https://doi.org/10.5061/dryad.mpg4f4r7d

We focused on the small fish medaka (Oryzias latipes, O. sakaizumii) to explore the genetic basis of the size-fecundity relationship. We demonstrate O. sakaizumii has genetically higher fecundity than O. latipes in a common garden experiment. Quantitative trait locus analysis using F2 interspecific hybrids showed that chromosome 23 is linked to the size-fecundity relationship. We hypothesize that adaptation to the habitat environment affects the evolution of the size-fecundity relationships in the two species. Thus, we also evaluate the size-fecundity relationship and spawning season length in the wild populations. We observed the proportions of mature males and females in the wild fish.

Description of the datasheet

evolution_fecundity_medaka_ver1_3
   ├ HabitatWaterTemperature_Log.csv: Record of habitat water temperature dataset
   |   Location: Place name
   |   Site: Setting point of temperature logger
   |   Temperature: water temperature (Celsius)
   |   Date: Month and Day in temperature record
   |   Month: Month in temperature record
   |   Year: Year in temperature record
   |
   ├ SpawningSeasonAssessment_Aomori_Okinawa.csv: Spawning observation dataset in the wild population
   |   date: Date of data collection in yyyymmdd format
   |   year: Year of data collection
   |   month: Month of data collection
   |   ordinal: Ordinal date number of data collection
   |   population: Collection site names (Okinawa or Aomori)
   |   sex: sex of the experimental individual (f: female, m: male)
   |   reproduct: Spawning or fertilization in two consecutive days (0: no observation, 1: observation)
   |   reproductSum: Days of spawning or fertilization in two consecutive days (0: no observation, 1: observation one day, 2: observation two days)
   |   reproductiveRate: reproductSum / 2 (days)
   |   firstEggNumber: Egg number on the first day of spawning assessment (Count)
   |   secondEggNumber: Egg number on the second day of spawning assessment (Count)
   |   averageEgg: Average value of the firstEggNumber and secondEggNumber (Count)
   |   dataset: Flag to determine whether to use for data analysis (0: not used, 1: used)
   |   SL: Standard length of each individual (mm)
   |   ExcludingReason: Description of reasons for exclusion from data analysis
   |   
   ├ labReared_G1eggNum_Aomori_Okinawa.csv: egg number dataset in the laboratory-reared G1 females
   |    Population:  Collection site names (Okinawa or Aomori)
   |    Species: Abbreviation of the scientific name of each species (lat: Oryzias latipes, sak: Oryzias sakaizumii)
   |    ExperimentSeries: Experimental series name of each observation
   |    PairID: Pair ID in the spawning observation experiment
   |    EggNum: Egg number in the spawning observation
   |    StandardLength: Standard length of experimental female (mm)
   |   
   ├ AFOM_F_SNP.csv: Genetic map dataset for AFOM strain of females (A: Aomori homo; H: Aomori/Okinawa hetero; B: Okinawa homo)
   ├ AFOM_M_SNP.csv: Genetic map dataset for AFOM strain of males (A: Aomori homo; H: Aomori/Okinawa hetero; B: Okinawa homo)
   ├ OFAM_F_SNP.csv: Genetic map dataset for OFAM strain of females (A: Okinawa homo; H: Aomori/Okinawa hetero; B: Aomori homo)
   ├ OFAM_M_SNP.csv: Genetic map dataset for OFAM strain of males (A: Okinawa homo; H: Aomori/Okinawa hetero; B: Aomori homo)
   |   
   ├ AFOM_F_behavior_mqm.csv: Phenotype dataset of AFOM females for QTL analysis
   ├ OFAM_F_behavior._mqmcsv: Phenotype dataset of OFAM females for QTL analysis
   |   id: Individual ID corresponding to SNP.csv
   |   pgm: “paternal grandmother” showed the cross direction 
   |   sex: Sex of each individual (0: female, 1: male)
   |   SL: Standard length (mm)
   |   avgEggNumber: Average egg number in two consecutive days (Count)
   |   fstWrappingRejection: Total number of wrapping rejections on the first day (Count)
   |   sndWrappingRejection: Total number of wrapping rejections on the second day (Count)
   |   fstSpawningLatency: Time to spend the spawning on the first day (second)
   |   sndSpawningLatency: Time to spend the spawning on the second day (second)
   |   spawning: Spawning observation over two consecutive days (0: no observation, 1: observation)
   |   
   ├ AFOM_M_behavior_mqm.csv: Phenotype dataset of AFOM males for QTL analysis
   ├ OFAM_M_behavior_mqm.csv: Phenotype dataset of AFOM males for QTL analysis
   |   id: Individual ID corresponding to SNP.csv
   |   pgm: “paternal grandmother” showed the cross direction 
   |   sex: Sex of each individual (0: female, 1: male)
   |   SL: Standard length (mm)
   |   fstQfreq: Frequency of quick circle on the first day (Count per second)
   |   fstHfreq: Frequency of approaching on the first day (Count per second)
   |   sndQfreq: Frequency of quick circle on the second day (Count per second)
   |   sndHfreq: Frequency of approaching in the second day (Count per second)
   |   fstMinCourtshipTime: Time to spend first courtship on the first day (second)
   └   sndMinCourtshipTime: Time to spend the first courtship on the second day (second)

