character alingnment Flashcards
informative macromolecules
DNA & proteins
Indirect inference of phylogeny
Characters that differ or are share Morphological Chromosomal Molecular Behavioral Ecological
Codes (states)
Binary, numerical, DNA and proteins
Homology in DNA
Locus Nucleotide position
Mutations in DNA & Kind of mutations
- Changes in DNA replications
- Errors by DNA polymerase
- Insertions
- Deletions
Keep in mind for Alingments
As hypothesis
- Number of substitutions
- Number of indels (insertion/deletion): gaps
- The most likely hypothesis
- Take the most parsimonius hypothesis
Errors in DNA polymerase
- Mutagenetic reagents
- radiation
- Genomin factors
Alignment & Problems
Columns in homologous positions
Sequences vary in length by insertions and deletions
Orthologous genes
The gen duplicate before speciation within the sp.
- Homologous genes
Paralogous genes
the gene duplicate after speciation, leading to two different genes.
Non homologous genes (no good phylogeny)
DNA vs Proteins
DNA
3 t more characters
than proteins
4 ch. states
No further editing
Proteins
3 times less
20 ch. states
RNA editing
How the morphological character states can change?
- Binary
- Continous data
- Ordered (Wagner)
- unordered (Fitch Parsimony): every step has the same likelihood. Change freely
- Irreversible: Carmin Sokal: when it goes back: infinito
- Present to absent many times, but just once the other way: Dollo
