An Introduction

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Nomenclature, Classification, Taxonomy,
Phylogenetics, Systematics,
An Introduction
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Nomenclature, Classification, Taxonomy,
Phylogenetics, Systematics,

• Nomenclature the naming of organisms
• Classification the assignment of taxa to groups
  of organisms
• Taxonomy Nomenclature Classification
• Phylogenetics Evolutionary patterns
  relationships among organisms
• Systematics Taxonomy Phylogenetics

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Biodiversity
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Estimated Numbers of Described Extant
Species _________________________________________
__________________________________________________
_ Taxon Common Name Number of described
species Percentage of total () __________________
__________________________________________________
________________________ Bacteria true
bacteria 9021 0.5 Archaea archaebacteria 259
0.01 Bryophyta mosses 15000 0.9 Lycopodiophyt
a clubmosses 1275 0.07 Filicophyta
ferns 9500 0.5 Coniferophyta
conifers 601 0.03 Magnoliophyta flowering
plants 233885 13.4 Fungi fungi 100800 5.8 "
Porifera" sponges 10000 0.6 Cnidaria
cnidarians 9000 0.5 Rotifera rotifers 1800
0.1 Platyhelminthes flatworms 13780 0.8 Mollu
sca mollusks 117495 6.7 Annelida annelid
worms 14360 0.8 Nematoda nematodes 20000 1.1
Arachnida arachnids 74445 4.3 Crustacea crus
taceans 38839 2.2 Insecta insects 827875 47
.4 Echinodermata echinoderms 6000 0.3 Chondricht
hyes cartilaginous fishes 846 0.05 Actinopterygi
i ray-finned bony fishes 23712 1.4 Lissamphibia
amphibians 4975 0.3 Mammalia mammals 4496 0
.3 Chelonia turtles 290 0.02 Squamata lizards
and snakes 6850 0.4 Aves birds 9672 0.6 Oth
er 193075 11.0 ______________________________
__________________________________________________
____________ The total number of described
species is assumed to be 1,747,851. This figure,
and the numbers of species for taxa are taken
from LeCointre and Guyader (2001) and Cracraft
(2002). Lecointre, G. and H. Le Guyader. (2001).
Classification phylogenetique du vivant. Paris,
France Belin. Cracraft, C. (2002). The seven
great questions of systematic biology an
essential foundation for conservation and the
sustainable use of biodiversity. Annals of the
Missouri Botanical Garden, 89, 127-144.      
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Are these numbers right?
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Are these numbers right?
There are known knowns. These are things we know
that we know. There are known unknowns. That is
to say, there are things that we know we don't
know. But there are also unknown unknowns. There
are things we don't know we don't know. Donald
Rumsfeld
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About right
Vertebrates 50,841 Flowering Plants 233,885
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Slight underestimates
Arthropods 941,159 Fungi 100,800
30,000,000 species
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Huge underestimates
Bacteria 9,021 Archaea 259
?
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Total number of described species
1,747,851 Estimated range of total number of
species in the world 3,600,000 to 117,700,000
Erwin TL. 1982. Tropical forests Their richness
in Coleoptera and other arthropod species. The
Coleopterist Bulletin 36(1) 74-75. Lecointre G
Le Guyader H. 2001. Classification phylogenetique
du vivant. Belin Paris. Cracraft C. 2002. The
seven great questions of systematic biology an
essential foundation for conservation and the
sustainable use of biodiversity. Annals of the
Missouri Botanical Garden 89127-144.
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30 of all animals are beetles Q What could
one conclude as to the nature of the Creator from
a study of his creation? A An inordinate
fondness for beetles! J. B. S. Haldane quoted
in Hutchinson, G. E. 1959. Homage to Santa
Rosalia or Why are there so many kinds of
animals? Am. Nat. 93 145-159
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Objectives

• Reconstruct the correct genealogical ties among
  taxa
• Estimate the time of divergence between taxa
• Chronicle the sequence of events along
  evolutionary lineages

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What is a species?
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Species Concepts

• Species concepts are linked to views on how
  species originate.
• Early views were associated with a creationist
  view and were non-evolutionary.
• Today, some species concepts take evolution into
  account and attempt to address problems that are
  associated with biological entities that are
  evolving rather than immutable.

