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

• Based on anatomical characteristics.– Morphology.– Fossil record.

Modern systematist uses two techniques to classify organisms:

• 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

• 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 OrganismsTwo 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.