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? 2 “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 3

We have a tendency to put things into categories. 4

A B C D E F Classifications often reflect evolutionary history 5

Phylogenetic trees are representations of evolutionary history 6

evolution phylogen* 2007 phylogen* 29,282 38% evolution 77, % ecolog* 62,761 82% ecolog* Figure courtesy of Brian Omeara 7

8 What is the difference between taxonomy and phylogeny?

(E) human Consider primates: Do humans make up a monophyletic group? Hylobatidae Pongidae Hominidae 9

Phylogeny based on a globin pseudogene suggests that humans and chimpanzees make up a single monophyletic group outgroup 10

Are there practical uses for phylogenetics? 11 Consider the “Tripoli Six”

Are there practical uses for phylogenetics? 12 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 later re-tried and sentenced to life. They were eventually released.

Trait Evolution Image courtesy of Brian Omeara 13

Rotifera Platyhelminthes Annelida Mollusca Nematoda Arthropoda Echinodermata Vertebrata gain Are the “Camera eyes” in molluscs and vertebrates homologous? 14

15

Phylogenetic tree as a reference for barcode-based species identification 16

? Barcode x Phylogenetic tree as a reference for barcode-based species identification 17

The Blue Line 18