DOI: 10.5061/dryad.qbzkh18pb
title: Ghost introgression in ricefishes of the genus Adrianichthys in an ancient Wallacean lake

description: Because speciation might have been promoted by ancient introgression from
 an extinct lineage, it is important to detect the existence of “ghost
 introgression” in focal taxa and examine its contribution to their
 diversification. In this study, we examined possible ghost introgression
 and its contributions to the diversification of ricefishes of the genus
 Adrianichthysin Lake Poso, an ancient lake on Sulawesi Island, in which
 some extinctions are known to have occurred. Population genomic analysis
 revealed that two extant Adrianichthys species, A. oophorus and A. poptae,
 are reproductively isolated from each other. Comparisons of demographic
 models demonstrated that introgression from a ghost population, which
 diverged from the common ancestor of A. oophorus and A. poptae, is
 essential for reconstructing the demographic history of Adrianichthys. The
 best model estimated that the divergence of the ghost population greatly
 predated the divergence between A. oophorus and A. poptae, and that the
 ghost population secondarily contacted the two extant species within Lake
 Poso more recently. Genome scans and simulations detected a greatly
 divergent locus, which cannot be explained without ghost introgression.
 This locus was also completely segregated between A. oophorus and A.
 poptae. These findings suggest that variants that came from a ghost
 population have contributed to the divergence between A. oophorusand A.
 poptae, but the large time-lag between their divergence and ghost
 introgression indicates that the contribution of introgression may be
 restricted.
description: # README for data set from Yamahira et al. 2023 Journal of Evolutionary
 Biology. The data set accompanies six Dryad data files. Uploaded: June
 2023 Revised: Contact: Kazunori Yamahira (yamahira@lab.u-ryukyu.ac.jp) ***
 ### File 1: File\_01\_13463\_RAD\_loci.fa The fasta file containing
 sequences of 13,463 RAD loci (51 bp) of 15 Adrianichthys oophorus and 54
 A. poptae individuals, which was used for genome scan by DnaSP. The
 sequence files are available from DDBJ/EMBL-EBI/NCBI Sequence Read Archive
 under the accession number DRA014904. *** ### File 2:
 File\_02\_4463\_SNPs.vcf The VCF file containing only the first SNP from
 each of 4,463 RAD loci among 15 *Adrianichthys* *oophorus* and 54 *A.
 poptae* individuals, which was used for phylogenetic and population
 structure analyses. REF and ALT alleles represent major and minor alleles,
 respectively, rather than reference and alternative. This is due to the
 specification of the populations program of the Stacks pipeline that was
 used to produce the file. The sequence files are available from
 DDBJ/EMBL-EBI/NCBI Sequence Read Archive under the accession number
 DRA014904. *** ### File 3: File\_03\_6275\_SNPs.vcf The VCF file
 containing 6,275 biallelic SNPs on 9,701 RAD loci among 15 *Adrianichthys*
 *oophorus* and 54 *A. poptae* individuals, which was used to create
 two-dimensional joint minor allele site frequency spectrum for
 fastsimcoal2 runs. REF and ALT alleles represent major and minor alleles,
 respectively, rather than reference and alternative. This is due to the
 specification of the populations program of the Stacks pipeline that was
 used to produce the file. The sequence files are available from
 DDBJ/EMBL-EBI/NCBI Sequence Read Archive under the accession number
 DRA014904. *** ### File 4: File\_04\_JSFS\_data The two-dimensional joint
 minor allele site frequency spectrum for the demographic model comparisons
 by fastsimcoal2. *** ### File 5: File\_05\_est\_and\_tpl The est and tpl
 files of each of the demographic models compared in fastsimcoal2. *** ###
 File 6: SplitsTree.nex The nexus file containing p-distances between 69
 individuals (15 *Adrianichthys* *oophorus* and 54 *A. poptae*
 individuals), which was used for building a phylogenetic network by
 SplitsTree.