PHYLOGENETICS

{
Introduction to
Phylogenetics
Dela Cruz, B.S.F
What is Phylogenetics?
gStudy of the evolutionary development of
organisms; "phylogenetic development
gIs the scientific discipline concerned with
describing and reconstructing the
patterns of genetic relationships among
species and among higher taxa.
gThe study of phylogeny.
Phylogeny
Species: A B C D
T
i
m
e

A

B

C

D
Time
A and B are most closely related because they share a common ancestor
( call the ancestor E) that C and D do not share
E
E
F
F
A+B+C are more closely related to each other than to D because they share
a common ancestor (F) that D does not share
Phylogenetic Tree
ga diagram showing the evolutionary
interrelations of a group of organisms
derived from a common ancestral form.
g convenient way of visually
representing the evolutionary history
of life.
Phylogenetic Tree
gRoot: the common ancestor of all
taxa.
gNode: a branchpoint in a tree.
gBranch: defines the relationship
between the taxa in terms of
descent and ancestry.
gClade: a group of two or more taxa
or DNA sequences that includes
both their common ancestor and all
their descendents.
Species A
Species E
Species D
Species C
Species B
Node
Root
Branch
Clade
]
Monophyletic group

Includes an ancestor
all of its descendants
A B C D
Paraphyletic group

Includes ancestor and
some, but not all of its
descendants
A B C D
Polyphyletic group

Includes two convergent
descendants but not their
common ancestor
A B C D
Cladistic Classification
Phylogenetic trees are usually based on
a combination of these lines of evidence:
g Fossil record
g Morphology
g Embryological patterns of
development
g Chromosomes and DNA
Taxonomy vs. Systematics
g In taxonomy, it is a
subdivision of systematics, is
the science of biological
classification.
g Focus on naming.
g In systematics, it is the study
of biological diversity and its
evolution.
g Focus on evolutionary trait.
Taxonomy
gThe science dealing with the description,
identification, naming, and classification
of organisms
g Practice of arranging organisms.
gAlso referred to the classifying of living
organisms.

Systematics
gthe study of relationships of
organisms, characters,
distributions, evolution,
classification.
gfundamental to all biological
science endeavors.
Classification vs.
Systematization
g In classification, the
taxonomist asks whether the
species being classified
contains the defining feature
of a certain taxonomic
grouping.
g Focus is on features.
g In systematization, the
taxonomist asks whether the
characteristics of a species
support the hypothesis that it
descends from the most
recent common ancestor of
the taxonomic group.
g Focus is on evolutionary
origin of those features.


Classification
gis the arrangement of organisms into
orderly groups based on their similarities.
g to clarify relationships among organisms.
g clearly the identity of organisms being
studied.
gStable names.
Systematization
g Explored the distinction between classification.
g Levels of organization concept.
g Understanding of the role and potential
contribution of cladistics.
{
Carolus Linnaeus
and Taxonomy
Antonio, B.L.S
{
Carl von Linn
Swedish botanist
Born on the 23
rd
of May
in Sweden
By the age of 8 yrs. old
= The Little Botanist.
Designed the
hierarchical
classification scheme
Father of Taxonomy
Binomial
Nomenclature
Carolus Linnaeus (1707-1778)
{
Publications
Systema Naturae (1735) -
classifying the natural world

Fundamentica botanica (1735) -
rules for classification

Genera Plantarum (1737) - short
descriptions of all 935 plants
genera

Flora Lapponica (1737) - Laplands

Critica botanica (1737) - the rules
for botanical nomenclature

Hortus Cliffortianus (1738) - the
plants in Cliffords garden

Classes Plantarum (1738), a
review of plant systems.

gThe Linnaean system of classification
was widely accepted by the early 19th
century and is still the basic framework
for all taxonomy in the biological
sciences today.
gAllowed for clear and easy descriptions
of plants, animals and minerals and
forms the basis for modern classification.
gThe binomial classification system
proposed by Linnaeus allowed him to
group organisms together based on
common structures, functions, and
resulting behaviors, which led to the
science of taxonomy.
Greatest contributions
g 4 specific categories
/ Class, Order, Genus & Species
g Divided the kingdom into many smaller
groups called Classes
g Gave the idea of using names for species and a
pattern where there are two words used in
each name
/ Genus as a noun
/ Species as an adjective
g Recognized species as the basic natural unit of
classification.

