1. Genes, gene families, and genomes How does genome evolution relate to development and paleontology? Understanding how genomes evolve How do we use genomic data to infer phylogeny?

3. Did the Cambrian Explosion actually happen?

4. Quartets Take fossils for AB and CD, plus molecular data, and extrapolate the age of the ancestor of ABCD.

5. Date estimates with 95% confidence intervals, given by quartets that passed the rate constancy test for the mitochondrial ( ) and 18S rRNA ( ) alignments, for two deep nodes: the split between vertebrates and echinoderms, and the split between deuterostomes (vertebrates and echinoderms) and protostomes

6. Phylogenetic Fuse Molecular dating suggests origins prior to diversification. Cambrian phylogenetic fuse Cooper & Fortey 1998 TREE

7. Can we reconcile fossil and molecular evidence?

8. Marine lakes in Palau (Philippines): a modern day analogue of Vendian conditions?

9. Jelly fish with photosynthetic symbioints Anemones that eat jellyfish Algal mat on lake floor (45 ft) Bacterial layer (90 ft)

10. Is there a link between macroevolution and genomics?

11. HOX genes Regulate development of segmentation in animals

12. Increasing complexity in vertebrates seems correlated with genome duplications

13. Copy ACopy B Gene duplication Two copies of original gene Copy B may be lost (e.g., lose function due to mutation) Copy B may evolve new function (A retains original function) Copy B may persist relatively unchanged (provides redundancy) Original gene Duplication event

14. Orthology and Paralogy ABC 123 456 123456 Orthologous Paralogous Gene duplication

15. Assumption: Gene tree = species tree ABC 123

16. Duplication and loss Duplication event Lineage goes extinct (gene loss) gene loss CB A 1 23

17. CB A 1 23 C B A 1 2 3 = incongruent gene and species trees

18. Is paralogy common?

19. Rhodopsin Gene duplication Gene loss (and/or) missing genes Complex relationship to species tree amphibian s sharks teleost fish mammals reptiles birds lampreys outgroups lungfish Key

20. Vertebrate gene families Number of sequences against number of species for gene families from the Hovergen database From Slowinski & Page, 1999 (Syst Biol 48:814)

21. Incongruent gene and species trees

22. d c b a b c d a 1 duplication 3 losses Embedding gene tree inside species tree

23. Gene tree parsimony We can identify duplications on gene trees, given a species tree Gene tree parsimony uses gene trees as characters, choosing the species tree that minimises duplications across a set of gene family trees James Cotton (PhD student) assembled 118 gene family trees from the Hovergen database...

24. Mitochondrial genomes (16,000 bp DNA) Nuclear genes (118 gene familes)

25. Why so many duplications in vertebrates? Possibly entire genome duplicated twice (2R hypothesis) Vertebrates Drosophila

26. Have there been genome duplications in vertebrates? Different hypotheses about the timing of genome duplication events (polyploidisation) during the evolution of vertebrates. Dark block indicates explosion of independent dupl. events along a single lineage. Rectangles indicate uncertainty in timing of events. Modified from Skrabenek & Wolfe, 1996 (Curr Op Genet Dev 8:694-).

27. Distribution of duplications

28. Summary Gene duplication and loss complicate interpretation of gene evolution Gene duplication very important in vertebrate evolution Genome duplication hypothesis still open (and controversial)