Lecture 11.

The
Contributions of
Systematics To
Evolutionary Biology
Darius Noel C. Minoza
Department of Biological Sciences
College of Arts and Sciences
Visayas State University
Introduction
•Common Misconception
•Classification of the living world is virtually
complete
•We can use any of a range of books to identify
and classify any common organism
Introduction
•However,
•Careful comparison of
several texts reveals
differences in treatments
•Examples
• Family placement of a species (Durian:
Bombacaceae, Malvaceae)
Introduction
•Hence,
•Taxonomists have been accused of:
✔Pervert desire to confuse things
✔Unscientific
✔Subjective
✔Lack of better things to do
Introduction
•Actually,
•Reflects ongoing differences in opinions
concerning the most appropriate
classification
•Continuing acquisition of additional
knowledge
•Active intellectual exchange and healthy
scientific debate
So what is TAXONOMY?
•Greek taxis (arrangement), nomos (law)
•Theory and practice of classifying
organisms (Mayr et al.)
•Recognizing, naming and classifying
organisms (Gullan & Cranston, 2000)
•How does it differ from systematics?
and what about
SYSTEMATICS?
•Latinized Greek word systema as applied to
systems of classification developed by early
naturalists especially Linnaeus (1735)
and what about SYSTEMATICS
•Scientific study of the kinds and diversity of
organisms and of any and all relationships
among them (Simpson, 1961)
•Study of the kinds and diversity of
organisms and their interrelationships
(Gullan & Cranston, 2000)
•Science of the diversity of organisms (Mayr,
1969)
Important aspects of the
definitions
•Organism
•Science/Scientific study
•Kinds
•Diversity
•Relationships
•Theory
•Practice
•Classifying
Classification
•Ordering of organisms into groups or
sets on the basis of relationships
•Ordering of populations and groups of
populations at all levels by inductive
procedures
•Most important aspects:
•Grouping
•Ranking
Identification
•Placing of individuals by deductive
procedures into previously established
classes
Nomenclature
•Application of distinctive names to each
of the groups recognized in a
classification system
Taxon
•A group of real organisms recognized as
a formal unit at any level of a hierarchic
classification
•”A taxonomic group of any rank that is
sufficiently distinct to be worthy of being
assigned to a definite category
Taxon: Two Important
Aspects
•Concrete zoological objects (organisms)
•Formally recognized by a taxonomist
•NOTE: races, biotypes, isolates, forms
become taxa only when they are
formally recognized as species or
subspecies
Taxonomic Categories
•Original Linnean hierarchy
•Only five within the animal kingdom
•Classis
•Ordo
•Genus
•Species
•Varietas (Linnaeus’ optional category for various
types of infraspecific variants; now discarded in
zoology)
Taxonomic Categories
•Linnaean hierarchy •Present standard
• Regnum • Kingdom
• Phylum (=Division)
• Classis • Class
• Ordo • Order
• Family
• Genus • Genus
• Species • Species
• Varietas
Additional Taxonomic
Categories
•Empire
•Domain
•Tribe (Between family and genus)
•Cohort (Between class and order in
some vertebrate groups but between
order and family among mites)
More detailed taxonomic
categories
•Super
•Sub
•Infra
•Informal categories
•Series
•Clade (Cladus)
•League (Legio)
•Section (Sectio)
More detailed taxonomic
categories
•Below the species, the only accepted
category in zoology is the subspecies
•In botany, additional infraspecific
categories aside from subspecies are:
•Variety (including cultivar, pathovar)
•Forma
Acceptable Abbreviations
•Genus – gen. or g.
•Species (singular) – sp.
•Species (plural) – spp.
•Subspecies (singular) – ssp. or subsp.
•Subspecies (plural) – sspp. or subspp. for
plants
•Variety – var. (cultivar – cv.; pathovar – pv.)
•Forma – f.
Classification of the Oriental
Weaver Ant
Kingdom Animalia
Subkingdom
Phylum Arthropoda
Subphylum Mandibulata
Superclass Hexapoda
Class Insecta
Subclass Pterygota
Infraclass Neuroptera
Classification of the Oriental
Weaver Ant
Supercohort
Cohort
Infracohort
Superoder Hymenopteroidea
Order Hymenoptera
Suborder Apocrita
Infraorder
Epifamily
Classification of the Oriental
Weaver Ant
Superfamily Vespoidea
Family Formicidae
Subfamily Formicinae
Infrafamily
Supertribe
Tribe Formicini
Subtribe Formicina
Infratribe
Classification of the Oriental
Weaver Ant
Genus Oecophylla
Subgenus Oecophylla
Species smaragdina
Subspecies smaragdina
Full scientific name
Oecophylla (Oecophylla) smaragdina smaragdina
(Fabricius)
Phylogenetics
•the unravelling of evolutionary history
•controversial area of biology
•morphology – provided much of the data upon
which relationships of organisms were
reconstructed
•some of the “ambiguity” and lack of clarity
regarding phylogeny of many groups
•blamed on inherent deficiencies of phylogenetic
information in morphological characters
Phylogenetics
•Other data sources explored
•Cytogenetic – mainly chromosome numbers
•Allozymes, isozymes (relies on differences in
electrophoretic mobility of proteins),
biochemical
•Nucleic acid sequence (DNA, RNA), data
(molecular)
Phylogenetics
•Increased use of sequence data (molecular)
•Attempts to resolve some unanswered
questions (esp. higher relationships of
insects etc.)
•Appropriate choice of taxa and genes,
molecules are providing resolution of some
phylogenetic questions that morphology has
been unable to answer
Phylogenetics
•Preferred approach to estimating
phylogenies:
1. Holistic
-Use data from as many sources as
possible
-Be constantly aware that:
-Not all similarities are equally informative in
showing phylogenetic patterns
Phylogenetic methods
•Methods that attempt to recover or
reconstruct the pattern produced by
phylogenetic history
•Rely on observations of living organisms and
fossils
Phylogenetic Methods
•Phenetics
•Cladistics
•Evolutionary Systematics
Phenetics
•Also known as traditional
taxonomy
•Quantitative or numerical
method for distinguishing
species based on
morphological grounds
•Based on overall
morphology, especially
quantitative data from
morphometric studies
Examples (Bivariate plot)
Examples (GM- Geometric
morphometrics)
Cladistics
•Quantitative method that
uses shared character to
create hypothesis
•Rely on assumptions
about ancestral
relationships as well as
current data
Consider these taxa

