Table 1.
Summary of differences in parasitism between E. quagga populations.
Figure 1.
Statistical comparisons of diversity indices at β-Fibr and ELA loci (DRA and DQA) across populations.
Genetic diversity indices plotted by population (Etosha: black, Kruger: gray) and locus. Diversity indices shown are: (A) average percent difference (APD), and (B) haplotype diversity (HD). Significant difference (p<0.05) between population means are indicated by an asterisk (*) and non-significance by NS.
Table 2.
Standard intra-population genetic diversity indices at neutral and ELA loci.
Table 3.
Unbiased intra-population genetic diversity indices independent of allele frequency.
Table 4.
Population differentiation estimates based on neutral and ELA loci.
Figure 2.
STRUCTURE plots of E. quagga from Etosha and Kruger.
Individual genetic clustering assignments under the model of K = 2 based on (A) neutral loci (13 microsatellites and the β-Fibr intron), (B) ELA-DRA, and (C) ELA-DQA. Percent assignment to each of two genetic clusters are shown for each individual genotype in plots. Population where an individual was sampled is indicated by the bar to the left of each plot (Etosha: black, Kruger: gray). The mean posterior probability (L(K)) ± 95% confidence interval and the rate of change in the log probability of the data between successive K values (ΔK) from K = 1 to 5, for each marker type are shown below each corresponding STRUCTURE plot.
Figure 3.
Bayesian skyline plots showing changes in population size over time.
Median estimates of effective population size (Ne), relative to generation time, is plotted over time (years before present) for (A) Etosha and (B) Kruger zebra populations. The 95% credibility interval is shown by gray shading.
Table 5.
Tests of neutrality and population equilibrium.
Figure 4.
Allele frequency distributions by locus and population.
Alleles presented in order of descending frequency at the (A) ELA-DRA, (B) ELA-DQA, and (C) β-Fibr intron by population, with Etosha shown in black and Kruger in gray. Allele sample sizes are as follows: Etosha (β-Fibr: 72, DRA: 144, DQA: 66) and Kruger (β-Fibr: 47, DRA: 62, DQA: 46). DQA allele frequencies were calculated excluding individuals with multi-locus genotypes.
Table 6.
Molecular detection of selection across codon sites at the ELA-DRA and DQA.
Figure 5.
Median-joining haplotype networks for ELA-DRA, ELA-DQA, and β-Fibr loci.
Circle size is proportional to haplotype frequency. Proportion of total alleles found in Etosha (black) and Kruger (gray) are shown, with sample sizes corrected by rarefaction. Haplotypes from Equus callabus are shown in white (GenBank accession numbers– β-Fibr: AY726647, DRA: L47174, M60100, L47172, AJ575295, FJ716134, DQA: L33909, U92505, U92506, U92507, U92508). Differences between haplotypes that were greater than one mutational step are notated in red italics. Insertion-deletion mutational events are represented by a red perpendicular line.