The tree of life triumphs and tribulations in

The tree of life, triumphs and tribulations in the age of genomics

Mora et al. , 2011.

BACTERIA PREDICTED: > 10, 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

GTo. L "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. . .

GTo. L 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 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 vegetal soul man

earth plants 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 “To. L” ? Us and the“To. L” ?

HGT-mechanisms

Comb of Life Recently, whole genome prokaryotic and Tree of Life (To. L) 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 1 0 All apomorphies in a tree can be categorized as HGT or no. HGT 0 1 COUNT AS HGTF

1 0 NO HGTF 0 1

8000 7000 TOT AL 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

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 no-HGT 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 ?

0 1 1 + 1 0 0 0 1 1 1 0 0 . . . species 3 1 0 0 species 5 1 1 0 species 4 Gene 1: Gene 2: Gene 3: . . species 2 species 1 Supermatrix for a tree of life Gene Content Partition + Amino Acid Alignment Partition 7, 000 Characters >1, 000 PIC

Climbing around the tree of life ? The “mother” of all Metazoa? Is there a “To. L” ? Us and the“To. L” ?

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 “To. L” ? Us and the“To. L” ?

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

John Gen ome Seq uenc e Smit h

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 IV V VI 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

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