Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes.
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, approximately 1-2 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.
Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark. mtpgilbert@gmail.com
M Thomas P
MT
Gilbert
Daniela I
DI
Drautz
Arthur M
AM
Lesk
Simon Y W
SY
Ho
Ji
J
Qi
Aakrosh
A
Ratan
Chih-Hao
CH
Hsu
Andrei
A
Sher
Love
L
Dalén
Anders
A
Götherström
Lynn P
LP
Tomsho
Snjezana
S
Rendulic
Michael
M
Packard
Paula F
PF
Campos
Tatyana V
TV
Kuznetsova
Fyodor
F
Shidlovskiy
Alexei
A
Tikhonov
Eske
E
Willerslev
Paola
P
Iacumin
Bernard
B
Buigues
Per G P
PG
Ericson
Mietje
M
Germonpré
Pavel
P
Kosintsev
Vladimir
V
Nikolaev
Malgosia
M
Nowak-Kemp
James R
JR
Knight
Gerard P
GP
Irzyk
Clotilde S
CS
Perbost
Karin M
KM
Fredrikson
Timothy T
TT
Harkins
Sharon
S
Sheridan
Webb
W
Miller
Stephan C
SC
Schuster
D000818:Animals; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000032:analysis / Q000235:genetics; D004606:Elephants / Q000145:classification* / Q000235:genetics*; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D006197:Hair / Q000737:chemistry; D008969:Molecular Sequence Data; D010163:Paleontology; D010802:Phylogeny; D017422:Sequence Analysis, DNA
D004272:DNA, Mitochondrial