Partie I

1
BIN1001 – Intégration biosciences/informatique
Devoir 4, session hiver 2005
À remettre le vendredi 1 Avril 2005, avant 17 :00
Partie I
Six positions nucléotidiques ont été extraites d’un alignement de génomes du HIV2. L’arbre
le plus parcimonieux a été obtenu en utilisant l’ensemble de l’alignement. Le but de l’exercice
est, pour ces six positions, de (1) trouver le nombre minimum de changements et (2)
proposer un scénario possible de l’histoire évolutive (c’est-à-dire les nucléotides ancestraux
à chaque nœud interne et l’ensemble des substitutions) qui soit le plus parcimonieux.
Position 1
/------------------------------------------------------------------------------ A
+------------------------------------------------------------------------------ A
| /-------------------------------------------------------------------- A
| | /--------------------------------------------------------- C
| | | /---------------------------------------------------- A
| | /----+ | /----------------------------------------------- C
| | | | | | /------------------------------------------ A
| | | \----+ | | /-------------------------- A
| | | | | | | /----- C
| | | \----+ | | /----+----- C
| | | | | /---------+ /-----+---------- C
| /----+ | | | | | /----+ /----- C
| | | | \----+ | | | \----------+----- C
| | | | | | \----+ /----- A
| | | | | | \---------------+----- A
| | | | | | /----- G
| | | | | | /----+----- G
| | | | \-----+ /-----+---------- G
| | | | | /----+---------------- G
| | \-----+ | /----+ /----- G
| | | | | \---------------+----- G
| | | | /----+ /----- G
| | | | | \--------------------+----- G
| | | \----+ /----- G
\----+ | \-------------------------+----- A
| | /----- G
| | /---------------+----- A
| | | /----- C
| | /----+ /----+----- G
| | | | /-----+---------- G
| | /----+ \----+---------------- C
| | | \-------------------------- T
| | | /----- A
| \------------------------------+ /----+----- A
| | /-----+---------- A
| \--------------+---------------- T
| /----- C
\-------------------------------------------------------------------+----- A

2
Position 2
------------------------------------------------------------------------------- G
+------------------------------------------------------------------------------ A
| /-------------------------------------------------------------------- T
| | /--------------------------------------------------------- A
| | | /---------------------------------------------------- G
| | /----+ | /----------------------------------------------- A
| | | | | | /------------------------------------------ A
| | | \----+ | | /-------------------------- G
| | | | | | | /----- G
| | | \----+ | | /----+----- G
| | | | | /---------+ /-----+---------- G
| /----+ | | | | | /----+ /----- G
| | | | \----+ | | | \----------+----- G
| | | | | | \----+ /----- G
| | | | | | \---------------+----- A
| | | | | | /----- A
| | | | | | /----+----- A
| | | | \-----+ /-----+---------- A
| | | | | /----+---------------- A
| | \-----+ | /----+ /----- A
| | | | | \---------------+----- A
| | | | /----+ /----- A
| | | | | \--------------------+----- A
| | | \----+ /----- A
\----+ | \-------------------------+----- A
| | /----- G
| | /---------------+----- A
| | | /----- T
| | /----+ /----+----- T
| | | | /-----+---------- A
| | /----+ \----+---------------- T
| | | \-------------------------- G
| | | /----- T
| \------------------------------+ /----+----- T
| | /-----+---------- T
| \--------------+---------------- A
| /----- A
\-------------------------------------------------------------------+----- G

3
Position 3
------------------------------------------------------------------------------- G
+------------------------------------------------------------------------------ A
| /-------------------------------------------------------------------- A
| | /--------------------------------------------------------- T
| | | /---------------------------------------------------- A
| | /----+ | /----------------------------------------------- A
| | | | | | /------------------------------------------ A
| | | \----+ | | /-------------------------- A
| | | | | | | /----- A
| | | \----+ | | /----+----- A
| | | | | /---------+ /-----+---------- A
| /----+ | | | | | /----+ /----- A
| | | | \----+ | | | \----------+----- A
| | | | | | \----+ /----- A
| | | | | | \---------------+----- A
| | | | | | /----- C
| | | | | | /----+----- C
| | | | \-----+ /-----+---------- C
| | | | | /----+---------------- C
| | \-----+ | /----+ /----- C
| | | | | \---------------+----- C
| | | | /----+ /----- C
| | | | | \--------------------+----- C
| | | \----+ /----- C
\----+ | \-------------------------+----- C
| | /----- G
| | /---------------+----- A
| | | /----- A
| | /----+ /----+----- G
| | | | /-----+---------- G
| | /----+ \----+---------------- G
| | | \-------------------------- T
| | | /----- G
| \------------------------------+ /----+----- G
| | /-----+---------- A
| \--------------+---------------- T
| /----- A
\-------------------------------------------------------------------+----- A

4
Position 4
/------------------------------------------------------------------------------ A
+------------------------------------------------------------------------------ G
| /-------------------------------------------------------------------- A
| | /--------------------------------------------------------- A
| | | /---------------------------------------------------- T
| | /----+ | /----------------------------------------------- T
| | | | | | /------------------------------------------ A
| | | \----+ | | /-------------------------- A
| | | | | | | /----- A
| | | \----+ | | /----+----- A
| | | | | /---------+ /-----+---------- A
| /----+ | | | | | /----+ /----- A
| | | | \----+ | | | \----------+----- A
| | | | | | \----+ /----- G
| | | | | | \---------------+----- G
| | | | | | /----- G
| | | | | | /----+----- G
| | | | \-----+ /-----+---------- A
| | | | | /----+---------------- A
| | \-----+ | /----+ /----- A
| | | | | \---------------+----- A
| | | | /----+ /----- A
| | | | | \--------------------+----- A
| | | \----+ /----- A
\----+ | \-------------------------+----- A
| | /----- C
| | /---------------+----- T
| | | /----- T
| | /----+ /----+----- T
| | | | /-----+---------- T
| | /----+ \----+---------------- A
| | | \-------------------------- T
| | | /----- A
| \------------------------------+ /----+----- A
| | /-----+---------- G
| \--------------+---------------- A
| /----- A
\-------------------------------------------------------------------+----- A

5
Position 5
/------------------------------------------------------------------------------ C
+------------------------------------------------------------------------------ C
| /-------------------------------------------------------------------- G
| | /--------------------------------------------------------- A
| | | /---------------------------------------------------- G
| | /----+ | /----------------------------------------------- G
| | | | | | /------------------------------------------ C
| | | \----+ | | /-------------------------- A
| | | | | | | /----- A
| | | \----+ | | /----+----- A
| | | | | /---------+ /-----+---------- A
| /----+ | | | | | /----+ /----- A
| | | | \----+ | | | \----------+----- A
| | | | | | \----+ /----- G
| | | | | | \---------------+----- G
| | | | | | /----- A
| | | | | | /----+----- A
| | | | \-----+ /-----+---------- A
| | | | | /----+---------------- A
| | \-----+ | /----+ /----- A
| | | | | \---------------+----- A
| | | | /----+ /----- A
| | | | | \--------------------+----- A
| | | \----+ /----- A
-----+ | \-------------------------+----- A
| | /----- A
| | /---------------+----- A
| | | /----- C
| | /----+ /----+----- C
| | | | /-----+---------- G
| | /----+ \----+---------------- C
| | | \-------------------------- A
| | | /----- G
| \------------------------------+ /----+----- G
| | /-----+---------- G
| \--------------+---------------- A
| /----- A
\-------------------------------------------------------------------+----- C