MIGRATION RATE AND POPULATION SIZE ESTIMATION using the coalescent and maximum likelihood or Bayesian inference Migrate-n version 3.2.16 [] Program started at Mon Sep 17 15:44:33 2012 Program finished at Thu Sep 20 08:44:20 2012
Options Datatype: Missing data:
Microsatellite data [Brownian motion] not included
Inheritance scalers in use for Thetas: 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 [Each Theta uses the (true) ineritance scalar of the first locus as a reference] Random number seed: (with internal timer) Start parameters:
914982295
Theta values were generated
from the FST-calculation
M values were generated
from the FST-calculation
Connection type matrix: where m = average (average over a group of Thetas or M, s = symmetric M, S = symmetric 4Nm, 0 = zero, and not estimated, * = free to vary, Thetas are on diagonal Population 1 pop_1 2 pop_2 3 pop_3 4 pop_4
1 * * * *
2 * * * *
3 * * * *
Migrate 3.2.16: (http://popgen.sc.fsu.edu) [program run on ]
4 * * * *
-- 2
Order of parameters: 1 Θ1 2 Θ2 3 Θ3 4 Θ4 5 M 2−>1 6 M 3−>1 7 M 4−>1 8 M 1−>2 9 M 3−>2 10 M 4−>2 11 M 1−>3 12 M 2−>3 13 M 4−>3 14 M 1−>4 15 M 2−>4 16 M 3−>4
Mutation rate among loci:
Mutation rate is constant for all loci
Analysis strategy:
Bayesian inference
Proposal distributions for parameter Parameter Theta M
Proposal Slice sampling Slice sampling
Prior distribution for parameter Parameter Prior Minimum Theta Uniform 0.000000 M Uniform 0.000000
Mean* 15.000000 100.000000
Markov chain settings: Number of chains Recorded steps [a] Increment (record every x step [b] Number of concurrent chains (replicates) [c] Visited (sampled) parameter values [a*b*c] Number of discard trees per chain (burn-in) Multiple Markov chains: Static heating scheme Migrate 3.2.16: (http://popgen.sc.fsu.edu) [program run on 15:44:33]
Maximum 30.000000 200.000000
Delta 3.000000 20.000000
Bins 1500 1500
Long chain 1 15000 75 1 1125000 15000
4 chains with temperatures
-- 3 12.00
Print options: Data file: Output file: Log file: Posterior distribution raw histogram file: Print data: Print genealogies [only some for some data type]:
Migrate 3.2.16: (http://popgen.sc.fsu.edu) [program run on 15:44:33]
3.00
1.50 1.00 Swapping interval is 1
m=0.01-4980gen&0.005-20gen_006.txt m=0.01-4980gen&0.005-20gen_006 1 to 0.5 4980-06 bayesfile Yes None
-- 4
Data summary Datatype: Number of loci:
Population 1 pop_1
2 pop_2
Migrate 3.2.16: (http://popgen.sc.fsu.edu) [program run on 15:44:33]
Migrate 3.2.16: (http://popgen.sc.fsu.edu) [program run on 15:44:33]
-- 36
Bayesian Analysis: Posterior distribution over all loci
Freq
Freq 0.020
0.020
0.015 0.010
0.010 0.005 0.000 0.0
0.2
0.5
0.8
Θ1
1.0
Freq
0.000 0.0
0.5
1.0
1.5
Θ2
Freq
0.020
0.020
0.015 0.010
0.010
0.005 0.000 0.0
0.5
Θ3
1.0
1.5
0.000 0.0
Freq
Freq
0.020
0.020
0.2
0.5
Θ4
0.8
1.0
0.015 0.010
0.010
0.005 0.000
0.000 0
2
4
6
M
2−>1
Migrate 3.2.16: (http://popgen.sc.fsu.edu) [program run on 15:44:33]
8
0
2
5
M
8 3−>1
10
-- 37 Freq
Freq
0.020
0.020
0.015 0.010
0.010
0.005 0.000
0.000 0
2
5
8
M
10
0
2
4
M
4−>1
Freq
Freq
0.020
0.020
0.015
0.015
0.010
0.010
0.005
0.005
0.000
6
8
1−>2
0.000 0
2
5
M
8
10
0
2
5
M
3−>2
Freq
8
10
4−>2
Freq
0.020 0.020 0.015 0.015 0.010
0.010
0.005
0.005
0.000
0.000 0
5
10
M
15
0
2
5
8
M
1−>3
Freq
Freq
0.020
0.020
0.015
0.015
0.010
0.010
0.005
