Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

Abstract

We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, Ϸ1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the 14 C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.mtDNA genome ͉ phylogeny ͉ ancient DNA ͉ next-generation sequencing A lthough ancient DNA analyses offer the potential to tackle a tantalizing range of otherwise unapproachable questions, the actual achievements of the field have been limited by the postmortem degradation of DNA. Even in well preserved specimens from arctic environments, number of specimens and amount of data per specimen are limited. Previous studies to assess the genetic structure of extinct species, including mammoths (1), have had to rely on short sequence intervals that were often only a few hundred nucleotides in length. This has made it difficult to obtain precise estimates of substitution rates and divergence times, particularly for species exhibiting low levels of genetic variation. Additionally, it is possible that the accuracy of these estimates has been compromised by the presence of sequence damage in the form of miscoding lesions, which can introduce significant biases in estimates of evolutionary parameters (2). These problems can be addressed by large-scale sequencing with manifold coverage, which will increase the amount of informative data while filtering out the spurious polymorphisms resulting from sequence damage. This should serve to increase both the precision and accuracy of demographic estimates.

The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

“…We identified a substantial amount of human DNA contamination in the thylacine samples, unlike in our earlier analysis of woolly mammoth bone (Poinar et al 2006;Gilbert et al 2007b) and hair shafts (Gilbert et al 2007a(Gilbert et al , 2008Miller et al 2008). For example, from the ethanol-preserved specimen (thylacine 2 in Table 1), we identified 44,493 reads (4.3%) that originated from the human nuclear genome and 136 reads from the human mitochondrial genome.…”

“…Library preparation for the thylacine and numbat hair samples were performed as previously described for the woolly mammoth (Gilbert et al 2007a(Gilbert et al , 2008, and all fragment sizes were retained. For the numbat liver sample, a gel extraction of fragments was performed, followed by library preparation as previously described (Miller et al 2008).…”

Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox ( Ovibos moschatus ) population dynamics

“…Thus, an alternate explanation for the loss is required. Intriguingly, the loss of a distinct mtDNA clade for mammoths has also been observed in this region at this time (15,16,38), suggesting the cause was not species-specific. Given that during MIS 3 both polar ice-core records and pollen, plant macrofossils, mammal, and insect remains indicate that the climate started to both fluctuate significantly and become increasingly warmer and wetter (39)(40)(41) (Fig.…”

Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens

“…Even with NGSTs' growing familiarity and broad range of applications such as ChIPseq, RNA-seq, and genome-wide association studies, NGSTs still have the potential to influence the field of population genetics and phylogenetics with new methods to obtain genomic sequences of rare, difficult to sample, or extinct species (Millar et al 2008). The ability to uncover the phylogenetic history of recently extinct species has rapidly improved due to the reduced cost and increased sequence capacity of NGSTs (Gilbert et al 2007(Gilbert et al , 2008Miller et al 2008Miller et al , 2009); however, obstacles do remain. The difficulties with applying NGSTs to phylogenetic problems do not lie with the sequencing technology itself, but with the preparative procedures for isolation and sequencing of large, orthologous DNA regions across multiple divergent species (Summerer 2009).…”