Phylogeny and Systematics

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Phylogeny and Systematics. Chapter 10. Taxonomy. Taxonomy produces a formal system for naming and classifying species to illustrate their evolutionary relationship. Taxonomy & Systematics. Taxonomy Formal system for naming and classifying species. Systematics
Phylogeny and Systematics

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Slide 1

Phylogeny and Systematics

Chapter 10

Slide 2


  • Taxonomy produces a formal system for naming and classifying species to illustrate their evolutionary relationship.

Slide 3

Taxonomy & Systematics

  • Taxonomy

    • Formal system for naming and classifying species.

  • Systematics

    • Broader science of classifying organisms based on similarity, biogeography, etc.

    • Systematic zoologists have three goals:

      • To discover all species of animals.

      • To reconstruct their evolutionary relationships.

      • To classify animals according to their evolutionary relationships.

Slide 4

Introduction of evolutionary theory into animal taxonomy changed taxonomist’s role from one of classification to systematization.

Classification denotes the construction of classes.

Grouping of organisms that possess a common feature called an essence used to define the class.


Slide 5

Systematization places groups of species into units of common evolutionary descent.

Character variation is used to diagnose systems of common descent.

No requirement that an essential character be maintained throughout the system for its recognition as a taxon.


Slide 6


  • In classification

    • Taxonomist asks whether a species being classified contains the defining feature of a particular taxonomic class.

  • In systematization

    • Taxonomist asks whether the characteristics of a species confirm or reject the hypothesis that it descends from the most recent common ancestor of a particular taxon.

Slide 7

Linnaeus and Classification

  • Carolus Linnaeus designed our hierarchical classification scheme.

    • Kingdom

    • Phylum

    • Class

    • Order

    • Family

    • Genus

    • Species

Slide 8

Linnaeus and Classification

  • All animals are placed in Kingdom Animalia.

  • Names of animal groups at each rank in the hierarchy are called taxa (taxon).

    • Each rank can be subdivided into additional levels of taxa.

      • Superclass, suborder, etc.

Slide 9

Linnaeus and Classification

Slide 10

Linnaeus and Classification

  • Binomial nomenclature is the system Linnaeus used for naming species.

    • Genus and species

    • Names are latinized and italicized, only the genus is capatilized.

    • Sitta carolinensis

Slide 11

Linnaeus and Classification

  • A trinomial name includes a subspecies epithet.

    • Ensatina escholtzii escholtzii

    • E. e. klauberi

Slide 12


  • Defining a species can be difficult.

  • Criteria:

    • Common descent

    • The smallest distinct groupings of organisms sharing a pattern of descent.

      • Morphological & molecular techniques

    • Members of a species must form a reproductive community that excludes other species.

Slide 13


  • The geographic range of a species is its distribution in space.

  • Evolutionary duration of a species is its distribution in time.

  • A worldwide species is cosmopolitan.

  • One with a very localized range is called endemic.

Slide 14

Typological Species Concept

  • The typological or morphological species concept relies on type specimens that represent the ideal form for the species. When trying to name a specimen, the type specimens were compared.

  • Scientists still name species by designating a type specimen.

Slide 15

The Biological Species Concept

  • The biological species concept emerged during the evolutionary synthesis.

    • “A species is a reproductive community of populations (reproductively isolated from others) that occupies a specific niche in nature.” Mayr 1982

    • Sibling species fit this category, but can only be differentiated with molecular techniques.

    • Lacks a temporal dimension.

    • Degree of reproductive isolation necessary?

    • Species that reproduce asexually?

Slide 16

Evolutionary Species Concept

  • The evolutionary species concept states that a single lineage of ancestor-descendant populations that maintains its identity from other such lineages and that has its own evolutionary tendencies and historical fate.

    • Definition accommodates both sexual and asexual forms as well as fossils.

Slide 17

Phylogenetic Species Concept

  • The phylogenetic species concept is defined as an irreducible (basal) grouping of organisms diagnosably distinct from other such groupings and within which there is a parental pattern of ancestry and descent.

    • Both asexual and sexual groups are covered.

Slide 18

Phylogenetic Species Concept

  • Main difference in practice between the evolutionary and phylogenetic species concepts:

    • The latter emphasizes recognizing as separate species the smallest groupings of organisms that have undergone independent evolutionary change.

    • Discerns the greatest number of species but may be impractical.

    • Disregards details of evolutionary process.

