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    Principles of Classification

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    - Systematics is the field of biology dealing with the diversity and evolutionary history of life. It includes taxonomy, which is the classification and naming of organisms. - Phylogenetic classification is based on the inferred evolutionary history and places organisms into groups reflecting their evolutionary relationships and patterns of common descent. It is advantageous over phenetic classification which is based only on overall similarity. - Phylogenetic trees or cladograms depict the evolutionary relationships between taxa, with more closely related taxa having a more recent common ancestor according to the tree. They are reconstructed using shared derived characteristics and other molecular and anatomical data.

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    Principles of Classification

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    - Systematics is the field of biology dealing with the diversity and evolutionary history of life. It includes taxonomy, which is the classification and naming of organisms. - Phylogenetic classification is based on the inferred evolutionary history and places organisms into groups reflecting their evolutionary relationships and patterns of common descent. It is advantageous over phenetic classification which is based only on overall similarity. - Phylogenetic trees or cladograms depict the evolutionary relationships between taxa, with more closely related taxa having a more recent common ancestor according to the tree. They are reconstructed using shared derived characteristics and other molecular and anatomical data.

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    Principles of Classification

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    - Systematics is the field of biology dealing with the diversity and evolutionary history of life. It includes taxonomy, which is the classification and naming of organisms. - Phylogenetic classification is based on the inferred evolutionary history and places organisms into groups reflecting their evolutionary relationships and patterns of common descent. It is advantageous over phenetic classification which is based only on overall similarity. - Phylogenetic trees or cladograms depict the evolutionary relationships between taxa, with more closely related taxa having a more recent common ancestor according to the tree. They are reconstructed using shared derived characteristics and other molecular and anatomical data.

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    340 views70 pages

    Principles of Classification

    Uploaded by

    Bio Sciences
    - Systematics is the field of biology dealing with the diversity and evolutionary history of life. It includes taxonomy, which is the classification and naming of organisms. - Phylogenetic classification is based on the inferred evolutionary history and places organisms into groups reflecting their evolutionary relationships and patterns of common descent. It is advantageous over phenetic classification which is based only on overall similarity. - Phylogenetic trees or cladograms depict the evolutionary relationships between taxa, with more closely related taxa having a more recent common ancestor according to the tree. They are reconstructed using shared derived characteristics and other molecular and anatomical data.

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    Phylogeny and the Tree of Life (Principles of classification)

    All life is interconnected by descent


    Bacterium Amoeba Pine tree Rattlesnake Humans

    How to determine the pattern of descent?

    Systematics - field of biology dealing with


    diversity and evolutionary history of life
    Includes Taxonomy: DINC
    Description Identification Nomenclature Classification

    Goal:
    Determine Evolutionary History (Phylogeny) of Life

    Description
    = assign features Character = a feature (e.g., petal color) Character states = two or more forms of a character (e.g., red, white).

    Identification
    = associate an unknown with a known How? One way: Taxonomic Key, e.g.,
    Tree . Species A Leaves simple . Species B Leaves pinnate ....... Species C Herb Flowers red . Species D Flowers white ... Species E

    Nomenclature
    Naming, according to a formal system. Binomial: Species are two names (Linnaeus): E.g., Homo sapiens Homo = genus name sapiens = specific epithet Homo sapiens = species name

    Nomenclature
    Hierarchical Ranks: Domain Kingdom Phylum Class Order Family Genus Species

    Classification
    Placing objects, e.g., life, into some type of order. Taxon = a taxonomic group (plural = taxa).

    How to classify life


    Phenetic classification
    Based on overall similarity

    Those organisms most similar are classified more closely together.

