Data from: A genome-wide phylogeny of the family Adrianichthyidae and redescription of the monotypic Horaichthys setnai

Data files

Sep 21, 2026 version files 411.03 MB

File_01_supermatrix.fas

246.09 MB
File_02_supermatrix.gene_positions.txt

87.66 KB
File_03_supermatrix.partitions.txt

419.97 KB
File_04_supermatrix.excl_3rd_codon_pos.fas

164.06 MB
File_05_supermatrix.excl_3rd_codon_pos.gene_positions.txt

87.03 KB
File_06_supermatrix.excl_3rd_codon_pos.partitions.txt

278.71 KB
File_07_raw_morphological_data.txt

5.04 KB
README.md

6.58 KB

Abstract

The family Adrianichthyidae comprises more than 40 species distributed across East, Southeast, and South Asia and represents an important system for studying evolutionary diversification in tropical and subtropical regions. However, incongruences between morphology-based taxonomy and molecular phylogenies remain unresolved, particularly regarding the systematic position of Oryzias setnai, a species endemic to western India that was originally described as Horaichthys setnai. Here, we reconstruct a comprehensive genome-wide nuclear phylogeny of Adrianichthyidae using thousands of single-copy orthologous genes identified by BUSCO (Benchmarking Universal Single-Copy Orthologs), incorporating a newly generated genome assembly for O. setnai. Our analyses robustly support O. setnai as sister to all other adrianichthyids, contrary to the morphology-based classification. Morphological re-examination confirms that O. setnai possesses numerous autapomorphies absent from Oryzias, including reproductive traits associated with internal fertilization, distinctive skeletal features, and a unique body morphology. Taken together, these data strongly support the reinstatement of the genus Horaichthys. Accordingly, we redescribe the species under its original combination, Horaichthys setnai. Notably, the lineage leading to this species exhibits a markedly elongated branch, indicating an accelerated rate of molecular evolution in a phylogenetically isolated lineage lacking close extant relatives. This combination of rapid molecular evolution and profound phylogenetic isolation provides new insights into the evolutionary processes underlying the emergence of morphological and reproductive autapomorphies, as well as lineage-specific variation in diversification rates.

README for the dataset from Anoop et al. 2026: A genome-wide phylogeny of the family Adrianichthyidae with a taxonomic revision of Horaichthys setnai. Zoological Journal of the Linnean Society. The dataset has five Dryad data files.

Contact: Kazunori Yamahira (yamahira@cs.u-ryukyu.ac.jp)

File_01: File_01_supermatrix.fas

The fasta file containing nucleotide sequences of concatenated BUSCO genes in multi-FASTA format, used for the RAxML analysis.

File_02: File_02_supermatrix.gene_positions.txt

The text file containing gene positions (1-based coordinates) of each BUSCO gene in the supermatrix.fas file. The first column lists OrthoDB v12 gene IDs; the second column indicates the starting position of each gene; the third column indicates the ending position of each gene.

File_03: File_03_supermatrix.partitions.txt

The text file containing partition information for the supermatrix.fas file used for the RAxML analysis.

File_04: File_04_supermatrix.excl_3rd_codon_pos.fas

The fasta file containing nucleotide sequences of concatenated BUSCO genes in multi-FASTA format, with third codon positions removed, used for the RAxML analysis.

File_05: File_05_supermatrix.excl_3rd_codon_pos.gene_positions.txt

The text file containing gene positions (1-based coordinates) of each BUSCO gene in the supermatrix.fas file, with third codon positions removed. The first column lists OrthoDB v12 gene IDs; the second column indicates the starting position of each gene.

File_06: File_06_supermatrix.excl_3rd_codon_pos.partitions.txt

The text file containing partition information for the supermatrix.fas file, with third codon positions removed, used for the RAxML analysis.

File_07: File_07_raw_morphological_data.txt

The text file containing raw morphometric and meristic data used in the redescription of Horaichthys setnai. Each column represents an individual specimen, and each row represents a morphological character or specimen information. Morphometric measurements are given in millimetres (mm). Meristic characters are counts of fin rays, scales, vertebrae, or fin positions. A dash ("-") indicates that the character did not apply to that specimen.

