Genetic basis for the evolution of pelvic-fin brooding, a new mode of reproduction, in a Sulawesian fish
Cite this dataset
Montenegro, Javier et al. (2024). Genetic basis for the evolution of pelvic-fin brooding, a new mode of reproduction, in a Sulawesian fish [Dataset]. Dryad. https://doi.org/10.5061/dryad.v6wwpzgwz
Abstract
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.
README: 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
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)
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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.
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File 2: File_2_Newick_for_PGLS.newick
The tree data used for phylogenetic generalized least squares (PGLS) analyses.
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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.
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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.
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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.
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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.
Funding
Japan Society for the Promotion of Science, Award: KAKENHI 16F16392
Japan Society for the Promotion of Science, Award: KAKENHI 19K16203
Japan Society for the Promotion of Science, Award: KAKENHI 19K16232
Japan Society for the Promotion of Science, Award: KAKENHI 17H01675
Japan Science and Technology Agency, Award: CREST JPMJCR20S2
University of the Ryukyus, Strategic Research Grant
University of the Ryukyus, Research Project Promotion Grant
University of the Ryukyus, Spatiotemporal Genomics Project
National Institute of Genetics, Collaborative Grant (B)