Appendix D. Effects of physical and chemical covariates on ecosystem and community-level general linear model results.

Effects of physical and chemical covariates on ecosystem and community-level general linear model results

Appendix B. List of functional groupings to which algal species were assigned.

List of functional groupings to which algal species were assigned

Appendix C. Complete summary of general linear model results.

Complete summary of general linear model results

Appendix A. Distribution of ambient nitrate concentrations and molar nitrate:orthophosphate ratios among streams used in this study, with photos of the experimental design and measured nutrient diffusion rates.

Distribution of ambient nitrate concentrations and molar nitrate:orthophosphate ratios among streams used in this study, with photos of the experimental design and measured nutrient diffusion rates

Appendix A. Responses of individual periphyton species to nutrient enrichment.

Responses of individual periphyton species to nutrient enrichment

Supplement 1. Original data used for all analyses and figures in the main article.

<h2>File List</h2><blockquote> <p><a href="Cardinale_et_al_2008dataset.txt">Cardinale_et_al_2008dataset.txt</a></p> </blockquote><h2>Description</h2><blockquote> <p>Cardinale_et_al_2008dataset.txt is a tab-delimited file that contains all of the original data used for all analyses and figures in Cardinale, B. J., D. Bennett, C. Nelson, and K. Gross. Does productivity drive diversity or vice versa?  Support for the multivariate productivity–diversity hypothesis in streams. <i>Ecology</i> 90:1227–1241. Column numbers, headings, descriptions, and column sums of numerical data for checking file upload are as follows: </p> -- TABLE: Please see in attached file. --</blockquote

Tempo and Mode of Gene Duplication in Mammalian Ribosomal Protein Evolution

<div><p>Gene duplication has been widely recognized as a major driver of evolutionary change and organismal complexity through the generation of multi-gene families. Therefore, understanding the forces that govern the evolution of gene families through the retention or loss of duplicated genes is fundamentally important in our efforts to study genome evolution. Previous work from our lab has shown that ribosomal protein (RP) genes constitute one of the largest classes of conserved duplicated genes in mammals. This result was surprising due to the fact that ribosomal protein genes evolve slowly and transcript levels are very tightly regulated. In our present study, we identified and characterized all RP duplicates in eight mammalian genomes in order to investigate the tempo and mode of ribosomal protein family evolution. We show that a sizable number of duplicates are transcriptionally active and are very highly conserved. Furthermore, we conclude that existing gene duplication models do not readily account for the preservation of a very large number of intact retroduplicated ribosomal protein (RT-RP) genes observed in mammalian genomes. We suggest that selection against dominant-negative mutations may underlie the unexpected retention and conservation of duplicated RP genes, and may shape the fate of newly duplicated genes, regardless of duplication mechanism.</p></div

Pipeline for ribosomal protein family analyses.

<p>Protein sequence for all parental ribosomal proteins were collected manually from Ensembl62. These were input to tBLASTn against whole genomes to capture all putative duplicates. The resulting duplicates were processed by Pseudopipe to determine the mechanism of duplication (DNA or RNA) and the fate of the duplicate (intact or pseudogenized). We then utilized our in-house pipeline steps of hierarchical clustering by local synteny³ in order to build our gene family trees after filtering false-positives and redundant entries. Final gene family analyses were conducted in 2 steps: 1) calculating the selective pressures on all gene duplicates using the Nei-Gojobori method against the species- and family-specific seed protein via an exon-based reconstruction, and 2) checking for expression signatures via EST analyses using the UCSC genome browser EST track for both human and mouse.</p

RP gene duplicates in 8 mammalian genomes.

<p>A) Distribution of duplication events in 8 mammalian genomes. B) Assessment of coverage or species-specific bias in ribosomal protein gene duplicates. C) Representation of DNA and RNA-mediated duplications in RP gene families. Abbreviations: Hs, <i>Homo sapiens</i> (human); Pt, <i>Pan troglodytes</i> (chimpanzee); Mmul, <i>Macaca mulatta</i> (Rhesus macaque); Mm, <i>Mus musculus</i> (house mouse); Rn, <i>Rattus norvegicus</i> (Norway rat); Bt, <i>Bos taurus</i> (cattle); Cf, <i>Canis familiaris</i> (dog); Md, <i>Monodelphis domestica</i> (gray short-tailed opossum); Gg, <i>gallus gallus</i> (chicken).</p

Likelihood Ratio Test statistics (LRT) for random site models.

a<p>Alternative model;</p>b<p>null model; 2Δℓ = 2(ℓ₁−ℓ₀), df degrees of freedom.</p><p>Likelihood Ratio Test statistics (LRT) for random site models.</p