Research article
Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution
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* Corresponding authors: Eske Willerslev ewillerslev@bio.ku.dk - Stephan C Schuster scs@bx.psu.edu
1 Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK-2100, Denmark
2 Centre for Macroevolution and Macroecology, School of Biology, Australian National University, Canberra, ACT 0200, Australia
3 Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, PA 16802, USA
4 Department of Integrative Biology, University of California, Berkeley, CA 9472-3140, USA
5 Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninsky Prospect, 119071 Moscow, Russia
6 Department of Paleontology, Faculty of Geology, Lomonosov Moscow State University, Leninskiye Gory, 119992 Moscow, Russia
7 Oxford University Museum of Natural History, Parks Road, Oxford, OX1 3PW, UK
8 Center for Conservation and Research of Endangered Wildlife (CREW), Cincinnati Zoo & Botanical Garden, 3400 Vine St, Cincinnati, OH 45220, USA
BMC Evolutionary Biology 2009, 9:95 doi:10.1186/1471-2148-9-95
Published: 11 May 2009Additional files
Additional file 1:
Figure S1. Nonsynonymous sites in mitochondrial cytb sequences of rhinoceroses, mapped onto the bovine structure [PDF:1PPJ] [22]. The nonsynonymous sites are shown in white, with those located in functionally relevant areas represented as orange spheres, and surrounded by boxes in the alignment. The prosthetic groups are represented in black, and bound inhibitors in brown (ant: antimycin; stig: stigmatellin). Sites that, when mutated in humans, are responsible for exercise intolerance, are depicted in red.
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Additional file 2:
Figure S2. Nonsynonymous sites in mitochondrial co1/co2/co3 sequences of rhinoceroses, mapped onto the bovine structure [PDF:1V54] [23]. The nonsynonymous sites are shown in white, with that located in a functionally relevant area represented as orange spheres, and surrounded by a box in the alignment. Prosthetic groups are represented as grey spheres.
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Additional file 3:
Table S1. Details of the primers used for gapfilling of the Javan rhinoceros mitochondrial genome.
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Additional file 4:
Table S2. Matrix of uncorrected p-distances for the whole mitochondrial genomes of six rhinoceros species, with distances between sister species given in bold.
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Additional file 5:
Table S3. Details of the components of the aligned mitochondrial genomes from six rhinoceroses, tapir, and horse.
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Additional file 6:
Table S4. Support for three candidate topologies estimated using Bayesian and maximum-likelihood phylogenetic analysis, using nine laurasiatherian outgroup species. In addition to the six rhinoceros sequences, the following outgroup taxa were included: Tapirus terrestris [GenBank:AJ428947], Equus caballus [GenBank:X79547], Hippopotamus amphibius [GenBank:NC_000889], Equus asinus [GenBank:NC_001788], Artibeus jamaicensis [GenBank:NC_002009], Ursus arctos [GenBank:NC_003427], Manis tetradactyla [GenBank:NC_004027], Bos taurus [GenBank:NC_006853], and Sorex unguiculatus [GenBank:NC_005435]. Phylogenetic analyses were performed on first and second codon positions only, using an unpartitioned GTR+I+G substitution model. Other settings in the Bayesian and likelihood-based analyses were as described in the main text, the only exceptions being the use of the heuristic tree-bisection-reconnection instead of a branch-and-bound search in the maximum-likelihood analysis, and the calculation of the bootstrap support values from 200 pseudoreplicates rather than 1,000.
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