Download Systematics and phylogeny

Systematics and phylogeny
Organizing life
• All organisms:
– Are composed of one or more cells
– Carry out metabolism
– Transfer energy with ATP
– Encode hereditary information in DNA
• Tremendous diversity of life
– Bacteria-----whales----sequoia trees
• Biologists group organisms based on shared characteristics
Taxonomy
• Field of biology concerned with identifying and naming
• Binomial system devised by Linnaeus
• Classification is how species and higher groups are placed into the taxonomic
hierarchy
Systematics
• Since fossil records are not complete, scientists rely on other types of
evidence to establish the best hypothesis of evolutionary relationships
• Systematics is the study of evolutionary relationships
• Phylogeny is a hypothesis about the evolutionary relationships among groups
Tree of life
• Darwin envisioned that all species were descended from a single common
ancestor
• He depicted this history of life as a branching tree
– Now called a cladogram
Cladogram
• Twigs of a tree represent existing species
• Joining of twigs and branches reflects the pattern of common ancestry back in
time to a single common ancestor
Phylogenies depict evolutionary relationships
Early trees
• Similarity may not accurately predict evolutionary relationships
– Early systematists relied on the expectation that the greater the time since
two species diverged from a common ancestor, more different would be
Evolution can happen quickly
Evolution is not unidirectional
Evolution is not always divergent
Evolutionary reversal can occur
Identifying inherited similarity
• Derived characteristic is similarity that is inherited from the most recent
common ancestor of an entire group
• Ancestral characteristic is similarity that arose prior to the common ancestor of
the group
Modern systematics - cladistics
• Only shared derived characters are considered informative about evolutionary
relationships
• To use the cladistic method, character variation must be identified as ancestral
or derived
Using characters
• Characters can be any aspect of the phenotype
– Morphology
– Physiology
– DNA
– Behavior
• Characters should exist in recognizable character states
Ancestral vs. derived characters
• Presence of hair is a shared derived feature of mammals
• Presence of lungs in mammals is an ancestral feature; also present in
amphibians and reptiles
Determination of ancestral versus derived
• First step in a manual cladistic analysis is to polarize the characters (are they
ancestral or derived)
– Outgroup comparison is used to assign character polarity
Cladistics
• When the group under study exhibits multiple character states, and one of
those states is exhibited by the outgroup, then that state is ancestral and other
states are derived
• Most reliable if character state is exhibited by several different outgroups
Teeth absence polarization
• Presence of teeth in mammals and reptiles is ancestral (also found in outgroup
of fish)
• Absence of teeth in birds and turtles is derived
Constructing a cladogram
• Clade is a group of species that share a common ancestor as indicated by the
possession of shared derived characters
• Clades are evolutionary units and refer to a common ancestor and all
descendants
• Synapomorphy is a derived character shared by clade members
Cladogram
• A simple cladogram is a nested set of clades
• Plesiomorphies are ancestral states
• Symplesiomorphies are shared ancestral states
Classifying vertebrates
Complications in cladistics
• Homoplasy is a shared character state that has not been inherited from a
common ancestor
– Results from convergent evolution and evolutionary reversal
• If there are conflicts among characters, use the principle of parsimony which
favors the hypothesis that requires the fewest assumptions
Parsimony and homoplasy
Building a cladogram with DNA
Limitations of use of parsimony
• Some characters evolve rapidly and principle of parsimony may be misleading
• Rate of DNA evolution can be high
– Mutations in non-functional sequences are not affected by natural selection,
but are affected by genetic drift
Statistical approaches
• Neighbor-joining method
• Maximum likelihood method
• Bayesian method
Molecular clock
• Branches in a cladogram can be dated using the fact that the rate of a
molecule is constant over time in a given group
Systematics and classification
• A monophyletic group includes the most recent common ancestor of the group
and all of its descendants (clade)
• A paraphyletic group includes the most recent common ancestor of the group,
but not all its descendants
• A polyphyletic group does not include the most recent common ancestor of all
members of the group
Mismatches
• Taxonomic hierarchies are based on shared traits, should reflect evolutionary
relationships
• Difficulties changing current perception
– i.e., dinosaurs as birds rather than reptiles
Monophyletic group
Paraphyletic group
Polyphyletic group
• Warm-blooded
Old classification system
New classification system
Phylogenetic species concept (PSC)
• Focuses on shared derived characters
• Species should be applied to groups of populations that have been evolving
independently of other groups
Strengths of PSC
• PSC can be applied to allopatric populations
• PSC can be applied to both sexual and asexual species
Weakness of PSC
Comparative biology
• Phylogenetics is the basis of all comparative biology
• Homologous structures are derived from the same ancestral source
• Homoplastic structures are not
Homologous behavior
Homoplastic convergence
• Saber teeth
– Occurred in different groups of extinct carnivores
– Similar body proportions
– Similar predatory lifestyle
– Most likely evolved independently at least 3 times
Distribution of saber-toothed mammals
Homoplastic convergence
• Plant conducting tubes
– Sieve tubes facilitate long-distance transport of food that is essential for the
survival of tall plants
– Brown algae also have sieve elements
– Closest ancestor a single-celled organism
Convergent evolution of conducting tubes
Evolution of complex characters occur in steps
• Birds adapted for flight
– wings, feathers, light bones, breastbone
• Initial stages of a character may evolve as an adaptation to some
environmental selective pressure different from current use
– First feather-like structure evolved in theropod phylogeny for insulation or
perhaps decoration
Testing hypotheses with phylogenies
• Larval dispersal in marine snails
– Some snails produce microscopic larvae that drift in the ocean currents
– Some species have larvae that settle to the ocean bottom and do not
disperse
– Fossils show increase in nondispersing snails
Increase through time in proportion of species whose larvae do not disperse
Competing hypotheses
• Evolutionary change from dispersing to nondispersing occurs more often than
change in the opposite direction
• Species that are nondispersing speciate more frequently, or become extinct
less frequently than dispersing species
• The two processes would result in different phylogenetic patterns
Hypothetical trees
Which hypothesis is more likely?
Loss of larval stage in marine invertebrates – non-reversible?
Alternative hypothesis
Species diversification
• Use phylogenetic analysis to suggest and test hypotheses about why some
groups have greater species richness than others
Evolutionary diversification of the Phytophaga
Evolution of disease
• HIV evolved from a simian viral counterpart SIV
– Current estimate: >39 million people infected; > 3 million die each year
– SIV found in 36 species of primates
Evolution of HIV
• HIV descended from SIV
• Independent transfers of different strains from different primate species
Disease transmission
• Evidence use to convict dentist for infecting patient