Who thought this was a good idea?

1. Who thought this was a good idea? http://www.youtube.com/watch?v=glii-kazad8

2. Corgis, dachshunds & achondroplaysia • How’d that happen?

3. Semester review • Flu viruses: how to reconstruct a tree-of-descent (phylogeny) • Blue eyes: it’s the same set of eyes, over and over again! • Milk drinking: genetically ‘solved’ by diff’t peoples in diff’t places • Sickle cell anemia: same mutation; different origins • That’s linkage • So is your recent proposal

4. Achondroplaysia: bone growth http://www.healthhype.com/achondroplasia.html

5. Papers • “Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication” Nature 464: 898-902 • “Genetic Structure of the Purebred Domestic Dog” Science 304: 1160-1164 • “An Expressed Fgf4 Retrogene is Associated with Breed-Defining Chondrodysplasia in Domestic Dogs” Science 325: 995-998 • “The Dog Genome: Sequence, Evolution, and Haplotype Structure” The Dog and Its Genome, Cold Spring Harbor Press 2006

6. Dog breeds are ‘real’ Each label marks five unrelated dogs of a breed Color indicates a pattern of sequences Note how each breed is different than others and individuals in it are same

7. FYI: ‘chunking’ dogs

8. Dachshund, corgi, basset hound Form hypotheses about short-legged dogs What predictions would you make about these breeds vs. other dog breeds?

9. Needles & Haystacks • All short-legged dogs have a specific form of the DNA chunk in a particular region of Chromo 18 • All other dogs lack that version of the chunk Ref. 3

10. TBA “An insert of about 5 kb starting at position 23,431,136 (fig. S1) was found by tiling poly- merase chain reaction (PCR) amplicons across the homozygous region. This insert was present in all dogs from the original eight breeds and 11 of 12 additional breeds that fit at least two of the three chondrodysplastic criteria (175 dogs from 19 breeds)” Ref. 3

11. Basset Hound Dachshund Corgis Where are ours? Flies in ointments Ref. 2

12. Stop! Think • How did dogs ‘happen’? • How did dog breeds ‘happen’?

13. Evolution, genes, individuals • Look around. There’s diversity in our little population here • How many ‘184 breeds’ could we create? • What would happen to the diversity in those subpopulations? • What if we selected for a PTC-tasting pool & a dimpled pool • What would be the eye color of each pool?

14. Population thinking • A species is a bunch of organisms that can interbreed • At any given time, then, it is not a genotype, but a collection of alleles • Hence the term ‘gene pool’ • To go back to an earlier lecture, evolution is defined simply as a change in the frequency of alleles in the gene pool

15. Looking back “Through… simulations, the experimental results were recapitulated using a dual-bottleneck population model for dog breeds, assuming commonly accepted mammalian mutation and recombination rates. With an initial domestication bottleneck... approximately 27,000 years ago (9000 generations) with an effective population size of 13,000, and a subsequent, breed-creation bottleneck, the simulated data successfully mimicked the [findings]. Modeling the second breed-creation bottleneck for individual dog breeds... breed creation about 50 generations ago (100–200 years) with a moderate bottleneck... recapitulates the experimental data and is consistent with historical records.” Ref. 4

16. River out of Eden* *Title of Richard Dawkins book