Download determining phylogen..

Exam I: Friday afternoon
•Exam covers lecture material and corresponding readings
•Chapter 22: Descent with modification: a Darwinian view of life
•Chapter 23 The evolution of populations
•Chapter 24 The origin of Species
•Chapter 25 Tracing phylogeny (omit last subunit; The science of
phylogenetic systematics)
•Two additional readings
•Coverage of topics on exam is approximately proportional to time spent in
lecture to those topics
Phylogeny and
Systematics
Taxonomic classification is
hierarchical and nested
•Linnean classification called
binomial nomenclature, in
reference to genus and specific
epithet
•Taxon is a generic term for any
taxonomic unit (level)
•Most inclusive taxon, not
shown here, is Domain
Systematics
•Study of biodiversity
•Inter-related goals of systematists and taxonomists
•Formally name and describe species
•Classify taxa; assign species to genera, genera to
families, etc., which may require establishing new
taxa
•Determine evolutionary relationships among
lineages; establish nested hierarchical
classifications (taxonomies) that superimpose
precisely on the branching pattern of the
corresponding phylogenetic tree
Bass
Phylogeny
evolutionary
history of a
species or a group
of related species
Frog
Snake
Bird
“Basal” or
“Ancestral” Lineage
Phylogenetic Tree or Cladogram. Depiction of a phylogeny.
Carries information only on order of branching (= speciation =
cladogenesis); no information about passage of time or amount
of phenotypic change.
Tunicate
Bass
Frog
Snake
Bird
Subphylum Vertebrata (fish,
amphibians,reptiles, birds)
Tetrapoda (frog, snake,
bird)
Amniota (snake, bird)
Vertebrata
Tunicate
Tetrapoda
Bass
Frog
Amniota
Snake
Bird
Determining monophyletic taxa is key to classifying organisms
according to their evolutionary history:
•Monophyletic taxon is one in which a single ancestor gave rise to
all species, and which includes all descendents of that single ancestor
•Paraphyletic taxon excludes one or more species descended from a
single ancestor
•Polyphyletic taxon includes species descended from two or more
ancestral forms not common to all members
Systematists classify organisms based on homologous
characters (traits)
•Remember; classify organisms ~ establish taxa ~ determine
evolutionary history
•Homologous character; character that is shared by two or
more taxa because those taxa inherited the character from a
common ancestor
•Expect shared character to be quite similar, perhaps, but
not identical among taxa, as a result of descent with
modification
•Homology indicates common ancestry, which is
information with which one can determine evolutionary
history
•Analagous character; character occurring in two or more taxa
because it evolved independently in each of those taxa,
•Analagies may arise through convergent evolution: taxa
occupy similar ecological roles and similar selective forces
Divergent Evolution of Homologous Characters Homologous
characters may “evolve away” from each other in structure
Aardvark, native to
central, southern and
eastern Africa
Giant Anteater (at a
termite mound), native
to Latin America from
Southern Mexico to
Northern Argentina
Pangolin, native to
Africa and southern
and southeastern
Asia
Convergent Evolution of Analogous Characters. Three distantly
related mammals have structural similarities (analogous characters,
homoplasious characters) due to convergent evolution. Each taxon
independently evolved morphological traits for feeding on ants and
termites.
The supporting structure of bird and
bat wings are homologous
structures; derived from a common
ancestor
The supporting structures of insect
wings are analogous to the structures
of bird and bat wings; evolved
independently.
Systematic investigation is based on analysis of
homologous characters (traits). Characters may be
morphological, molecular, behavioral, physiological..
Shoot
develops
from
axillary bud
Thorn
develops
from
axillary bud
Spine
develops
from midrib
of leaf
Spine of
Japanese
barberry is a
modified leaf
Thorn of
downy
hawthorn is a
modified
stem
Analagous traits, or homoplasies, in two distantly related plant taxa
Evolutionary relationships can also be determined
through analysis of macromolecules; DNA, RNA and
proteins
•Molecular biology provides powerful tools for systematics
•Nucleotide sequences and therefore amino acid sequences,
are inherited; both undergo descent with modification
following divergence of one lineage into two
•Extent of sequence differences between taxa is an indicator,
an estimator, of time since divergence from a common
ancestor
•DNA , RNA and proteins are used to classify organisms and
determine evolutionary relationships
Phylogenetic Analyses Based On DNA-DNA Hybridizations
Melting tempertature
curve for DNA of T4
bacteriophage.
T50 = 84 deg C
Phylogenetic tree based on systematics.