    Problem with phenetic classification:


    Can be arbitrary, e.g., classify these:

    Phylogenetic classification
    Based on known (inferred) evolutionary history. Advantage:
    Classification reflects pattern of evolution Classification not ambiguous

    lineage or clade TIME

    Cladogram or Phylogenetic Tree

    = representation of the history of life

    TAXA

    lineage or clade TIME

    Cladogram or Phylogenetic Tree

    TAXA

    TIME speciation

    Cladogram or Phylogenetic Tree

    Ingroup group studied


    Outgroup group not part of ingroup, used to root tree

    Fig. 26-5

    Branch point (node)

    Taxon A
    Taxon B Sister taxa

    Taxon C
    ANCESTRAL LINEAGE Taxon D

    Taxon E
    Taxon F Common ancestor of taxa AF Polytomy

    Apomorphy (derived trait)

    = a new, derived feature E.g., for this evolutionary transformation scales --------> feathers (ancestral feature) (derived feature)

    Presence of feathers is an apomorphy for birds.

    Taxa are grouped by apomorphies


    Apomorphies are the result of evolution. Taxa sharing apomorphies underwent same evolutionary history should be grouped together.

    Principle of Parsimony
    That cladogram (tree) having the fewest number of steps (evolutionary changes) is the one accepted. Okhams razor: the simplest explanation, with fewest number of ad hoc hypotheses, is accepted.

    Other methods of phylogeny reconstruction:


    Maximum Likelihood or Bayesian analysis
    Uses probabilities Advantage: can use evolutionary models.

    TAXA

    E
    apomorphy (for Taxon D)

    apomorphies (for Taxa B & C) TIME

    apomorphy (for Taxa B,C,D,E,F)

    Cladogram or Phylogenetic Tree

    Sequentially group taxa by shared derived character states (apomorphies)


    TAXA Leopard

    Lancelet (outgroup)
    Lamprey

    Tuna

    Vertebral column (backbone) Hinged jaws Four walking legs Amniotic (shelled) egg Hair (a) Character table

    0 0 0 0 0

    1 0 0 0 0

    1 1 0 0 0

    1 1 1 0 0

    1 1 1 1 0

    1 1 1

    Tuna Vertebral column Salamander Hinged jaws Four walking legs Turtle

    1 Amniotic egg 1 (b) Phylogenetic tree Hair Leopard

    Fig. 26-11

    DNA sequence data most important type of data 1

    Deletion

    Insertion
    Fig. 26-8a

    DNA sequence data - alignment 3

    Fig. 26-8b

    Each nucleotide position = Character Character states = specific nucleotide

    Homology
    Similarity resulting from common ancestry.
    E.g., the forelimb bones of a bird, bat, and cat.

    Homoplasy (analogy)
    Similarity not due to common ancestry
    Reversal loss of new (apomorphic) feature, resembles ancestral (old) feature. Convergence (parallelism) gain of new, similar features independently.

    Convergent evolution: spines of cacti & euphorbs

    Cactus

    Euphorb

    Convergent evolution: spines of cacti & euphorbs

    euphorb spines

    cactus spines

    Leg-less lizards
    Both examples of reversal within Tetrapods: loss of a derived feature forelimbs. Example of convergence relative to one another! Independently evolved.

    Snake
    snakes legged lizards leg-less lizards

    *
    *= loss of legs

    gain of legs (Tetrapods)

    Convergent evolution: wings of some animals evolved independently

    Fig. 26-7

    Convergent evolution: Australian mole and N. Am. mole

    Gene Duplication can occur!

    Ancestral gene

    Ancestral species Speciation with divergence of gene

    Species A

    Orthologous genes

    Species B

    (a) Orthologous genes

    Orthology genes homologous

    Species A Gene duplication and divergence

    Paralogous genes Species A after many generations (b) Paralogous genes


    Fig. 26-18

    Paralogy genes not homologous

    Common ancestry
    TAXA

    TIME common ancestor (of taxon D, E, & F) common ancestor (of taxon A & taxa B-F)

    Cladogram or Phylogenetic Tree

    Monophyletic Group
    a group consisting of:
    a common ancestor + all descendents of that common ancestor

    TAXA

    D
    monophyletic group

    TIME common ancestor (of taxon D, E, & F) common ancestor (of taxon A & taxa B-F)

    Cladogram or Phylogenetic Tree

    TAXA

    D
    monophyletic group

    TIME common ancestor (of taxon D, E, & F) common ancestor (of taxon A & taxa B-F)

