The tree of life,

triumphs and

tribulationsin 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 evidencefor the occurrence of evolution.

2. Darwin provided a mechanism for howevolution 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 of 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; and 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, and 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 pigeon 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 evidencefor the occurrence of evolution.

2. Darwin provided a mechanism for howevolution worked - NATURAL SELECTION

3. Changed the way we “think” about the Natural World

What did Darwin do right?

1,Darwin provided overwhelming evidencefor the occurrence of evolution.

2. Darwin provided a mechanism for howevolution worked - NATURAL SELECTION

3. Changed the way we “think” about the Natural World

A. Population Thinking

"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

GToLAs 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).

Letter to J. D. Hooker dated June 8, 1858.

• "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. ''

What did Darwin do right?

1,Darwin provided overwhelming evidencefor the occurrence of evolution.

2. Darwin provided a mechanism for howevolution worked - NATURAL SELECTION

3. Changed the way we “think” about the Natural World

A. Population ThinkingB. Tree Thinking

"Thus, as I believe, species are multiplied, and genera areformed. '’ (the Origin)

plants animals manearth

plants animals manearth

plants animals manearth

vegetal soul

plants animals manearth

vegetal soul

animal soul

plants animals manearth

vegetal soul

animal soul

rational soul

plants animals manearth

vegetal soul

animal soul

rational soul

With apologies toOlivier Rieppel

?

Is there a “ToL” ?

Climbing around the tree of life

The “mother” of all Metazoa?

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

01

01

COUNT AS HGTF

COUNT AS HGTF

10

10

All apomorphies in a treecan be categorized as HGT or noHGT

01

01

1010

NO HGTF

01

8000

7000

6000

5000

4000

3000

2000

1000

0

genefamilies

0 50 100 150 200 250 300

- E value

Figure 2

HGT measured as per gene and per total

The extent of Horizontal Gene Transfer

1.00.90.80.70.60.50.40.30.20.10.0

0 50 100 150 200 250 300

Rholf

CFI

Figure 3

And By removing genes expected of HGT at different e valuesresulting trees were unresolved at crucial nodes, dissolving well-established relationships.

Removing HGT makes things worse !!Part 2

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 ?

Gene ContentPartition

Amino Acid AlignmentPartition

+ +

Supermatrix for a tree of life

7,000,000 Characters>1,000,000 PIC

?

Is there a “ToL” ?

Climbing around the tree of life

The “mother” of all Metazoa?

Us and the“ToL” ?

How to arrange major groups of animals??

Nervous system

-+

+

+

+

2 2 (3) 1

Placozoa

-

6 5 (6) 5

?

Is there a “ToL” ?

Climbing around the tree of life

The “mother” of all Metazoa?

Us and the“ToL” ?

360 feet long

Each step is 75 MY

Earth is formed4.5 billion years ago

Life begins on planet3.5 billion years ago

Complex Eukaryotes Evolve – 500 millionYears ago

Dinosaurs go extinct65 million years ago

Earth is formed4.5 billion years ago

Life begins on planet3.5 billion years ago

Complex Eukaryotes Evolve – 500 millionYears ago

Dinosaurs go extinct65 million years ago

At the very end is a humanhair. Its width representsthe amount of time Homosapiens has been senescent.

30,000-60,000 YEARS AGO

What do fossil genomes tell us?

We like to do “it”

30,000-60,000 YEARS AGO

John Smith

Genome Sequence

What can human genomes tell us about ourselves

1.Natural Selection

2.Relationships

3.Variation

When Human Genomes were first sequencedit was shown that the average number of singlenucleotide polymorphisms between any two peoplewas 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 SNPsto over 20 million total.

Many of these SNP variants are “rare” in that they appear inthe genomes of only one or a few genomes so far sequenced.

Single Nucleotide Polymorphism

As of this year over 20 million single nucleotidepolymorphisms have been discovered in humangenomes.

A recent study from U Penn found 3 to 5 million novel SNPs in the genomes of people from Africa.

Natural Selection

Either direct measuresor proxies (linkagedisequilibrium, Fst) aremeasured along length of the genome.

Departures fromneutral expectationare detected.

Such regions are candidates forbeing under selection.

What can human genomes tell us about ourselves

1.Natural Selection

2.Relationships

3.Variation

Y chromosomeX chromosome

Chromosome 20

Using common SNP variants

Y Chromosome

10 5 1

X Chromosome

10 5 1

Chromosome 20

10 5 1

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.

Colbert Ma LongoriaCaucasian

Asian

African

Colbert Ma LongoriaCaucasian

Asian

African

BACTERIA PREDICTED: > 10,000,000 DESCRIBED AND CATALOGUED: 7,000