Rekonstruktion stammbaum

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ChristophSchmid22

Kleine praktische Übung zu Grundlagen der Evolution

Bildung

1
“Tage der
Genforschung”
Rekonstruktion eines
Stammbaums
●
FMI, 16. Mai 2019
●
Christoph Schmid /
Kenji Shimada

2
Rekonstruktion der
Abstammung
●
Lebewesen verändern sich langsam
über Generationen
●
Unter gewissen Umständen können
solche Änderungen zur Auftrennung
in verschiedene Arten führen
●
Ein vereinfachtes Beispiel, wie man
aus dem heutigen Zustand und
genetischen Informationen die
Geschichte der Entwicklung
zurückverfolgen kann

4
Evolution einer Sequenz
ACGTCGTATG
ACGTCTTATG
ACGTCATATG

5
Evolution einer Sequenz
ACGTCGTATG
ACGTCTTATG
ACGTCATATG
ACGTCACATG
ACGTCAGATG
ACTTCTTATG
ACATCTTATG

6
Evolution einer Sequenz
ACGTCGTATG
ACGTCTTATG
ACGTCATATG
ACGTCACATG
ACGTCAGATG
ACTTCTTATG
ACATCTTATG
AAGTCACATG
ATGTCACATG
ACGTCAGGTG
ACGTCAGCTG
ACTACTTATG
ACTCCTTATG
ACATGTTATG
ACATATTATG

7
Gegenwärtiger Zustand
AACATAGTCG
AACATTGTCG
AAGGTCGTCG
AAGCTCGTCG
ATTATCTACG
ATTATCTCCG
ATTATCATGG
ATTATCATAG
?

8
Verschiedenheits-matrix
AACATAGTCG
AACATTGTCG
AAGGTCGTCG
AAGCTCGTCG
ATTATCTACG
ATTATCTCCG
ATTATCATGG
ATTATCATAG

9
Verschiedenheits-matrix
0
0
0
0
0
0
0
0
AACATAGTCG
AACATTGTCG
AAGGTCGTCG
AAGCTCGTCG
ATTATCTACG
ATTATCTCCG
ATTATCATGG
ATTATCATAG
=> Distanz zwischen identischen Sequenzen = 0

10
Verschiedenheits-matrix
0
0
0
0
0
0
0
0
AACATAGTCG
AACATTGTCG
AAGGTCGTCG
AAGCTCGTCG
ATTATCTACG
ATTATCTCCG
ATTATCATGG
ATTATCATAG
=> Distanzen reziprok, untere Matrix-Hälfte redundant!

11
Platziere die Sequenzen
passend im Stammbaum
●
Distanz ~= Summe der horizontalen Längen im Stammbaum (vertikale Position nicht entscheidend)

13
Verschiedenheits-matrix
0 3 5 1 5 5 3 5
0 5 3 5 5 1 5
0 5 1 3 5 3
0 5 5 3 5
0 3 5 3
0 5 1
0 5
0
AACATAGTCG
AACATTGTCG
AAGGTCGTCG
AAGCTCGTCG
ATTATCTACG
ATTATCTCCG
ATTATCATGG
ATTATCATAG

14
AACATAGTCG
AACATTGTCG
AAGGTCGTCG
AAGCTCGTCG
ATTATCTACG
ATTATCTCCG
ATTATCATGG
ATTATCATAG
Platziere die Sequenzen
passend im Stammbaum
●
Distanz ~= Summe der horizontalen Längen im Stammbaum (vertikale Position nicht entscheidend)

15
Offenkundigste Vereinfachungen
In realen Anwendungen
➔
haben Genomsequenzen verschiedene Längen
charakteristisch für die Art (zB. Mensch: 3* 109 Basenpaare)
➔
geschehen Veränderungen nicht so schön regelmässig, und
nicht nur an einer Position
➔
kann eine bestimmte Position in getrennten Arten mehrmalig
verändert werden
➔
ist die Erbinformation mehrfach redundant (DNA
Doppelstrang, doppelter Chromosomensatz)
➔
gibt es viele Veränderungen in einem Individuum, die nicht
charakteristisch sind für die Art
➔

16
Erweiterungen
Kleine Programmierübungen:
●
Berechnung der Distanzen zwischen
vorgegebenen DNA Sequenzen
●
Darstellung eines möglichen
Stammbaumes aus einer vorgegebenen
Distanzmatrix