{
Species
Guadana, S.M.F.
Bacosa, M.A.B.
{
Guadana, S.M.F
Introduction and
Criteria for Species
gDefining a species can be difficult.
gCriteria:
/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.
gThe geographic range of a species
is its distribution in space.
gEvolutionary duration of a
species is its distribution in time.
gA worldwide species is
cosmopolitan.
gOne with a very localized range is
called endemic.
{
Species
Typological
Species Concept
gThe 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.

In a Nutshell
gThe person who first described a
species is called the Authority thus
the name of the person and date of
publication follows the scientific
name

gDidelphis marsupialis Linnaeus 1758
{
Bacosa, M.A
Biological Species
Concept
The Biological Species
Concept

/The biological species concept defines a
species as members of populations that
actually or potentially interbreed in nature, not
according to similarity of appearance.
/A species is a reproductive community of
populations (reproductively isolated from
others) that occupies a specific niche in
nature.

Example
Organisms may appear to be alike and be different in species.
For example, The western meadowlarks and the eastern meadowlarks
look almost identical to each other, yet do not interbreed to each other-
thus they separate species in this concept.
Sturnella neglecta Sturnella magna
*Organisms may be different in appearance but may be in the
same species. Many characteristics may vary in a single species.
Evolutionary Species
Concept
g all organisms, past and present, belong to
some evolutionary species.
g a species is a lineage of ancestral descendant
populations which maintains its identity from
other such lineages and which has its own
evolutionary tendencies and historical fate.
Typological Species Concept
g 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.

*The morphological species concept is applicable
particularly to situations in which the potential
for mating along with postzygotic barriers to reproduction
cannot easily be determined.
{
Dizon, J.
Phylogenetic Species
Concept
Phylogenetic Species Concept
Defined as an irreducible (basal)
groupings of organisms diagnosably
distinct from other such groupings and
within which there is a parental pattern of
ancestry and descent
It is a technique for identifying
organisms to species using sequences
informationfrom a standard gene
present in all animals.
DNA Barcoding
{
Taxonomic Characters
and Phylogenetic
Reconstruction
Cuello, R. O.
Goal of Systematics:

gTo understand the evolutionary tree that
relates all extant and extinct species by
identifying organismal features

EVOLUTIONARY TREE =
PHYLOGENY
ORGANISMAL FEATURES =
CHARACTERS
Characters
g Found by observing patterns of similarity
among:
- Morphological
- Chromosomal
- Molecular features
- Behavioral or Ecological
{ { Homologous

gShared characters that
result from common
ancestry

- Similar charac.
- Common Ancestry


Homoplasy

gIndependent
evolution of similar
characters that are
NOT homologous

- Similar charac.
Not common
ancestry

Homologous
Analogous
gThe observed features are similar
but not of common descent of
ancestry

gA potential misconception in
constructing a phylogeny is
similarity due to convergent
evolution, called analogy, rather
than shared ancestry.

Convergent Evolution
Similar adaptations in organisms from
different evolutionary images are
produced by similar environmental
pressures and natural selection.

Analogous structures or molecular sequences that
evolved independently are also called homoplasies.



Analogous
Analogies are the result of convergent evolution
{
Shared Primitive and
Shared Derived
Characteristics
Cuello, R.O.
Javiniar, V.Y.S.
gA 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: All Mammals have backbone,
but so do other vertebrates.

gA shared derived character:
/ An evolutionary novelty unique to
a particular clade.
/A character that is only observed
within the group

Example: All mammals have hair, and no
other animals have hair.

ANCESTRAL CHARACTER
STATES
/The form of the character that was
present in the common ancestor of
the entire group.

DERIVED CHARACTER STATES
/Variant forms of the character arose
later

gDetermining polarity of a character
involves determining which state is
ancestral.

POLARITY
- The states of characters used in a cladistic
analysis, either original or derived.
- 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.
- OUTGROUP - INGROUP
/Character groups found in the study groups
but not the outgroups are derived.
OUTGROUP - INGROUP
CLADES
ga group of organisms that evolved from a
common ancestor

gA clade corresponds to a unit of
evolutionary common descent.

gare organisms or species that share derived
character states and form a subset within a
larger group.



