Transcript phylogenetic_trees

Phylogenetic Trees
• Understand the history and diversity of life.
• Systematics.
– Study of biological diversity in evolutionary
context.
– Phylogeny is evolutionary history.
– Goal: Account for evolutionary history of all
species to origin of life.
Systematics Approaches
Modern systematist uses two techniques to classify
organisms:
• Based on anatomical
characteristics.
– Morphology.
– Fossil record.
• Based on molecular
characteristics.
– Genetic information.
• Nucleic acids.
• Proteins.
– Involves sequencing.
Phylogenetic Trees
• Organize comparative
information and form
hypothesis.
• Phylogenetic tree is a
diagram of the hypothesis.
– Traces evolutionary
relationships.
– Records the classifications
of organisms.
• Monophyletic groups share
a common ancestor.
• Polyphyletic groups do not
share a common ancestor.
Anatomical Characterization
• Degree of anatomical similarities between organisms
indicates evolutionary relatedness.
• Two major approaches.
– Characterizing the morphology of live animals:
• Description of physical characteristics.
• Unfeasible if extinct or unresolvable by microscopy (too
small).
– Studying fossil record:
• Array of fossils in layered rock.
• Radiometric dating determines age.
• Oldest ~ 3.5 billion years.
Molecular Techniques
• Protein sequencing:
– Digest a polypeptide, separate and sequence the fragments.
– Reconstruct sequence by matching regions of sequence
overlap.
– Algorithms provide local and global comparisons of protein
sequence data against a database.
– Advantages: Obtaining disulfide bond position and detecting
modified amino acids.
– Drawbacks: Only looking at genes that code for proteins (small
fraction of genome).
• Nucleic acid sequencing:
– mRNA, rRNA, genomic DNA.
– Automated high-throughput chain termination method cranks out
10,000 bp/day.
– Advantages: More complexity yields identification of new
lineages and viral strains.
– Drawbacks: Much nongene junk DNA, introns within gene, not
many genomes sequenced.
Protein Data
• Compare protein sequences of alike proteins for different
species.
• Comparison of sequences orders the divergence of species in
relative time.
• Problems with “molecular clock.”
– Proteins evolve at different rates.
– Changes in generation time or metabolic rate may affect a mutation
rate.
Nucleic Acid Data
• NCBI website BLAST alignment for 2 different HIV strains
(HIV-1 and HIV-2).
• Help characterize the different strains of HIV and their
evolutionary relationship to one another.
Tree Construction
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Based on comparisons of anatomical or sequence information.
Reference outgroup is more recent and closely related to the study groups,
but not as closely related as the study groups are to each other.
Distance of the branch from outgroup represents relative time of origin.
Between nodes ancestor changes from primitive to more recent condition.
Classifying Organisms
Two modern analytical taxonomic methods
– Phenetics:
• Classification based entirely on measurable similarities and
differences; no assumptions of homology are made.
• Compares as many anatomical characteristics as possible to
determine relatedness.
• Skeptics claim that phenotypic similarity alone is not sufficient
to judge phylogenetic relationships.
– Cladistics:
• Orders organisms along a phylogenetic tree in branches.
• Describes the extent of divergence between the branches. For
molecular sequence alignments, two major computational
approaches (PHYLIP and MEGA software):
– Distance-based: The overall distance between all sequence pairs
is calculated to construct a tree.
– Character-based: Individual substitutions along sequence pairs
are used to derive ancestral relationships.
Conclusion
• Data of two main types are used to determine
evolutionary relatedness: anatomical and molecular.
• Systematists construct phylogenetic trees to
represent inferred relationships between organisms.
• The strongest support for any phylogenetic
hypothesis is agreement between molecular data and
anatomical evidence (from living or fossilized
organisms).
• To represent the history and diversity of life in one
classification system is a goal far from realization.