Slide 19

Investigating the Tree of Life

  • A major goal of systematics is to infer the evolutionary tree or phylogeny – the evolutionary history of a species or group of related species.

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  • Phylogenies are inferred by identifying organismal features, characters, that vary among species.

    • Morphological

    • Chromosomal

    • Molecular

    • Behavioral or ecological

Slide 21


  • Shared characters that result from common ancestry are homologous.

  • Independent evolution of similar characters that are NOT homologous is called homoplasy.

Slide 22

Sorting Homology from Analogy

  • A potential misconception in constructing a phylogeny is similarity due to convergent evolution, called analogy, rather than shared ancestry.

Slide 23

Sorting Homology from Analogy

  • Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages.

Slide 24

Sorting Homology from Analogy

  • Analogous structures or molecular sequences that evolved independently are also called homoplasies.

Slide 25

Shared Primitive and Shared Derived Characteristics

  • A shared primitive (ancestral) character:

    • Is a homologous structure that predates the branching of a particular clade from other members of that clade.

    • Is shared beyond the taxon we are trying to define.

    • Example – mammals all have a backbone, but so do other vertebrates.

Slide 26

Shared Primitive and Shared Derived Characteristics

  • A shared derived character is an evolutionary novelty unique to a particular clade.

    • All mammals have hair, and no other animals have hair.

Slide 27


  • The form of the character that was present in the common ancestor of the entire group is called ancestral.

  • Variant forms of the character arose later and are called derived character states.

  • Determining polarity of a character involves determining which state is ancestral.

Slide 28


  • Polarity is determined by using outgroup comparison.

    • An outgroup is closely related, but not part of the group being examined (the ingroup).

    • If a character is found in both the study group and the outgroup, it is considered ancestral for the study group.

    • Character groups found in the study groups but not the outgroups are derived.

Slide 29


  • Clades are organisms or species that share derived character states and form a subset within a larger group.

    • A synapomorphy is a derived character shared by the members of the clade.

    • A clade corresponds to a unit of evolutionary common descent.

    • A nested hierarchy is formed by the derived states of all characters in a study group.

Slide 30


  • Ancestral character states for a taxon are called plesiomorphic.

  • Sharing these ancestral characters is called symplesiomorphy.

    • Symplesiomorphies, unlike synapomorphies, do not provide information on nesting of clades – groups with derived characters get left out.

Slide 31


  • The nested hierarchy of clades can be represented as a cladogram that is based on shared synapomorphies.

Slide 32


  • A phylogenetic tree is another way of representing evolutionary relationships.

    • Branches represent real lineages that occurred in the evolutionary past.

    • Includes information about ancestors, duration of evolutionary lineages, amounts of evolutionary change that has occurred.

Slide 33

Sources of Phylogenetic Information

  • Characters used to construct cladograms can be found using:

    • Comparative morphology – examine shapes and sizes of organismal structures, including developmental origins.

    • Comparative biochemistry – examine sequences of amino acids and nucleotides to identify variable characters.

    • Comparative cytology – uses variation in numbers, shapes, and sizes of chromosomes and their parts.

Slide 34


  • A theory of taxonomy allows us to rank taxonomic groups.

    • Two popular theories

      • Evolutionary taxonomy

      • Phylogenetic systematics

    • Both based on evolutionary principles, sometimes results conflict.

Slide 35


  • A valid clade is monophyletic.

    • Signifying that it consists of the ancestor species and all its descendants.

Slide 36


  • A paraphyletic clade is a grouping that consists of an ancestral species and some, but not all, of the descendants.

Slide 37


  • A polyphyletic grouping includes numerous types of organisms that lack a common ancestor.

Slide 38

Traditional Evolutionary Taxonomy

  • Evolutionary taxonomy utilizes common descent and the amount of adaptive evolutionary change to rank higher taxa.

    • Sometimes this type of classification includes paraphyletic groupings.

Slide 39

Phylogenetic Systematics

  • Phylogenetic systematics, or cladistics, emphasizes common descent and is based on cladograms.

    • All taxa must be monophyletic.

    • Cladistic taxonomists have moved chimpanzees, gorillas, and orangutans into the family Hominidae with humans.

    • Humans and chimps form a sister group, as do the human/chimp group and gorillas.

Slide 40

Theories of Taxonomy

  • Both evolutionary and cladistic taxonomy:

    • Accept monophyletic groups.

    • Reject polyphyletic groups.

