Priors used for approximate bayesian computation (abc) analyses. N1= Effective population size



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Table S1 Priors used for approximate bayesian computation (ABC) analyses. N1= Effective population size (Ne) of Nothofagus cunninghamii from Tasmania; N2 = Ne of Nothofagus cunninghamii from central highland Victoria; NA= Ne of the ancestral population; NF1 = Ne of the founding population for Tasmania, NF2 = Ne of the founding population for VictoriaT1 and T2 = times of divergence in generations of the respective populations; DB = the duration of the bottleneck associated with the foundation of new populations. Conditions were set so that DB-3 and 10-5 mutations per locus per generation.


Parameter

Minimum

Maximum

Effective Population size







N1

10

10000

N2

10

10000

NA

10

10000

NF1

10

10000

NF2

10

10000

Time scale in generations







T1

10

10000

T2

10

10000

DB

10

10000

Mutation model







Mean mutation rate

1.00E-05

1.00E-03

Individual locus mutation rate

1.00E-05

1.00E-02

Mean coefficient P

1.00E-01

3.00E-01

Individual locus coefficient P

1.00E-02

9.00E-01

Mean SNI rate

1.00E-08

1.00E-05

Individual locus SNI rate

1.00E-09

1.00E-04


Table S2 Results of ABC analyses for estimated historical parameters of Nothofagus cunninghamii based scenario 3. N1= Effective population size (Ne) of Tasmania; N2 = Ne of central highland Victoria; t1 = time of divergence in generations; NA= Ne of the ancestral population; µmic_1= mean mutation rate; pmic = number of repeat motifs added or removed from the microsatellite in each mutation step and snimic = the single insertion nucleotide rate. Means, medians, modes and quantiles are given.


Parameter__N1__N2__t1__NA'>Parameter

N1

N2

t1

NA

µmic_1

pmic_1

snimic_1

mean

9.31E+03

1.45E+03

2.96E+02

1.27E+03

8.32E-04

2.73E-01

8.22E-06

median

9.50E+03

1.23E+03

2.24E+02

7.21E+02

8.55E-04

2.87E-01

9.86E-06

mode

9.98E+03

9.34E+02

1.67E+02

2.32E+02

1.00E-03

3.00E-01

1.00E-05

q025

7.53E+03

4.03E+02

5.94E+01

5.64E+01

5.32E-04

1.70E-01

5.52E-07

q050

7.98E+03

4.94E+02

7.70E+01

1.00E+02

5.83E-04

1.94E-01

1.35E-06

q250

9.02E+03

8.46E+02

1.49E+02

3.53E+02

7.44E-04

2.62E-01

7.52E-06

q750

9.79E+03

1.73E+03

3.44E+02

1.51E+03

9.43E-04

3.00E-01

1.00E-05

q950

9.97E+03

3.17E+03

7.05E+02

4.48E+03

1.00E-03

3.00E-01

1.00E-05

q975

9.98E+03

4.03E+03

9.05E+02

6.18E+03

1.00E-03

3.00E-01

1.00E-05


Table S3 Mean relative bias of the ABC analyses for estimated historical parameters of Nothofagus cunninghamii based on the present data sets for scenario 3. Parameters are explained in the caption for Fig. S1.

Parameter

Means

Medians

Modes

N1

0.064

0.0689

0.1366

N2

0.088

0.0358

-0.056

t1

0.206

0.119

0.0144

NA

1.273

1.089

0.5872

µmic_1

0.236

0.138

0.0061

pmic_1

0.04

0.0256

-0.0345

snimic_1

14.035

4.2132

-0.7812

Table S3 Posterior probabilities of all 12 scenarios estimated with a maximum of 1% of the simulated datasets. n = the number of simulated datasets closest to the observed used to estimate the posterior.


Scenario













n



















6858

13716

20574

27432

34290

41148

48006

54864

61722

68580

1

0.0042

(0.0000-0.0954)



0.007

(0.0000-0.0667)



0.0098

(0.0000-0.0558)



0.0108

(0.0000-0.0491)



0.0118

(0.0000-0.0454)



0.0123

(0.0000-0.0421)



0.0126

(0.0000-0.0396)



0.013

(0.0000-0.0378)



0.0134

(0.0000-0.0365)



0.0138

(0.0000-0.0356)



2

0.409

(0.2836-0.5345)



0.3932

(0.3034-0.4829)



0.3801

(0.3065-0.4537)



0.3702

(0.3062-0.4342)



0.3648

(0.3072-0.4224)



0.3579

(0.3053-0.4106)



0.3526

(0.3037-0.4014)



0.3483

(0.3026-0.3941)



0.3454

(0.3021-0.3887)



0.343

(0.3019-0.3842)



3

0.3257

(0.2012-0.4501)



0.3645

(0.2831-0.4459)



0.3765

(0.3126-0.4404)



0.383

(0.3271-0.4389)



0.3879

(0.3371-0.4387)



0.3934

(0.3464-0.4404)



0.3969

(0.3530-0.4409)



0.3987

(0.3573-0.4402)



0.3993

(0.3600-0.4387)



0.3993

(0.3618-0.4368)



4

0.0048

(0.0000-0.0960)



0.0064

(0.0000-0.0664)



0.0064

(0.0000-0.0530)



0.0068

(0.0000-0.0458)



0.0069

(0.0000-0.0411)



0.0071

(0.0000-0.0375)



0.0073

(0.0000-0.0348)



0.0076

(0.0000-0.0330)



0.0081

(0.0000-0.0318)



