Microsatellite genotypes

This file contains raw genotypes for 17 microsatellite loci for two species of Rattus- R. rattus and R. satarae sampled in seven locations in Western Ghats

Model-checking to measure the discrepancy between the model parameter posterior combination and the real dataset for the three alternative demographic scenarios for the Upper Subansiri population of the Arunachal macaque.

<p>The summary statistics using datasets simulated with the prior distributions of the parameters, the observed data and the datasets from the posterior predictive distributions are represented on the plane of the first two principal components. The model (Scenario 2) fits the data well, as the cloud of datasets simulated from the prior (small green dots), datasets from the posterior predictive distribution (larger green dots) and the observed dataset (yellow circles) overlap completely.</p

Comparison of the three possible alternative demographic scenarios for the Upper Subansiri population.

<p>(A) Estimates of the posterior probability of each scenario and their comparison. Direct estimate: The number of times that a given scenario is found closest to the simulated datasets once the latter, produced under several scenarios, have been sorted by ascending distances to the observed dataset. Logistic regression: A polytomic weighted logistic regression was performed on the first closest datasets with the proportion contributed by each scenario as the dependent variable and the differences between the summary statistics of the observed and simulated datasets as the independent variables. The intercept of the regression, corresponding to an identity between simulated and observed summary statistics, was taken as the point estimate. In addition, 95% confidence intervals were computed <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097061#pone.0097061-Cornuet3" target="_blank">[41]</a>. In all these cases, Scenario 2 explained the observed data best. (B) Principal component analysis: Visual information on how data sets simulated under each scenario are close to the observed data set. Here too, Scenario 2 fits the observed data best <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097061#pone.0097061-Cornuet3" target="_blank">[41]</a>.</p

Possible alternative scenarios of the demographic history of the Upper Subansiri population.

<p>When tested using the ABC approach, Scenario 2 was best fit with the data (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097061#pone-0097061-t002" target="_blank">Table 2</a>). The details of each scenario parameterisation have been given in the Methods. The time-scale is indicated by the arrow on the left. T<i>₁</i> ranges between 20 and 4000 generations. Time has been measured backward in generations before the present. Gen: Generation.</p

Bayesian skyline plot reconstruction of past population size trajectory for the Upper Subansiri population.

<p>The plot is the product of female effective population size (f<i>N_e</i>) and mutation rate (<i>μ</i>) through time, assuming a substitution rate of 0.1643 substitutions per nucleotide per million years <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097061#pone.0097061-Chakraborty2" target="_blank">[29]</a>. The lower and upper 95% confidence interval for the Upper Subansiri TMRCA is also shown. LGM, Last Glacial Maximum, approximately 18 to 20 thousand years before present.</p

Model specifications and prior distributions for demographic parameters and locus-specific mutation model parameters.

<p>UN: Uniform distribution, with two parameters – minimum and maximum values; GA: Gamma distribution with three parameters – minimum and maximum values and shape parameter value; LU: Log-Uniform distribution with two parameters – minimum and maximum values. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097061#pone-0097061-g002" target="_blank">Figure 2</a> for the demographic parameters of each model tested. The mutation model parameters for the microsatellite loci were the mutation rate (<i>μ_mic</i>), the parameter determining the shape of the gamma distribution of individual loci mutation rate (<i>P</i>), and the Single Insertion Nucleotide rate (<i>SNI</i>).</p

Demographic parameters estimated under the best-supported demographic scenario (Scenario 2) of a recent population decline in the Upper Subansiri population of Arunachal macaques.

<p>Population sizes are given in effective number of diploid individuals. Time estimates were calibrated by assuming a generation time of 5 years <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097061#pone.0097061-Harvey1" target="_blank">[44]</a>.</p

Supporting tables from Social structure of the harem-forming promiscuous fruit bat, <i>Cynopterus sphinx</i>, is the harem truly important?

File contains supplementary tables S1 to S4

significant association index

List of significant association inde

Figure S1 from Social structure of the harem-forming promiscuous fruit bat, <i>Cynopterus sphinx</i>, is the harem truly important?

Frequency distribution of the observed association index