La Coalescencia. wooding/TreeToy/ Mozilla Firefox.
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Transcript of La Coalescencia. wooding/TreeToy/ Mozilla Firefox.
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La Coalescencia La Coalescencia
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Especiación incipiente en el género Orestias en el Altiplano sur
Jimena Guerrero Fabiola Peña
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O. chungarensis
O.laucaensis
O.piacotensis
O. parinacotensis
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10 etapas:
1. Obtener las secuencias
2. Alinear las secuencias
3. Sitios Polimorficos
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4. Calcular los índices de diversidad (S, K, H, Π)
5. Realizar el test D de Tajima (y otros)
6. Construir la red de haplotipos (network)
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7. Inferencia demográfica a partir de la mismatch (crecimiento instantáneo)
8. Inferencia demográfica en base al modelo de crecimiento exponencial
9. Detectar variaciones de la taza de coalescencia visualizando una genealogía
10. Conclusiones
BEAST
Lamarc
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Abrir Orestias.nex
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Etapa 4. Calcular los índices de diversidad (S, K, H, Π)
1. Número de sitios polimórficos S
2. Número de haplotipos K
3. Diversidad H = 1 - pi2 (pi
2 : frecuencia del haplotipo i)
4. Número promedio de diferencias entre 2 secuencias
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Etapa 5. Realizar el test D de Tajima (y otros)
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Estadística de Tajima (D) = 2Ne
1
1
1)(
n
i iSE
E() = sensible a las frecuencias
2 estimadores de :
sólo al número de mutaciones
D 0 equilibrio mutación-deriva
D > 0 faltan haplotipos raros (cuello de botella)
D < 0 exceso de haplotipos raros (crecimiento)
)(n
n
aSVar
aS
D
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Etapa 6. Construir la red de haplotipos (network)
Generar orestias.rdf
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orestias.rdf
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Etapa 7. Construir la distribución del número de diferencias entre pares de secuencias
Rogers and Harpending 1992 (pdf)
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8. Inferencia demográfica en base al modelo de crecimiento exponencial
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Paso 1: Copiar “Orestias.xml” en el mismo directorio que Lamarc
Paso 2:
orestia.xml
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Paso 3: cambiar parametros
A
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G
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X
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Listo!!!!
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A
G
X
. iniciar programa
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Paso 5: abrir archivo Nt orestias.xls e incorporar los valores de g y
Paso 6: incorporar el valor de u
(esta vez por sitio y por año)
U = 2.10-8
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Etapa 9. Detectar variaciones de la taza de coalescencia visualizando una genealogía
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http://evolve.zoo.ox.ac.uk/webapps/skyline.html
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t = 0.495 x 1/u
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BEASTBayesian Ecological Analysis of Statistical Trends
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Estudio de caso N°4:
Conectividad en Galaxias maculatus
Pilar Salinas
Maculatus.nex (2 grupos: lago y Fiordo)
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Bajo Pascua
Fiordo
Lago
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fiordo lago
K
S
H
Pi
Tajima
Fu
-Network (todos juntos)
-Mismatch y estimacion tiempo expansion cuando relevante
-Fluctuate (lago.phy – fiordo.phy)