Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus)
Version of Record online: 7 FEB 2013
© 2013 The Authors. Ecology and Evolution published by Blackwell Publishing Ltd.
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Ecology and Evolution
Volume 3, Issue 3, pages 655–666, March 2013
How to Cite
Ecology and Evolution 2013; 3(3): 655–666
- Issue online: 11 MAR 2013
- Version of Record online: 7 FEB 2013
- Manuscript Accepted: 24 DEC 2012
- Manuscript Revised: 17 DEC 2012
- Manuscript Received: 12 NOV 2012
- Swedish Research Council. Grant Number: 2009-693
- NSF. Grant Number: DEB-IOS 0923088
Figure S1. Individual FST estimates (y-axis) and their corresponding P-values (x-axis scaled as 2*abs(0.975–0.5)) for all SNPs identified in the three genes when analyzed using the BAYESFST method (Beaumont and Balding 2004). The vertical dashed red line indicates the threshold for significance (P = 0.05). Values to the right of the vertical bar would be significant at the 0.05 level. The SNPs associated with pathogen load are indicated in green (SNP1558) and red (SNP1620).
Figure S2. Plots of pair-wise linkage disequilibrium between SNPs with minor allele frequenc y >10% located within each of the genes HSP90α(a, b) and LCP1 (c, d) for the Alabama population (a, c) and the Arizona population (b, d), respectively. The horizontal bar indicates the sequenced region and the vertical lines show positions of SNPs with minor allele frequency >10% along the stretch. SNsP numbers are given below the horizontal bar and numbers within diamonds denote the r2-values. The level of LD is also indicated by the shading of the diamond representing a SNP pair, the darker the shading the higher the LD (white indicates r2-values = 0 and black indicates r2-values = 1). CD74 did only contain a single pair of SNPs with MAF > 10% and is therefore omitted from the figure.
Figure S3. Schematic of the relative position of primers for each of the three genes. Primer sequences are given in Table S1. Forward primers are in red and reverse primers in blue. Black horizontal bars indicate the sequence region analyzed for each gene.
Table S1. Primer combinations used for amplification of the upstream region of the three candidate genes. As a result of varying GC content and several polymorphic length variants more than one primer combination had to be used to cover the region. The specific PCR settings for each amplicon are available upon request. For approximate locations see Figure S3.
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