Download homoplasy

Phylogenies
Reconstructing the Past
The field of systematics
• Studies
– the mechanisms of evolution
• evolutionary agents
– the process of evolution
• speciation events
– the products of evolution
• discovery, nomenclature, classification,
tools for identification of extant organisms
Phylogenetic Analysis
• Phylogeny
– chronicle of the descent of a group of
organisms from a common ancestor
– illustrated as a branching, tree-like diagram
• anagenesis operating along branches
• cladogenesis producing new branches
– shows the origins of different groups from
an ancestral group
Phylogenetic Reconstruction
• a phylogenetic tree (cladogram) is a hypothesis
of events in the evolution of a group
– based on the analysis of characters of extant
organisms
– identifies the speciation events (branch
points) in the evolution of the group
– estimation of time spans or identification of
ancestral organisms is extraneous
Phylogenetic Reconstruction
• an ideal data set…
– the complete morphological and genetic
description of each member of the lineage
• better than nothing…
– the complete fossilized remains of each
member of a lineage
• One approach that’s always feasible…
– inference from extant members
Phylogenetic Reconstruction
• clues to the phylogenetic history of a group
– homologies
• two features descended from a common
ancestral feature are homologous
• may or may not resemble each other
• may or may not perform the same
functions
Figure 25.2
Figure 1.2
tetrapod limbs homologs
bat, bird,
insect wings not homologs
Figure 25.2
leaf homologs in flowering plants
Figure 25.3
Phylogenetic Reconstruction
• clues to the phylogenetic history of a group
– common ancestry is inferred from the
presence of homologous traits
• traits inherited from a distant ancestor are
shared by many taxa
• traits inherited from a recent ancestor are
shared by few taxa
Homoplasies
• traits that are similar due to something other
than inheritance from a common ancestor
– convergent evolution
– parallel evolution
– evolutionary reversal
Homoplasies
• traits that are similar due to something other
than inheritance from a common ancestor
– convergent evolution
Figure: three plants that all look like cactus but c
Three distinct families -
Euphrobiaceae
Cactaceae
Asclepiadaceae
Homoplasies
• traits that are similar due to something other
than inheritance from a common ancestor
– convergent evolution
– parallel evolution
Figure: butterfly/moth wings with similar
patterns
Homoplasies
• traits that are similar due to something other
than inheritance from a common ancestor
– convergent evolution
– parallel evolution
– evolutionary reversal
Figure: Magnolia & grass
Phylogenetic Reconstruction
• steps in the reconstruction of a phylogeny
– identification of members of the group
• key homologous traits
e.g. a vertebral column
– selection of characters
• characters with traits that differ in the
group
–ancestral vs. derived
–(plesiomorphies vs. apomorphies)
Phylogenetic Reconstruction
=>during the history of a lineage, some traits
change from the ancestral condition
ancestral => derived
=>taxa that change pass on the changes
=>closely related taxa share traits from a
recent ancestor and a distant ancestor
=>distantly related taxa share traits from a
distant ancestor only
Phylogenetic Reconstruction
• steps in the reconstruction of a phylogeny
– identification of ancestral and derived
character states
• select an outgroup
–traits shared with the outgroup are
ancestral
– distinguish between homologies and
homoplasies
• assume similar traits are homologous
–other characters will test the assumption
Table 25.1
phylogeny of selected vertebrates
Figure 25.5
dealing with the real world
• unrecognized homoplasies happen
– multiple trait changes, reversals,
convergence, parallels
• each analysis produces multiple possible trees
– some trees explain the evolution of the
group by assuming many speciation events
– some trees explain the evolution of the
group by assuming few speciation events
• how to select the right tree?
dealing with the real world
• selecting the right tree
– can’t be done (with certainty)
– Principle of Parsimony
• the best hypothetical tree is the one that
requires the fewest unverified assumptions
(events)
• the best tree is the shortest tree, for now
• new data, new insights, may provide
evidence supporting a different tree
dealing with the real world
• selecting the right tree
– Maximum Likelihood
• analyzes trees using additional
information
–certain possible events are more likely
than others and are given greater weight
e.g. transitions are more likely than
tranversions
dealing with the real world
• final trees are often inconclusive, so
– consensus trees combine results from
several best-scoring trees
– “unresolved” nodes support multiple
branches
dealing with the real world
• cladistic analysis is a highly documented
hypothetical process
– assumptions are explicit
– taxon selection criteria are explicit
– character/trait selection criteria are explicit
– homoplasy identification is explicit
– software choices are explicit
– tree reconciliation is explicit
shared developmental features
may demonstrate links
between taxa with
little adult similarity
Figure 25.4
Useful Characters for Phylogenies
• heritable, quantifiable characters
– morphological characters
– anatomical characters
– developmental biology
– molecular traits
• proteins
• nucleic acids
Dendroica fusca hierarchy
Figure 25.6
Classification of Organisms
• Biological Classification uses a hierarchical
system
– a taxon is identified by diagnostic
characteristics
– lower taxa belong to higher taxa along with
sister taxa
Rosa gallica hierarchy
Figure 25.6
Classification of Organisms
• Biological Classification uses a hierarchical
system
– the taxonomic hierarchy is information rich
• diagnostic characters are reliable as
predictors
Classification of Organisms
• Biological Classification applies a unique
name to each species
– A binomial is applied to each species
• every known species possesses a binomial
• each binomial is applied to only one
species
• binomial nomenclature is accepted
universally among scientists
Campanula sp.
Campanulaceae
Three different species, all called
“Bluebells”
Mertensia sp.
Boraginaceae
Endymion sp.
Liliaceae
Classification of Organisms
• Biological Classification applies a unique
binomial to each species
– common names are insufficient
• unregulated
• incomplete
Arabidopsis
thaliana
the
primary
flowering plant
molecular
model system
a.k.a.
Arabidopsis
thaliana
Classification of Organisms
• Biological Classification applies a unique
binomial to each species
– binomials consist of two parts
• Genus name: e.g. Echinocactus
• specific epithet: E. enneacanthus
Classification of Organisms
• Biological Classification applies a unique
binomial to each species
– binomials replaced polynomial phrase
names
• Linnaeus is credited with development of
binomial nomenclature, ~1750