Hybridization between two parapatric ranid frog species in the northern Sierra Nevada, California, USA

Abstract

Contact zones between species provide a unique opportunity to test whether taxa can hybridize or not. Cross‐breeding or hybridization between closely related taxa can promote gene flow (introgression) between species, adaptation, or even speciation. Though hybridization events may be short‐lived and difficult to detect in the field, genetic data can provide information about the level of introgression between closely related taxa. Hybridization can promote introgression between species, which may be an important evolutionary mechanism for either homogenization (reversing initial divergence between species) or reproductive isolation (potentially leading to speciation). Here, we used thousands of genetic markers from nuclear DNA to detect hybridization between two parapatric frog species (Rana boylii and Rana sierrae) in the Sierra Nevada of California. Based on principal components analysis, admixture, and analysis of heterozygosity at species diagnostic SNPs, we detected two F1 hybrid individuals in the Feather River basin, as well as a weak signal of introgression and gene flow between the frog species compared with frog populations from two other adjacent watersheds. This study provides the first documentation of hybridization and introgression between these two species, which are of conservation concern.

Flow modification associated with reduced genetic health of a river-breeding frog,Rana boylii

“…To produce a genomic resource for frog species with large genome sizes, we interrogated a significant fraction of the R. boylii genome using RAD sequencing with SbfI (Miller et al 2007, Baird et al 2008, Ali et al 2016. Paired-end Illumina sequence data were generated using 24 R. boylii individuals (Data S4) and de novo locus discovery and contig extension were carried out as previously described (Miller et al 2012, Sağlam et al 2016, Peek et al 2019 using the alignment program Novoalign and the PRICE assembler (Ruby et al 2013). This resulted in a set of 77,544 RAD contigs ranging from 300 to 800 bp which served as a de novo partial reference assembly for all subsequent downstream analyses (Data S5).…”

“…A total of 345 individual frog samples were prepared for sequencing following the RAD Capture (Rapture) methods outlined in Ali et al (2016) and detailed in Peek et al (2019). We generated RAD libraries from the samples, quantified the libraries using a Fragment Analyzer (Agilent Technologies, Santa Clara, CA) and pooled them, performed capture on the pooled library with the 120 bp baits described above, and sequenced the resulting Rapture library with paired-end Illumina sequencing.…”

“…Sequencing Data (ANGSD) (Korneliussen et al 2014) was used for all population genetic analyses as it does not require calling genotypes and is suitable for lowcoverage sequencing data (Korneliussen et al 2013, Fumagalli et al 2013. ANGSD analyses were conducted following details from Peek et al (2019).…”

Spatial and temporal patterns of environmental DNA detection to inform sampling protocols in lentic and lotic systems

“…Management of these species is further complicated by their similarities in appearance, which can make identification in the field difficult. They occasionally hybridize, but hybrids do not appear to successfully reproduce (Peek et al ). By relying on genetic material, instead of phenotypic characteristics, the collection of eDNA has the potential not only to more accurately monitor the distribution of these two vulnerable amphibians, but also detect the fungus Bd that has impacted both species.…”

Rapture-ready darters: choice of reference genome and genotyping method (whole-genome or sequence capture) influence population genomic inference inEtheostoma

“…A hybrid method that uses restriction-associated DNA sequencing (RADseq) combined with targeted enrichment of a user-defined subset of hundreds to thousands of RAD loci, termed 'Rapture' (Ali et al 2016) has great potential as a rapid and efficient method for generating repeatable highthroughput genomic data at low cost and high efficiency. Rapture assays have so far been developed and applied to salmon (Ali et al 2016), Tasmanian devils (Margres et al 2018), marine turtles (Komoroske et al 2019), frogs (Peek et al 2019), and sea lampreys (Sard et al 2020). The application of Rapture has mainly focused on population genomics within species, although Rapture loci developed for one species have been shown to be useful for studying hybridization among closely related species (Peek et al 2019) and across species within slowlyevolving lineages (Komoroske et al 2019).…”