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Lecture V
How to Determine Evolutionary Relationships:
Concepts in Phylogeny and Systematics
Textbook Reading: pp 425-433, 435-437 in chapter 23:
Reconstructing and using Phylogenies
Nature 413, 277 - 281 (2001) Skeletons of terrestrial cetaceans and the relationship of whales to
artiodactyls. J. G. M. Thewissen, E. M. Williams, L. J. Roe & S. T. Hussain. See webpage for link to pdf
of this paper, and summary/persptive of this paper
Taxonomic classification is
hierarchical and nested
•Taxonomy is the science of the
classification (=naming) of
organisms
•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
Bass
Frog
Snake
Bird
“Basal” lineage
Phylogeny history of descent of a group of organisms from their common ancestor
Phylogenetic Tree or Cladogram. Depiction of a phylogeny. Carries information only on
branching relationships; no information about passage of time or amount of phenotypic
change. Each branching point (node) reflects a divergence (ie, speciation, cladogenesis)
event that took place in the species that is the most recent common ancestor to the
descendents of that cladogenesis event
Lineage Organisms in an ancestor-descendent relationship
Tunicate
Bass
Frog
Snake
Bird
Vertebrata (fish, amphibians,reptiles,
birds)
Tetrapoda (frog, snake, bird)
Amniota (snake, bird)
The nested polygons here show taxonomic groupings, but with no regard for
“inclusion” or “exclusion” of ancestors common to the groupings
Vertebrata
Tunicate
Tetrapoda
Bass
Frog
Amniota
Snake
Bird
The nested polygons here do show taxonomic groupings, but with regard for
“inclusion” or “exclusion” of ancestors common to the groupings
Determining monophyletic taxa is key to classifying organisms according
to their evolutionary history:
•Monophyletic taxon is one in which a single ancestor gives rise to all
species, and which includes all descendents of that single ancestor
•Paraphyletic taxon excludes one or more species descended from the most
recent common ancestor of the taxon
•Polyphyletic taxon excludes the most recent common ancestor of all
members of the taxon
A taxon that includes only A and B would be
paraphyletic
A taxon that includes B, C and D would be
polyphyletic
A taxon that includes D, E and F would
be monophyletic
“SCHOOLS” OF SYSTEMATICS
TRADITIONAL EVOLUTIONARY TAXONOMY [Simpson
and others]
•Establish taxa based on common ancestry (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.”
George Gaylord Simpson (19021984). Mammalian Paleontologist,
regarded as one of the architects of the
modern synthesis. Formulated the
principles of evolutionary taxonomy
•paraphyletic taxa may be acceptable
PHYLOGENETIC SYSTEMATICS (CLADISTICS)
[Hennig]
•Establish taxa based on clades; monophyletic taxa only
•Powerful methodological and analytic tool for determining
relationships
•The tools of cladistics now represent the prevailing
approach to determining relationships; the philosophy of
strict monophyly wrt classification is still under debate -bears on definition - concept- of species
Willi Hennig (1913-1976). Hennig is
best known for developing
phylogenetic systematics, a coherent
theory of the investigation and
presentation of the relations that exist
among species.
http://www.cladistics.org/about/hennig.html
Systematists classify organisms and determine evolutionary relationships
based on analysis of homologous characters (traits)
•Systematic investigation is based on analysis of homologous characters (traits);
characters may be morphological, molecular, behavioral, physiological..
•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
Divergent Evolution of Homologous Characters Homologous
characters may “evolve away” from each other in structure
•Analagous character; character occurring in two or more lineages because it evolved
independently in each of those lineages,
•Analagies may arise through convergent evolution: lineages occupy similar ecological
roles and similar selective forces
•Misinterpretation of analagous characters for homologus ones may lead to erroneous
conclusions regarding phylogenetic relationships and unintended taxanomic groupings
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 structures 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.
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
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.
“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) to produce an
optimal tree, perhaps a concensus tree
•Seek congruence
•Product: Phylogenetic Hypothesis
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.
“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) to produce an
optimal tree, perhaps a concensus tree
•Seek congruence
•Product: Phylogenetic Hypothesis
Reconstruct the phylogeny of three closely related bird species
Species A
Species B
Species C
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
Species B
Species C
Hooked Bill
Hooked Bill
No Hooked Bill
Crested Head
No Crested Head
Crested Head
Webbed Toes
Webbed Toes
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
Outgroup Closely
related species that
we know diverged
from ancestral
lineage before our
three species of
interest diverged
Ingroup
Outgroup
Closely related
species that
Outgroupfrom
diverged
Species A
ancestral
Speciesbefore
B
lineage
ourSpecies
threeC
speciesH=hooked
of bill
interestC=crest
W=webbed toes
diverged
Species A
Species B
Species C
Transformation Series
Bill Shape
Head Plumage
Toe Condition
H-
C-
W-
H+
C+
W+
H+
C-
W+
H-
C+
W-
+=species has trait
-=species lacks trait
?
(ingroup)
(outgroup)
Assume character state seen in outgroup is ancestral character state.
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 hypothesis requires
evolutionaryW+
transformations to
our
threeA
Species
H+
C+ Thisfive
phylogenetic
hypothesis
explain
the distribution
of character
species of
states among taxa under investigation
Species B
H+
C- requires four evolutionary
W+
interest
Wtransformations to explain
WCdivergedC
Species
HC+ the distribution of
W-character
(outgroup)
HC-
states among taxa under
Assume character state seen ininvestigation
outgroup is ancestral.
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
Evolutionary relationships may be determined through analysis of
molecular characters; 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
Normal RBC’s and normal
hemoglobin
Sickled RBC’s and sickle-cell
hemoglobin
Phenotypic consequence of a point mutation - a substitution
Molecules evolve at different rates, some, at constant rates
Raven and Johnson 1999)
Hemoglobin Evolution
•Gene duplication Multigene Families
•Evolution of molecular function
Tetrameric Human hemoglobin
•Gene family
-two or more genes in a genome,
identical or highly similar in
nucleotide sequence
-descended from the same ancestral
gene
•Origin of gene families
-Repeated gene duplication from
errors during DNA replication and
recombination
•Globin gene families are wellstudied across taxa for sequence,
structure and function
•Hemoglobin multigene families in
humans
•Alpha globin family (on chr. 16)
•Beta globin family (on chr. 13)
•Hemoglobin families probably
descended from a myoglobin-like
ancestral gene
Evolution of the
Globin Gene
•Genes encoding proteins
have undergone continual
evolution, accumulating
increasing numbers of
changes over time
•Length of lines
corresponds to number of
nucleotide substitutions
in the gene
Raven and Johnson 1999