Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae

  title={Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae},
  author={Johannes Krause and Paul H. Dear and Joshua L. Pollack and Montgomery Slatkin and H. Spriggs and Ian Barnes and Adrian M. Lister and Ingo Ebersberger and Svante P{\"a}{\"a}bo and Michael Hofreiter},
In studying the genomes of extinct species, two principal limitations are typically the small quantities of endogenous ancient DNA and its degraded condition, even though products of up to 1,600 base pairs (bp) have been amplified in rare cases. Using small overlapping polymerase chain reaction products, longer stretches of sequences or even whole mitochondrial genomes can be reconstructed, but this approach is limited by the number of amplifications that can be performed from rare samples… 
Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes
Five new complete mitochondrial DNA genomes of Siberian woolly mammoth are reported, sequenced with up to 73-fold coverage from DNA extracted from hair shaft material, demonstrating the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence.
Short sequence effect of ancient DNA on mammoth phylogenetic analyses
All of the phylogenetic trees, based on either the partial or the complete cyt b gene, reject the relationship constructed by the whole mitochondrial genome, showing the occurrence of an effect of sequence length of cytochrome b gene on mammoth phylogenetic analyses.
Complete Mitochondrial Genome and Phylogeny of Pleistocene MammothMammuthus primigenius
It is demonstrated that well-preserved mitochondrial genome fragments, as long as ~1,600–1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species, and the sequence of the complete mitochondrial genome is reported—the oldest mitochondrial genome sequence determined to date.
Paleogenomics in a Temperate Environment: Shotgun Sequencing from an Extinct Mediterranean Caprine
This study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences.
Proboscidean Mitogenomics: Chronology and Mode of Elephant Evolution Using Mastodon as Outgroup
The complete mitochondrial genome of the extinct American mastodon is sequenced from an Alaskan fossil that is between 50,000 and 130,000 y old, extending the age range of genomic analyses by almost a complete glacial cycle and concluding that the first sequence of mastodon DNA ever reported is obtained.
The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis
The genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.
The Neandertal genome and ancient DNA authenticity
It is argued that only direct assays of DNA sequence positions in which Neandertals differ from all contemporary humans can serve as a reliable means to estimate human contamination, and a similar ‘boot‐strap’ approach is suggested in which interim approaches are applied until sufficient data for more definitive directAssays are acquired.
True single-molecule DNA sequencing of a pleistocene horse bone.
The first "true single molecule sequencing" of ancient DNA is reported, suggesting that paleogenomes could be sequenced in an unprecedented manner by combining current second- and third-generation sequencing approaches.
Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution
Satisfactory resolution of the rhinoceros phylogeny may not be achievable without additional analyses of substantial amounts of nuclear DNA, and there are significant limitations with single-locus phylogenetics.


Phylogenetic Position of Mammoth and Steller's Sea Cow Within Tethytheria Demonstrated by Mitochondrial DNA Sequences
DNA sequences from mitochondrial cytochrome b gene segments for the extinct woolly mammoth and Steller's sea cow and the extant Asian elephant and the Western Indian manatee allow us to construct the phylogeny for the Tethytheria.
Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution
This first molecular view of the break-up of Gondwana provides a new temporal framework for speciation events within other Gondwanan biota and can be used to evaluate competing biogeographical hypotheses.
Molecular phylogeny of the extinct ground sloth Mylodon darwinii.
Phylogenetic analyses using homologous sequences from all extant edentate groups suggest that Mylodon darwinii was more closely related to the two- toed than the three-toed sloths and, thus, that an arboreal life-style has evolved at least twice among sloths.
Complete mitochondrial DNA geonome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis
  • O. Haddrath, A. Baker
  • Biology
    Proceedings of the Royal Society of London. Series B: Biological Sciences
  • 2001
Most of the major ratite lineages fit the vicariance biogeography hypothesis, the exceptions being the ostrich and the kiwi, which require dispersal to explain their present distribution.
Nuclear DNA sequences from late Pleistocene megafauna.
The nuclear sequences retrieved from the mammoths suggest that mammoths were more similar to Asian elephants than to African elephants and under some circumstances, nucleotide sequence differences between alleles found within one individual can be distinguished from DNA sequence variation caused by postmortem DNA damage.
Molecular and morphological evidence on the phylogeny of the Elephantidae
The results highlight the need for multiple markers and close attention to within–taxon variation and outgroup selection in both morphological and molecular phylogenetics, and support the mammoth–African elephant relationship.
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed, and this dating may pose a problem for the widely believed hypothesis that the bipedal creatureAustralopithecus afarensis, which lived some 3.7 million years ago, was ancestral to man and evolved after the human-ape splitting.
Genetic analyses from ancient DNA.
The precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences are discussed, which highlight some significant results and areas of promising future research.