“Genetic evidence of range-wide population declines in an Australian marsupial prior to European settlement”

Anna Brüniche-Olsen, Stephanie L. Hazlitt, Mark D.B. Eldridge

SUPPLEMENTARY MATERIAL

S1. Description of population structure analysis.

To assess structure among the 12 sampled brush-tailed rock-wallaby colonies we used the Bayesian clustering method implemented in STRUCTURE v2.3.4 (Pritchard et al. 2000). Based on genotype the sample is partitioned into the most likely number of clusters (K) that maximises linkage equilibrium and Hardy-Weinberg equilibrium within the clusters. We used on MCMC with a burn-in of 1×105 iterations followed by 2×105 iterations for K from 1–13. For each value of K we applied 5 MCMC runs. STRUCTURE HARVESTER v0.694 (Earl & vonHoldt 2012) was used to identify the most likely K-value following the delta-K method (Evanno et al. 2005). We used CLUMPP (Jakobsson & Rosenberg 2007) to permute the clustering output from STRUCTURE and visualised the results in DISTRUCT v1.1 (Rosenberg 2004).

Figure S2. Posterior density distributions from MSVAR under the exponential model using identical priors were used for N0and N0. Current (log(N0)) and ancestral (log(N0)) effective population sizes are given for the North (a) and South (b) regions and for the populations within each region. Solid lines correspond to current effective population sizesand dashed lines correspond to ancestral effective population sizes. Priors indicated with dotted grey lines and the distributions are colored corresponds to the population/region colors used in Figure 1.

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Table S3. Genetic diversity indices for brush-tailed rock-wallaby populations sampled across Southeastern Australia based on eight microsatellite loci.

State / Population / n / AO / AR / HO / HE / FIS / P-value / Bonferroni corrected P-value
Queensland / Crows Nest NP / 12 / 2.9 / 2.0 / 0.448 / 0.457 / 0.019 / 0.259 / 0.008
Emu Creek / 10 / 3.5 / 2.7 / 0.612 / 0.614 / 0.002 / 0.477 / 0.025
Farm Creek East / 10 / 3.5 / 2.7 / 0.663 / 0.551 / -0.203 / 0.013 / 0.004
Farm Creek / 11 / 4.1 / 2.5 / 0.577 / 0.591 / 0.023 / 0.317 / 0.010
Hurdle Creek / 54 / 5.4 / 2.8 / 0.629 / 0.622 / -0.011 / 0.393 / 0.017
New South Wales / Armidale / 12 / 3.4 / 2.6 / 0.677 / 0.591 / -0.145 / 0.017 / 0.005
Bowmans Road / 20 / 5.1 / 3.3 / 0.725 / 0.713 / -0.082 / 0.779 / 0.050
Drews Creek / 20 / 4.4 / 2.9 / 0.638 / 0.645 / 0.010 / 0.342 / 0.013
Jenolan Caves / 30 / 3.3 / 3.5 / 0.524 / 0.670 / -0.113 / 0.036 / 0.006
Martindale / 7 / 4.3 / 2.2 / 0.732 / 0.471 / -0.027 / 0.016 / 0.005
Victoria / Rocky Plains Creek / 8 / 3.3 / 1.6 / 0.429 / 0.347 / 0.165 / 0.029 / 0.006
Little River / 8 / 2.3 / 2.2 / 0.438 / 0.513 / -0.260 / 0.076 / 0.007

Sample size (n), observed number of alleles (AO), effective number of alleles (AR), observed (HO) and expected heterozygosity(HE), and inbreeding coefficient (FIS).

Table S4. Results from BAYESASS for the 12 sampled brush-tailed rock-wallaby colonies. Proportion of immigrants in each population (row) from different source populations (column) is given. The diagonal indicated with bold represent the proportion of individuals in the population with no mixed ancestry. Mean and SD are given and M>0.15 are indicated with italics.

