historical perspective: organizing life
Organic life beneath the shoreless waves
Was born and nurs'd in ocean's pearly caves;
First forms minute, unseen by spheric glass,
Move on the mud, or pierce the watery mass;
These, as successive generations bloom,
New powers acquire and larger limbs assume;
Whence countless groups of vegetation spring,
And breathing realms of fin and feet and wing.
Erasmus Darwin. The Temple of Nature. 1802
Linnaean classification for humans
•
•
•
•
•
•
•
•
• people have always been fascinated with
classification of organisms
• Linnaeus developed classification hierarchy
• Lamarck and others suggested “inheritance of
acquired traits”
• Charles Darwin proposed natural selection
• Mendelian genetics supported Darwin’s theory
• phylogenetics: study of evolutionary relationships
among organisms
• molecular-based phylogenetic tree reconstruction
• applications in understanding molecular function,
pathogenic diseases, antibiotic resistance
• in the future: role of lateral gene transfer
illustration in “Origin of the Species”
Domain: Eukaryota
Kingdom: Metazoa
Phylum: Chordata
Class: Mammalia
Order: Primata
Family: Hominidae
Genus: Homo
Species: Homo sapiens
1
the tree of life
the tree of life
http://tolweb.org/tree/
what molecules to use when reconstructing trees?
• small subunit (SSU) ribosomal RNA: "It is
abundant,... it has slow- and fast-moving portions
("hour hands and minute hands"), and it has a
universally conserved structure. Two other
factors...are its obviously ancient and essential
fundamental function...and its interaction with
many other coevolved cellular RNA's and
proteins... least liable of all genes to experience
interspecific lateral gene transfer" Doolittle, 1999
• leads to unrooted tree
rooting the tree of life
• Schwartz-Dayhoff developed the paragolous gene
outcrop method, used to root the tree of life
• organisms in all major groups have genes
encoding elongation factors : EF1A (EF-Tu), and
EF-2, (EF-G).
• these genes are paragalous genes, that is, products
of gene duplication that happened before split
from universal ancestor.
• tree made from these two sequences should have
two major subtrees, one per paralog, each having
topology of universal tree.
2
rooting the tree of life
A
rooting the tree of life
A, EF1A
E
A, EF2
E, EF1A
E, EF2
B
B,EF1A
root!
the human kinome
B, EF2
measuring evolutionary distance
• which hypothesis is correct?
•“A molecular time scale for human evolution”,
•by Wilson and Sarich, Proc Natl Acad Sci USA 1969.
3
measuring evolutionary distance
measuring evolutionary distance
• “The bulk of the available sequence information is
consistent with the hypothesis that for any given
protein, such as hemoglobin, the probability of an
amino acid substitution occurring in a given
interval of time is the same in every lineage. [...]
Regardless of the reason for this regularity in
protein evolution, however, its existence opens the
exciting possibility that protein molecules can be
used as evolutionary clocks.”
measuring evolutionary distance
... tree of life?
• “The Clock Approach.-Since regularity appears to have
characterized the evolution of ape, human, and monkey
hemoglobins and albumins, the close similarity of the ape
and human proteins must imply that these species diverged
from one another much more recently than did monkeys
from apes and man, as shown in phylogeny B (Fig. 1).
According to immunological criteria, the albumins of
chimpanzee, gorilla, and man are only about one sixth as
different from one another as they are from the albumin of
the rhesus monkey. It then follows from the regularity test
that the African apes and man diverged about six times
more recently than did rhesus monkey and man. As the
time of divergence between men and monkeys
(Hominoidea and Cercopithecoidea) can scarcely be
greater than about 30 million years, we have calculated
that the lineages leading to man and the African apes
diverged about 5 million years ago.”
4
resources
• “A molecular time scale for human evolution”, by Wilson
and Sarich, Proc Natl Acad Sci USA 1969.
• Phylogenetic classification and the universal tree, W. Ford
Doolittle, Science 1999
• “Biology's next revolution”, by Goldenfeld and Woese,
Nature 2007. “The emerging picture of microbes as geneswapping collectives demands a revision of such concepts
as organism, species and evolution itself.”
• NIH phylogenetics factsheet:
http://www.ncbi.nlm.nih.gov/About/primer/phylo.html
• tree of life website: http://tolweb.org/tree/
5