Open Access Highly Accessed Research article

Evolution of cichlid vision via trans-regulatory divergence

Kelly E O’Quin*, Jane E Schulte, Zil Patel, Nadia Kahn, Zan Naseer, Helena Wang, Matthew A Conte and Karen L Carleton

Author Affiliations

Department of Biology, University of Maryland, College Park, MD, 20742, USA

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BMC Evolutionary Biology 2012, 12:251  doi:10.1186/1471-2148-12-251

Published: 26 December 2012

Additional files

Additional file 1:

Excel file of sequencing and assembly statistics of all P0 and F2 used in this study.

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Additional file 2:

Table of primers used to amplify and genotype polymorphisms at candidate gene markers and re-sequence RAD-seq loci.

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Additional file 3:

Table of genotyping errors for 11 markers inferred from RAD-seq, including updated association valuesc. c P-value following ANOVA of cycle-sequencing genotypes and opsin expression of 5611 with RH2B; 20245 with RH2A and LWS; and 28586 with SWS2B, SWS2A and RH2B.

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Additional file 4:

Supplemental text discussing genotyping error and RAD-seq.

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Additional file 5:

Linkage map of the cichlid genome along with eQTL positions for cichlid opsin gene expression.

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Additional file 6:

Table of the identity, sequence, and map-position of all RAD-seq markers used in this study.

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Additional file 7:

Distribution of opsin gene expression values among genotypic classes at eQTL loci. Genotypic classes include individuals that are homozygous for Aulonocara baenschi alleles (AA), homozygous for Tramitichromis intermedius alleles (TT), or heterozygous (AT). Marker loci are from the eQTL peaks indicated in Figure 2 and Table 2. Bars represent mean ± 1 SEM. The number of individuals varies among plots, though the average number of individuals is n = 62.60±4.06 SEM.

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Additional file 8:

Excel file of 32 5-bp barcodes used to label F2 DNA in each reduced-representation RAD-seq library.

Format: XLSX Size: 41KB Download file

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