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Species Concepts

• There are many difficulties associated with the
  definition of species.
• Concepts that work well for some groups of
  organisms do not necessarily work for other
  organisms. Also, concepts that work well for
  extant species do not always apply to the case of
  fossil species.

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1. The Typological Species Concept

• Species are discrete, stable, and unchanging.
• The concept dates back to Aristotle.
• Linnaeus, who held a creationist view, defined a
  type (typus) specimen for each species and
  provided it with a Latin binomial.
• Individuals were assigned to a species if they
  had the characteristic morphology of the type.

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1. The Typological Species Concept
Most Typological Species Are Defined on the basis
on morphology morphospecies
Other Typological Species May be Defined on the
basis on serotype (serospecies), genotype
(genospecies)
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Clusiella albiflora
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nomenclature
Cabramatta New South Wales, 11101959 C. E.
Chadwick on trunk of dead Acacia fulcata.
Jaczyk, F. (1966). Ein neue Laemosaccus aus
New-Südwales (Australien). Annalen des
Naturhistorischen Museums in Wien 63 213-214.
Laemosaccus chadwicki Jaczyk
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1. The Typological Species Concept

• The basic Linnaean system remains in place today
  despite its non-evolutionary stance on the origin
  of species.
• The idea of morphospecies has practical value,
  especially for paleontologists that must rely
  heavily on morphological features.

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2. The Phenetic or Numerical Taxonomy Species
Concept

• A species is defined as a set of organisms that
  resemble one another and is distinct from other
  sets (no ideal type).
• A modern outgrowth of the typological concept.
  Evolutionary change is acknowledged, but
  phenotypic similarity is used for defining
  species.
• Numerical measurements of as many characters as
  possible are used to define clusters of organisms.

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4 legs
black
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3. The Biological Species Concept

• The biological species concept was proposed by
  Theodosius Dobzhansky in the 1930s. It has been
  elaborated on and reworked by Verne Grant, Julian
  Huxley and Ernst Mayr.
• Mayrs definition Species are groups of
  interbreeding natural populations that are
  reproductively isolated from other such groups.

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3. The good things about the Biological Species
Concept

• Species are cohesive gene pools that are held
  together by gene flow. Organisms in a species are
  defined by the exchange of genes, or at least by
  the potential to exchange genes. Gene flow is the
  glue that holds a species together.
• Biological species are reproductively isolated
  from each other. Reproductive isolation severes
  the ties that bind populations together and
  allows populations to diverge from each other.

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4. The bad things about the Biological Species
Concept

• The concept applies to sexually reproducing
  species and has no application to asexual
  organisms.
• The concept cannot readily be applied to fossils
  or museum specimens.
• Overlapping ranges and partial interbreeding
  render the biological species concept difficult
  to apply in practice.

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4. The Evolutionary/Phylogenetic Species
Concept (the theory)

• Promoted mainly by George Gaylord Simpson
• An evolutionary species is a lineage
  (ancestor-descendant populations), evolving
  separately from others and with its own unitary
  evolutionary role and historical tendencies.

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4. The Evolutionary/Phylogenetic Species
Concept (the practice)

• A species is the smallest diagnosable cluster of
  individual organisms within which there is a
  parental pattern of ancestry and descent.
• Species are not recognized strictly in terms of
  whether they can be diagnosed, i.e., whether or
  not they have unique morphological, biochemical,
  or physiological phenotypes.

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4. The good things about the Phylogenetic
Species Concept

• This species definition derives from an
  evolutionary perspective of ancestry and descent.
  
• It results in a natural hierarchical
  classification.

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Carolus Linnaeus (1707-1778)
The Linnaean hierarchy
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4. The bad things about the Phylogenetic
Species Concept

• The definition of species is arbitrary.

