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Supplemental Information

Supplemental Text S1 - Details on the model and three case studies

Supplementary text includes model derivation, detailed description of three case studies, and extended Materials and Methods.

DOI: 10.7287/peerj.preprints.2249v1/supp-1

Codon bias vs. expression gauged by different experiments for partially overlapping gene sets

A, 95% CIs for Spearman correlation coefficients between codon bias (tAI or CAI) and gene expression. Main part: correlations determined for yeast genes common to the original study (in bold) and each of the alternative studies, for which expression was gauged on the basis of any possible combination of experimental input data on protein and mRNA abundances and marked by two-letter shortcuts (see Supplemental Text S1). n = sample size. B, 95% CIs for correlation differences, determined by an approximate method for dependent groups, are shown separately for overlapping (blue) and non-overlapping (red) correlations (see Supplemental Text S1). The original Ne/Wh correlation from Tuller et al. (2010) is compared to all the alternative correlations derived from other data sources. The relaxation of constraints of the calculations of correlation differences does not change the conclusions drawn from the more restrictive analysis presented in Figure 2, main text.

DOI: 10.7287/peerj.preprints.2249v1/supp-2

Codon bias vs. expression gauged by different experiments for gene sets treated as independent

A, 95% CIs for Spearman correlation coefficients between codon bias (tAI or CAI) and gene expression. Main part: correlations determined for yeast genes of known expression, gauged by any possible combination of experimental input data on protein and mRNA abundances and marked by two-letter shortcuts (see Supplemental Text S1). n = sample size. B, 95% CIs for correlation differences, determined by an approximate method for independent groups (see Supplemental Text S1). The original Ne/Wh correlation from Tuller et al. (2010) is compared to all the alternative correlations derived from other data sources.. The conclusions drawn from Figure 2, main text, hold even if the sets of genes are treated as independent.

DOI: 10.7287/peerj.preprints.2249v1/supp-3

The effect of folding energy on correlation between tAI and translation efficiency - revisited

A,C, Reproduction of Figure 3A and 3C from Tuller et al (2010) supporting the statement that folding energy modulates the strength of association between codon bias and translation efficiency. The bars show correlations between tAI and translation efficiency for five equal-sized bins of E.coli and S.cerevisiae genes divided according to folding energy of their mRNAs. We added 95% CIs to these correlations (red lines). B,D, 95% CIs for correlation differences calculated for each pair of bins. It is not possible to identify the difference sign for any single pair, meaning that the presented data do not provide evidence of the modulating role of folding energy.

DOI: 10.7287/peerj.preprints.2249v1/supp-4

Median dN, median X-autosome dN differences and contrasts in three studies of Drosophila.

A, 95% CIs for median divergence in dN for X-linked and autosomal loci for three contradicting studies. Bootstrap CIs are shown in brackets, n = sample size. B, 95% CIs for the median dN difference between X-linked and autosomal loci for each study. CIs obtained in a wilcox.test R method (dark purple) are consistent with the p-values reported previously by Begun et al. (2007). However, the CIs obtained by bootstrap do not confirm statistical significance, demonstrating that in the NHST-focused reasoning even a tiny shift of the CI limits, caused by application of other statistical methods, may result in a dramatic change in conclusions. C, 95% CIs for contrasts, i.e., the differences of dN differences, calculated between the X-autosome dN differences for genes analysed by two contradicting studies. Their signs cannot be determined, and thus no controversy between the studies may be claimed.