Apomorphy
- A derived or specialised character.
Synapomorphy
- is a derived character shared by the
members of the clade.

/A nested hierarchy is formed by the
derived states of all characters in a
study group.

Plesiomorphic
Ancestral character states for a taxon.
Symplesiomorphic
A character shared by a number of
groups, but inherited from ancestors
older than the last common ancestor.

/Symplesiomorphies, unlike synapomorphies,
do not provide information on nesting of
clades groups with derived characters get
left out.

Cladogram
gNested hierarchy of clades
that is based on shared
synapomorphies.
gA branching diagram


Phylogenetic tree
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.

Cladogram vs.
Phylogenetic Tree
Sources of Phylogenetic
Information
gCharacters used to construct
cladograms can be found using:
/Comparative Morphology
/Comparative Biochemistry
/Comparative cytology

Comparative morphology
examine shapes and sizes of
organismal structures, including
developmental origins.
Examples: Skull or limb bones, scales,
hairs, feathers
*Can be observed in fossils as well as
living specimens

_ examine sequences of amino acids and
nucleotides to identify variable characters.
_ Most common evidence used

Examples:
Protein or DNA sequence comparison
* Occasionally fossils have remnants of DNA
preserved, but not easy to recover
Comparative cytology
_ uses variation in numbers,
shapes, and sizes of
chromosomes and their parts.

*Only used for living organisms
{
Theories of
Taxonomy
Javiniar, V.Y.S.
Baria, C.K.T.
Theories of Taxonomy
gAllows us to rank taxonomic
groups.
/Two popular theories
[Evolutionary taxonomy
[Phylogenetic systematics
/Both based on evolutionary
principles, sometimes results
conflict.
CLADISTICS
g A valid clade is monophyletic.
/Signifying that it consists of the ancestor
species and all its descendants.
- ANCESTOR - DESCENDANTS




CLADISTICS
gA paraphyletic clade is a grouping that consists
of an ancestral species and some, but not all, of
the descendants.
- ANCESTOR & SOME DESCENDANTS



CLADISTICS
gA polyphyletic grouping includes numerous
types of organisms that lack a common ancestor.
ANCESTOR - DESCENDANTS


{
Traditional
Evolutionary
Taxonomy
Baria, C. K. T.
gTwo different evolutionary principles:
/common descent
/ amount of adaptive evolutionary change
gMust have a single evolutionary origin and
must show unique adaptive features
gGeorge Gaylord Simpson and Ernst Mayer
/Formulated the principles of evolutionary
taxonomy


g A branch on an evolutionary tree is
considered a higher taxon if it
represents a distinct adaptive zone
/A taxon that constitutes a distinct
adaptive zone is termed a grade
gEvolutionary taxa may be either monophyletic or
paraphyletic


Phylogenetic
Systematics
Phylogenetic Systematics
g emphasizes common descent
g based on cladograms
g Willi Hennig. Hennigian
systematics
g All taxa must be monophyletic
g Sister group
/To express common descent of
groups without constructing
paraphyletic taxa
gBoth 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.

{
Current State of
Animal Taxonomy
Naluz, P. K. C.
Was established using
principles of evolutionary
systematics and has been
revised recently in part using
principles of cladistics
PhyloCode:
A New System of
Nomenclature
Principles of the PhyloCode:
REFERENCE
CLARITY
UNIQUENESS
STABILITY
PHYLOGENETIC CONTEXT
TAXONOMIC FREEDOM
PARSIMONY

In general, parsimony is the principle that the simplest
explanation that can explain the data is to be preferred.

In the analysis of phylogeny, parsimony means that a
hypothesis of relationships that requires the smallest
number of character changes is most likely to be
correct.
Maximum Parsimony Principle as
employed in phylogenetics states that the most
probable course of cladogenesis is the one that
can explain the distribution of the individual
forms of traits within the phylogenetic tree
through the smallest number of anagenetic
changes.
Maximum likelihood
Maximum likelihood is also a criterion, similar to maximum
parsimony. But here the aim is not to find the shortest tree, but
the tree that most likely explains the data under the assumed
evolutionary model.

