Introductory Phylogenetics and the Blue line in DNA Subway

Sheldon McKay

DNALC, Cold Spring Harbor Laboratory

March 28, 2012

Why is the tree of life important?

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“Knowledge of evolutionary relationships is fundamental to biology, yielding new insights across the plant sciences, from comparative genomics and molecular evolution, to plant development, to the study of adaptation, speciation, community assembly, and ecosystem functioning.”

Tree of Life: Classification and Phylogeny

Image from http://tolweb.org/tree

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We have a tendency to put things into categories.

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AB C

DE

F

Classifications often reflect evolutionary history

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Phylogenetic trees are representations of evolutionary history

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evolution

phylogen*

2007

phylogen*29,28238%

evolution77,816100%

ecolog*62,76182%

ecolog*

Figure courtesy of Brian Omeara 7

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What is the difference between taxonomy and phylogeny?

(E) human

Consider primates: Do humans make up a monophyletic group?

Hylobatidae Pongidae

Hominidae

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Phylogeny based on a globin pseudogene suggests thathumans and chimpanzees make up a single monophyletic group

outgroup

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Are there practical uses for phylogenetics?

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Consider the “Tripoli Six”

Are there practical uses for phylogenetics?

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Six Medical aid workers who arrived in Libya were accused of causing an HIV outbreak amongst 400 children at a Libyan hospital.

Forensic phylogenetic analysis showed that the strains of HIV and HCV were prevalent in the hospital well before the team arrived in 1990

The six were convicted and sentenced to death anyway. They were laterre-tried and sentenced to life. They were eventually released.

Trait Evolution

Image courtesy of Brian Omeara

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Rotifera Platyhelminthes Annelida Mollusca Nematoda Arthropoda Echinodermata Vertebrata

gain gain

Are the “Camera eyes” in molluscs and vertebrates homologous?

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http://phe.rockefeller.edu/barcode/blog/wp-content/uploads/2006/12/titmice-tree2.gif

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Phylogenetic tree as a reference for barcode-based species identification

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? Barcode x

Phylogenetic tree as a reference for barcode-based species identification

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The Blue Line

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