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.
Gilbert
M Thomas P
MT
Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark. mtpgilbert@gmail.com
Drautz
Daniela I
DI
Lesk
Arthur M
AM
Ho
Simon Y W
SY
Qi
Ji
J
Ratan
Aakrosh
A
Hsu
Chih-Hao
CH
Sher
Andrei
A
Dalén
Love
L
Götherström
Anders
A
Tomsho
Lynn P
LP
Rendulic
Snjezana
S
Packard
Michael
M
Campos
Paula F
PF
Kuznetsova
Tatyana V
TV
Shidlovskiy
Fyodor
F
Tikhonov
Alexei
A
Willerslev
Eske
E
Iacumin
Paola
P
Buigues
Bernard
B
Ericson
Per G P
PG
Germonpré
Mietje
M
Kosintsev
Pavel
P
Nikolaev
Vladimir
V
Nowak-Kemp
Malgosia
M
Knight
James R
JR
Irzyk
Gerard P
GP
Perbost
Clotilde S
CS
Fredrikson
Karin M
KM
Harkins
Timothy T
TT
Sheridan
Sharon
S
Miller
Webb
W
Schuster
Stephan C
SC
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