Results of a recent study analysing complete mitogenomes from North American mammoth populations were consistent with this hypothesis.
Furthermore, this study found evidence of hybridisation and potential male mediated gene flow between North American woolly mammoths, Columbian mammoths, Jefferson’s mammoth and pygmy mammoth.
Morphology-based taxonomic identifications are provided as rectangular bars to the right of sample names.
Nodes leading to major clades are labeled and highlighted as magenta dots, with the inferred t MRCA (95% highest posterior density of node ages, magenta numbers below the branch leading to the clade).
Posterior probability for each clade is provided either as black numbers along branch leading to major clades, or indicated as 95% by the presence of a black dot.
The timescale is offset by 4651 years, which is the age of the youngest sample in the data set. Figure 1 shows the maximum clade credibility (MCC) mammoth mitochondrial genealogy resulting from a Bayesian phylogenetic analysis of the relaxed data set, using a strict molecular clock and the root-and-tip calibration approach; the results from the strict data set are provided in Figure S2.
Here, we combine hybridization-based targeted capture and high-throughput sequencing to generate 54 complete mammoth mitochondrial genomes, including 22 from temperate localities across Eurasia.
We incorporate these into a globally extensive data set totalling 143 mammoth mitochondrial genomes sampled from across the northern hemisphere.
For each sample, de-multiplexing, mapping and duplicate removal resulted in between 367 and 211,184 unique mitochondrial reads, which is equivalent to 1-fold to 819-fold coverage of the mitochondrial genome (Table S1).
To evaluate potential error associated with missing and low-coverage data and to include the largest number of individuals possible, we adopted two strategies for consensus calling and filtering (see Methods) that resulted in two data sets: a relaxed alignment of 117 mammoth mitochondrial genomes and a strict alignment of 70 mitochondrial genomes.