•Data used in this analysis includes comparison of
genomes by DNA-DNA hybridization
•Note: this molecular approach help determine that
lesser panda isn’t a bear (an Ursid) – it’s a racoon
relative (a Procyonid)
Pattern of
speciation
that explains
the diversity
of
Galapagos
Finches
Seed Eaters
?
Seed Eaters
2 of the 3 competing
hypotheses on
phylogeny of seed
eating Galapagos
Finches
Seed
G. fuliginosa diverged
first; G. fortis and G.
magnirostris are sister
Eaters
species
G. magnirostris
diverged first; G. fortis
and G. fuliginosa are
Seed sister
Eaters
species
Phylogenetic Systematics
Dr. Willi Hennig (1913-1976)
•The history of diversification is recorded through descent with
modification
•Modification exists in the form of evolutionary transformation of
characters from one state to another state.
•Plesiomorphy: Ancestral character state
•Apomorphy: Derived character state
•Synapomorphy Derived character state that is exclusively shared
by a subset of taxa under investigation.
•A synapomorphy is evidence that taxa bearing it are descended from
the same common ancestor -- the ancestor in which the derived
character arose.
?
Seed Eaters
Species A
Species B
Species C
Reconstruct the phylogeny of three closely related bird species
Determine characters to use for analysis
•bill shape (derived character state: hooked;ancestral= not hooked)
•head feathers (derived = crest; ancestral = no crest)
•toe condition (derived = webbed; ancestral = no webbing)
Species A
Hooked Bill
Species B
Hooked Bill
Species C
No Hooked Bill
Crested Head
Webbed Toes
No Crested Head
Webbed Toes
Crested Head
No Webbed Toes
•Character states variously arise in lineages.
•Character states variously accumulate in lineages, in
descendents of the ancestor in which the character states arose
A
B
?
C
“Cladistic” or “Phylogenetic” Analysis: Procedural Outline
SELECT ORGANISMS
•Identify the ingroup
•Select an appropriate outgroup
BUILD TRANSFORMATION MATIX
•Select characters for analysis
•Assign character states
•Determine polarity of character states
ANALYZE AND INTERPRET DATA
•Subject data to optimization algorithm
(usually parsimony criteria)
•Product: optimal tree, perhaps a concensus tree
•Seek congruence
•Product: Phylogenetic Hypothesis
Closely related
species that we
know diverged
from ancestral
lineage before
our three
species of
interest
diverged
(outgroup)
?
(ingroup)
Outgroup
Species A
Species B
Species C
Closely related
Transformation Series
species that
diverged from Bill Shape
Head Plumage
Toe Condition
ancestral
? (ingroup)
Outgroup
HCWlineage before
our
threeA
Species
H+
C+
W+
species of
Species B
H+
CW+
interest
divergedC
Species
HC+
W-
(outgroup)
Assume character state seen in outgroup is ancestral character state.
H- C- W-
H+ C+ W+
H+ C- W+
OG
A
H- C+ W-
B
C+
C
Outgroup
Species A
Species B
Species C
Closely related
W+Series
C+
Transformation
species that
diverged from Bill Shape
Head PlumageH+
Toe Condition
ancestral
? (ingroup)
Outgroup
HCWlineage before
our
threeA
Species
H+
C+ This phylogenetic
W+hypothesis
species of
Species B
H+
C- requires four evolutionary
W+
interest
transformations to explain
WdivergedC
Species
HC+ the distribution of
W-character
(outgroup)
C-
states among taxa under
Assume character state seen ininvestigation
outgroup is ancestral.
H-
H- C- W-
H+ C- W+
H+ C+ W+
OG
B
H- C+ W-
A
C+
C
W+
Outgroup
Species A
Species
B
Species C
W+
H+
Closely related
W+
C+
H+
Transformation
Series
species that
C+ Condition
diverged from Bill Shape
Head PlumageH+
Toe
ancestral
? (ingroup)
Outgroup
HCWlineage before
This phylogenetic
our
threeA
Species
H+
C+ Thishypothesis
W+hypothesis
phylogenetic
requires
five
species of
four evolutionary
evolutionary
Species B
H+
C- requires
W+
interest
Wtransformations
to explain
transformations
to explain
WCdivergedC
Species
HC+ the distribution
W-character
of
the distribution
of character
(outgroup)
HC-
states
among
taxataxa
under
states
among
under
Assume character state seen ininvestigation
outgroup is ancestral.
