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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:
Monotremes
Marsupials
Placental
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