DOI: 10.5061/dryad.v6wwpzgwz
title: Genetic basis for the evolution of pelvic-fin brooding, a new mode of reproduction, in a Sulawesian fish

description: Modes of reproduction in animals are diverse, with different modes having
 evolved independently in multiple lineages across a variety of taxa.
 However, an understanding of the genomic change driving the transition
 between different modes of reproduction is limited. Several
 ricefishes (Adrianichthyidae) on the island of Sulawesi have a
 unique mode of reproduction called “pelvic-fin brooding,” wherein
 females carry externally fertilized eggs until hatching using
 their pelvic fins. The phylogenomic analysis demonstrated pelvic-fin
 brooders to have evolved at least twice in two distant clades of the
 Adrianichthyidae. We investigated the genetic architecture of the
 evolution of this unique mode of reproduction. Morphological analyses and
 laboratory observations revealed that females of pelvic-fin brooders have
 longer pelvic fins and a deeper abdominal concavity and that they can
 carry an egg clutch for longer than non-brooding adrianichthyids,
 suggesting that these traits play important roles in this reproductive
 mode. Quantitative trait locus mapping using a cross between a pelvic-fin
 brooder Oryzias eversi and a
 non-brooding O. dopingdopingensis reveals different
 traits involved in pelvic-fin brooding to be controlled by different loci
 on different chromosomes. Genomic analyses of admixture detected no
 signatures of introgression between two lineages with pelvic-fin brooders,
 indicating that introgression is unlikely to be responsible for
 the repeated evolution of pelvic-fin brooding. These findings
 suggest that multiple independent mutations may have contributed to the
 convergent evolution of this novel mode of reproduction.
description: # Genetic basis for the evolution of pelvic-fin brooding, a new mode of
 reproduction, in a Sulawesian fish
 [https://doi.org/10.5061/dryad.v6wwpzgwz](https://doi.org/10.5061/dryad.v6wwpzgwz) README for data set from Javier et al. 2022 Molecular Ecology. The data set accompanies six Dryad data files. Uploaded: October 2021 Contact: Kazunori Yamahira ([yamahira@lab.u-ryukyu.ac.jp](mailto:yamahira@lab.u-ryukyu.ac.jp)) \-------------------------------------------------------------------------------- **File 1: File_1_Phenotype_17_species.txt** The phenotypes data for the 17 Sulawesi-endemic adrianichthyid species. Standard length, pelvic-fin length, the extent of abdominal concavity, and the number of days for which eggs were carried are measured for each female. Measurement units are included within the files. Three females per species were included, except for *Adrianichthys poptae* for which measurements were repeated three times using one female. NA indicates that it is not applicable. \-------------------------------------------------------------------------------- **File 2: File_2_Newick_for_PGLS.newick** The tree data used for phylogenetic generalized least squares (PGLS) analyses. \-------------------------------------------------------------------------------- **File 3: File_3_Phenotype_laboratory_cross.txt** The phenotypes data for F1 and F2 hybrid individuals between the cross of an *Oryzias eversi* female and an *O. dopingdopingensis* male. Standard length, pelvic-fin length, the extent of abdominal concavity, and the number of days for which eggs were carried are measured for each female. Information of .fastq files used for genotyping is also listed for each individual. "-" indicates that data was not obtained. \-------------------------------------------------------------------------------- **File 4: File_4_20_species_599749477bp_alignment.vcf.gz** The .vcf file containing alignments of 20 Sulawesi-endemic species/populations with a total length of 599,749,477 bp, which was used in genome scanning of significant loci detected by QTL mapping. \-------------------------------------------------------------------------------- **File 5: File_5_9_species_380264237bp_alignment.vcf.gz** The .vcf file containing alignments of nine Sulawesi-endemic species with a total length of 380,264,237 bp, which was used in f4 statistics and SAGUARO analysis. \-------------------------------------------------------------------------------- **File 6: File_6_P_distance_among_20_species_within_QTL_95CI.txt** The .csv file containing P-distance matrices among 20 Sulawesi-endemic species/populations within 1-kb sliding windows within 95% Bayesian credibility intervals of significant loci detected by QTL mapping.