investigation
H-
Choosing Among Competing Hypotheses:
The Parsimony Principle
•The Parsimony Principle holds that, all other things being equal,
the hypothesis requiring the fewest number of evolutionary
transformations has the highest likelihood of being the correct
hypothesis
Using Phylogenies to Test Hypotheses
McGregor’s Viper, Phillipines
not
(Scanlon and Lee 2000)
George Gaylord Simpson
(1902-1984)
Mammalian Paleontologist,
regarded as one of the
architects of the modern
synthesis
Formulated the principles of
evolutionary taxonomy
“SCHOOLS” OF SYSTEMATICS
TRADITIONAL EVOLUTIONARY TAXONOMY [Simpson]
•Establish taxa based on common descent (clades) and or extent of
adaptive evolutionary change:
•evolutionary groups that represent adaptive zone constitute
legitimate higher taxa -- a grade
•adaptive zone; “…characteristic reaction and mutual relationship
between environment and organism, a way of life and not a place
where life is led.”
•paraphyletic taxa may be acceptable
PHYLOGENETIC SYSTEMATICS (CLADISTICS) [Hennig]
Establish taxa based on:
• clades; monophyletic taxa only
Tunicate
Bass
You establish the
taxon...
PHYLUM: REPTILAVES
snake
bird
Frog
Snake
Bird
Tunicate
Bass
Frog
Snake
Bird
You establish the
taxon...
Monophyletic taxon:
PHYLUM: REPTILAVES
snake
bird
Includes all and only all the
descendents of the most
recent common ancestor of
the group (taxon)
Tunicate
Bass
You establish the
taxon...
PHYLUM: AMPHIREPTA
frog
snake
Frog
Snake
Bird
Tunicate
Bass
Frog
Snake
Bird
You establish the
taxon...
Paraphyletic taxon:
PHYLUM: AMPHIREPTA
frog
snake
Includes common ancestor
to all members of the group
(taxon), but not all
descendents of the common
ancestor
Tunicate
Bass
Frog
You establish the
taxon...
PHYLUM: ICHTHYREPTILAVES
bass
snake
frog
Snake
Bird
Tunicate
Bass
Frog
Snake
Bird
You establish the
taxon...
Polyphyletic taxon:
PHYLUM: ICHTHYREPTILAVES
bass
snake
frog
Taxon does not include most
recent common ancestor of
all its members
mammals turtles plesiosaurs
ichthyosaurs snakes crocodilians dinosaurs
dinosaurs
& lizards
(ornithischians) (saurischians)
Phylogeny of Amniotes
birds
Species A
Species B
Species C
H+ W+ C+
H+ W+ C-
H- W- C+
•Character states variously arise in lineages.
•Character states accumulate in lineages, in descendents of the
ancestor in which the character states arose
TETRAPOD
autopod
phase III colinear hox
expression
SARCOPTERYGIANS
zeugopod
reduction of dermal fin elements
leaborate fin endoskeleton
GNATHOSTOMES
2 sets of paired appendages
serial homology
fin axis
VERTEBRATES
paired appendages
a/p polarity of fin structure
Posterior hox genes expressed
in both appendages
Hox genes expressed along body axis
Pattern of
speciation
that explains
the diversity
of
Galapagos
Finches
2. Phylogeny and Systematics.
Lecture Topics
•Biodiversity
•History of Biodiversity (Macroevolution)
•Pattern = Nested lineages
•Process = Cladogenesis
• Systematics
•Scientific Inquiry
•Analytic Approach to Determining Evolutionary History (Phylogeny)
•The Purposes and Uses of Phylogenies
Prevailing
hypothesis:
Birds diverged
in early
Jurassic
Period from
Theropod
Dinosaurs
Alternative
hypothesis:
Birds diverged
from ancestral
Crocodilian
Birds from
Croc Ancestors
Birds from Theropod Dinosaurs
Cretaceous Period
Jurassic Period
Triassic Period
Permian Period
The Practice and Objectives of Systematists
•Determine evolutionary history of taxa (biodiversity)
•reconstruct phylogeny
•Classify taxa accordingly, into a nested hierarchical
taxonomy that superimposes precisely on the branching
pattern of the corresponding phylogenetic tree
•Two schools of thought among systematists as to
whether this objective should be universally applied.
The Practice and Objectives of Systematists
•Determine evolutionary history of taxa (biodiversity)
•reconstruct phylogeny
•Classify taxa accordingly, into a nested hierarchical
taxonomy that superimposes precisely on the branching
pattern of the corresponding phylogenetic tree
•Two schools of thought among systematists as to
whether this objective should be universally applied.
Phylogenetic tree
and dates of
divergence for
humans, apes and
old world
monkeys based
on DNA-DNA
hybridization
studies