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Why species are not independent data points and what to do about it: correlation on independent contrasts
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Independent contrasts can be calculated between all nodes: X4 - X5 X2 - X3 X6 - X7 X1 - X8 Ancestral reconstruction: tricky Assumption of a constant rate of evolution along each node - ancestral value is an average of those for its descendants X6 = (X2+X3)/2 different branch lengths - the average is weighted by branch length
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Phylomatic: An on-line tool for plant phylogenies
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An example: species A-H, traits X and Y, phylogeny with equal branch lengths Traits for deeper nodes as mean values of sister lineages
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X Y 12 15 4 20 3 18 2 23 20 5 10 10 38 3 25 8 (((A,B),(C,D)),((E,F),(G,H))); (((A:2,B:3):3,(C:2,D:4):3):2,((E:16,F:19) :17,(G:12,H:10):32):18); Phylogeny without branch lengths Phylogeny with branch lengths Compare: one of many independent contrasts software options Data [with variability within species]
![X Y (((A,B),(C,D)),((E,F),(G,H))); (((A:2,B:3):3,(C:2,D:4):3):2,((E:16,F:19) :17,(G:12,H:10):32):18); Phylogeny without branch lengths Phylogeny with branch lengths Compare: one of many independent contrasts software options Data [with variability within species]](http://images.slideplayer.com/25/7838671/slides/slide_5.jpg "X Y (((A,B),(C,D)),((E,F),(G,H))); (((A:2,B:3):3,(C:2,D:4):3):2,((E:16,F:19) :17,(G:12,H:10):32):18); Phylogeny without branch lengths Phylogeny with branch lengths Compare: one of many independent contrasts software options Data [with variability within species]")
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And now, an exercise for you:
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