Crows Nest NP / Emu Creek / Farm Creek East / Farm Creek / Hurdle Creek / Armidale / Martindale / Drews Creek / Bowmans Road / Jenolan Caves / Rocky Plains Creek / Little River
Crows Nest NP / 0.851 (0.035) / 0.014 (0.013) / 0.014 (0.013) / 0.013 (0.013) / 0.016 (0.015) / 0.014 (0.013) / 0.013 (0.012) / 0.013 (0.013) / 0.014 (0.013) / 0.013 (0.013) / 0.014 (0.014) / 0.013 (0.013)
Emu Creek / 0.018 (0.017) / 0.683 (0.015) / 0.015 (0.015) / 0.016 (0.015) / 0.164 (0.033) / 0.015 (0.015) / 0.014 (0.014) / 0.015 (0.015) / 0.015 (0.014) / 0.015 (0.014) / 0.015 (0.014) / 0.015 (0.015)
Farm Creek East / 0.015 (0.014) / 0.014 (0.013) / 0.682 (0.014) / 0.016 (0.015) / 0.167 (0.031) / 0.015 (0.014) / 0.016 (0.014) / 0.015 (0.014) / 0.015 (0.014) / 0.016 (0.015) / 0.015 (0.015) / 0.015 (0.015)
Farm Creek / 0.015 (0.013) / 0.015 (0.014) / 0.015 (0.014) / 0.682 (0.015) / 0.172 (0.032) / 0.015 (0.014) / 0.015 (0.014) / 0.015 (0.014) / 0.014 (0.014) / 0.014 (0.014) / 0.014 (0.013) / 0.015 (0.014)
Hurdle Creek / 0.005 (0.005) / 0.006 (0.005) / 0.006 (0.005) / 0.005 (0.005) / 0.943 (0.015) / 0.005 (0.005) / 0.005 (0.005) / 0.005 (0.005) / 0.005 (0.006) / 0.005 (0.005) / 0.005 (0.005) / 0.005 (0.005)
Armidale / 0.013 (0.013) / 0.013 (0.013) / 0.014 (0.013) / 0.014 (0.013) / 0.013 (0.012) / 0.852 (0.035) / 0.014 (0.013) / 0.013 (0.012) / 0.013 (0.013) / 0.014 (0.013) / 0.014 (0.013) / 0.014 (0.014)
Martindale / 0.017 (0.016) / 0.017 (0.017) / 0.018 (0.017) / 0.018 (0.018) / 0.017 (0.017) / 0.017 (0.017) / 0.801 (0.039) / 0.019 (0.017) / 0.024 (0.021) / 0.017 (0.016) / 0.016 (0.016) / 0.018 (0.017)
Drews Creek / 0.010 (0.010) / 0.010 (0.009) / 0.010 (0.009) / 0.009 (0.009) / 0.010 (0.009) / 0.011 (0.010) / 0.010 (0.010) / 0.890 (0.028) / 0.011 (0.011) / 0.010 (0.010) / 0.010 (0.010) / 0.010 (0.010)
Bowmans Road / 0.010 (0.010) / 0.010 (0.010) / 0.011 (0.010) / 0.010 (0.010) / 0.011 (0.010) / 0.013 (0.012) / 0.011 (0.010) / 0.012 (0.011) / 0.882 (0.030) / 0.010 (0.010) / 0.010 (0.010) / 0.011 (0.011)
Jenolan Caves / 0.008 (0.007) / 0.007 (0.007) / 0.008 (0.008) / 0.007 (0.008) / 0.007 (0.007) / 0.007 (0.007) / 0.008 (0.008) / 0.008 (0.008) / 0.008 (0.008) / 0.918 (0.021) / 0.008 (0.008) / 0.007 (0.008)
Rocky Plains Creek / 0.017 (0.016) / 0.017 (0.015) / 0.017 (0.016) / 0.017 (0.016) / 0.016 (0.015) / 0.016 (0.015) / 0.016 (0.016) / 0.017 (0.015) / 0.017 (0.016) / 0.017 (0.016) / 0.819 (0.037) / 0.016 (0.014)
Little River / 0.016 (0.016) / 0.017 (0.016) / 0.016 (0.015) / 0.017 (0.015) / 0.016 (0.015) / 0.017 (0.016) / 0.017 (0.016) / 0.016 (0.015) / 0.017 (0.016) / 0.018 (0.017) / 0.149 (0.034) / 0.684 (0.017)

Table S5. Results from BAYESASS for the twoSTRUCTURE inferred clusters (K=2). Proportion of immigrants in each population (row) from different source populations (column) is given. The diagonal represent the proportion of individuals in the population with no mixed ancestry. Mean and SD are given.

North / South
North / 1.00 (0.00) / 0.00 (0.00)
South / 0.00 (0.00) / 1.00 (0.00)

Figure S6. Posterior density distributions from MSVAR under the exponential model. Current (log(N0)) and ancestral (log(N0)) effective population sizes are given for the North (a) and South (b) regions and for the populations within each region. Solid lines correspond to current effective population sizesand dashed lines correspond to ancestral effective population sizes. The time of change (T) in population size are given as log(T) for North (c) and South (d) regions. In all four plots priors are indicated with dotted grey lines and the distributions are colored corresponds to the population/region colors used in Figure 1.

Figure S7. Precision in parameter estimates from a) the population (K=8) and b) the regional (K=2) ABC analysis. Results are based on 500 pseudo-observed datasets (“pods”) simulated under the most likely demographic scenario (‘free’ model). Results are presented as ‘relative median error’ (RMAE) and depict RMAE for the prior information on parameters (without data) and RMAE for the posterior information (including data). The parameters correspond to: current (N0) and ancestral (N1) population sizes, timing of population decline (Tpopulation–name or ), region decline (Tregion–name), and time of divergence between the two regions (Tsplit). The mutation model is described by the mutation rate (μ), the parameter for change in length of repeat length (P), and the frequency of ‘single nucleotide inserts’ (SNI).

References

Earl D, vonHoldt B (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources4, 359-361.

Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology14, 2611-2620.

Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics23, 1801-1806.

Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics155, 945-959.

Rosenberg NA (2004) distruct: a program for the graphical display of population structure. Molecular Ecology Notes4, 137-138.

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