0.0086

(0.0000-0.0309)



5

0.0092

(0.0000-0.0996)



0.0104

(0.0000-0.0699)



0.0121

(0.0000-0.0583)



0.0136

(0.0000-0.0521)



0.0146

(0.0000-0.0484)



0.0151

(0.0000-0.0452)



0.0153

(0.0000-0.0426)



0.0156

(0.0000-0.0407)



0.016

(0.0000-0.0394)



0.0162

(0.0000-0.0383)



6

0.0003

(0.0000-0.0925)



0.0003

(0.0000-0.0613)



0.0004

(0.0000-0.0478)



0.0004

(0.0000-0.0400)



0.0004

(0.0000-0.0353)



0.0005

(0.0000-0.0315)



0.0005

(0.0000-0.0286)



0.0005

(0.0000-0.0265)



0.0006

(0.0000-0.0248)



0.0006

(0.0000-0.0235)



7

0.0786

(0.0000-0.1612)



0.0594

(0.0045-0.1143)



0.0586

(0.0158-0.1014)



0.0587

(0.0229-0.0944)



0.0579

(0.0264-0.0893)



0.0579

(0.0299-0.0859)



0.0583

(0.0328-0.0837)



0.059

(0.0356-0.0825)



0.06

(0.0380-0.0819)



0.0609

(0.0402-0.0817)



8

0.0368

(0.0000-0.1247)



0.0342

(0.0000-0.0926)



0.0342

(0.0000-0.0796)



0.0339

(0.0000-0.0719)



0.0332

(0.0000-0.0666)



0.0326

(0.0029-0.0623)



0.0325

(0.0055-0.0594)



0.0325

(0.0077-0.0574)



0.0319

(0.0087-0.0551)



0.0316

(0.0097-0.0535)



9

0.0395

(0.0000-0.1253)



0.0303

(0.0000-0.0874)



0.0282

(0.0000-0.0726)



0.0275

(0.0000-0.0646)



0.0269

(0.0000-0.0595)



0.0273

(0.0000-0.0562)



0.0277

(0.0015-0.0539)



0.0284

(0.0042-0.0525)



0.0289

(0.0064-0.0514)



0.0293

(0.0081-0.0505)



10

0.0292

(0.0000-0.1166)



0.0269

(0.0000-0.0848)



0.0264

(0.0000-0.0714)



0.0276

(0.0000-0.0651)



0.0273

(0.0000-0.0603)



0.0273

(0.0000-0.0566)



0.0276

(0.0011-0.0541)



0.0277

(0.0033-0.0521)



0.0277

(0.0049-0.0505)



0.0277

(0.0062-0.0492)



11

0.0166

(0.0000-0.1056)



0.0168

(0.0000-0.0756)



0.015

(0.0000-0.0607)



0.014

(0.0000-0.0522)



0.0139

(0.0000-0.0475)



0.0135

(0.0000-0.0434)



0.0132

(0.0000-0.0403)



0.0129

(0.0000-0.0379)



0.0128

(0.0000-0.0362)



0.0128

(0.0000-0.0348)



12

0.046

(0.0000-0.1312)



0.0506

(0.0000-0.1069)



0.0523

(0.0085-0.0962)



0.0535

(0.0167-0.0902)



0.0544

(0.0220-0.0867)



0.0552

(0.0263-0.0840)



0.0555

(0.0293-0.0817)



0.0557

(0.0315-0.0799)



0.056

(0.0333-0.0786)



0.0562

(0.0349-0.0775)






Figure S1 Proportion of membership of clusters identified using Structure assuming 2 clusters. Note the high incidence of the typically Tasmanian cluster (red) in the two southernmost Victorian populations. Barriers (predicted with BARRIER version 2.2) to gene flow are indicated by grey lines; the thickness of the edge of a barrier is proportional to the extent of the barrier and the adjacent numbers relate to the number of times the barrier was observed across samples.



Figure S2. The 12 scenarios tested for ABC analysis. The colours represent populations that are either observed (red for Victoria and dark blue for Tasmania) or inferred past populations (other colours). A change in colour represents formation of a new population.



Figure S3 The partitioning of genetic variance in N. cunninghamii based on (a) 10 loci, and (b) 12 loci. The 10 locus analysis should provide a less biased estimate of the partitioning of variance because it excludes the two loci with high levels of null alleles, which can cause overestimation of among individual variance. The levels are: between states, among populations within states, among subpopulations within populations, among individuals within subpopulations and within individuals, as identified by AMOVA.

a) Tasmania

b) Victoria

Figure S4 Plots of genetic distance versus geographic distance for (a) Tasmanian subpopulations, and (b) Victorian subpopulations. Mantel tests showed very highly significant associations between geographic and genetic distances within Victoria both including and excluding the isolated Kinglake population (P = 0.006 and P<0.001, respectively), but no significant association within Tasmania (P = 0.125).

Figure S5. Relationships between allelic richness (Ar) and altitude of all subpopulations in (a) Tasmania and (b) Victoria.

supp materials allele frequency histograms1.tif

supp materials allele frequency histograms2.tif

Figure S6 Allele frequency histograms showing the count of alleles across all 12 loci within six allele frequency classes within each of the 18 Nothofagus cunninghamii populations from Tasmania (a-k) and Victoria (l-r).

Figure S7 The posterior distribution (green lines) and prior distribution (red lines) of the effective populations size of (a) Tasmanian populations, (b) Victorian populations and (c) the time in generations of the divergence of these populations. The numbers in brackets are the median values of the posterior.

a)


b)




c)



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