Research article
Distinct patterns of mitochondrial genome diversity in bonobos (Pan paniscus) and humans
-
* Corresponding author: Wolfram S Kunz wolfram.kunz@ukb.uni-bonn.de
1 Division of Neurochemistry, Department of Epileptology and Life&Brain Center, University Bonn, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
2 Harvard Medical School, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA
BMC Evolutionary Biology 2010, 10:270 doi:10.1186/1471-2148-10-270
Published: 2 September 2010Additional files
Additional file 1:
Figure S1. Neighbor-joining tree of Pan paniscus hypervariable region I sequences using Pan troglodytes as outgroup. Previously published sequences are shown by their GenBank accession numbers. Complete Pan paniscus mtDNA sequences described in this study are marked by dots. Scale bar, evolutionary distance (substitutions per nucleotide position).
Format: PDF Size: 272KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 2:
Figure S2. Detailed phylogenetic tree of complete Pan paniscus mtDNA sequences displaying all detected polymorphic positions. For each branch, strictly branch-specific mutations are listed on the left-hand side of the line, while homoplasic mutations (occurring also in other independent branches) on the right-hand side. Stars indicate the lack of the specific bonobo-allele (representing a 'backwards' mutation to the human reference). A list of such 'backwards' mutating sites is shown at the root (top). PPRefCOD and PPRefDL, coding and D-loop regions of the only previously reported Pan paniscus mtDNA sequence [GenBank:NC_001644].
Format: PDF Size: 41KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 3:
Figure S3. Ratios of non-synonymous to synonymous mutations in mitochondrial protein coding genes. dN/dS ratios of within-group polymorphic sites in the mitochondrial encoded subunits of complexes I, III, IV and V in Pan paniscus and diverse human haplogroups. Numbers of analyzed individual sequences are shown in brackets.
Format: PDF Size: 78KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 4:
Table S1. Non-synonymous mutations in mitochondrial genes of complex V. Scoring of amino acid changes according to Betts and Russell [44]. Positive values indicate favored changes, zero neutral changes, negative values disfavored changes in membrane proteins.
Format: PDF Size: 60KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 5:
Table S2. Human haplogroup definitions used in the study. Haplogroups defined by the presence (+) or the absence (-) of specific mutations as compared to the revised Cambridge Reference Sequence [18].
Format: PDF Size: 59KB Download file
This file can be viewed with: Adobe Acrobat Reader