    • Differ on accepting paraphyletic groups.

      • Traditional evolutionary taxonomy does.

      • Phylogenetic systematics does not.

    • Difference has important evolutionary implications.

Slide 41

Theories of Taxonomy

  • Current State of Animal Taxonomy:

    • Modern animal taxonomy was established using evolutionary systematics and recent cladistic revisions.

    • PhyloCode

      • New taxonomic system

      • Being developed as an alternative to Linnean taxonomy.

      • Replaces Linnean ranks with codes that denote the nested hierarchy of monophyletic groups conveyed by cladograms.

    • The terms “primitive,” “advanced,” “specialized” and “generalized” are used for specific characteristics and not for groups as a whole.

Slide 42

Maximum Parsimony and Maximum Likelihood

  • Systematists can never be sure of finding the single best tree in a large data set.

    • Narrow the possibilities by applying the principles of maximum parsimony and maximum likelihood.

Slide 43


  • Among phylogenetic hypotheses the most parsimonioustree is the one that requires the fewest evolutionary events to have occurred in the form of shared derived characters.

    • Occam’s Razor

Slide 44


  • The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be foundthat reflects the most likely sequence of evolutionary events.

Slide 45

Phylogenetic Trees as Hypotheses

  • The best hypotheses for phylogenetic trees are those that fit the most data: morphological, molecular, and fossil.

Slide 46

Molecular Systematics

  • Much of an organism’s evolutionary history is documented in its genome.

  • Comparing nucleic acids or other molecules to infer relatedness is a valuable tool for tracing organisms’ evolutionary history.

Slide 47

Major Divisions of Life

Aristotle’s two kingdom system included plants and animals.

One-celled organisms became a problem

Haeckel (1866) proposed Protista for single-celled organisms.

R.H. Whittaker (1969) proposed a five-kingdom system to distinguish prokaryotes and fungi.

Slide 48

Major Divisions of Life

  • Woese, Kandler and Wheelis (1990) proposed three monophyletic domainsabove kingdom level—Eucarya, Bacteria and Archaea—based on ribosomal RNA sequences.

Slide 49

Major Division of Life

  • More revisions are necessary to clarify taxonomic kingdoms based on monophyly.

  • “Protozoa”

    • Neither animals nor a valid monophyletic taxon.

  • “Protista”

    • Not a monophyletic kingdom.

    • Most likely composed of seven or more kingdoms.

Slide 50

Major Subdivisions of the Animal Kingdom

Traditional groupings based on embryological and anatomical characters:

Branch A (Mesozoa): phylum Mesozoa, the mesozoa

Branch B (Parazoa): phylum Porifera, the sponges and phylum Placozoa

Branch C (Eumetazoa): all other phyla

Slide 51

Branch C (Eumetazoa): all other phyla

Grade I (Radiata): phyla Cnidaria, Ctenophora

Grade II (Bilateria): all other phyla

Division A (Protostomia): Protostome characteristics

Acoelomates: phyla Platyhelminthes, Gnathostomulida, Nemertea

Pseudocoelomates: phyla Rotifera, Gastrotricha, Kinorhyncha, Nematoda, Nematomorpha, Acanthocephala, Entoprocta, Priapulida, Loricifera

Eucoelomates: phyla Mollusca, Annelida, Arthropoda, Echiurida, Sipunculida, Tardigrada, Onychophora.

Major Subdivisions of the Animal Kingdom

Slide 52

Major Subdivisions of the Animal Kingdom

  • Division B (Deuterostomia): Deuterostome characteristics

    • phyla Phoronida, Ectoprocta, Chaetognatha, Brachiopoda, Echinodermata, Hemichordata, Chordata

Slide 53

Major Subdivisions of the Animal Kingdom

Recent molecular phylogenetic studies have challenged traditional classification of Bilateria.

Grade II: Bilateria

Division A: (Protostomia):

Lophotrochozoa: phyla platyhelminthes, Nemertea, Rotifera, Gastrotricha, Acanthocephala, Mollusca, Annelida, Echiurida, Sipunculida, Phoronida, Ectoprocta, Entoprocta, Gnathostomulida, Chaetognatha, Brachiopoda

Ecdysozoa: phyla Kinorhyncha, Nematoda, Nematomorpha, Priapulida, Arthropoda, Tardigrada, Onychophora, Loricifera

Division B (Deuterostomia):

phyla Chordata, Hemichordata, Echinodermata

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