    Cladogram or Phylogenetic Tree

    TAXA

    D
    monophyletic group

    TIME common ancestor (of taxon D, E, & F) common ancestor (of taxon A & taxa B-F)

    Cladogram or Phylogenetic Tree

    TAXA

    D
    monophyletic group

    TIME common ancestor (of taxon D, E, & F) common ancestor (of taxon A & taxa B-F)

    Cladogram or Phylogenetic Tree

    TAXA

    D
    monophyletic group

    TIME common ancestor (of taxon D, E, & F) common ancestor (of taxon A & taxa B-F)

    Cladogram or Phylogenetic Tree

    TAXA

    TIME speciation

    Cladogram or Phylogenetic Tree

    TAXA

    C A

    B B

    F C

    E D

    D E

    A F

    TIME speciation

    Cladogram or Phylogenetic Tree Cladograms can be flipped at nodes, show same relationships

    Fig. 26-13

    One can date divergence times with molecular clock and fossils
    Drosophila

    Lancelet

    Zebrafish

    Frog

    Chicken

    Human

    Mouse
    PALEOZOIC 542 251 MESOZOIC CENOZOIC 65.5 Present

    Millions of years ago

    Relationship
    = recency of common ancestry i.e., taxa sharing a common ancestor more recent in time are more closely related than those sharing common ancestors more distant in time.

    Example:
    Are fish more closely related to sharks or to humans?

    Shark

    Fish

    Humans

    TIME

    Shark

    Fish

    Humans

    TIME common ancestor of Fish and Humans

    common ancestor of Sharks, Fish, and Humans

    Vertebrata Osteichthyes Shark Fish Humans

    TIME

    monophyletic group common ancestor of Fish and Humans

    common ancestor of Sharks, Fish, and Humans

    Example:
    Are crocodyles more closely related to lizards or to birds?

    Turtles

    Lizards & Snakes

    Crocodyles

    Birds

    "Reptilia"
    Turtles Lizards & Snakes Crocodyles Birds

    Paraphyletic group
    Consist of common ancestor but not all descendents Paraphyletic groups are unnatural, distort evolutionary history, and should not be recognized.

    "Reptilia"
    Turtles Lizards & Snakes Crocodyles Birds

    Reptilia here paraphyletic


    "Reptilia"
    Turtles Lizards & Snakes Crocodyles Birds

    Re-defined Reptilia monophyletic

    Reptilia
    Turtles Lizards & Snakes Crocodyles Birds

    Reptilia
    Turtles Lizards & Snakes Dinosaurs Crocodyles Birds

    Importance of a name: Did humans evolve from apes?

    Orangatan Gorilla

    Chimpanzees Humans

    Pongidae Hominidae Great Apes Orangatan Gorilla Chimpanzees Humans

    Pongidae Pongidaeor Hominidae Great Apes


    Orangatan Gorilla Chimpanzees Humans

    Pongidae or Hominidae
    Orangatan Gorilla Chimpanzees Humans

    Pongidae or Hominidae
    Orangatan Gorilla Chimpanzees Humans

    We are human, but we are also apes.


    We share unique human features. We also share features with other apes (and with other animals, plants, fungi, bacteria, etc.). Humans didnt evolve from apes, humans are apes.

    Importance of systematics & evolution:


    1) Foundation of biology - study of biodiversity 2) Basis for classification of life 3) Gives insight into biological processes: speciation processes adaptation to environment 4) Can be aesthetically/intellectually pleasing!

    E.g., schistosomiasis

    Schistosomiasis:
    knowledge of species diversity and evolutionary history of primary host can aid in controlling parasite (Schistosoma, a fluke)

    Phylogeny of Oncomelania snails

    All of life is interconnected by descent.


    TAXA

    lineage or clade TIME

    Cladogram or Phylogenetic Tree

    There are no higher or lower species.


    TAXA

    lineage or clade TIME

    Cladogram or Phylogenetic Tree

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