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Open Access Highly Accessed Research article

A genetic polymorphism evolving in parallel in two cell compartments and in two clades

Ward B Watt12*, Richard R Hudson3, Baiqing Wang1 and Eddie Wang14

Author Affiliations

1 Department of Biology, Stanford University, Stanford, CA 94305-5020, USA

2 Rocky Mountain Biological Laboratory, Crested Butte, CO 81224, USA

3 Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA

4 Present address: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 0213, USA

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BMC Evolutionary Biology 2013, 13:9  doi:10.1186/1471-2148-13-9

Published: 12 January 2013

Additional files

Additional file 1:

Amplifying and sequencing primers for study of Colias PEPCK. Amplifying primers are of course used for sequencing as well. ″5end″ and ″3end″ primers are located in 5- and 3-untranslated regions (UTRs). S and A denote sense and antisense primer directions, respectively. Overlapping gene subsets amplified for sequencing: MVY-S-5end and MLH-S2-5end / A1005 (one each per individual); S511C / A1519C; and S1487 / A3end. Primer numbers denote primers’ 3-terminal nucleotide positions in the gene.

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Additional file 2:

Reference sequences of PEPCK (GTP; EC 4.1.1.32) from diverse taxa and bioinformatics sources.

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Additional file 3::

Tests of linkage disequilibrium among varying amino acid sites. Abbreviations: amino acids, standard one-letter codes; obs, observed; exp, expected; D, linkage disequilibrium = pX1pX4 – pX2pX3; GYates(1), G statistic with Yates’ correction and 1 degree of freedom; Fisher’s exact, test of that name [ref]; P, probability of this or more extreme result by chance alone. a) tests of sites polymorphic in both Colias species. Site variant frequencies in main text Table 2. Correction of significance threshold for multiple tests by Dunn-Sidak method [ref], 6 tests, α = 0.0085. No linkage disequilibria are significant. b) tests of Arg/Lys 11, polymorphic only in mitochondrial 5exon of C. eurytheme, and the other polymorphic sites in that species. Site frequencies at site 11: Arg 0.556, Lys 0.444; other site frequencies as above. 3 tests, α = 0.017. No linkage disequilibria are significant.

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Additional file 4:

Alignment of Rattus PEPCK (PDB 2qew) with Colias PEPCK (allele GDV) as amino acid sequences. Alignment generated with Modeller [19]. “*” denotes identity of residue between sequences.

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Additional file 5:

Absence/presence of polymorphic amino acid variable bonds with sidechains of nearby invariant amino acids in Colias PEPCK. Abbreviations: H bond, hydrogen bond; Ǻ, Ǻngstrom unit of length; vdW, van der Waals; marg, marginal. Alleles identified by one-letter amino acid codes at each of the three polymorphic sites shared between species. Invariant amino acid sites bonding to variable amino acids are identified by number prior to bond length in Ǻ. 272-503 H bonds engage the backbone carbonyl of amino acid 503. All bond types, including distance criteria for marginal or absent van der Waals contacts, are discussed in the main text and many are illustrated in Figures 6, 7, 8.

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