Module 6

Module 6 - Trees Readings: HtDP, section 14, 15, 16 We will...

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Unformatted text preview: Trees Readings: HtDP, section 14, 15, 16 We will cover the ideas in the text using different examples and different terminology. The readings are still important as an additional source of examples. CS 135 Fall 2008 06: Trees 1 Phylogenetic trees A phylogenetic tree is a data structure recording information about the evolution of species. It contains two kinds of information. One kind is about modern species, such as humans (Homo Sapiens). The tree will contain several modern species. In our example, for space reasons, we will represent the information about a modern species by one number, its current population. For humans, this is about 6.5 billion. CS 135 Fall 2008 06: Trees 2 The other kind of information represents evolutionary history. A “speciation event” leads to a splitting of one species into two distinct species (for example, through physical separation). For instance, humans and chimpanzees diverged about five million years ago. The second kind of information in a phylogenetic tree represents such events, as computed from genomic data. CS 135 Fall 2008 06: Trees 3 We will represent the information about the ancient species that was split by an assigned name and the time elapsed since the speciation event (in millions of years). The next slide contains a small example. Some of the population data is fictitious, and in general, each branch of a speciation event can lead to another speciation event. CS 135 Fall 2008 06: Trees 4 human 6.5 bil chimp 100000 rat 1 bil fruitFy 100 bil chicken 15 bil primate 5 mammal 65 vertebrate 320 animal 535 worm 50 bil invertebrate 530 CS 135 Fall 2008 06: Trees 5 Most trees in computer science are drawn branching downward, except where it is more natural to branch upwards, as in the ancestor family tree example in HtDP. The drawing, however, is just a visualization. We will use data definitions to be more precise about our data and derive templates. Since we have both ancient and modern species, we start with a definition of mixed data, using the terminology “taxonomic unit” or “taxon” for a species. CS 135 Fall 2008 06: Trees 6 Data definition: a taxon is a t-modern or a t-ancient . ( define-struct t-modern ( name pop )) ( define-struct t-ancient ( name age left right )) A t-modern is a ( make-t-modern name pop ) , where name is a string and pop is a number. A t-ancient is a ( make-t-ancient name age left right ) , where name is a string, age is a number, and left and right are taxons. CS 135 Fall 2008 06: Trees 7 ( define human ( make-t-modern " Homo Sapiens " 6500000000 )) ( define chimp ( make-t-modern " Pan Troglodytes " 100000 )) ( define rat ( make-t-modern " Rattus Norvegicus " 1000000000 )) ( define worm ( make-t-modern " Caenorhabditis Elegans " 50000000000 )) ( define fruit-fly ( make-t-modern " Drosophila Melanogaster " 100000000000 )) ( define chicken ( make-t-modern " Gallus Gallus " 15000000000 )) CS 135 Fall 2008 06: Trees 8 ( define primate ( make-t-ancient " Primate " 5 human chimp...
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This note was uploaded on 10/21/2010 for the course CS 135 taught by Professor Vasiga during the Fall '07 term at Waterloo.

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Module 6 - Trees Readings: HtDP, section 14, 15, 16 We will...

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