Table 3. Bayesian coalescent estimates of divergence times (thousands of years before present—ky BP) among red deer mtDNA D-loop haplotypes (670 bp) at the Iberian Peninsula level and among the European lineages (haplogroups A, B and C; 329 bp) at the European level, inferred using an evolutionary rate estimated in this study*.
Estimates from between-species fossil calibration method used in Skog et al. [19] are also shown.
| Analysis | mtDNA D-loop | This study | Skog et al. [19] | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Average | 95% HPD lower | 95% HPD upper | ESS | Average | 95% HPD lower | 95% HPD upper | ESS | ||
| Iberian level | All haplotypes | 24.2 | 12.1 | 38.4 | 3.289 | ||||
| (H7)/(H04/10/20) | 20.7 | 6.9 | 35.0 | 1.612 | |||||
| (H09)/(H04/10/20) | 20.0 | 8.4 | 33.5 | 1.933 | |||||
| (H26/27/27’/28)/ (H04/10/20) |
19.3 | 6.9 | 33.4 | 1.399 | |||||
| European level | Haplogroup A/B/C | 131.1 | 81.5 | 187.2 | 4.006 | - | - | - | - |
| Haplogroup A/B | 128.3 | 78.6 | 185.7 | 4.310 | 303.7 | 209.1 | 411.0 | 7.123 | |
| Haplogroup A/C | 131.1 | 81.5 | 187.2 | 4.006 | 272.3 | 175.3 | 384.7 | 4.384 | |
| Haplogroup B/C | 131.0 | 81.4 | 187.2 | 3.995 | 295.2 | 207.1 | 398.6 | 6.613 | |
* Calculations were done using a mutation rate of 3.849x10-7 nucleotide substitutions per site per year for the D-loop region (see details in Materials and Methods), while in Skog et al. [19] a mutation rate of 1.03x10-7 was used. At the Iberian level, the divergence time between the private evolutionary sub-lineages (H7—dark blue; H09 –orange; and H26/27/27’/28– pink; color codes as Fig 6) and mtDNA haplotypes central to the phylogenetic network (H4/10/20 –brown color Fig 6) were obtained. The average and 95% highest posterior density interval (HDP) together with effective samples sizes (ESS) are indicated.