The tree of
life, triumphs
and
tribulations
in the age of
genomics
Mora et al., 2011.
BACTERIA
PREDICTED: > 10,000,000
DESCRIBED AND CATALOGUED: 7,000
Two simple kinds of questions can be asked
• 1. What are the relationships of organisms?
• 2. How do we use these relationships to
understand the natural world better?
What did Darwin do right??
1. Darwin provided overwhelming evidence
for the occurrence of evolution.
2. Darwin provided a mechanism for how
evolution worked - NATURAL SELECTION
The diversity of the breeds is something astonishing.
Compare the English carrier and the short-faced tumbler,
and see the wonderful difference in their beaks, entailing
corresponding differences in their skulls. The carrier, more
especially the male bird, is also remarkable from the
wonderful development of the carunculated skin about the
head, and this is accompanied by greatly elongated eyelids,
very large external orifices to the nostrils, and a wide gape o
f mouth. The short-faced tumbler has a beak in outline almost
like that of a finch; and the common tumbler has the singular
and strictly inherited habit of
flying at a great height in a compact flock, and tumbling in the
air head over heels. The runt is a bird of great size, with long, massive beak and large
feet; some of the sub-breeds of
runts have very long necks, others very long wings and tails,
others singularly short tails.
The barb is allied to the carrier, but, instead of a very long beak,
has a very short and very broad one. The pouter has a much
elongated body, wings, and legs; a
nd its enormously developed crop, which it glories in inflating, may well excite astonishment and
even laughter. The turbit has a very short and conical beak, with a line of reversed feathers down
the breast; and it has the habit of continually expanding slightly the upper part of the oesophagus.
The Jacobin has the feathers so much reversed along the back of the neck that they form a hood, a
nd it has, proportionally to its size, much elongated wing and tail feathers. The trumpeter and laugher,
as their names express, utter a very different coo from the other breeds. The fantail has thirty or even
forty tail-feathers, instead of twelve or fourteen, the normal number in all members of the great pigeo
n family; and these feathers are kept expanded, and are carried so erect that in good birds the
head and tail touch; the oil-gland is quite aborted.
What did Darwin do right?
1,Darwin provided overwhelming evidence
for the occurrence of evolution.
2. Darwin provided a mechanism for how
evolution worked - NATURAL SELECTION
3. Changed the way we “think” about the Natural World
What did Darwin do right?
1,Darwin provided overwhelming evidence
for the occurrence of evolution.
2. Darwin provided a mechanism for how
evolution worked - NATURAL SELECTION
3. Changed the way we “think” about the Natural World
A. Population Thinking
GToL
"The affinities of all the beings of the same class have
sometimes been represented by a great tree. I believe this
simile largely speaks the truth. The green and budding twigs
may represent existing species; and those produced during each
former year may represent the long succession of extinct species
...
GToL
As buds give rise by growth to fresh buds, and these, if
vigorous, branch out and overtop on all a feebler branch, so
by generation I believe it has been with the Tree of Life,
which fills with its dead and broken branches the crust of
the earth, and covers the surface with its ever branching
and beautiful ramifications" (Charles Darwin, 1859).
• "I will try to leave out all allusion to genera
coming in and out ... till when I discuss the
'Principle of Divergence,' which along with
'Natural Selection,' is the keystone of my
book; and I have very great confidence it is
sound. ''
Letter to J. D. Hooker dated June 8, 1858.
What did Darwin do right?
1,Darwin provided overwhelming evidence
for the occurrence of evolution.
2. Darwin provided a mechanism for how
evolution worked - NATURAL SELECTION
3. Changed the way we “think” about the Natural World
A. Population Thinking
B. Tree Thinking
"Thus, as I believe, species are multiplied, and genera are
formed. '’ (the Origin)
earth
plants
animals
man
earth
plants
animals
man
earth
plants
animals
vegetal soul
man
earth
plants
animals
animal soul
vegetal soul
man
earth
plants
animals
man
rational soul
animal soul
vegetal soul
earth
plants
animals
man
rational soul
animal soul
vegetal soul
With apologies to
Olivier Rieppel
Climbing around the tree of life
?
The “mother” of all Metazoa?
Is there a “ToL” ?
Us and the“ToL” ?
HGT-mechanisms
Comb of Life
Recently, whole genome prokaryotic and Tree of Life (ToL) phylogenetics has been viewed
as a useless, inscrutable endeavor because of the prevalence of horizontal gene transfer
(HGT). Specifically, Bapteste et al (2007) claim:
“it is safer to assume a comb-like topology of life”.
This “safe” topology would be a soft polytomy, or the lack of resolution at deep nodes in
the tree due to the inability, because of HGT, of the data at hand to resolve a
bifurcating relationship.
