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

@article{Krause2006MultiplexAO,
  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},
  journal={Nature},
  year={2006},
  volume={439},
  pages={724-727}
}
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… 
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References

SHOWING 1-10 OF 42 REFERENCES
Phylogenetic Position of Mammoth and Steller's Sea Cow Within Tethytheria Demonstrated by Mitochondrial DNA Sequences
TLDR
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
TLDR
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.
TLDR
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
TLDR
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.
TLDR
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
TLDR
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
TLDR
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.
TLDR
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.
...
...