DOI: 10.7287/peerj.preprints.2249v1/supp-5

dS comparisons in X-linked and autosomal coding sequences

A, 95% CI for the weighted mean divergence dS of genes allocated on the X chromosome (red) and autosomes 2 and 3 (dark blue); subsets of autosomes (light blue) contain loci from: 2nd chromosome (2), 3rd chromosome (3), left arms of chromosomes 2 and 3 (L), and right arms of chromosomes 2 and 3 (R). CIs limits are shown in brackets, n = sample size. B, 95% CIs for the median divergence difference between: X-linked (X) and autosomal (A) loci (in bold); loci from the 2nd and 3rd autosome; and loci from the left and right arms of autosomes. CIs obtained in a wilcox.test R method (dark purple) are consistent with p-values reported in the original study by Begun et al. (2007). Bootstrap CIs are in light purple. The difference sign depends on the lineage and calculation method used (pairwise or lineage-specific). Note that all lineage-specific dS differences between the 2nd and 3rd autosome are statistically significant, and so is the L- R dS difference in D.melanogaster. C, 95% CIs for contrasts, i.e., the differences of divergence differences, calculated between X-autosome and inter/intra-autosomal divergence differences. Contrasts for the opposite inter/intra-autosomal divergence differences (i.e., 3 vs. 2 and R vs. L) are in grey. All dS differences between X and autosomes are indistinguishable from at least one inter/intra-autosomal difference, for which the hypothesis of faster evolution has never been proposed. This indicates that the reference data set from Begun et al. (2007) does not provide enough precision to distinguish the faster-X effect from dS fluctuations that naturally occur within autosomes.

DOI: 10.7287/peerj.preprints.2249v1/supp-6

dN comparisons in X-linked and autosomal coding sequences

A,B,C, Markings as per Supplemental Fig 5. B, The size and position of CIs are very similar between X-autosomes and the dN comparisons of inter/intra-autosomes. C, All dN differences between X and autosomes are indistinguishable from at least one inter/intra-autosomal difference, for which the hypothesis of faster evolution has never been proposed. This indicates that the reference data set from Begun et al. 2007 does not provide enough precision to distinguish the faster-X effect from dN fluctuations that naturally occur within autosomes.

DOI: 10.7287/peerj.preprints.2249v1/supp-7

Divergence comparisons in X-linked and autosomal introns

A,B,C, Marking as per Supplemental Fig. 5. C, Most comparisons show that the divergence differences of X vs. autosomes cannot be distinguished from at least one inter/intra-autosomal difference, calculated over the same set of gene elements. Only for lineage-specific divergence in D.melanogaster is the observed X-autosome divergence difference negative and larger (in absolute value) than any of the inter- or intra-autosomal differences. This suggests faster evolution of autosomal introns. However, due to limitations of our analysis, the biological significance of this effect still needs further confirmation.

DOI: 10.7287/peerj.preprints.2249v1/supp-8

Divergence comparisons in X-linked and autosomal intergenic regions

A,B,C, Marking as per Supplemental Fig. 5. C, All comparisons show that divergence differences of X vs. autosomes cannot be distinguished from at least one inter/intra-autosomal difference, calculated over the same set of gene elements. This indicates that, for intergenic regions, the reference data set from Begun et al. (2007) does not provide enough precision to distinguish the faster-X effect from divergence fluctuations that naturally occur within autosomes.

DOI: 10.7287/peerj.preprints.2249v1/supp-9

Divergence comparisons in X-linked and autosomal 3'UTRs

A,B,C Marking as per Supplemental Fig. 5. C, In all cases, except the lineage-specific divergence comparison for D.melanogaster, the X-autosome divergence differences are positive and at least somewhat larger than inter/intra-autosomal differences. From all analysed genetic elements, only the UTR case may support the faster-X evolution hypothesis in Drosophila, but only if the biological significance of this effect is further confirmed by other studies.

DOI: 10.7287/peerj.preprints.2249v1/supp-10

Divergence comparisons in X-linked and autosomal 5'UTRs

A,B,C Marking as per Supplemental Fig. 5. C, In all cases, except the lineage-specific divergence comparison for D.melanogaster, the X-autosome divergence differences are positive and at least somewhat larger than inter/intra-autosomal differences. From all analysed genetic elements, only the UTR case may support the faster-X evolution hypothesis in Drosophila, but only if the biological significance of this effect is further confirmed by other studies.

DOI: 10.7287/peerj.preprints.2249v1/supp-11

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Marlena Siwiak conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Tomasz Wyszomirski conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Piotr Zielenkiewicz conceived and designed the experiments, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

The research in this article did not generate, collect or analyse any raw data or code.

Funding

Part of this study was carried out at the Biological and Chemical Research Centre, University of Warsaw, established within the project co-financed by European Union from the European Regional Development Fund under the Operational Programme Innovative Economy, 2007--2013. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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