Additional file 1: Table S1. of Early evolutionary history and genomic features of gene duplicates in the human genome

Evolutionary and genomic features of 184 gene duplicates with low synonymous divergence in the human genome. (PDF 262 kb

Fitness measures at MA generation 100 under osmotic stress

Fitness of C. elegans mutation accumulation (MA lines) following 100 consecutive generations of spontaneous MA. The MA experiment was conducted under benign laboratory conditions. Fitness was tested under hyperosmotic conditions (200mM salt concentration in NGM plates). Manual measurements of two fitness-related traits, survivorship to adulthood and productivity, in long-term mutation accumulation (MA) lines of C. elegans maintained at population bottlenecks of N = 1, 10 and 100 individuals and the pre-MA ancestral control. Data is presented, where available for 20 N=1 lines (lines 1A-1T), ten N=10 lines (10A-10J), five N=100 lines (100A-100E) and 20 ancestral control lines (C1-C20). Where possible, data was collected for five replicates per experimental line. Productivity was measured by the total number of offspring produced by a virgin hermaphrodite over eight days or until day of expiration prior to eight days. Survivorship to adulthood was measured by isolating ten L1 larvae and determining the fraction that had survived to adulthood at 36 hours after initial sequestration. Survivorship data values range from 0-1, with a 0 value representing 100% mortality prior to reaching adulthood, and a value of 1 representing 100% survivorship

Fitness measures at MA generation 300 under osmotic stress

Fitness of C. elegans mutation accumulation (MA lines) following 300 consecutive generations of spontaneous MA. The MA experiment was conducted under benign laboratory conditions. Fitness was tested under hyperosmotic conditions (200mM salt concentration in NGM plates). Manual measurements of two fitness-related traits, survivorship to adulthood and productivity, in long-term mutation accumulation (MA) lines of C. elegans maintained at population bottlenecks of N = 1, 10 and 100 individuals and the pre-MA ancestral control. Data is presented, where available for 20 N=1 lines (lines 1A-1T), ten N=10 lines (10A-10J), five N=100 lines (100A-100E) and 20 ancestral control lines (C1-C20). Where possible, data was collected for five replicates per experimental line. Productivity was measured by the total number of offspring produced by a virgin hermaphrodite over eight days or until day of expiration prior to eight days. Survivorship to adulthood was measured by isolating ten L1 larvae and determining the fraction that had survived to adulthood at 36 hours after initial sequestration. Survivorship data values range from 0-1, with a 0 value representing 100% mortality prior to reaching adulthood, and a value of 1 representing 100% survivorship

Mutation Accumulation Generation 172 Fitness Data

Productivity and survivorship to adulthood for MA lines following 172 consecutive generations of mutation accumulation and the ancestral controls. Column 1 corresponds to the line identifier (MA line or ancestral control line). Column 2 lists the replicate number for each line (where possible, we aimed for five replicates within each line). Columns 3-10 list the worm productivity corresponding to Days 1-8 of the productivity assay. Column 11 is the total productivity summed across Days 1-8. Column 12 lists the number of surviving adults from a pool of L1 larvae initially isolated. Column 13 is the final value for survivorship to adulthood and ranges from 0 to 1 (corresponding to 0 to 100% survivorship to adulthood). Dashes in cells represent lack of data due to hermaphrodite mortality during the assay or inability to enter the replicate line into assay due to sterility or mortality in preceding generations

Mutation Accumulation Generation 409 Fitness Data

Productivity and survivorship to adulthood for MA lines following 409 consecutive generations of mutation accumulation and the ancestral controls. Column 1 corresponds to the line identifier (MA line or ancestral control line). Column 2 lists the replicate number for each line (where possible, we aimed for five replicates within each line). Columns 3-10 list the worm productivity corresponding to Days 1-8 of the productivity assay. Column 11 is the total productivity summed across Days 1-8. Column 12 lists the number of surviving adults from a pool of L1 larvae initially isolated. Column 13 is the final value for survivorship to adulthood and ranges from 0 to 1 (corresponding to 0 to 100% survivorship to adulthood). Dashes in cells represent lack of data due to hermaphrodite mortality during the assay or inability to enter the replicate line into assay due to sterility or mortality in preceding generations

Mutation Accumulation Generation 300 Fitness Data

Productivity and survivorship to adulthood for MA lines following 300 consecutive generations of mutation accumulation and the ancestral controls. Column 1 corresponds to the line identifier (MA line or ancestral control line). Column 2 lists the replicate number for each line (where possible, we aimed for five replicates within each line). Columns 3-10 list the worm productivity corresponding to Days 1-8 of the productivity assay. Column 11 is the total productivity summed across Days 1-8. Column 12 lists the number of surviving adults from a pool of L1 larvae initially isolated. Column 13 is the final value for survivorship to adulthood and ranges from 0 to 1 (corresponding to 0 to 100% survivorship to adulthood). Dashes in cells represent lack of data due to hermaphrodite mortality during the assay or inability to enter the replicate line into assay due to sterility or mortality in preceding generations

Mutation Accumulation Generation 100 Fitness Data

Productivity and survivorship to adulthood for MA lines following 100 consecutive generations of mutation accumulation and the ancestral controls. Column 1 corresponds to the line identifier (MA line or ancestral control line). Column 2 lists the replicate number for each line (where possible, we aimed for five replicates within each line). Columns 3-10 list the worm productivity corresponding to Days 1-8 of the productivity assay. Column 11 is the total productivity summed across Days 1-8. Column 12 lists the number of surviving adults from a pool of L1 larvae initially isolated. Column 13 is the final value for survivorship to adulthood and ranges from 0 to 1 (corresponding to 0 to 100% survivorship to adulthood). Dashes in cells represent lack of data due to hermaphrodite mortality during the assay or inability to enter the replicate line into assay due to sterility or mortality in preceding generations

Additional file 11: Supplemental Data S3. of Rapid Increase in frequency of gene copy-number variants during experimental evolution in Caenorhabditis elegans

List of ORFs contained in eight overlapping duplications and deletions in experimental C. elegans lines following 180–212 generations of population expansion under competitive conditions. Duplication/deletion breakpoint coordinates and ORFs contained therein are based on Wormbase version WS243. (PDF 116 kb