Dr. Walter Salzburger
Molecules as documents of evolutionary history
Documents of Evolutionary History | 2
“The most rational, universal and informative molecular phylogeny will be built on semantophoretic molecules alone”
Zuckerkandl and Pauling (1965) Documents of Evolutionary History | 3
Linus Carl Pauling (1901-1994)
! quantum chemistry (USA)
! Nobel Prize (1954) for his work “on the nature of chemical bonds”
! Nobel Peace Price (1962) for his campaign against nuclear testing
! founder of molecular biology; influential in the fields of molecular evolution, molecular medicine, etc.
Documents of Evolutionary History | 4
Emile Zuckerkandl (1922-)
! biologist (Austria, USA)
! protein chromatography and electrophoresis in Linus Pauling’s lab
! Zuckerkandl & Pauling (1962): concept of molecular clocks
! founder of molecular evolution; founding editor of the Journal of Molecular Evolution Documents of Evolutionary History | 5
! Semantophoretic molecules, semantides are molecules that carry information of genes of transcripts thereof: DNA, mRNA, polypeptides (proteins)
! Episemantic molecules are synthesized under the control of (tertiary) semantides but in the absence of a template.
! Asemantic molecules are not produced by the organism and do not express information that this organism contains (e.g. vitamins, phosphate ion).
“It is plain that asemantic molecules are not worthy in inquiries about phylogenetic relationships.”
Zuckerkandl and Pauling (1965)
Documents of Evolutionary History | 6
The comparison of homologous semantophoretic molecules yields threefold information:
! the approximate time of existence
! the probable amino-acid sequence of the ancestor
! the lines of descent along which changes occurred
Zuckerkandl and Pauling (1965) Documents of Evolutionary History | 7
Nucleic acids: basis of all life on Earth
Documents of Evolutionary History | 8
Three domains of life Documents of Evolutionary History | 9
Three domains of life
16S rRNA
Carl Woese (1928-)
Documents of Evolutionary History | 10 cellular processes: rRNA subunits Documents of Evolutionary History | 11 genomic architecture: Hox gene clusters
anterior posterior Swalla (2006)
Documents of Evolutionary History | 12 mutational difference: foxp2 in apes Fisher & Marcus (2006) Documents of Evolutionary History | 13 molecular evolution of foxp2 in apes
chimpanzee
gorilla orangutan
1 mutation rhesus
Enard et al. (2002)
Documents of Evolutionary History | 14
diagram of evolutionary history
(phylogenetic) treehuman phylogeny chimpanzee
gorilla evolutionaryorangutan tree 1 mutation rhesus Documents of Evolutionary History | 15
“The stream of heredity makes phylogeny: in a sense, it is phylogeny. Complete genetic analysis would provide the most priceless data for the mapping of this stream”
Simpson (1945)
George G. Simpson (1902-1984)
Documents of Evolutionary History | 16
mutational change inheritance + Documents of Evolutionary History | 17
...CCGGCCTAGTC...... CCGGCCTATTC...... CCGGCCTAGTC...... CCGGCCTATTC...... CCGGCCTAGTC...... CCGGCCTATTC...... CCGGCCTAGTC...... CCGGCCTATTC...... CCGGCCTATTC...... CCGGCCTATTC...... CCGGCCTATTC...... CCGGCCTATTC...... CCGGCCTATTC...... CAGGCTTATTC...... CCGGCCTATTC...... CAGGCTTATTC... space ...CCGGCCTATTC...... CCGGCTTATTC...... CAGGCTTATTC...... CCGGCCTATTC...... CCGGCTTATTC...... CAGGCTTATTC...... CCGGCCTATTC...... CCGGCTTATTC...... CCGGCCTATTC...... CCGGCTTATTC...... CCGGCTTATTC...... CCGGCTTATTC...... CCGGCTTATTC...... CCGGCTTATTC...... CCGGCTTATTC...... CCGGCTTATTC...
time
Documents of Evolutionary History | 18
...CCGGCCTAGTC...
...CCGGCCTATTC...
...CAGGCTTATTC...... CCGGCCTATTC...
...CCGGCTTATTC...
...CCGGCTTATTC...
