DOI: 10.5061/dryad.mpg4f4r7d
title: Evolution of size-fecundity relationship in medaka fish from different latitudes

description: In most fishes, the number of offspring increases with maternal body size.
 Although this size-fecundity relationship often varies among species as a
 result of the coevolution of life-history traits, the genetic basis of
 such size-fecundity relationships remains unclear. We explored the genetic
 basis underlying this size-fecundity relationship in two small medaka
 species, Oryzias latipes and O. sakaizumii. Our findings showed that O.
 sakaizumii has a higher fecundity than O. latipes, and quantitative trait
 locus analysis using interspecific F2 hybrids showed that chromosome 23 is
 linked to the size-fecundity relationship. In particular, the genes igf1
 and lep-b in this region are known to be associated with life-history
 traits, including somatic growth, gonad maturation, and offspring numbers
 in various taxa. Because O. sakaizumii is distributed at higher latitudes
 and has a shorter spawning season than O. latipes in the wild, we propose
 that the relatively high fecundity observed in O. sakaizumii is an
 adaptation to high latitudes. We also discuss the potential ecological
 ramifications associated with the evolution of increased fecundity in this
 species.
description: # Evolution of size-fecundity relationship in medaka fish from different
 latitudes
 [https://doi.org/10.5061/dryad.mpg4f4r7d](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](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](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](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](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](https://feb2023.archive.ensembl.org)