The variables are as follows:

Voucher number: Institutional voucher number assigned to each specimen.
Sex: Sex of the specimen (Female or Male).
Total length (mm): Distance from the anterior-most point of the head to the posterior-most point of the caudal fin.
Standard length (mm): Distance from the anterior-most point of the head to the posterior end of the hypural plate, excluding the caudal fin.
Head length (mm): Distance from the anterior-most point of the head to the posterior margin of the operculum.
Pectoral-fin length (mm): Distance from the origin of the pectoral fin to the tip of the longest ray.
Pelvic-fin length (mm): Distance from the origin of pelvic-fin to tip of longest ray.
Dorsal-fin length (mm): Distance from the origin of dorsal-fin to tip of longest ray.
Anal-fin length (mm): Distance from the origin of anal-fin to the tip of the longest ray.
Anal-fin base length (mm): Distance from the origin of the first anal-fin ray to the posterior base where the last anal ray meets the body.
Pre-dorsal length (mm): Distance from the anterior-most point of the head to the origin of the dorsal fin.
Pre-anal length (mm): Distance from the anterior-most point of the head to the origin of the anal fin.
Body depth at anal-fin origin (mm): Maximum vertical depth of the body at the anal-fin origin.
Body width at anal-fin origin (mm): Maximum transverse width of the body at the anal-fin origin.
Caudal-peduncle length (mm): Distance between the insertion of the anal fin and the posterior end of the hypural plate.
Caudal-peduncle depth (mm): Maximum vertical depth of the body at the middle ofthe caudal peduncle.
Caudal-fin length (mm): Distance from the posterior-most point of the hypural plate to the end of the caudal fin ray.
Gonopodium length (mm): Distance measured from the anterior base of the modified reproductive fin to the distal tip of the longer ray. This character does not apply to females and is indicated by "-".
Snout length (mm): Distance from the anterior-most point of the head to the anterior margin of the eye.
Eye diameter (mm): Diameter between the anterior margin and the posterior margin of the eye.
Interorbital width (mm): Minimum transverse distance between the dorsal margins of the eyes.
Head depth at eye (mm): Maximum vertical depth of the head measured through the centre of the eye
Head width at eye (mm): Maximum transverse width of the head measured through the centre of the eye.
Dorsal-fin rays: Number of rays in the dorsal fin.
Pectoral-fin rays: Number of rays in the pectoral fin.
Pelvic-fin rays: Number of rays in the pelvic fin.
Anal-fin rays: Number of rays in the anal fin.
Caudal-fin rays/ Principal caudal-fin rays: Number of principal caudal-fin rays, excluding procurrent rays. The count includes the unbranched rays forming the dorsal and ventral margins of the caudal fin and all intervening rays. The notation i,4+4, i indicates one unbranched ray on each side and four branched rays in each of the upper and lower lobes.
Procurrent rays (upper): Number of small, unbranched fin rays along the dorsal margin of the caudal peduncle, excluding the principal caudal-fin rays.
Procurrent rays (lower): Number of small, unbranched fin rays along the ventral margin of the caudal peduncle, excluding the principal caudal-fin rays.
Lateral line scales: Scales bearing the lateral-line canal from the head to the end of the vertebral column (end of the hypural plate).
Total vertebrae: Total number of vertebral centra in the vertebral column.
Abdominal vertebrae: Number of vertebrae anterior to the caudal vertebrae that lack haemal spines, extending from the first vertebra of the vertebral column to the last vertebra without a haemal spine.
Caudal vertebrae: Number of vertebrae bearing haemal arches or haemal spines, extending posteriorly from the first caudal vertebra to the end vertebra of the vertebral column.
Position of pelvic-fin: Position of the pelvic-fin origin, expressed as the number of the corresponding vertebral position.
Position of anal-fin: Position of the anal-fin origin, expressed as the number of the corresponding vertebral position.
Position of dorsal-fin: Position of the dorsal-fin origin, expressed as the number of the corresponding vertebral position.