•Monophyletic
-Descendants of a
single common
ancestor
Consider these taxa

•Paraphyletic
-Do not include all
descendants of a
single common
ancestor
Consider these taxa

•Polyphyletic
-Do not share
common
ancestor and have
multiple origins
Evolutionary Systematics
•Also referred to as Classical Evolutionary
Systematics/Taxonomy, Evolutionary
Taxonomy
•Uses estimates of derived similarity
•UNLIKE Cladistics
✔Estimates of the amount of evolutionary change are
included with the branching pattern in order to
produce a classification
Evolutionary Systematics
•Emphasizes distinctness
•Grants higher taxonomic status to taxa
separated by “gaps”
•May be due to accelerated morphological
innovation in a lineage and/or extinction of
intermediate linking forms
Phylogenetic Methods
•The case of the ants
•Highly specialized
•Many unique features
•Looks very different from nearest relatives
•Frequently given superfamily rank (Formicoidea)
within Hymenoptera (evolutionary taxonomy)
Phylogenetic Methods
•The case of the ants
•Phylogenetic study indicates
•Family Formicidae in the Superfamily Vespoidea (a
group of solitary,semi-social and social wasps
Phylogenetics
•Paraphyletic groups – avoid if possible
because their only defining features are
ancestral characters shared with other
indirect relatives
•Thus, absence of wings in paraphyletic
apterygotes is an ancestral feature shared
by many other invertebrates
Phylogenetics
•Polyphyletic groups – their mixed ancestry
means that such groups are biologically
uninformative
•Such taxa are artificial and should never be
included in any classification
Phylogenetics
•Current classification of most organisms
1. Mix all three practices
2. Most orders based on groups (taxa) with
most distinctive morphology
3. Such morphologically distinct groups are not
necessarily monophyletic
Phylogenetics
•Current classification of most organisms
•Some are almost certainly paraphyletic
•However, it is unlikely that any higher-level
groups are polyphyletic
Phylogenetics
•Colloquial terms
•Flies – cover disparate groupings from
mayflies (Ephemeroptera) to true flies
(Diptera)
•Bugs - ! ! !
Phylogenetics
•Refinements continue
•Classification: should reflect our developing
understanding of phylogeny
•Current classification – combination of
traditional views variably reconciles with
phylogeny
Three Schools of Taxonomy
•Consider how the three schools of taxonomy
will classify groups of animals that were first
taught to us as kids -
•Four-legged (tetrapods), amniotic
vertebrates (mammals, birds, reptiles)
Classification of Amniote
Tetrapods (Evolutionary Taxonomy)
Class Mammalia
Class Reptilia
Subclass Testudines (turtles)
Subclass Squamata (lizards, snakes, crocodiles)
Class Aves
Classification of Amniote
Tetrapods (Phenetics)
•Class Mammalia
•Class Reptilia
•Subclass Testudines
•Subclass Squamata
•Class Aves
Classification of Amniote
Tetrapods (Cladistics)
•Class Mammalia
•Class Reptilia
•Subclass Testudines
•Subclass Sauria
•Infraclass Squamata (lizards, snakes)
•Infraclass Archosauria (crocodiles, birds)
• Order Crocodilia
• Order Aves
 Naming based on current data
Naming based on past data

