4. Speciation Biological species definition: “... groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups.” - Mayr, 1942

5. Ring Species

6. Displays all OUT at predefined cutoffs User defined OUT algorithms: nearest-neighbor (single- linkage) furthest-neighbor (complete linkage) Average-neighbor (UPGMA) Schloss, et al, AEM, in press Schloss, et al, AEM, in press

7. How do you define an Operational Taxanomic Unit (OTU)? SSU rRNA surveys have traditionally used a 3% or 1% identity cut-off. “…organisms that have less than 97.0% sequence homology will not reassociate to more than 60%…”

8. Overview of K-means Algorithm Randomly assign sequences to K clusters Calculate centroid for each cluster Assign each sequence to centroid with which it shares the highest identity Recalculate centroids based on new clusters Reiterate steps until…

9. Dotur : Defined distance = 0.01 Complete-linkage 98 sequences PAM : 93 clusters

10. Speciation Biological species definition: “... groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups.” - Mayr, 1942 Speciation in plants: –Galeopsis tetrahit, which was made artificially by hybridizing G. pubescens and G. speciosa - Müntzing, 1930 –Two species of primrose - deVries, 1905 & Digby, 1912 –Raphanobrassica - Karpchenko, 1927 –8 more examples Speciation in animals: –Apple maggot flies (Rhagoletis pomonella) - Feder et al, 1988 –Gall Former flies (Eurosta solidaginis) - Craig et al, 1993 –Fruit flies (Drosophila paulistorum) - Dobzhansky & Pavlovsky, 1971

14. Sutter, et al, Science, Sutter, et al, Science, April 6, 2007 April 6, 2007

15. QTL & Fixed Mutations in Dogs Sutter, et al, Science, Sutter, et al, Science, April 6, 2007 April 6, 2007

16. SNP 5 in Dogs Sutter, et al, Science, Sutter, et al, Science, April 6, 2007 April 6, 2007

17. Apple Maggot & Hawthorn Berry Maggot Flies Rhagoletis pomonella

19. Fig. 17-18, p.273

23. -Vila, et al. 1997

24. Phylogeny of dogs Lindblad-Toh et al, Nature, 2005