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Rekonstruktion stammbaum

1. 1 “Tage der Genforschung” Rekonstruktion eines Stammbaums ● FMI, 16. Mai 2019 ● Christoph Schmid / Kenji Shimada

2. 2 Rekonstruktion der Abstammung ● Lebewesen verändern sich langsam über Generationen ● Unter gewissen Umständen können solche Änderungen zur Auftrennung in verschiedene Arten führen ● Ein vereinfachtes Beispiel, wie man aus dem heutigen Zustand und genetischen Informationen die Geschichte der Entwicklung zurückverfolgen kann

3. 3 Evolution einer Sequenz ACGTCGTATG

4. 4 Evolution einer Sequenz ACGTCGTATG ACGTCTTATG ACGTCATATG

5. 5 Evolution einer Sequenz ACGTCGTATG ACGTCTTATG ACGTCATATG ACGTCACATG ACGTCAGATG ACTTCTTATG ACATCTTATG

6. 6 Evolution einer Sequenz ACGTCGTATG ACGTCTTATG ACGTCATATG ACGTCACATG ACGTCAGATG ACTTCTTATG ACATCTTATG AAGTCACATG ATGTCACATG ACGTCAGGTG ACGTCAGCTG ACTACTTATG ACTCCTTATG ACATGTTATG ACATATTATG

7. 7 Gegenwärtiger Zustand AACATAGTCG AACATTGTCG AAGGTCGTCG AAGCTCGTCG ATTATCTACG ATTATCTCCG ATTATCATGG ATTATCATAG ?

8. 8 Verschiedenheits-matrix AACATAGTCG AACATTGTCG AAGGTCGTCG AAGCTCGTCG ATTATCTACG ATTATCTCCG ATTATCATGG ATTATCATAG

9. 9 Verschiedenheits-matrix 0 0 0 0 0 0 0 0 AACATAGTCG AACATTGTCG AAGGTCGTCG AAGCTCGTCG ATTATCTACG ATTATCTCCG ATTATCATGG ATTATCATAG => Distanz zwischen identischen Sequenzen = 0

10. 10 Verschiedenheits-matrix 0 0 0 0 0 0 0 0 AACATAGTCG AACATTGTCG AAGGTCGTCG AAGCTCGTCG ATTATCTACG ATTATCTCCG ATTATCATGG ATTATCATAG => Distanzen reziprok, untere Matrix-Hälfte redundant!

11. 11 Platziere die Sequenzen passend im Stammbaum ● Distanz ~= Summe der horizontalen Längen im Stammbaum (vertikale Position nicht entscheidend)

12. 12 Lösungen

13. 13 Verschiedenheits-matrix 0 3 5 1 5 5 3 5 0 5 3 5 5 1 5 0 5 1 3 5 3 0 5 5 3 5 0 3 5 3 0 5 1 0 5 0 AACATAGTCG AACATTGTCG AAGGTCGTCG AAGCTCGTCG ATTATCTACG ATTATCTCCG ATTATCATGG ATTATCATAG

14. 14 AACATAGTCG AACATTGTCG AAGGTCGTCG AAGCTCGTCG ATTATCTACG ATTATCTCCG ATTATCATGG ATTATCATAG Platziere die Sequenzen passend im Stammbaum ● Distanz ~= Summe der horizontalen Längen im Stammbaum (vertikale Position nicht entscheidend)

15. 15 Offenkundigste Vereinfachungen In realen Anwendungen ➔ haben Genomsequenzen verschiedene Längen charakteristisch für die Art (zB. Mensch: 3* 109 Basenpaare) ➔ geschehen Veränderungen nicht so schön regelmässig, und nicht nur an einer Position ➔ kann eine bestimmte Position in getrennten Arten mehrmalig verändert werden ➔ ist die Erbinformation mehrfach redundant (DNA Doppelstrang, doppelter Chromosomensatz) ➔ gibt es viele Veränderungen in einem Individuum, die nicht charakteristisch sind für die Art ➔

16. 16 Erweiterungen Kleine Programmierübungen: ● Berechnung der Distanzen zwischen vorgegebenen DNA Sequenzen ● Darstellung eines möglichen Stammbaumes aus einer vorgegebenen Distanzmatrix