Module 6 - Trees Readings HtDP 16 We will cover the ideas...

Info icon This preview shows pages 1–4. Sign up to view the full content.

View Full Document Right Arrow Icon
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
Image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
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 fruitfly 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
Image of page 2
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 )) ( define mammal ( make-t-ancient " Mammal " 65 primate rat )) ( define invertebrate ( make-t-ancient " Invertebrate " 530 fruit-fly worm )) ( define vertebrate ( make-t-ancient " Vertebrate " 320 mammal chicken )) ( define animal ( make-t-ancient " Animal " 535 vertebrate invertebrate )) CS 135 Fall 2008 06: Trees 9
Image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
Image of page 4
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern