Figure 1.
Sampling sites and geographic distribution of the northern muriqui.
Map highlighting the southeast section of Brazil with sampled populations overlaid on the northern muriqui distribution, which is based on [36] (left, state acronyms: BA – Bahia, MG – Minas Gerais, ES – Espírito Santo, RJ – Rio de Janeiro). Sampling sites and some of the landscape features at SMJ are shown on the large map (right).
Table 1.
Sampled localities, number of sampled individuals, and molecular diversity indices (h, haplotype diversity; π, nucleotide diversity; s, number of polymorphic sites).
Figure 2.
Nine alternative scenarios tested with the Approximates Bayesian Computation approach.
Only the four best sampled populations were included (PESB, PERD, RPPN-FMA, and SMJ). The scenarios are organized in three groups of three each. The first group includes scenarios that depicts a rapid or star-like divergence event among the populations (1, 2, and 3). Scenario 1 assumes that one large population split into four populations during the Holocene (t1). Scenarios 2 and 3 push the splitting event further back in time (during the last glacial maximum, t2, and earlier, t3, respectively). The second group includes three scenarios (3, 4, and 5) representing sequential or step-wise divergence among the populations in different times. The third group includes scenarios with sequential divergences and assumes that the population RPPN-FMA (FMA) diverged after an admixture event. Different branch colors represent putative changes in effective population sizes (see Figure S1 for prior set up). The posterior probability of each scenario is shown on the lower left-hand side of its respective diagram.
Figure 3.
Rarefaction analysis showing the changes in haplotype richness relative to successive increments in sample sizes.
Rarefaction curves of two groups of populations sampled for at least ten individuals. The test was significant for the differences in haplotype richness between these groups (t = 12.5, df = 19, P<0.0001). The mean number of haplotypes found in 10 samples randomly drawn from the group PERD/PESB/SMJ was 7.0 (SD = 1.3), whereas the mean was roughly half as much (X = 3.5, SD = 0.2) for the groups found in smaller areas (RPPN-FMA/RPPN-MS).
Figure 4.
Haplotype network, haplotype distributions, and intrapopulation genetic distances.
Median-joining network depicting haplotype relationships is shown on the left side. The areas of the circles are proportional to the relative abundance of each haplotype (the smallest circle represents 1 sample, the largest circle represents 33 samples). Each node between two haplotypes or median vectors (small open circles) accounts for one mutational step (transition or transversion), unless indicated by two vertical dashes, which account for two transitions. A star shows the single transversion detected in the respective node (h21–h22). The map on the right side shows the haplotype frequencies (pie charts) within each population. Each color represents one of the 23 haplotypes. The chart area is scaled to the sample size. The bar graph (inset) in the center of the figure displays the lower and upper bound genetic distances calculated between pairs of haplotypes within each proposed management unit (MU) population. While the lower bound distances were the same in all groups (0.3%, gray section of each bar), intrapopulation divergences (black sections of each bar) did not deviate substantially from the overall (TOTAL) level.
Table 2.
Pairwise ΦST between muriqui social groups for RPPN-FMA (upper left) and Santa Maria do Jetibá (lower right).
Figure 5.
Bayesian skyline plot depicting the population size of northern muriquis over time.
Bayesian skyline plot showing an overall stable population size in northern muriquis. A modest population decline near the end of the last glacial maximum (roughly 10000 years ago) may have occurred and it is possibly associated with the recent population subdivision shown in the ABC analysis (see Fig. 2). The solid line is the median, and the shaded area around it is the 95% HPD estimate of the historic female effective population size (Nef) not corrected for generation time (τ). Timing of events was estimated assuming a substitution rate of 3.7×10−8 s/s/y (2.1×10−8<μ<6.0×10−8 s/s/y, see text for details). Time is shown from 0 (present) to 120 kya (the lower estimate of the 95% HPD around tMRCA).