Transcript Table of Contents

Reconstructing and Using
Phylogenies
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Reconstructing and Using Phylogenies
• Phylogenetic Trees
• Steps in Reconstructing Phylogenies
• Reconstructing a Simple Phylogeny
• Biological Classification and Evolutionary
Relationships
• Phylogenetic Trees Have Many Uses
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Phylogenetic Trees
• Systematics, the scientific study of the diversity
of organisms, reveals the evolutionary
relationships between organisms.
• Taxonomy, a subdivision of systematics, is the
theory and practice of classifying organisms.
• Information about evolutionary relationships can
be of great value.
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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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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
• The distinction between ancestral and derived
traits is very important in reconstructing
phylogenies.
• A particular trait may be ancestral or derived,
depending on the group of interest.
• In a phylogeny of rodents, continuously growing
incisors are an ancestral trait because all rodents
have them.
• In a phylogeny of mammals, continuously growing
incisors are a derived trait unique to the rodents.
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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.
Figure 25.3 Homologous Structures Derived from Leaves
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Steps in Reconstructing Phylogenies
Creating a phylogeny:
1. Select a group of organisms to classify (the
ingroup) and an appropriate outgroup.
2. Choose the characters that will be used in
the analysis and identify the possible forms
(traits) of the character.
3. Determine the ancestral and derived traits.
4. Distinguish homologous from homoplastic
traits.
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Steps in Reconstructing Phylogenies
• Systematists use many characters to reconstruct
phylogenies, including physiological, behavioral,
molecular, and structural characters of both living
and fossil organisms.
• The more traits that are measured, the more
inferred phylogenies should converge on one
another and on the actual evolutionary pattern.
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Steps in Reconstructing Phylogenies
• An important source of information for systematists
is morphology, which describes the sizes and
shapes of body parts.
• Early developmental stages of many organisms
reveal similarities to other organisms, but these
similarities may be lost in adulthood.
• The notochord of larval sea squirts is an example.
• The fossil record provides much morphological
data and reveals when lineages diverged.
Figure 25.4 A Larva Reveals Evolutionary Relationships
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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.
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Biological Classification and
Evolutionary Relationships
• The system of biological classification used today
was developed by Carolus Linnaeus in 1758.
• His two-name system is referred to as binomial
nomenclature.
• The first name identifies the genus; the other name
identifies the species.
• Using this system, scientists throughout the world
can refer unambiguously to the same organisms by
the same names.
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Biological Classification and
Evolutionary Relationships
• The name of the taxonomist who first proposed
the species is often added to the name.
• Homo sapiens Linnaeus is the name of the
modern human species.
• The generic name is always capitalized, whereas
the specific name is not, and both names are
italicized.
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Biological Classification and
Evolutionary Relationships
• Abbreviations:
 For references to more than one species in a
genus, the abbreviation “spp.” is used in place of
the names of all the species (Drosophila spp.
means more than one species of the genus
Drosophila).
 If the identity of the species is uncertain, the
abbreviation “sp.” may be used (Drosophila sp.).
 If an organism is referred to numerous times, the
genus is abbreviated (D. melanogaster for
Drosophila melanogaster).
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Biological Classification and
Evolutionary Relationships
• Any group of organisms that is treated as a unit is
called a taxon (plural, taxa).
• In the Linnaean system species and genera are
further grouped into higher taxonomic categories.
• The category above genus is family. Family
names end with the suffix “-idae” for animals and
“-aceae” for plants.
• Families in turn are grouped into orders, classes,
phyla, and kingdoms.
Figure 25.6 Hierarchy in the Linnaean System
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Biological Classification and
Evolutionary Relationships
• Biological classification systems and unique
names are important for several reasons.
 They are aids to memory and precise
communication.
 They improve the ability to infer relationships
among organisms, and are also useful for
predictions in scientific investigations.
 The discovery of precursors of cortisone in
some yam species of the genus Dioscorea
stimulated a successful search for higher
concentrations of the drug in other species
of Dioscorea.
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Biological Classification and
Evolutionary Relationships
• Most taxonomists today believe that biological
classification systems should reflect evolutionary
relationships and that taxonomic units should be
monophyletic.
• A monophyletic group (or clade) contains all the
descendants of a particular ancestor and no other
organisms.
• A polyphyletic taxon contains members with
more than one recent common ancestor.
• A paraphyletic group contains some, but not all,
of the descendants of a particular ancestor.
Figure 25.7 Monophyletic, Polyphyletic, and Paraphyletic Taxa
Figure 25.8 Phylogeny and Classification (Part 1)
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Phylogenetic Trees Have Many Uses
• Studies of characiform fishes illustrate how
phylogenetic analyses can help determine when
lineages split.
• The 1,400 species of these freshwater fishes vary
greatly in size, shape, and diet.
• Closely related species have been found on both
sides of the Atlantic Ocean.
• Genetic differences in the rRNA of both groups
are great enough to be consistent with a split
caused by the separation of Africa from South
America, about 90 million years ago.
Figure 25.10 Dating Lineage Splits
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Phylogenetic Trees Have Many Uses
• A plausible phylogeny enables biologists to
answer a variety of questions about the history of
the group.
• For example, molecular and geological data have
been used to reconstruct a phylogeny of Lake
Victoria’s cichlid fishes.
• Initially, the radiation that produced more than 500
species was assumed to have occurred over a
period of about 750,000 years.
• Recent geological evidence suggests, however,
that the lake dried up completely between 15,600
and 14,700 years ago.
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Phylogenetic Trees Have Many Uses
• Biologists determined that the hundreds of diverse
cichlids could not have evolved in such a short time.
• A new phylogeny of the cichlids of Lake Victoria and
other lakes in the region was developed using 300
mtDNA sequences.
• This phylogeny suggested that the ancestors of the
Lake Victoria cichlids came from the much older lake
Kivu.
• The phylogeny also indicated that some of the
cichlid lineages found only in Lake Victoria split at
least 100,000 years ago, suggesting that the lake
did not completely dry up about 15,000 years ago.
Figure 25.11 Origins of the Cichlid Fishes of Lake Victoria (Part 1)
Figure 25.11 Origins of the Cichlid Fishes of Lake Victoria (Part 2)