Topic : Phylogenetic Reconstruction

I. Systematics = Science of biological diversity. Systematics uses taxonomy to reflect phylogeny (evolutionary history).

- Based on cladistic analysis (will define shortly)

II. Taxonomy = identify, name and classify organisms.

Carl Linneaus (Swedish Prof. 1707-1778)

Binomial nomenclature, Genus species

III. Hierarchial Taxonomic Grouping: Plants

• Kingdom

• Phylum

• Class

• Order - names end in “ales”

• Family - names end in “aceae”

• Genus

• species

Table. Classification of Large Ground Finch and Common Buttercup

Figure: The connection between classification and phylogeny

IV. Classification and Phylogeny

• After the publication of Charles Darwin’s book On the Origin of Species (1859) differences and similarities among organisms became to be seen as the result of their evolutionary history = phylogeny.

• Phylogenetic Trees = trace evolutionary relationships among taxa.

• taxa (plural) taxon (singular) = named taxonomic unit at any level.

V. Types of Phylogenetic Trees

• Monophyletic = members of taxa result from single common ancestor. Only legitimate taxa derived from cladograms!

• Polyphyletic = members of taxa result from more than one common ancestor.

Figure: Monophyletic versus and polyphyletic groups

VI. Homology vs. Analogy

• Homologous Traits = Common origin.

• Similarity in structure = reflects common ancestry

• Characters reflect ancestral past.

• Examples:

Figure:  Homologous structures: anatomical signs of evolution

VI. Homology vs. Analogy

• Analogy = similarity in gross appearance and function DOES NOT reflect common ancestry.

• = traits or characters exhibit a common function BUT different evolutionary origins.

• Analogy DOES reflect similar selective pressures ----> Convergent Evolution.

• Ex., bird and insect wings,

• succulence in plants,

• Monotremes, marsupial, placental mammals

Figure: Convergent evolution and analogous structures: cactus and euphorb

Three types of Mammals:

MonotremesMarsupialsPlacental

VII. Molecular Markers aid Systematics

Two Approaches:

1) Sequence of amino acids in proteins – of human genome only 2%

2) Sequence of nucleotides in nucleic acids DNA and RNA comparisons via sequencing, restriction mapping and hybridization.

• Much data now held in electronic data bases.

• Goal: Identify and compare homologous DNA sequences among taxa.

How to identifying homologous nucleotide sequences:

1. Select appropriate portion of genome to compare.

• Often mtDNA segments for recently diverged taxa.

• Often rRNA genes for distantly related taxa – evolves slowly.

• Example: Aligning segments of DNA

• Today utilize sophisticated computer programs to analyze differences between sequences.

Figure: Aligning segments of DNA

Molecular Clock utility:

• Goal is to provide an independent assessment for the origin of taxonomic groups in time.

• Based on the fact: some proteins, cytochrome C and some mitochondrial genomes evolve at a constant rate of evolution over time.

• Thus, Molecular clocks are calibrated in actual time = graphing differences in sequences against time.

• However, some proteins and nucleic acids evolve at different rates.

• Molecular clocks also assume constant Mutation Rate?

• Utility may be minimal

Figure: Dating the origin of HIV-1 M with a molecular clock: In 2000 estimated invasion of aids into humans in 1930s. Evidence also for multiple origins of AIDs invading humans as well.

VIII. Science of Phylogentic Systematics

B. Cladistics - uses novel homologies to define branch points.

• Location of branch point = relative time of origin between taxa.

• Location of branch point = extent of divergence between branches or how different 2 taxa have become since diverging from a common ancestor.

• Recent branch versus deeper branch

VIII. Science of Phylogentic Systematics

C. Cladistic Analysis

• Clade = evolutionary branch

• Cladistic analysis groups organisms by order in time, clades arose along a dichotomous tree.

• Each branching point indicates a novel homology unique to the species on the branch.

• Uses ONLY homologies to construct trees!!!

• DOES NOT use level of divergence.

Figure: Cladistics and taxonomy:

Figure: Constructing a cladogram

VIII. Science of Phylogentic Systematics

C. Cladistic Analysis

• Uses outgroup comparison = to recognize primitive traits members of the study group AND to establish a starting point for the tree.

• Outgroup = Species or a group of species relatively closely related to study group BUT clearly NOT as related as any study group members are to each other.

• Outgroup & study group may share primitive characters, likely shared a common ancestor.

VIII. Science of Phylogentic Systematics

C. Cladistic Analysis• First, outgroup determines shared primitive character

states.

• Next, examine synapomorphies = shared derived character states to construct the tree.

• Synapomorphies = novel homologous traits that evolved in an ancestor common to all species on ONE branch BUT not on other branch.

• Parsimony = simplest tree using the fewest changes to show evolutionary relationships.

Figure: Constructing a cladogram

Figure: Parsimony and the analogy-versus-homology pitfall: 4 chambered heart is analogous NOT homologous

VIII. Science of Phylogentic Systematics

C. Cladistic Analysis Limitations

• Since focus solely on phylogenetic branching cladistic analysis accepts ONLY monophyletic study groups.

• Preferred approach is to use a combination of characters to design trees for study groups including: molecular, morphological, anatomical, ultrastructural, and developmental.

Figure: When did most major mammalian orders originate?

• The END FOR NOW