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Is there a perfect "species concept?
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5. The Intuitive Species Concept
Hard-core pornography I shall not today
attempt to define the kinds of material I
understand to be embraced within that shorthand
description, and perhaps I could never succeed in
intelligibly doing so. But I know it when I see
it. Justice Potter Stewart 1964 Jacobellis vs.
Ohio
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5. The Intuitive Species Concept
Nor shall I here discuss the various definitions
which have been given of the term species. No one
definition has as yet satisfied all naturalists
yet every naturalist knows vaguely what he means
when he speaks of a species. I look at the
term species as one arbitrarily given, for the
sake of convenience, to a group of organisms
resembling each other. Charles Darwin. 1859.
The Origin of Species.
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How construct a phylogeny?

• Look at a large number of characters
• Generate all possible trees
• Select the most parsimonious tree
• A maximum parsimony tree is an ad hoc hypothesis

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Types of characters

• Morphology
• Ultrastructure
• Embryology
• Ethology
• Paleontology
• Biochemistry
• Molecular Biology

Complex Genetics
Simple Genetics
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Advantages of Molecular Data 1. Molecular
entities are strictly heritable.
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Advantages of Molecular Data 2. The description
of molecular characters is unambiguous.
The third amino acid in the preproinsulin of the
rabbit (Oryctolagus cuniculus) is always serine,
and the homologous position in the preproinsulin
of the golden hamster (Mesocricetus auratus) is
always leucine. Morphological descriptions
frequently contain such ambiguous modifiers as
"thin," "reduced," "slightly elongated,"
"partially enclosed," and "somewhat flattened."
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Advantages of Molecular Data 3. There is some
regularity to the evolution of molecular
traits.
e.g., transitions occur more frequently than
transversions, functional parts evolve slower
than nonfunctional parts.
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Advantages of Molecular Data 4. Molecular data
are amenable to quantitative treatment.
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Advantages of Molecular Data 5. Homology
assessment is easier than with morphological
traits.
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Advantages of Molecular Data 6. Molecular data
are robust to evolutionary distance.
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Advantages of Molecular Data 7. Molecular data
are abundant.
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Evolutionary relationships are illustrated by
means of a phylogenetic tree or a dendogram.
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Ernst Heinrich Haeckel 1834-1919
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A phylogenetic tree or dendrogram is a graph
composed of nodes and branches, in which only one
branch connects any two adjacent nodes (binary
trees).
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Rooted trees
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Taxon (singular) Taxa (plural)
A taxon is a species or a group of species that
has been given a name, e.g., Homo sapiens (modern
humans) or Lepidoptera (butterflies). There are
codes of biological nomenclature which seek to
ensure that every taxon has a single and stable
name, and that every name is used for only one
taxon.
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Clades

• Strictly A clade is a group of all the taxa that
  have been derived from a common ancestor plus the
  common ancestor itself.
• In molecular phylogenetics A clade is a group of
  taxa under study that share a common ancestor,
  which is not shared by any other species outside
  the group.

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Paraphyletic Taxa

• A taxon whose common ancestor is shared by any
  other taxon is called a paraphyletic taxon or an
  invalid taxon.

Reptiles are paraphyletic.
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• A named taxon that lacks phylogenetic validity,
  but is nonetheless used, is called a convenience
  taxon.

a convenience fish
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A character is a well-defined feature that in a
taxonomic unit can assume one out of two or more
mutually exclusive character states.
Mutually exclusive If David is tall, David
cannot be short.
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Character
Continuous
Discrete
Binary
Multistate
Unordered
Ordered
Unpolar
Polar
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Temporal Polarity of Character States Character
states may be ranked by relative antiquity
into (1) primitive or ancestral
(plesiomorphy) (2) derived or novel (apomorphy)
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Taxonomic Distribution of Character States A
primitive state that is shared by several taxa is
a symplesiomorphy. A derived state that is
shared by several taxa is a synapomorphy. A
derived character state unique to a particular
taxon is an autapomorphy. A character state
that is shared by several taxa due to
convergence, parallelism and reversals, rather
than due to common descent, is a homoplasy.
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homoplasy
apomorphy (autapomorphy)
synapomorphy
symplesiomorphy
D
C
C
B
A
A
B
A
C
A
A
A
plesiomorphy
A
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Homoplasy
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How construct a phylogeny?