Description of the script and intermediate file structure

wildpopulation_spawning_aomori_okinawa 
　├ Fig2_a_sizeFecundityRelationship.R: Script of R making the figure size-fecundity relationship
　└ Fig2_c_matureProportion_Aomori_Okinawa.R :
　　　　　Script of R making the seasonal change in the mature proportion of males and females

labReared_G1eggNum_aomori_okinawa 
　├ labReared_G1eggNum_Aomori_Okinawa.csv: egg number dataset in the laboratory-reared G1 females
　└ Fig2b_labRearedG1_eggNum_aomori_okinawa_ver1.R:
　　　　　Script of R making boxplot of the laboratory-reared G1 females

qtl_analysis 
　├ QTLanalysis_MQM_AFOM_F_ver1.R: Script of QTL analysis of LOD score and permutation test for AFOM females
　├ QTLanalysis_MQM_OFAM_F_ver1.R: Script of QTL analysis of LOD score and permutation test for OFAM females
　├ QTLanalysis_MQM_AFOM_M_ver1.R: Script of QTL analysis of LOD score and permutation test for AFOM males
　├ QTLanalysis_MQM_OFAM_M_ver1.R: Script of QTL analysis of LOD score and permutation test for OFAM males
　├ QTLanalysis_Fig3c_eggNum_chr23.R: Script of R making scatterplot between body size and egg number
　├ QTLanalysis_FigS2_EffectPlot_ver2.R: Script of R making boxplot for genetic marker and phenotype
　└ QTLanalysis_Table1_PVE.R: Script of R calculating genome-wide and QTL of Phenotypic variance explained (PVE)

