Transcript Taxonomy lecture

Reconstructing and Using
Phylogenies
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• Systematics:
the study of biologicalPhylogeny: the evolutionary history of a species
diversity in an
evolutionary context
• Taxonomy, a
subdivision of
systematics, is the
theory and practice of
classifying organisms.
• The fossil record:
the ordered array of
fossils, within layers,
or strata, of
sedimentary rock
• Paleontologists:
scientists who study
fossils
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• Sedimentary rock: rock formed
from sand and mud that once
settled on the bottom of seas,
lakes, and marshes
• Dating:
• 1- Relative~ geologic time scale;
sequence of species
• 2- Absolute~ radiometric dating;
age using half-lives of radioactive
isotopes
The fossil record
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Biogeography: the study of the past and present distribution of species
• Pangaea-250 mya
√ Permian extinction
• Geographic isolation-180 mya
• √ African/South American
reptile fossil similarities
• √ Australian marsupials
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• Permian extinction (250
million years ago): 90%
of marine animals;
Pangea merge
• Cretaceous extinction
(65 million years ago):
death of dinosaurs, 50%
of marine species; low
angle comet
Mass extinction
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• The tracing of evolutionary
relationships (phylogenetic
tree)
• Linnaeus
• Binomial nomenclature
• Genus, specific epithet
• Homo sapiens
• Taxon (taxa)
Phylogenetics
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• Cladistic Analysis: taxonomic approach
that classifies organisms according to the
order in time at which branches arise along
a phylogenetic tree (cladogram)
• Clade: each evolutionary branch in a
cladogram
• Types:
• 1- Monophyletic single ancestor that
gives rise to all species in that taxon and to
no species in any other taxon; legitimate
cladogram
• 2- Polyphyletic members of a taxa are
derived from 2 or more ancestral forms not
common to all members; does not meet
cladistic criterion
• 3- Paraphyletic lacks the common
ancestor that would unite the species; does
not meet cladistic criterion
Phylogenetic Trees
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Phylogenetic Trees
• A phylogeny is a hypothesis proposed by a
systematist that describes the history of descent
of a group of organisms from their common
ancestor.
• A phylogenetic tree represents that history.
• A lineage is represented as a branching tree, in
which each split or node represents a speciation
event.
• Systematists reconstruct phylogenetic trees by
analyzing evolutionary changes in the traits of
organisms.
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Phylogenetic Trees
• Systematists expect traits inherited from an
ancestor in the distant past to be shared by a
large number of species.
• Traits that first appeared in a more recent
ancestor should be shared by fewer species.
• These shared traits, inherited from a common
ancestor, are called ancestral traits.
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A Cladogram
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Phylogenetic Trees
• Any features (DNA sequences, behavior, or
anatomical feature) shared by two or more
species that descended from a common ancestor
are said to be homologous.
• For example, the vertebral column is homologous
in all vertebrates.
• A trait that differs from its ancestral form is called
a derived trait.
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Phylogenetic Trees
• To identify how traits have changed during
evolution, systematists must infer the state of the
trait in an ancestor and then determine how it has
been modified in the descendants.
• Two processes make this difficult:
 Convergent evolution occurs when
independently evolved features subjected to
similar selective pressures become superficially
similar.
 Evolutionary reversal occurs when a character
reverts from a derived state back to an ancestral
state.
Figure 25.2 The Bones Are Homologous, but the Wings Are Not
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Phylogenetic Trees
• Convergent evolution and evolutionary reversal
generate homoplastic traits, or homoplasies:
Traits that are similar for some reason other than
inheritance from a common ancestor.
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Phylogenetic Trees
• Distinguishing derived traits from ancestral traits
may be difficult because traits often become very
dissimilar.
• An outgroup is a lineage that is closely related to
an ingroup (the lineage of interest) but has
branched off from the ingroup below its base on
the evolutionary tree.
• Ancestral traits should be found not only in the
ingroup, but also in outgroups. Derived traits
would be found only in the ingroup.