0.005
0.000
10
2−>3
0.000
Migrate 3.2.16: (http://popgen.sc.fsu.edu) [program run on 15:44:33]
0
5
M
4−>3
10
0
2
5
M
8 1−>4
10
-- 38 Freq
Freq
0.020
0.020
0.015 0.010
0.010
0.005 0.000
0.000 0
2
5
M
8 2−>4
Migrate 3.2.16: (http://popgen.sc.fsu.edu) [program run on 15:44:33]
10
0
2
5
M
8 3−>4
10
-- 39
Log-Probability of the data given the model (marginal likelihood)
Use this value for Bayes factor calculations: BF = Exp[ ln(Prob(D | thisModel) - ln( Prob( D | otherModel) or as LBF = 2 (ln(Prob(D | thisModel) - ln( Prob( D | otherModel)) shows the support for thisModel]
(1a, 1b and 2) is an approximation to the marginal likelihood, make sure the program run long enough! (1a, 1b) and (2) should give a similar result, (2) is considered more crude than (1), but (1) needs heating with several well-spaced chains, (1b) is using a Bezier-curve to get better approximations for runs with low number of heated chains [Scaling factor = 98.178015
Migrate 3.2.16: (http://popgen.sc.fsu.edu) [program run on 15:44:33]
-- 41
Acceptance ratios for all parameters and the genealogies
Parameter
Accepted changes
Ratio
Θ1 Θ2 Θ3 Θ4 M 2−>1 M 3−>1 M 4−>1 M 1−>2 M 3−>2 M 4−>2 M 1−>3 M 2−>3 M 4−>3 M 1−>4 M 2−>4 M 3−>4
This section reports potential problems with your run, but such reporting is often not very accurate. Whith many parameters in a multilocus analysis, it is very common that some parameters for some loci will not be very informative, triggering suggestions (for example to increase the prior range) that are not sensible. This suggestion tool will improve with time, therefore do not blindly follow its suggestions. If some parameters are flagged, inspect the tables carefully and judge wether an action is required. For example, if you run a Bayesian inference with sequence data, for macroscopic species there is rarely the need to increase the prior for Theta beyond 0.1; but if you use microsatellites it is rather common that your prior distribution for Theta should have a range from 0.0 to 100 or more. With many populations (>3) it is also very common that some migration routes are estimated poorly because the data contains little or no information for that route. Increasing the range will not help in such situations, reducing number of parameters may help in such situations.
Param 9 (Locus 2): Upper prior boundary seems too low! Param 8 (Locus 3): Upper prior boundary seems too low! Param 7 (Locus 7): Upper prior boundary seems too low! Param 12 (Locus 9): Upper prior boundary seems too low! Param 16 (Locus 19): Upper prior boundary seems too low! Param 15 (Locus 20): Upper prior boundary seems too low! Param 2 (Locus 21): Upper prior boundary seems too low! Param 15 (Locus 24): Upper prior boundary seems too low! Param 8 (Locus 27): Upper prior boundary seems too low! Param 13 (Locus 27): Upper prior boundary seems too low! Param 4 (Locus 30): Upper prior boundary seems too low! Param 5 (Locus 30): Upper prior boundary seems too low! Param 13 (Locus 30): Upper prior boundary seems too low!
Migrate 3.2.16: (http://popgen.sc.fsu.edu) [program run on 15:44:33]
Migrate-n version 3.2.16 []. Program started at Mon Sep 17 15:44:33 2012. Options. Datatype: Microsatellite data [Brownian motion]. Missing data: not included.
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