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