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5-Animals: Scientists sequence complete genome of Woolly Mammoth

------------------------------- GENET-news -------------------------------

TITLE:  Scientists Sequence Complete Genome of Woolly Mammoth
SOURCE: University of Massachusetts Medical School, USA, posted at:
DATE:   07 Feb 2006

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Scientists Sequence Complete Genome of Woolly Mammoth

Scientists have completed the oldest mitochondrial genome sequence from
the 33,000-year-old remains of a woolly mammoth; results show mammoths
and Asian elephants are a sister species that diverged soon after their
common ancestor split from the lineage of the African elephant.

Some 10,000 years after the last of their kind wandered the North
American and Eurasian wilderness, woolly mammoths (Mammuthus primigenius)
remain a fascinating subject of study for scientists, with implications
for understanding the evolutionary origins of present day mammals.
Mammoths and elephants belong to one of the most ancient mammalian groups
and various recent studies have debated the genetic relationships between
them. Now, scientists at the University of Massachusetts Medical School
and the Russian Academy of Medical Sciences have weighed in on the issue,
with results supported by the oldest mitochondrial genome sequence
determined to date from the remains of a mammoth that died approximately
33,000 years ago.

In "Complete mitochondrial genome and phylogeny of Pleistocene mammoth
Mammuthus primigenius," published in the February 7 issue of PLoS
Biology, a publication of the Public Library of Science (PLoS), Evgeny I.
Rogaev, PhD, a professor of psychiatry at UMass Medical School and
professor of genetics at the Russian Academy of Medical Sciences, with
colleagues from the Brudnick Neuropsychiatric Research Insitute at UMass
Medical School, Russian Academy of Sciences, Moscow State University and
the University of California-San Diego, report the sequence of the
complete mitochondrial genome (16,842 base pairs) of a woolly mammoth
extracted from permafrost-preserved remains from the Pleistocene epoch, a
period of time usually dated from between 1.6-1.9 million to about 10,000
years before present. Their study demonstrates that the woolly mammoth
and the Asian elephant are a sister species that diverged soon after
their common ancestor split from the lineage of the African elephant.

Dr. Rogaev and colleagues used extracted DNA from segments of a woolly
mammoth leg with intact muscle and skin tissue that was found in the
Enmynveem River valley in northeastern Siberia in 1986 and radio-carbon
dated to be between 33,750 and 31,950 years old. They found that the DNA
extracted from the well preserved tissue, while degraded, was
nevertheless of remarkable quality and quantity. Using polymerase chain
reaction (PCR) techniques that allow for investigators to make a
significant number of copies of a gene and thus create a template for
sequencing, the scientists used different DNA extracts from the mammoth
muscle tissue to reconstruct the complete mitochondrial genome in
laboratories in Moscow in 2000, and independently, at UMass Medical
School a few years later.

While DNA is present inside the nucleus of every cell of the body, DNA in
the cell's mitochondria offers investigators valuable information on
evolutionary development. Distinct from nuclear DNA, mitochondrial DNA
possesses its own genome of about 16,500 base pairs that exists outside
of the cell nucleus. And whereas nuclear DNA undergoes the process of
recombination, where sections of DNA from the mother and the father are
mixed resulting in a more distorted genetic history, mitochondrial DNA,
which is inherited only from the mother, allows for the tracing of a more
direct genetic line.

Using the mitochondrial genome they had sequenced, Rogaev and his fellow
scientists sought to uncover the evolutionary relationship between the
extinct woolly mammoth and the Asian and African savanna elephants.
Analysis of the creatures from the study of their biological form and
structure have yielded conflicting results; for example, while dental
characteristics suggest a closer relationship between the woolly mammoth
and the Asian elephant, an examination of the structure of the trunk tip
supports a grouping of the woolly mammoth with the African elephant.

To resolve this evolutionary mystery, Rogaev and colleagues sequenced
complete mitochondrial genomes of the African and Asian elephants. Their
subsequent analysis indicated that the woolly mammoth shared a common
ancestor with the Asian elephant more recently than with the African
elephant. This conclusion corroborates a paralleled and independent study
of a younger mammoth (~12,000 years old) from the Max Planck Institute in
Leipzig, Germany as reported in Nature in December 2005.

Because the modern populations of African and Asian elephants are quite
highly diverse genetically, the investigators also sought to determine if
the same was true of different woolly mammoths living through the
Pleistocene. Interestingly, in comparing the mammoth mitochondrial genome
sequence to the longest mitochondrial DNA sequences available from other
individual mammoths, the authors of this study found that the mammoths
were highly similar, suggesting a relatively low genetic diversity of
mammoth maternal lineages in a population spanning vast territory in
Northern Siberia. These preliminary results suggest that Siberia was
occupied by a relatively homogeneous population of woolly mammoth
throughout the late Pleistocene. The scientists hope that further
sequencing of mitochondrial genomes of other mammoth specimens can
clarify the diversity of the ancient mammoth population.

Although previous studies have shown that the problem with using ancient
DNA in evolutionary studies is that DNA modifications can lead to
artifact mutations accumulating in postmortem material and, therefore,
produce errors in sequences; the strategies and data provided by Rogaev
et al demonstrate that their long genomic sequence is essentially free
from such artifacts and that the mammoth genome is authentic. Further,
they have demonstrated that large DNA fragments can be isolated from
ancient specimens recovered from permafrost conditions and that the
complete genes can be directly cloned or reconstructed for animals that
disappeared from the earth many thousand years ago.

"The reconstruction of an animal's evolutionary history based on complete
mitochondrial sequence analysis is a powerful method to determine the
relationship between closely related extinct and extant species," said
Rogaev. "However, data from both mitochondrial and nuclear DNA may offer
further information on the development of a species. Given the unique
quality of some specimens from mammoths found in Siberia, nuclear DNA may
potentially be recovered and used for further confirmation of the results
of this study."


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