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

1. The tree of life, triumphs and tribulationsin the age of genomics

2. Mora et al., 2011.

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

4. 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?

5. 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

6. 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.

7. 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

8. 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

10. GToL

11. 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).

12. "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.

15. 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

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

23. earth plants animals man

24. earth plants animals man

25. earth plants animals man vegetal soul

26. earth plants animals man animal soul vegetal soul

27. earth plants animals man rational soul animal soul vegetal soul

28. earth plants animals man rational soul animal soul vegetal soul With apologies to Olivier Rieppel

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

32. HGT-mechanisms

33. 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.

35. 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

36. 01 COUNT AS HGTF 01 01 10 10 COUNT AS HGTF All apomorphies in a tree can be categorized as HGT or noHGT 01

37. 10 10 NO HGTF 01

38. 8000 7000 6000 5000 4000 3000 2000 1000 0 TOT AL n-HGT HGT gene families 0 50 100 150 200 250 300 - E value Figure 2

39. The extent of Horizontal Gene Transfer HGT measured as per gene and per total

40. 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 Rholf CFI 0 50 100 150 200 250 300 Figure 3

41. 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.

42. Three tests for a vertical tree of life • Does a massively concatenated matrix give a resolved tree ? • Is the resulting tree ROBUST ? • Is the resulting tree biologically meaningful ?

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

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

48. How to arrange major groups of animals??