• Look at a large number of characters
• Generate all possible trees
• Select the most parsimonious tree
• A maximum parsimony tree is an ad hoc hypothesis

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Searching for the maximum-parsimony tree
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How construct a phylogeny?

• Look at a large number of characters
• Generate all possible trees
• Select the most parsimonious tree
• A maximum parsimony tree is an ad hoc hypothesis

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Phylogenetic approaches 1. distance-matrix
(based on distance measures - phenetics) 2.
character-state (based on character states -
cladistics) 3. maximum likelihood (based on both
character states and distances)
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Parsimony Methods
Willi Hennig 1913-1976
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Occams razor
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Pluralitas non est ponenda sine neccesitate.
(Plurality should not be posited without
necessity.) William of Occam or Ockham (ca.
1285-1349) English philosopher Franciscan monk
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MAXIMUM PARSIMONY Maximum parsimony involves the
identification of a topology (from among all
possible topologies) that requires the smallest
number of evolutionary changes to explain the
observed differences among the OTUs under study.
In maximum parsimony, we use discrete character
states, and the shortest pathway leading to these
character states is chosen as the best or maximum
parsimony tree. Often two or more trees with
the same minimum number of changes are found, so
that no unique tree can be inferred. Such trees
are said to be equally parsimonious.
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Inferring the maximum parsimony tree 1.
Identify all the informative sites. 2. For each
possible tree, calculate the minimum number of
changes at each informative site. 3. Sum up the
number of changes over all the informative sites
for each possible tree. 4. Choose the tree
associated with the smallest number of changes as
the maximum parsimony tree.
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The informative sites that support the internal
branches in the inferred tree are deemed to be
synapomorphies. All other informative sites are
deemed to be homoplasies.
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How construct a phylogeny?

• Look at a large number of characters
• Generate all possible trees
• Select the most parsimonious tree
• A maximum parsimony tree is an ad hoc hypothesis

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What, if anything, are whales?
At the morphological level, whales have many
autapomorphies (e.g., lack of hind feet), which
constitute insurmountable obstacles to
phylogenetic reconstruction.
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others
Mysticeti
Cetacea
Odontoceti
others
Tylopoda
Suiformes
Ancodonta
Suina
Tragulidae
Artiodactyla
Pecora
Ruminantia
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others
Ballen whales
Whales
Toothed whales
others
Camels
Pig-like
Hippopotamuses
Pigs
Mouse deer
Even-toed ungulates
Pecorans
Ruminants
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Because I said so! (1945)
George Gaylord Simpson (1902-1984)
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Balaenoptera musculus Blue whale
Mysticeti
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Physeter macrocephalus Sperm whale
Phocoena phocoena Harbor porpoise
Odontoceti
Tursiops truncatus Bottle-nose dolphin
Orcinus orca Killer whale
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Odontoceti

Mysticeti
Cetacea
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Tragulus napu Larger Malay Mouse Deer
Tragulus javanicus Lesser Malay Mouse Deer
Tragulidae
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Antilocapra americana Pronghorn
Giraffa camelopardalis Giraffe
Oreamnos americanus Mountain goat
Pecora
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Tragulidae
Pecora
Ruminantia
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Pecari tajacu Collared peccary
Sus barbatus Bearded pig
Suina
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Hippopotamus amphibius Hippopotamus
Ancodonta
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Ancodonta
Suina
Suiformes
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Camelus bactrianus Bactrian camel
Lama glama Llama
Tylopoda
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Suiformes


Tylopoda
Ruminantia
Artiodactyla
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Molecular study revision of cetacean and
artiodactyl phylogeny
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