Chapter 26

Phylogeny-Methods for Classification of Organisms

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Introduction to Phylogeny

  • All organisms:-

    • Composed of one or more cells.

    • Carry out metabolism.

    • Transfer energy with ATP.

    • Encode DNA.

  • Tremendous diversity exists

  • Biologists group organisms based on shared characteristics.

Categorizing Species Traits

  • Traits shared due to common ancestry classify organisms by evolutionary history.

Carl Linnaeus: Taxonomy Pioneer

  • Carl Linneaus [Swedish; 1707–1778]

  • Professor of Botany, Uppsala University

  • Developed:-

    • A system of Taxonomy.

    • Use of binomial nomenclature.

  • Applied his system to all plants and animals known at the time.

Linnaean Taxonomy

  • Carolus Linnaeus developed taxonomy based on resemblances (grouping similar species).

  • Key features:-

    • Two-part names (binomial nomenclature).

    • Hierarchical classification.

Hierarchical Ranks

  • A group at any level of hierarchy: taxon.

  • Scientific name: binomial (genus species).

Genus and Species

  • The two lowest ranks are Genus and Species

  • An organism’s name is constructed by combining the Genus with the Species designation

  • Genus is Capitalized but the species designation is lower case, and both are italicized or underlined

  • Humans belong to the Genus Homo and the species designation of modern humans is Homo sapiens

Classification and Phylogeny

  • Evolutionary history is a branching diagram: Phylogenetic tree.

Linnaean System Limitations

  • Molecular data show hierarchy is inadequate.

  • Taxonomic ranks not monophyletic.

  • Artificial grouping.

Linnaean Resemblances vs. Evolution

  • Linnaean system based on resemblances and NOT evolutionary relationships.

  • While it distinguishes groups, it doesn't show evolutionary relationships.

Two Classification Systems Summary

  1. Linnaean system is based on resemblances and NOT on evolutionary relationships - hierarchical ranks are based on degree of resemblance and not ancestor-descent relationship

  2. Phylogenetic tree: hierarchical ranks are based on ancestor-descent relationship

Linking Classification and Phylogeny

  • Linnaean system does not always reflect relationships.- Species losing key features may be misclassified.

    • Embryogenesis may show relatedness, not adulthood.

    • DNA evidence may support reclassification.

Bases for Classification

  • Difficulties in aligning Linnaean classification with phylogeny have led many systematists to propose that classification be based entirely on evolutionary relationships.

Classification and Evolutionary Relationships

  • Proposed to base classification only on evolutionary relationships.

  • Only groups including ancestor and descendants would be named.

Phylogenies and Systematics

  • Phylogeny: Evolutionary history.

  • Systematics: Classifying organisms and determining their evolutionary relationships.

  • Systematists construct phylogenies (evolutionary trees).

Visualizing Phylogenetic Relationships

  • Phylogenetic trees are hypothesis about relationships.

  • Branch point: Divergence from common ancestor.

  • Evolutionary lineage: Ancestral sequence to taxon.

  • Sister taxa: Groups sharing a recent common ancestor.

Phylogenetic Tree Caveats

  • Trees show descent, not necessarily phenotypic similarity.

  • Trees do not indicate when species evolved or the amount of change in a lineage

  • Do not assume a taxon evolved from its neighbor.

Tree Diagrams

  • Phylogenetic trees can be drawn horizontally, vertically, or diagonally without changing the relationships between groups

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Tree Branches and Taxa

  • Tree branches can be rotated around a branch point without changing what they convey about evolutionary relationships

  • The order in which taxa appear at the branch tips is not significant

Summary of Key Concepts

  • A lineage that diverges from all other members of the group early in the history of the group is called a basal taxon

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Understanding Ancestor-Descendant Relationships

  • One of the great challenges of modern science is to understand the history of ancestor–descendant relationships that unites all forms of life on Earth, from the earliest single-celled organisms to the complex organisms we see around us today.

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Phylogenies: Data Sources

  • Data on morphology, genes, & biochemistry useful for evolutionary relationships.

  • Features from common ancestry are most useful.

Homologies: Molecular & Morphological

  • Phenotypic and genetic similarities due to shared ancestry: homologies.

  • Similar morphology or DNA: Closely related.

  • Morphological divergence: Great even when genetically similar.- Hawaiian silverswords range in size from trees to shrubs.

Sorting Homology from Analogy

  • Distinguish homology (shared ancestry) from analogy (convergent evolution).

  • Analogy: Superficial similarities evolve in unrelated species responding to natural selection by adapting to similar conditions.- Ex: Australian "mole" and African golden mole show adaptation to similar lifestyles, not shared ancestry

Homology Defined

  • Homology: Similarity from shared ancestry, another form of evolution evidence

  • Related species can have similar features but function differently

Anatomical Homologies

  • Homologous structures: Anatomical resemblances variations of a structural theme from common ancestor.- Mammal forelimbs have same bones, different functions.

Anatomical Evidence for Evolution

  • Homologous structures: Different appearances/functions, same body part in common ancestor.

  • Mammal forelimbs: Homologous structures.

  • Different functions, same ancestor structure

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Anatomical and Molecular Homologies

  • Comparative embryology: anatomical homologies not visible in adult organisms

  • Vertebrate embryos have a post-anal tail and pharyngeal arches.

  • Arches develop into structures with very different functions in adults from different vertebrate groups

Evidence through Anatomy

  • Vestigial structures: Features served a function in ancestor now remains.

  • Snakes arose from ancestors with legs, some skeletons retain vestiges of pelvis.

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    Convergent Evolution

  • Biogeography: the study of the geographic distribution of species

  • Some plants and animals have similar appearance but are only distantly related

  • Convergent evolution: the independent development of similar structures in organisms that are not directly related

    *Convergent evolution is usually seen in animals and plants that live in similar environments

Resemblance Due to Convergent Evolution

*Convergent evolution is the evolution of similar, or analogous, features in distantly related groups

*Analogous traits arise not through common ancestry, but through independent adaptation to similar environments

*For example, the sugar glider is an Australian marsupial that superficially resembles the flying squirrel, a North American eutherian

Convergent evolution in burrowers

*Superficial similarities evolve in unrelated species through convergent evolution in response to natural selection to similar environmental conditions

*For example, similarities between the Australian “mole” and the African golden mole result from adaptation to similar lifestyles, not shared ancestry

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Mammals

  • Marsupials and placentals

    *Marsupials: young are born in an immature condition and held in a pouch until they develop

  • Placentals: young are not born until they can safely survive in the external environment

Convergence among fast-swimming predators

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Evaluation of Molecular Data

  • Evaluating sections of a sequence using DNA requires alignment.

    *closely related species vary little along the DNA sequence

    *More sequence similarity correlates with homology