Phylogeny
Systematics
Taxonomy
Ambiguity in everyday
names
Binomial
Genus
Specific epithet
Taxon
Phylogenic tree
Misclassification
Issue with Linnaean system
PhyloCode
Disadvantages
Chapter 26: Phylogeny and the Tree of Life
Evolutionary history of a species or a group of species
A practice focused on classifying organisms and determining their evolutionary
relationships; used to construct phylogenies; use data ranging from fossils to
molecules & genes to infer evolutionary relationships
26.1 Phylogenies Show Evolutionary Relationships
 Organisms share many characteristics because of common ancestry, since an
organism likely shares many of its genes, metabolic pathways, & structural
proteins with its close relatives
 How organisms are named & classified
Binomial Nomenclature
 Common, everyday names for organisms may refer to >1 species, and
sometimes they don’t accurately reflect the kind of organism they signify
 Two-part format of the scientific name; came up by Carolus Linnaeus
 First part of the name to which the species belongs
 Unique for each species within the genus
 First letter of genus is capitalized & entire binomial is italicized
Hierarchical Classification
 Linnaeus also grouped species into a hierarchy of increasingly inclusive
categories
 Species that appear to be closely related are grouped into the same genus
o Ex: leopard, African lion, tiger, & jaguar belong in same genus
 Related genera are place into the same family
 Related families are placed into orders
 Related orders are placed into classes
 Related classes are placed into kingdoms
 Related kingdoms are placed into domains
 Did King Phillip Come Over For Great Sex?
 Named taxonomic unit at any level of the hierarchy
 Characters useful for classifying one group of organisms may not be
appropriate for other organisms; larger categories often aren’t comparable
between lineages
 The placement of species into orders, classes, phyla, kingdoms, & domains
don’t necessarily reflect evolutionary history
Linking Classification and Phylogeny
 Branching diagram that can be used to represent evolutionary history of a group
of organisms
 The branching pattern often matches how taxonomists have classified groups of
organisms nested within more inclusive groups
 But sometimes, taxonomists have placed a species within a genus to which it is
not most closely related.
 One reason for misclassification may be that over the course of evolution, a
species has lost a key feature shared by its relatives
 Doesn’t tell us anything about the groups’ evolutionary relationships to one
another
 Such difficulties in aligning Linnaean classification with phylogeny have led
proposals that classification be based entirely on evolutionary relationships
 Only names groups that include a common ancestors & all of its descendants
 Changes the way taxa are defined, but groups would no longer have ranks
attached to them, like family or class.
 Some commonly recognized groups would become part of other groups
previously of the same rank
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for both classification
systems
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Ex: because birds evolved from a group of reptiles, Aves would be considered a
subgroup of Reptilia
Phylogenetic tree reps a hypothesis about evolutionary relationships
These relationships often are depicted as a series of dichotomies, two-way
branch points
Each branch point reps the divergence of 2 evolutionary lineages from a
common ancestor
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Key points about
phylogenetic trees
Practical applications
Ex: maize (corn)
Ex: what is the species identity of
food being sold as whale meat?
Taxa B & C are sister taxa,
groups of organisms that
share an immediate common
ancestor, & thus are each
other’s closest relatives
This tree is rooted- a branch
point within the tree reps the
most recent common
ancestor of all taxa in the
tree
Basal taxon- lineage that
diverges early in the history
of a group & lies on a branch
that originates near the common ancestor of the group (like G lies on a branch
that originates near the common ancestor of the group)
 Lineage leading to taxa D – F includes a polytomy- a branch point from which
>2 descendant groups emerge; signifies that evolutionary relationships among
the taxa are not yet clear
What We Can & Can’t Learn From Phylogenetic Trees
1. They’re intended to show patterns of descent, not phenotypic similarity
a. Although closely related organisms often resemble one another due to
common ancestry, the may not if their lineages have evolved at
different rates
i. Ex: even though crocodiles are more closely related to birds
than lizards, they look more like lizards because morphology
has changed dramatically the bird lineage
2. The sequence of branching in a tree doesn’t necessarily determine the actual
(absolute) ages of the particular species
a. Doesn’t show when a species (e.g. wolf) evolved more recently than
another (e.g. otter)
b. Shows only that the most recent common ancestor of the two species
lived before the most recent common ancestor of the wolf & coyote (2).
