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Open Access Research article

Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen

Sergios-Orestis Kolokotronis12, Ross DE MacPhee3 and Alex D Greenwood34*

  • * Corresponding author: Alex D Greenwood agreenwo@odu.edu

  • † Equal contributors

Author Affiliations

1 Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA

2 Department of Ecology, Evolution, and Environmental Biology, Columbia University, 1200 Amsterdam Avenue, MC5557, New York, NY 10027, USA

3 Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA

4 Department of Biological Sciences, Old Dominion University, Mills Godwin Building, Room 108E, Norfolk, VA 23529-0266, USA

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BMC Evolutionary Biology 2007, 7:67  doi:10.1186/1471-2148-7-67

Published: 27 April 2007

Additional files

Additional file 1:

PCR products generated from hair and blood of modern muskoxen. An example of the three PCR products amplified from hair and blood of two muskoxen. An ethidium bromide stained 2% agarose gel is shown with a ladder for each reaction. PCR A, B, and C correspond to primer combinations HV.1L+HV.1H, HV.2L+HV.2H, and published muskox primers [15], respectively. 1, water negative control, 2, ladder, 3, male muskox hair DNA, 4, same muskox blood DNA, 5, a second unrelated muskox blood DNA sample.

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Additional file 2:

Alignments of the overlapping regions of the 1.1 kb PCR products to muskox control region sequences from GenBank. Long PCR fragments are aligned to short PCR fragments from modern and Pleistocene muskoxen, as well as all Ovibos moschatus control region sequences retrieved from GenBank and the serow control region sequence from GenBank. Names describe muskox individual (C or E), tissue of origin (H for hair, B for blood), and clone number. For additional sequences included, see Additional file 4 for haplotype descriptions. Clones CBL.10 and CHL.5 aligned very poorly at the 5'-end of the sequence and were trimmed. The sequences extend beyond what is shown. Nucleotides identical to the first sequence are indicated by a dot and gaps/missing data by a dash. Long fragment sequences were submitted to GenBank (GenBank: EF566449EF566462).

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Additional file 3:

Pairwise Relative Rate Test results. Significant likelihood ratio tests (LRT) of pairwise combinations of sequences evolving at different rates. The evolutionary rate of the outgroup was independently calculated in all 3-taxon trees. Branch lengths denote the number of substitutions per site. Results are listed by ascending order of significance.

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Additional file 4:

Explanation of haplotypes. Collapsed sequences into haplotypes treating gaps as 5th state. The frequency is calculated within the same individual muskox and clone type (e.g. hair or blood).

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