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Speciation

Speciation. Biological species definition: “... groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups.” - Mayr, 1942. Ring Species. Schloss, et al , AEM, in press. Displays all OUT at predefined cutoffs

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Speciation

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

  2. Ring Species

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

  4. 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%…”

  5. 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…

  6. 93 clusters • Dotur: • Defined distance = 0.01 • Complete-linkage • 98 sequences • PAM: • 93 clusters

  7. 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

  8. Sutter, et al, Science, • April 6, 2007

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

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

  11. Apple Maggot & Hawthorn Berry Maggot Flies Rhagoletis pomonella

  12. Fig. 17-18, p.273

  13. -Vila, et al. 1997

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

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