c. To indicate when wolves & otters evolved, the tree would need to
include additional divergences in each evolutionary lineage & the dates
of when those splits occurred
d. Usually, if unspecified, the line length is not proportional to time
3. Don’t assume that a taxon on a phylogenetic tree evolved from the taxon next
to it
Adding Phylogenies
 form a phylogeny of maize based on DNA data, 2 species of wild grasses may
be maize’s closest living relatives. These 2 relatives may be useful as reservoirs
of beneficial alleles that can be transferred so cultivated maize by crossbreeding or genetic engineering
 another use of phylogenetic trees was used to investigate whether whale meat
samples had been illegally harvested from whale species protected under law
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Homologies
Ex: mammals
Ex: molecular scale
Similarity in ancestry
Ex: Hawaiian flowers
Analogy
Convergent evolution
Ex: mole-like animals
Distinguishing between
homology & analogy
Ex: bats & birds
Scientists bought 13 samples of whale meat from Japanese fish markets. They
sequenced a specific part of the mitochondrial DNA from each sample &
compared their results with the comparable DNA sequence from known whale
species
 To identify the species of the sample, a phylogenetic tree was constructed,
showing patterns of relatedness among DNA sequences rather than among taxa
 The phylogeny indicated that meat from humpack, fin, & Minke whaels caught
in the northern hemisphere was being sold illegally in some Japanese fish
markets
26.2 Phylogenies are Inferred from Morphological & Molecular Data
 To infer phylogeny, info about morphology, genes, & biochemistry of the
organisms, which are all features that result from common ancestry, of which
these features reflect evolutionary relationships
Morphological and Molecular Homologies
 Phenotypic & genetic similarities due to shared ancestry
 Similarity in number & arrangement of bones in the forelimbs of mammals is
due to their descent from a common ancestor
 Genes or other DNA sequences are homologies if they’re descended from
sequences carried by a common ancestor
 Organisms that share very similar morphologies or similar DNA sequences are
more likely to be more closely related than organisms with vastly different
structures or sequences
 But sometimes, morphological divergence between related species can be great
& their genetic divergence small
 These species vary dramatically in appearance throughout the islands, but their
genes are very similar
 Molecular data can be used to estimate divergence times
Sorting Homology from Analogy
 Similarity due to convergent evolution
 Similar environmental pressures & natural selection produce similar
(analogous) adaptations in organisms from different evolutionary lineages
 2 mole like animals are very similar in external appearance, but their internal
anatomy, physiology, & reproductive systems are very dissimilar: Australian
mole are marsupials (their young complete their embryonic development in a
pouch on the outside of the mother’s body), while North American moles are
eutherians (their young complete their embryonic development in the uterus
within the mother’s body)
 Genetic comparisons & the fossil record show that the common ancestor of
these moles lived 140 million years ago, about the time when marsupial &
eutherian mammals diverged
 This common ancestor & most of its descendants weren’t mole-like, but
analogous characteristics evolved independently in these 2 mole lineages
 Distinguishing between homology & analogy is critical in reconstructing
phylogenies
 Both birds & bats have adaptations that enable flight, which implies that bats
are more closely related to birds than they are to cats, which can’t fly. But a
closer examination reveals that a bat’s wing is more similar to the forelimbs of
cats & other mammals than to a bird’s wing
 Bats & birds descended from a common tetrapod ancestry that lived ~320
million years ago. This common ancestor couldn’t fly. Although the skeletal
systems of bats & birds are homologous, their wings aren’t
 Fossil evidence documents that bat & bird wings arose independently from the
Homoplasies
Complexity of comparisons
Ex: skulls
Ex: gene level
After sequencing molecules
Deceptive similarities
Solutions
Distinguishing between
analogy & homology
Cladistics
Forelimbs of different tetrapod ancestors
A bat’s wing is analogous, not homologous to a bird’s wing
Analogous structures that arose independently
The complexity of the characters being compared helps us distinguish between
homology & analogy as well. The more elements that are similar in the 2
complex structures, the more likely it is that they evolved from a common
ancestor
 Skulls of adult human & adult chimpanzee both consist of many bones fused
together. The compositions of the skulls match almost perfectly. It is unlikely
that such complex structures that match in so many details have separate
origins. The genes involved in the development of both skulls were inherited
from a common ancestor
 If genes in 2 organisms share many portions of their nucleotide sequences, it’s
likely that the genes are homologous
Evaluating Molecular Homologies
 Aligning comparable sequences from the species being studied. If the
sequences differ only at a few sites, the species are likely very closely related,
while distantly related species have different bases at many sites and different
lengths, because insertions & deletions accumulate over long periods of time
 Two sequences could appear very similar, i.e. the first base of one sequence has
been deleted, shifting the sequence back one nucleotide
 Computer programs have been constructed that estimate the best way to align
comparable DNA segments of differing lengths
 These molecular comparisons reveal
that many differences have
accumulated in the comparable
genes of Australian & North
America mole.
