DOI: 10.5061/dryad.p8cz8wb1q
title: Data from: Allopatric divergence and secondary contact within a single river system in a freshwater fish group

description: Because riverine fishes can disperse along linear river corridors and even
 between tributaries, allopatric divergence within river systems is limited
 to large rivers. Within small rivers, such as island rivers, allopatric
 divergence rarely occurs, and no cases of secondary contact have been
 reported to date. Two congeneric riverine ricefishes, Oryzias
 dopingdopingensis and O. landangiensis, are found in the Doping-doping and
 Cerekang Rivers, respectively, on Sulawesi Island, which are connected via
 estuarine waters. These two species are suggested to have diverged in
 allopatry within this single river system. Phylogenetic and population
 genetic structure analyses using genome-wide single nucleotide
 polymorphisms revealed that Oryzias individuals recently
 discovered from the downstream Cerekang River are phylogenetically
 distinct not only from O. dopingdopingensis in the Doping-doping River but
 also from O. landangiensis in the upstream Cerekang River. Species tree
 analysis and demographic model inference revealed that the downstream
 Cerekang Oryzias diverged from upstream Cerekang Oryzias in allopatry
 approximately 57,000 generations ago, and they came into secondary contact
 with each other approximately 22,000 generations ago. Thereafter, the
 upstream Cerekang population split into two populations, O. landangiensis
 and O. dopingdopingensis, approximately 14,000 generations ago. We are not
 aware of any freshwater fish groups that may have experienced both
 allopatric divergence and secondary contact within such a small single
 river system. The allopatric divergence and secondary contact within the
 Cerekang–Doping-doping River system can be explained by assuming that a
 lake once existed in this region, where many tectonic lakes have formed
 and disappeared because of the collision and/or juxtaposition of tectonic
 subdivisions since the Pliocene/Pleistocene. Gene flow from O.
 landangiensis to the downstream Cerekang Oryzias is also evident. Although
 the secondary contact between the upstream and downstream Cerekang
 populations was estimated to have occurred more than 40,000 years ago,
 they are still not completely homogenized within the linear corridor of
 the Cerekang River. This stagnation of homogenization can be explained by
 their weak dispersal ability, which may reflect past adaptation to
 lacustrine environments.
description: # Data from: Allopatric divergence and secondary contact within a single
 river system in a freshwater fish group Uploaded: January 2025 Revised:
 Contact: Kazunori Yamahira
 ([yamahira@lab.u-ryukyu.ac.jp](mailto:yamahira@lab.u-ryukyu.ac.jp))
 \-------------------------------------------------------------------------------- File 1: Sample_list.txt The text file containing the data listed below. *Species*: Species of each sample *River*: Name of the river where each sample was collected *Site_ID*: ID of sites where each sample was collected *Individual_ID*: ID of each sample *Coordinate*: Coordinate of collection sites *Collection_date*: Date of sample collection *Sex*: Sex of each sample *Accession_no._for_ND2*: DNA Data Bank of Japan (DDBJ) for mitochondrial ND2 sequences *Accession_no._for_ddRAD-seq_reads*: DDBJ Sequence Read Archive accession numbers (DRR no.) for raw reads of ddRAD-sequencing *Run_file*: Name of fastq files deposited to DRR *ddRAD-seq_read_count*: Read count of each fastq file *Percentage_of_heterozygous_sites*: Percentage of heterozygous sites in each sample *Reference*: Reference of each sample