As with parsimony, we have to evaluate all possible trees to
find out which one is the best (according to our criterion).
A C A B A B
|__| |__| |__|
| | | | | |
B D C D D C
With respect of the TAXON A, there are three hypothesis.
HYPOTHESIS 1 is much better!
{
Major Divisions of Life
Cabiles, M. A. F. E.

+ Aristotle (1800s) -2 Kingdoms namely
the Plant Kingdom and Animal
Kingdom
+ Ernst Haeckel (1866) proposed the
new kingdom Protista(single celled
organisms) to include all single-celled
organisms

+R.H. Whittaker(1969)- proposed five kingdom system
that incorporated the basic prokaryote-eukaryote
division
Monera (Prokaryotes)
Protista(Unicellular Organism)
Plantae(Multicellular Photosynthesizing
Organisms, higer plants and multicellular algae)
Fungi ( molds,yeasts, fungi that obtain food
absorption)
Animalia (invertebrates except protozoa and
vertebrates)
+Woese, Kandler and Wheelis(1990)
Recognize three monophyletic group
domains above the kingdom level
based on Ribosomal RNA sequences.
- Eucarya(all eukaryotes)
- Bacteria( true bacteria)
- Archaea(prokaryotes)
Clarifications:
Protozoa
Neither animals nor are they a valid monophyletic
taxon at any level.

Protista
Invalid because it is not monophyletic

Animal-like Protista
Now divided into seven or more phyla
{
Major subdivision of
the Animal Kingdom
Groupings based on embryological and anatomical characters.
Aratea, Jasmine
SUBDIVISIONS
BRANCH A: MESOZOA
BRANCH C: EUMETAZOA
BRANCH B: PARAZOA
MESOZOA
g Mesozoa are small vermiform (form of a
worm) animals formed by a few cells (among
20 and 30 cells, depending on the species)
arranged in two layers that are not equivalent
to the layers of metazoans. All mesozoans live
as parasites of marine invertebrates and their
cycle of life is very complex and insufficiently
known. Its locomotion is carried out by cilia.
g Rhombozoan mesozoans
is a phylum of tiny parasites that live in the renal
appendages of cephalopods.


g Orthonectid mesozoans
are found in the body spaces of various marine
invertebrates including tissue spaces & Gonads
PARAZOA
gThe Parazoa are an ancestral
subkingdom of animals, literally
translated as "beside the animals".

gIncludes Phylum Porifera &
Placazoa
EUMETAZOA
GRADE II: Bilateria
GRADE I: Radiata
DIVISION A (Prostostomia) DIVISION B (Deuterostomia)

Protostome - First embryonic opening
becomes the mouth.

Deuterostomes - Second embryonic opening
becomes the mouth.
Comparison
/ CLEAVAGE
Comparison
/ FATE OF BLASTOPORE
Comparison
/ COELOM FORMATION
References
g http://www.biocab.org/Mesozoa.html
g http://www.thefreedictionary.com/embryological
g http://rocklin.k12.ca.us
g http://www.nhm.ac.uk/nature-online/science-of-natural-
history/biographies/linnaeus/index.html
g http://anthro.palomar.edu/animal/animal_1.htm
g http://medical-dictionary.thefreedictionary.com/phylogenetic
g http://biology.unm.edu/ccouncil/Biology_203/Summaries/Phyloge
ny.htm
g http://eol.org/info/312
g http://www.biologyjunction.com/classification%20of%20life.ppt
g http://www.dellpassovoy.com/Taxonomy].ppt
g http://www.seas.gwu.edu/~simhaweb/cs177/fall2003/lecture9.ppt
g http://www.hartnell.cc.ca.us/faculty/jhughey/Files/TAXONOMY.P
PT
g http://hymenoptera.tamu.edu/courses/ento601/pdf/Kavanaugh_19
78.pdf
g http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Taxonomy.html



g http://www.palass.org/modules.php?name=palaeo&se
c=newsletter&page=20
g http://evolution.berkeley.edu/evosite/evo101/IIC1Hom
ologies.shtml
g http://www.geol.umd.edu/~tholtz/G204/lectures/204tol
.html
g http://www.insecta.bio.pu.ru/z/syst_I_1.htm
g http://www.zoology.siu.edu/king/304/ch12.htm