Identify all gene families with more than one gain on the optimal
tree. (multiple 0 --> 1 changes called HGTF’s)
Test if the exclusion of
HTGFs improves
phylogenetic resolution or
consistency by removing
misleading, homoplastic
phylogenetic signal
01
COUNT AS HGTF
01
01
10
10
All apomorphies in a tree
can be categorized as HGT or noHGT
COUNT AS HGTF
01
10
10
NO HGTF
01
8000
7000
n-HGT
6000
5000
gene
families
4000
3000
2000
1000
0
0
50
100
150
200
250
300
- E value
Figure 2
The extent of Horizontal Gene Transfer
HGT measured as per gene and per total
tree
cd tree
AA tree
P/A tree
per gene
per total
0.179
6.80%
0.188
7.20%
0.181
6.90%
Rholf
CFI
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.0
Combined
0
50
100
150
200
250
300
Figure 3
Removing HGT makes things worse !!
Part 2
And
By removing genes expected of HGT at different e values
resulting trees were unresolved at crucial nodes, dissolving well-established relationships.
Three tests for a vertical tree of life
1. Does a massively concatenated matrix give a resolved tree ?
2. Is the resulting tree ROBUST ?
3. Is the resulting tree biologically meaningful ?
Supermatrix for a tree of life
Gene Content
Partition
+
+
Amino Acid
Alignment
Partition
7,000,000 Characters
>1,000,000 PIC
Climbing around the tree of life
?
The “mother” of all Metazoa?
Is there a “ToL” ?
Us and the“ToL” ?
How to arrange major groups of animals??
+
+
+
+
2
2 (3)
1
Nervous system
Placozoa
-
6
5 (6)
5
Climbing around the tree of life
?
The “mother” of all Metazoa?
Is there a “ToL” ?
Us and the“ToL” ?
360 feet long
Each step is 75 MY
Earth is formed
4.5 billion years ago
Life begins
on planet
3.5 billion
years ago
Complex Eukaryotes
Evolve – 500 million
Years ago
Dinosaurs go extinct
65 million years ago
Earth is formed
4.5 billion years ago
Life begins
on planet
3.5 billion
years ago
Complex Eukaryotes
Evolve – 500 million
Years ago
At the very end is a human
hair. Its width represents
the amount of time Homo
sapiens has been senescent.
Dinosaurs go extinct
65 million years ago
30,000-60,000 YEARS AGO
What do fossil genomes tell us?
We like to do “it”
30,000-60,000 YEARS AGO
What can human genomes tell
us about ourselves
1.Natural Selection
2.Relationships
3.Variation
Single Nucleotide Polymorphism
When Human Genomes were first sequenced
it was shown that the average number of single
nucleotide polymorphisms between any two people
was around 0.1% of the entire genome.
With only a few genomes sequenced this meant that
there were a few million SNPs discovered
Subsequent studies have increased the number of SNPs
to over 20 million total.
Many of these SNP variants are “rare” in that they appear in
the genomes of only one or a few genomes so far sequenced.
As of this year over 20 million single nucleotide
polymorphisms have been discovered in human
genomes.
A recent study from U Penn found 3 to 5 million
novel SNPs in the genomes of people from Africa.
Natural Selection
Either direct measures
or proxies (linkage
disequilibrium, Fst) are
measured along
length of the genome.
Departures from
neutral expectation
are detected.
Such regions are
candidates for
being under selection.
What can human genomes tell
us about ourselves
1.Natural Selection
2.Relationships
3.Variation
Using common SNP variants
Y chromosome
X chromosome
Chromosome 20
10
5
1
Y Chromosome
10
5
1
X Chromosome
10
5
1
Chromosome 20
What can human genomes tell
us about ourselves
1.Natural Selection
2.Relationships
3.Variation
What do Stephen Colbert and Charles
Darwin have in common?
What do Stephen Colbert and Charles
Darwin have in common?
• Would Charles Darwin pay for a DNA ancestry
test?
• Is Stephen Colbert really as he puts it “the
inescapable black hole of white people”?
1*
2*
I
II
III
IV
V
VI
VII
VIII
IX
X
AIMs
• Ancestral Informative Markers – AIMs
• “Cherry Pick” a Set of SNPs and use the “All
swans are white” approach
• All people with Caucasian AIMs are Caucasian
and so on.
Caucasian
Colbert
Ma
Longoria
Asian
African
Caucasian
Colbert
Ma
Longoria
Asian
African
BACTERIA
PREDICTED: > 10,000,000
DESCRIBED AND CATALOGUED: 7,000