• The gene cannot be subject to transfer between species (lateral transfer). • The gene must display an appropriate level of sequence conservation for the divergences of interest. • The gene must be sufficiently large to contain a record of the historical information.
16S ribosomal RNA • Part of the ribosome • Required for translation of mRNA into protein. • Present in all bacterial (16S rRNA), archaeal and eukaryotic cells (18S rRNA)
Ribosomal RNAs are used as evolutionary chronometers because they... A. Are found in all living things. B. Evolve slowly but not too slowly. C. Can be sequenced relatively easily. D. Do not have variable regions. E. A, B, and C
• Estimate of the historical branching order of the species by the number of sequence changes. Comparison of rRNA sequences
Rooted versus Unrooted Trees Rooted trees Rooted trees reflect the most basal ancestor of the tree in question.
Rooted vs unrooted trees Unrooted trees Unrooted trees do not imply a known ancestral root.
Comparing Domains Property Eukarya Archaea Bacteria Organelles yes no no Mode of uptake endocytosis transport by membrane proteins transport by membrane proteins Multicellular yes no no RNA polymerase 12 proteins 9-12 proteins 4 proteins Ribosome 80S 70S* 70S* Cell walls none or cellulose proteins, pseudomurien, lattice None or Gram (-) or (+) Lipids ester-linked ether-linked ester-linked *proteins comprising the Archaeal ribosome are homologous to Eukaryotic proteins
WHY LIMIT TO 16S RNA?
Promiscuous microbes and traditional species Science 2008, 320:1031-1033 Microbes acquire new genes and traits, for example antibiotic resistance Genes acquired through conjugation, bacteriophage, and from the environment Species definition traditionally depends upon genes flowing vertically, parents to offspring DNA sequence data indicates that genes are moving freely between species multiple parents, how do you define species and taxonomic relationships?