time Documents of Evolutionary History | 19
Ernst Haeckel (1834-1919)
Documents of Evolutionary History | 20
! Phylogeny of plants based on morphological characters
liverworts hornworts mosses tracheophyta
multicell. ! true lignin rhyzoids ! ! branched sporoph. non-synchr. oil bodies ! spore production ! ! xylem pseudo-elaters ! ! phloem lunularic acid ! ! perine layer on spores
elaters in sporangium ! ! ability to distinguish D-methionine ! stomates
Bremer (1985) Documents of Evolutionary History | 21
Molecular phylogeny of Cetacea and Artiodactyla
Ursing & Arnason (1998)
Documents of Evolutionary History | 22
phylogeny, evolutionary tree “leaf”, operational taxonomic unit (OTU)
terminal node
internal node
root Documents of Evolutionary History | 23 phylogeny, evolutionary tree
terminal node
root
Documents of Evolutionary History | 24 phylogeny, evolutionary tree
A B C D E Documents of Evolutionary History | 25
Venn diagram
A B C D E
Documents of Evolutionary History | 26
Venn diagram
A B C D E
Nested parentheses
((A , B), (C, (D , E)) Documents of Evolutionary History | 27
((A , B), (C, (D , E))
A B C D E E D C B A
C B B C D D A A E E
Documents of Evolutionary History | 28
Rooted and unrooted trees
E D C B A C D B
TIME E A rooted tree unrooted tree
- has a defined “root” - no defined direction
- and therefore a defined - no information about direction ancestry Documents of Evolutionary History | 29
The resolution of trees
E D C B A E D C B A
unresolved (star-tree) fully resolved
E D C B A polytomy
partially resolved
Documents of Evolutionary History | 30
The basic kinds of threes
A B C D A B C D A B C D 0 2 1 2 4 1 1 4 cladogram phylogram dendrogram (“additive tree”) (“ultrametric tree”)
shows relative shows branch tips are aequidistant recency of lengths/amount of from the root, nodes common ancestry evolutionary change reflect evoluionary time Documents of Evolutionary History | 31
Tree terminology I: outgroup, ingroup and sistergroup
sister ingroup group outgroup A B C D E
root
Documents of Evolutionary History | 32
! A character can be - in relative terms - ancestral or derived. Ancestral character stages are referred to as plesiomorphies, derived ones as apomorphies.
Sarcopterygii Polypteriformes Chondrostei Teleostei
swimm bladder lung Documents of Evolutionary History | 33
Tree terminology II: ancestral/derived character states
apomorphy plesiomorphy autapomorphy
A A G G A G G G A G G G G G mutation
synapomorphy homoplasy
A A G G A G G A
A G G G G G
Documents of Evolutionary History | 34
! A monophyletic group contains a common ancestor and all of its descendants
Deuterostomia et al.:
Monophyletic groups are natural. Looking at the animal phylogeny Deuterostomia on the right, many of the major animal clades* are monophyletic, e.g.,: ! Deuterostomia Ecdysozoa ! Ecdysozoa ! Lophotrochozoa
*clade is in fact a synonym Lophotrochozoa of monophyletic group Hofer & Salzburger (2005) Documents of Evolutionary History | 35
! A paraphyletic group contains a common ancestor and some, but not all of its descendants
‘Reptilia’: ‘reptiles’ The ‘Reptilia’ are a paraphyletic group. The species included in the ‘Reptilia’ still resemble their ancestor morphologically. The birds birds, however, have evolved crocodiles lizards turtles more rapidly and no longer resemble their ancestor but have evolved a variety of derived characters. Note that if a group is not monophyletic, its name is put in quotation marks.
Documents of Evolutionary History | 36
! A polyphyletic group is a set of taxa descended from more than one common ancestor
‘Vultures’: ‘Vultures’ ‘Vultures’ are a polyphyletic grouping comprised of birds that have independently evolved similar morphology and habits from different ancestors. New World Vultures storks birds of prey Old World Vultures www.wikipedia.com www.haveyouseenmybird.com Documents of Evolutionary History | 37
Molecular clocks
“The persistence of memory”, Salvador Dalí (1931)
Documents of Evolutionary History | 38
“Soft watches, biologically speaking, are the giant Dalinian DNA molecules which constitute the factors of eternity”
Dalí (~1961)
Salvador Dalí (1904-1989) Documents of Evolutionary History | 39
! Molecular clock is the theory that molecules evolve at an approximately constant rate
! The difference between the form of a molecule in two species is then proportional to the time since divergence from a common ancestor
! The molecular clock hypothesis is a testable prediction
Documents of Evolutionary History | 40
molecular clock in hemoglobin
human/ kangaroo 100 human/ dog/ cow cow 75 rabbit/ rodent
llama/ 50 horse/ cow human/ donkey rodent goat/ horse/ cow cow 25 pig/ Nucleotide substitutions cow sheep/ cow 0 0 25 50 75 100 125 Millions of years ago Kimura (1993) Documents of Evolutionary History | 41
molecular clock in hominoids as revealed by DNA hybridiation common chimp pygmy chimp human gorilla orangutan common gibbon siamang gibbon Old World monkeys 0 0
1 5
2 10 3 15 4 20 5 25
% difference in DNA 6 before present (in Myr) 7 30
8 35 Sibley & Ahlquist (1987)
Documents of Evolutionary History | 42
Is there a universal molecular clock?
Rate of amino acid Rate of nucleotide Gene evolution evolution Albumin 0.92 6.08 "-globin 0.56 4.92 #-globin 0.78 3.36 Immunoglobin V 1.1 5.87 Parathyroid hormoneno!1.0 4.57 Relaxin 2.59 8.98 Ribosomal S14 0.02 2.18 average (45 genes) 0.74 4.25 Li (1997), Ridley (2004) in changes per 10" years for an average site Documents of Evolutionary History | 43
Relative rate test: rate constancy in a molecule in two independent lineages?
k=x+y l=y+z m=x+z Sarich and Wilson (1977)
Documents of Evolutionary History | 44 and K/T boundary
Bininda-Emonds et al. (2007) mammalian radiation