all the species in the group.

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A cladogram is used to track relationships by shared derived characters inherited from a common ancestor. Clades are defined by an evolutionary novelty at the branching point, which constitues a shared derived character (homology) for the clade (ingroup). An outgroup does not possess that character.

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Constructing a cladogram.
(a) Character table. A 0 indicates that a character is absent, a 1 indicates that a character is present. (b) Cladogram. Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny.

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Similar environmental pressures and natural selection can produce similar (analogous) adaptations in organisms from different evolutionary lineages: convergent evolution An elongated body, large front paws, small eyes, thicken skin, and a tapered nose all evolved independently in the marsupial Australian mole and eutherian North American mole.

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Traditional taxonomy uses a hierarchical classification where species are placed into groups belonging to more comprehensive groups (taxa). Starting from the most comprehensive taxon, Linnaeus classified organisms into kingdom, phylum, class, order, family, genus, and species. Leopards and humans both belong to kingdom Animalia, phylum Chordata, but while leopards are in order Carnivora, humans are in order Primates. A taxon above kingdom called domain was added after Linnaeus proposed these 7 levels.

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What are the evolutionary relationships among a human, a mushroom, and a tulip? Despite appearances, molecular evidence has revealed that animals, including humans, and fungi, such as mushrooms, are more closely related to each other than either are to plants.

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The tree of life. Based on rRNA gene sequences, living organisms are divided into 3 domains: Bacteria, Archaea, and Eukarya. Eukarya and Archaea appear to share a common ancestor, are more closely related to each other than to Bacteria. Note: Archaea and Bacteria are "prokaryotes" that lack organelles such as a nucleus. The lack of organelles is not a shared derived character, thus "prokaryotes" do not constitute a clade.

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Identifying homologous DNA.

  1. Ancestral DNA segments from 2 species are identical.
  2. Deletion and insertion mutations shift these sequences as the 2 species diverge.
  3. Homologous regions no longer align.
  4. Homologous regions realign after a computer program adds gaps in sequence 1.

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A phylogenetic tree shows evolutionary relationships by homology. A homology is a shared derived character, such as hair among the mammals, inherited from a common ancestor.