 The differences indicate that their
lineages have diverged a lot since
their common ancestor, so they’re
not closely related
 But the high degree of gene
sequence similarity among the
silverswords indicates that they’re
very closely related, despite their
morphological differences
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Two sequences that resemble each other at many points along their length most
likely are homologous, but in organisms that don’t appear closely related, the
bases may simply be coincidentally similar to another sequence, (molecular
homoplasies)
 Discipline that uses data from DNA & other molecules to determine
evolutionary relationships
26.3 Shared Characters are Used to Construct Phylogenetic Trees
 Only homology reflects evolutionary history
Cladistics
 Common ancestry is the primary criterion used to classify organisms
 Biologists attempt to place species into groups called clades, each of which
includes an ancestral species & all of its descendants
Nested
Ex: cats & dogs
Monophyletic
Paraphyletic
Polyphyletic
Shared ancestral character
Ex: mammals & backbones
Shared derived character
Ex: mammals & hair
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Clades are nested within larger clades
The cat group (Felidae) represents a clade within a larger clade (Carnivora) that
also includes the dog group (Canine)
 A toxon is equivalent to a clade only if it is monophyletic- consists of an
ancestra species and all of its descendants
 Consists of ancestra species and some, but not all of its descendants
 Includes taxa with different ancestors
Shared Ancestral & Shared Derived Characters
 Originated in an ancestor of the taxon
 All mammals have backbones, but a backbone doesn’t distinguish mammals
from other vertebrates (since they all have backbones).
 An evolutionary novelty unique to a clade
 Hair is a character shared by all mammals, but not found in their ancestors.
 Whether a particular character is considered ancestra or derived
Inferring Phylogenies Using Derived Characters
 It is possible to determine the clade in which each shared derived character first
appeared and to use that info to infer evolutionary relationships
 A species or group of species from an evolutionary lineage that’s known to
have diverged before the lineage that includes the species we are studying (the
ingroup)
 A suitable outgroup can be based on evidence from morphology, paleontology,
embryonic, development, & gene sequences
 By comparing members of the ingroup with each other & with the outgroup, we
can determine which characters were derived at the various branch points of
vertebrate evolution
 Based on which characteristics are present in the members, we can identify the
branch point in the clade
Proportional branch lengths
Phylogenetic trees with Proportional Branch Lengths
 So far, the lengths of the branches do not indicate the degree of evolutionary
change in each lineage. The chronology represented by the branching pattern is
relative rather than absolute
 The branch length reflects the number of changes that have taken place in a
particular DNA sequence in that lineage.
 Branch length reflects the time since certain members diverged from a common
ancestor
Equal spans of time
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All different lineages that descend from a common ancestor have survived for
the same number of years
These equal spans of chronological time can be represented in a phylogenetic
tree because whose branches are proportional to time
This tree draws on fossil data to place branch points in context of geological
time