Outcome of Sperm Competition Trials

Outcome of Sperm Competition Trial

Lenz_ParasiteData

Individual parasite data for community comparison among habitats and host species

Sperm concentration and velocity measurements

Sperm concentration and velocity measurement

Lenz_ParasiteData

Parasite data for experimental fish. Tab-delimited and ready for input into R

Lenz_MappedAssembly.fasta

contains the output of the mapping assembly of the normalized cDNA reads against the ENSEMBL transcript

Lenz_ESTmatrix_Normalized

SuperSAGE tag count data for each detected gene and sample library. Tags are filtered according to description in the manuscript and tag count is normalized to 1 Mio tags per library. See accompanying files for sample description. Gene IDs are from ENSEMBL. Ready for input into R

Lenz_24SuperSAGElibraries

contains the 24 individual libraries with sequenced SuperSAGE tags and their frequencies

Lenz_SampleIdentification

Table with information on origin, treatment and attributes for each SuperSAGE library sample

CNV proportions across genomic regions and homozygous deletions.

<p>(<b>A</b>) Proportion of deletions (white) and duplications (black) overlapping four mutually exclusive genomic categories; entirely within intergenic regions, entirely within intronic regions, partially overlapping a gene including an exonic region, or completely overlapping at least one gene. (<b>B</b>) Read depth coverage (grey histograms) along a gene (blocks are exons) for one representative individual from each population, showing CNV deletions. Examples include an intronic loss from a small G protein signaling modulator 3 gene (<i>SGSM3</i>) in Atlantic individuals, an exonic partial gene loss of a carbonic anhydrase gene (<i>CA4</i>) in Norwegian individuals, and the complete gene loss of a pogo transposable element with <i>KRAB</i> domain gene (<i>POGK</i>) in Atlantic individuals.</p

Relationship between young genes and CNVs.

<p>(<b>A</b>) Five mutually-exclusive gene categories based on orthology and paralogy: Non LSGs (Non-Lineage Specific Gene singletons), Non-LSG paralogs (Non-Lineage Specific Gene paralogs), Non-LSG LSD (Non-Lineage Specific Genes that are Lineage-Specific Duplicates), LSG LSD (Lineage-Specific Genes that are Lineage-Specific Duplicates) and LSG singletons (Lineage-Specific Gene singletons). Young genes are determined from broader overlapping categories, inferred as having no detectable orthologs (LSGs: lineage-specific genes) or recent paralogs (LSDs: lineage-specific duplications). LSGs are normally singletons but can also be duplicated, in which case they are both LSGs and LSDs (LSG LSD). LSGs and LSDs were found to have characteristic properties of young genes such as short gene lengths, narrow gene expression and rapid molecular evolution (<b><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004830#pgen.1004830.s038" target="_blank">S1 Text</a></b>). The relationship of corresponding genes across and within species (orthologs and paralogs) is represented for each category, wherein “>1” represents paralogs and “0” represents no detectable ortholog. For example, non-LSG singletons have a one-to-one relationship between sticklebacks and at least one other species, non-LSG paralogs have a many-to-many relationship due to an old duplication event (black dot in tree), and non-LSG LSD have a one-to-many relationship due to a recent duplication event along the stickleback lineage (purple dot in tree). The number of autosomal protein-coding genes belonging to each category is reported below each category name. (<b>B</b>) Proportion of genes (both protein-coding and RNA) completely encompassed within CNV regions (deletions in white, duplications in black, both deletion and duplication in stripes). (<b>C</b>) Overlap between protein-coding genes in segmental duplication (SD genes), CNV genes, and LSGs and LSDs. The majority of SD genes are LSGs and LSDs, many of which are also CNV genes.</p