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
 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.
Taxonomy
 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.
Taxonomy
 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.
Taxonomy
 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.
Linnaeus and Classification
 Carolus Linnaeus designed our hierarchical
classification scheme.
 Kingdom
 Phylum
 Class
 Order
 Family
 Genus
 Species
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.
Linnaeus and Classification
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
Linnaeus and Classification
 A trinomial name
includes a
subspecies epithet.
 Ensatina escholtzii
escholtzii
 E. e. klauberi
Species
 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.
Species
 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.
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.
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?
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.
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.
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.
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.
Phylogeny
 Phylogenies are inferred by identifying organismal
features, characters, that vary among species.
 Morphological
 Chromosomal
 Molecular
 Behavioral or ecological
Phylogeny
 Shared characters that result from common ancestry
are homologous.
Sorting Homology from
Analogy
 A potential misconception in constructing a phylogeny
is similarity due to convergent evolution, called
analogy, rather than shared ancestry.
Sorting Homology from
Analogy
 Convergent evolution
occurs when similar
environmental
pressures and natural
selection produce
similar (analogous)
adaptations in
organisms from
different evolutionary
lineages.
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.
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.
Phylogeny
 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.
Phylogeny
 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.
Phylogeny
 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.
Phylogeny
 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.
Phylogeny
 The nested hierarchy of clades can be
represented as a cladogram that is based
on shared synapomorphies.
Phylogeny
 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.
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.
Taxonomy
 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.
Cladistics
 A valid clade is
monophyletic.
 Signifying that it
consists of the
ancestor species
and all its
descendants.
Cladistics
 A paraphyletic
clade is a grouping
that consists of an
ancestral species
and some, but not
all, of the
descendants.
Cladistics
 A polyphyletic
grouping includes
numerous types of
organisms that lack
a common ancestor.
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.
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.
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.
 The terms “primitive,” “advanced,” “specialized” and
“generalized” are used for specific characteristics and not for
groups as a whole.
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.
Parsimony
 Among phylogenetic hypotheses the most
parsimonious tree is the one that requires the fewest
evolutionary events to have occurred in the form of
shared derived characters.
 Occam’s Razor
Parsimony
 The principle of
maximum
likelihood states
that, given certain
rules about how DNA
changes over time, a
tree can be found
that reflects the most
likely sequence of
evolutionary events.
Phylogenetic Trees as Hypotheses
 The best hypotheses for phylogenetic trees are those
that fit the most data: morphological, molecular, and
fossil.
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.
Major Divisions of Life
 Aristotle’s two kingdom system included plants
and animals.
 One-celled organisms became a problem
 Haeckel (1866) proposed Protista for singlecelled organisms.
 R.H. Whittaker (1969) proposed a five-kingdom
system to distinguish prokaryotes and fungi.
Major Divisions of
Life
 Woese, Kandler and Wheelis
(1990) proposed three
monophyletic domains above
kingdom level—Eucarya,
Bacteria and Archaea—based
on ribosomal RNA sequences.
Major Divisions 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.
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
Major Subdivisions of the Animal
Kingdom
 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
 Division B (Deuterostomia): Deuterostome
characteristics
 phyla Phoronida, Ectoprocta, Chaetognatha,
Brachiopoda, Echinodermata, Hemichordata,
Chordata
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