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Steps in Reconstructing Phylogenies
• Molecular traits are also useful for constructing
phylogenies.
• The molecular traits most often used in the
construction of phylogenies are the structures of
nucleic acids (DNA and RNA) and proteins.
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Steps in Reconstructing Phylogenies
• Comparing the primary structure of proteins:
 Homologous proteins are obtained and the
number of amino acids that have changed since
the lineages diverged from a common ancestor
are determined.
• DNA base sequences:
 Chloroplast DNA (cpDNA) and mitochondrial
DNA (mtDNA) have been used extensively to
study evolutionary relationships.
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Steps in Reconstructing Phylogenies
• Relationships between apes and humans were
investigated by sequencing a hemoglobin
pseudogene (a nonfunctional DNA sequence
derived early in primate evolution by duplication of
a hemoglobin gene).
• The analysis indicated that chimpanzees and
humans share a more recent common ancestor
with each other than they do with gorillas.
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Reconstructing a Simple Phylogeny
• A simple phylogeny can be constructed using
eight vertebrates species: lamprey, perch, pigeon,
chimpanzee, salamander, lizard, mouse, and
crocodile.
• The example assumes initially that a derived trait
evolved only once during the evolution of the
animals and that no derived traits were lost from
any of the descendant groups.
• Traits that are either present (+) or absent (–) are
used in the phylogeny.
Table 25.1 Eight Vertebrates Ordered According to Unique Shared Derived Traits (Part 1)
Table 25.1 Eight Vertebrates Ordered According to Unique Shared Derived Traits (Part 2)
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Reconstructing a Simple Phylogeny
• Examining the table reveals that the chimpanzee
and mouse share two traits: mammary glands
and fur.
• Since mammary glands and fur are absent in the
other animals, the traits can be attributed to a
common ancestor of the mouse and
chimpanzee.
• Using similar reasoning, the remaining traits are
assigned to common ancestors of the other
animals until the phylogenetic tree is complete.
• Note that the group that does not have any
derived traits (the lamprey) is designated as an
outgroup.
Figure 25.5 A Probable Phylogeny of Eight Vertebrates
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Reconstructing a Simple Phylogeny
• The example phylogeny was simplified by the
assumption that derived traits appear only once
in a lineage and were never lost after they
appeared.
• If a snake were included in the group of animals
used in the phylogeny, the assumption that traits
are never lost would be violated.
• Lizards, which have limbs and claws, are the
ancestors of snakes, but these structures have
been lost in the snake.
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Reconstructing a Simple Phylogeny
• Systematists use several methods to sort out the
complexities of phylogenetic relationships.
• The most widely used method is the parsimony
principle.
• This principle states that one should prefer the
simplest hypothesis that explains the observed
data.
• In reconstruction of phylogenies, this means
minimizing the number of evolutionary changes
that need to be assumed over all characters in all
groups in the tree.
• In other words, the best hypothesis is one that
requires fewest homoplasies.
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Reconstructing a Simple Phylogeny
• The maximum likelihood method is used
primarily for phylogenies based on molecular data
and requires complex computer programs.
• Determining the most likely phylogeny for a given
group can be difficult. For example, there are
34,459,425 possible phylogenetic trees for a
lineage of only 11 species.
• A consensus tree is the outcome of merging
multiple likely phylogenetic trees of approximately
equal length. In a consensus tree, groups whose
relationships differ among the trees form nodes
with more than two branches.
Figure 25.8 Phylogeny and Classification (Part 1)
Figure 25.8 Phylogeny and Classification (Part 2)
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Biological Classification and
Evolutionary Relationships
• The traditional class Reptilia is paraphyletic
because it does not include all descendants of its
common ancestor; birds are excluded.
• This emphasizes that birds have evolved unique
derived traits since they separated from reptiles,
and are thus a distinct grade.
• The current tendency is to change classifications
to eliminate paraphyletic groups; however, some
of the familiar taxonomic categories (such as
reptiles) are paraphyletic and will probably remain
in use.