gene_Info_ensembl
　├ qtl_HdrR_genome_liftover
　│ 　　 　├ liftover_ASM31367v1_ASM223467v1_qtlMarker
　│ 　　 　│　　　　└ flo_HdrR_sanger_to_HdrR_pacBio.txt: Shell script for “liftover” to convert genomic coordinates
　│　　　　└ estimate_cM_position
　│ 　　 　 　　   ├ QTLmarker_cM_position.csv: Genetic map and genomic coordinates dataset in QTL analysis
　│　　　　 　　 ├ interpolate_QTL_cM_position_ver2.R:
　│　　　　 　　 │ Script of R to interpolate the centiMorgan and physical position based on genetic map
　│　 　 　　　　├ interporated_cM_physicalPosition.csv: Intermediate file for conversion of physical position
　│　 　 　　　　├ qtl_candidateRegion.csv: Dataset for 95%CI in six QTL regions
　│ 　　 　 　　   └ QTL_95CI_interpolate_cMtoPOS.bed: Output file to convert the physical position in ASM223467v
　├ shinyGO_080_geneEnrichment
　│ 　　 　├ chr12_standardLengthQTL
　│ 　　 　│　　　　├ chr12_standardLength_Genes.txt: Gene ID list 
　│ 　　 　│　　　　├ enrichment_all_chr12_standardlength.csv: results of all GO terms in enrichment analysis
　│ 　　 　│　　　　├ enrichment_top20_chr12_standardlength.csv: results of top 20 GO term in enrichment analysis
　│ 　　 　│　　　　└ chr12_standardlength_shingyGO_080_2024-09-12.png: Screenshot of ShinyGO
　│ 　　 　├ chr13_spawningLatencyQTL
　│ 　　 　│　　　　├ chr13_spawningLatencyQTL_Genes.txt: Gene ID list 
　│ 　　 　│　　　　├ enrichment_all_chr13_spawningLatency.csv: results of all GO terms in enrichment analysis
　│ 　　 　│　　　　├ enrichment_top20_chr13_spawningLatency.csv: results of top 20 GO term in enrichment analysis
　│ 　　 　│　　　　└ chr13_spawningLatency_shingyGO_080_2024-09-12.png: Screenshot of ShinyGO
　│ 　　 　├ chr18_spawningLatencyQTL
　│ 　　 　│　　　　├ chr18_spawningLatencyQTL_Genes.txt: Gene ID list 
　│ 　　 　│　　　　├ enrichment_all_chr18_spawningLatency.csv: results of all GO terms in enrichment analysis
　│ 　　 　│　　　　├ enrichment_top20_chr18_spawningLatency.csv: results of top 20 GO term in enrichment analysis
　│ 　　 　│　　　　└ chr18_spawningLatency_shingyGO_080_2024-09-12.png: Screenshot of ShinyGO
　│ 　　 　├ chr20_courtshipFrequencyQTL
　│ 　　 　│　　　　├ chr20_courtshipFrequencyQTL_Genes.txt: Gene ID list 
　│ 　　 　│　　　　├ enrichment_all_chr20_courtshipFrequency.csv: results of all GO terms in enrichment analysis
　│ 　　 　│　　　　├ enrichment_top20_chr20_courtshipFrequency.csv: results of top 20 GO term in enrichment analysis
　│ 　　 　│　　　　└ chr20_courtshipFrequency_shingyGO_080_2024-09-12.png: Screenshot of ShinyGO
　│ 　　 　├ chr23_eggNumberQTL
　│ 　　 　│　　　　├ chr23_eggNumberQTL_Genes.txt: Gene ID list 
　│ 　　 　│　　　　├ enrichment_all_chr23_eggNumber.csv: results of all GO terms in enrichment analysis
　│ 　　 　│　　　　├ enrichment_top20_chr23_eggNumber: results of top 20 GO term in enrichment analysis
　│ 　　 　│　　　　└ chr23_eggNumber_shingyGO_080_2024-09-12.png: Screenshot of ShinyGO
　│ 　　 　└ chr24_wrappingRejectionQTL
　│ 　　 　  　　　　├ chr24_wrappingRejection_Genes.txt: Gene ID list 
　│ 　　 　  　　　　├ enrichment_all_chr24_wrappingRejection.csv: results of all GO terms in enrichment analysis
　│ 　　 　  　　　　├ enrichment_top20_chr24_wrappingRejection.csv: results of top 20 GO terms in enrichment analysis
　│ 　　 　  　　　　└ chr24_wrappingRejection_shingyGO_080_2024-09-12.png: Screenshot of ShinyGO
　└ qtl_candidate_gtf_geneExtract
　 　 　 　　　　├ GeneName_Exon_region_extraction.txt:
　　　 　　 　　 │              Shell script for extraction of geneID and gene name in QTL regions
　 　 　 　　　　├ qtl_geneList_Oryzias_latipes.ASM223467v1.109.txt:
　　　 　　 　　 │              Output file of “GeneName_Exon_region_extraction.txt”
　 　 　 　　　　├ geneOntology_biomart_ver2.R:
　　　 　　 　　 │              Script of R to obtain the Gene ontology term information via biomaRt
　 　 　 　　　　└ gene_GOterm_mergedDF.csv: Output file of “geneOntology_biomart_ver2.R”

Sharing/Access information

Original data of the genetic map was derived from the following sources:

• Kawajiri M, Yoshida K, Fujimoto S, et al. (2014) Ontogenetic stage-specific quantitative trait loci contribute to divergence in developmental trajectories of sexually dimorphic fins between medaka populations. Mol Ecol, 23(21):5258–5275. https://doi.org/10.1111/mec.12933

• Kawajiri M, Fujimoto S, Yoshida K, et al. (2015) Genetic Architecture of the Variation in Male-Specific Ossified Processes on the Anal Fins of Japanese Medaka. G3; Genes

  Genomes

  Genetics, 5(12):2875–2884. https://doi.org/10.1534/g3.115.021956

• Oryzias latipes MEDAKA1 (Reference sequence, HdrR strain, Old version): http://ftp.ensembl.org/pub/release-93/fasta/oryzias_latipes/dna/Oryzias_latipes.MEDAKA1.dna.toplevel.fa.gz
• ASM223467v1 (Reference sequence, HdrR strain): http://ftp.ensembl.org/pub/release-105/fasta/oryzias_latipes/dna/Oryzias_latipes.ASM223467v1.dna.toplevel.fa
• Ensemble, Gene database for Oryzias_latipes.ASM223467v1.109: https://feb2023.archive.ensembl.org