Reptiles
Sauropsida
Three Schools of
Taxonomy
•Note similar examples among insects and
many other groups of organisms
•More expected to be revealed by
•Molecular data
•More detailed morphological data
(ultrastructure)
Trees: What they are
•Cladogram – a tree-like diagram showing
hierarchic relationships, to depict relative
recency of such relationships, without
connoting degree of difference
•Phylogenetic trees or cladograms are
diagrammatic representations of
phylogenetic relationships
Cladogram
Trees: What they are
•Dendrogram – a tree-like diagram intending
to show both relationships (branching or
“cladogenesis”) and degree of difference
(divergence or “anagenesis”) (evolutionary
taxonomy)
Trees: What they are
•Phenogram – a diagram representing
hierarchic relationships obtained by applying
phenetic techniques, whereby data are
clustered at levels (phenetics)
Trees: What they are
•Cladograms result from analyses of sets of
data – morphological and or molecular
•Can only be as good as the available data
could support
•Therefore, cladograms are diagrams
depicting hypotheses of relationships
Trees: terminologies
•Character – a feature showing a variation(s)
that define a group
•Character-state – one of the various
conditions of a feature (character) obtained
across a group of taxa
•Character-state tree – graphic
representation of the coding of a character
Trees: terminologies
•Apomorphy- advanced or derived character;
a group-defining character (adj. apomorphic)
•Pleisomorphy- “primitive” character;
ancestral character; not group defining at the
level at which it is being observed; the
quality being primitive (adj. pleisomorphic)
Trees: terminologies
•Synapomorphy- shared derived character
•Symplesiomorphy- shared primitive
character
Figure 4.5, pg. 116
Trees: What they are and
how they are constructed
•Parsimony
–seeks the simplest explanation that requires the
least amount of change (fewest steps)
•Most parsimonious tree (MPT) – for a given
data set, tree(s) of minimum length as
computed with parsimony as main criterion
•Consensus tree – depicts “compromise” of all
MPTs
Parsimony
Parsimony
Parsimony
Parsimony
Parsimony
Trees: What they are and
how they are constructed
•Data matrix- information in tabular form on
characters (columns) for a set of taxa (rows)
•Terminal taxon – taxon for which data are
actually coded in a cladistic analysis
•Hypothetical ancestor – node in a
cladogram representing the deduced set of
attributes for two or more terminal taxa
Data Matrix
Data Matrix
Trees: How they are
constructed
•Selection of ingroup and outgroup taxa
1. For rooting of trees
2. Character polarity
i. Character analysis
ii. Construction of data matrix
iii. Coding methods
iv. For molecular data – alignment of nucleic
acid sequence
Trees: How many trees?
•Number of possible rooted bifurcating trees
for 1 to 22 taxa
-Can range from 1 to 13,113,070,
457,687,988,603,440,625
-Now possible through available
software/programs
Trees
Trees
Trees
Types of Phylogenetic
Analysis Methods
1. Phenetic
i. UPGMA (Demonstration)
ii. Fitch-Margoliash method
iii. Neighbor joining method
2. Cladistic
iv. Parsimony
v. Maximum Likelihood
Distance Methods
•Optimal tree is generated by calculating an
estimate of the evolutionary distance between all
pairs of sequences first
Example
Example (A and B)
Example (A and C)
Example (A and D)
Example (A and E)
Example (A and F)
Example
Example
How to prove?
Let us try!

•Measure
distance
between
branch tips
Let us try!

•Count the
number
of nodes
between
species
Let us try!
•Compare
time to a
common
ancestor
Let us try!

•Compare
number of
shared
monophyletic
groups
Assessing Confidence Level
of Phylogenetic Trees
•Bootstrap Method
•Randomly generates new data sets from
the original set (1000 replicates is most
common)
•Computes the number of times that a
particular grouping (or branch) appeared
in the tree.
Sample Studies on
Phylogenetic Analysis
Sample Studies in
Phylogenetic Analysis
Samples studies on
Phylogenetic Analysis
Workflow in Phylogenetic
Analysis