DOI: 10.5061/dryad.2jm63xt33
title: Data from: Molecular evidence of introgression between water frog species (Anura: Telmatobiidae) in the high Andes

description: Contact zones are classical natural laboratories to study speciation.
 Several evolutionary outcomes are expected from hybridization depending on
 the degree of reproductive isolation, ranging from the formation of hybrid
 swarms in early stages of speciation to the reinforcement of species
 differences when speciation is complete. The genus Telmatobius is a high
 Andean, diverse, but poorly known group of neotropical frogs. Although
 hybridization between diverged species is frequent in amphibians, it has
 not been observed in this group. Here, we studied hybridization processes
 among three neighboring Telmatobius species that inhabit different
 altitudes in the same desertic basin using nuDNA SNP and mitochondrial DNA
 data. The results suggest that the Chilean population of Telmatobius
 peruvianus has hybridized to different degrees with the species T. pefauri
 and T. marmoratus. We detected mitochondrial and nuclear introgression
 from T. peruvianus to T. pefauri and what appears to be historical
 introgression between T. marmoratus and T. peruvianus. No first-generation
 hybrids nor parental genotypes were detected in admixed localities,
 suggesting that the inferred hybridization processes did not occur
 recently and several generations of backcrossing have passed in
 geographical isolation. Instead of representing stable hybrid zones,
 hybrid populations show a degree of genetic differentiation from parental
 populations. In this group of amphibians, nearly 2 million years of
 allopatric divergence have not been enough to develop reproductive
 isolation between diverged species. Data used in the genetic analyses of
 Fibla et al. (2025) are provided. These include: a genlight file (nuDNA
 SNPs matrix) including all samples, two separate genlight files (nuDNA
 SNPs matrices) representing both parental schemes and a fasta file
 consisting of D-loop DNA sequences matrix.
description: # Data from: Molecular evidence of introgression between water frog
 species (Anura: Telmatobiidae) in the high Andes Dataset DOI:
 [10.5061/dryad.2jm63xt33](https://doi.org/10.5061/dryad.2jm63xt33) ##
 Description of the data and file structure Raw SNP data from Dart (50,688
 SNPs) were filtered using the dartR library (Mijangos et al., 2022)
 implemented in the R program (R core Team, 2024). To improve the quality
 of our dataset and reduce genotyping errors, we retained only one SNP in
 the reads containing two or more SNPs (39,390 SNPs retained). We
 eliminated: i) loci with a read depth below five or above 200 (31,234 SNPs
 retained), ii) loci with &lt; 99% reproducibility (23,926 SNPs retained),
 iii) monomorphic loci (23,926 SNPs retained), iv) loci with &gt; 10%
 missing data (12,758 SNPs retained), v) individuals with &gt;5% missing
 data (93 individuals retained), and vi) all SNPs with a minimum allele
 frequency (MAF) &lt;1% (11,550 SNPs retained). We also eliminated all loci
 identified as under selection by using three different approaches (10,516
 SNPs retained): i) a method based on likelihood implemented in the
 outflank function of the dartR library, ii) a Bayesian method implemented
 in the BayeScan program (Foll et al., 2008), and iii) a method based on
 the relationship between F~ST~ and heterozygosity of the *fsthet* library
 (Flanagan et al., 2017), implemented in R. Loci with significant
 departures from Hardy–Weinberg equilibrium in all sampling sites were also
 removed (8,898 SNPs retained) using the dartR library. Finally, loci
 showing linkage disequilibrium &gt;0.5 in all sampling sites were filtered
 with PLINK 2.0 software (Chang et al., 2015). The final SNP dataset (all
 localities) consisted of 6,328 unlinked SNPs and 93 individuals. SNP
 datasets including parental schemes by separate underwent the same
 filtering process. DNA sequence matrix (Fasta file) consisted of a
 fragment of the mitochondrial control region (CR; 945-bp approx.) that was
 amplified using the primers and conditions specified in Fibla et al.
 (2023). PCR products were sequenced using the Sanger method by Macrogen
 Inc. (Korea). The sequences obtained were aligned and manually edited in
 BioEdit v.7.2.0 software (Hall, 1999). The DNA sequence matrix used in the
 analyses was constructed using the ClustalW algorithm for multiple
 alignments integrated within BioEdit v.7.2.0. References Chang, C. C., C.
 C. Chow, L. C. A. M. Tellier, S. Vattikuti, S. M. Purcell, and J. J. Lee.
 2015. Second-generation PLINK: rising to the challenge of larger and
 richer datasets. GigaScience 4: s13742-015-0047-8. Fibla, P.,
 Rojas‐Hernández, N., Méndez, M. A., and Véliz, D. 2025. Molecular Evidence
 of Introgression Between Water Frog Species (Anura: Telmatobiidae) in the
 High Andes. *Molecular Ecology*, e70122. Fibla, P., Sáez, P. A.,
 Cruz-Jofré, F and Méndez, M. A. 2023. Drainage network morphology
 influences population structure and gene flow of the Andean water frog
 Telmatobius pefauri (Anura: Telmatobiidae) of the Atacama Desert, Northern
 Chile. Zoological Studies 62: 44. Flanagan, S. P., and A. G. Jones. 2017.
 Constraints on the Fst-heterozygosity outlier approach. Journal of
 Heredity 108: 561–573. Foll, M., and O. E. Gaggiotti. 2008. A genome scan
 method to identify selected loci appropriate for both dominant and
 codominant markers: a bayesian perspective. Genetics 180: 977–993. Hall,
 T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor
 and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series
 41, no. 41: 95–98. Mijangos, J. L., B. Gruber, O. Berry, C. Pacioni, and
 A. Georges. 2022. dartR v2: an accessible genetic analysis platform for
 Conservation, Ecology and Agriculture. *Methods in Ecology and Evolution
 *13: 2150–2158. R Core Team. 2024. R: a language and environment for
 statistical computing. R Foundation for Statistical Computing. ### Files
 and variables #### File: Telmatobius_Fibla_et_al.fas **Description:** DNA
 sequences (D-Loop) matrix, FASTA file. #### File: gl_all_locs
 **Description:** SNPs matrix, genlight file, all localities. #### File:
 gl_marmoratus_x_peruvianus **Description:** SNPs matrix, genlight file,
 parental scheme: T. marmoratus x T. peruvianus. #### File:
 gl_peruvianus_x_pefauri **Description:** SNPs matrix, genlight file,
 parental scheme: T. peruvianus x T. pefauri. ## Code/software The DNA
 sequence matrix (FASTA file) was constructed using the ClustalW algorithm
 for multiple alignments integrated within BioEdit v.7.2.0. The SNPs
 matrices were obtained using the DartR package in R 4.2.2 software. SNPs
 genlight files can be read using the following commands (in R
 environment): ``` install.packages("dartR") ``` ```
 library(dartR) ``` ``` gl_object&lt;- readRDS(file.choose()) ``` ```
 gl_object ``` ## Access information Other publicly accessible locations of
 the data: * DNA sequences were also deposited in Genbank (GenBank
 PX380050-PX380096)