Published August 31, 2022 | Version v1
Journal article Embargoed

Evidence of backcross inviability and mitochondrial DNA paternal leakage in sea turtle hybrids

Authors/Creators

  • 1. Leibniz Institute for Zoo and Wildlife Research
  • 2. University of Ferrara
  • 3. Fundação Projeto Tamar
  • 4. Kwata NGO
  • 5. BOREA, National Museum of Natural History (MNHN), CNRS
  • 6. Universidade Federal de Minas Gerais

Description

This dataset contains ddRAD data used in our sea turtles genomics research on hybridization in Brazil. In this paper, we analyzed hybridization patterns, population structure and relatedness between southwest Atlantic population with a focus on Brazilian populations with high frequency of interspecific hybrids. Source code for the R2SCO pipeline is available at https://github.com/mazzoni-izw/mazzoni-begendiv/ and raw sequencing data is available on on NCBI Sequence Read Archive (SRA) database under BioProject PRJNA857276. Data uploaded here contain:

  • Hybrids_SNPs.vcf: SNP dataset for population analyses.
  • Hybrids_SNPs_DP15.recode.vcf: SNP dataset for population analyses filtered for a minimum coverage (DP) of 15
  • R2SCO-MseI-EcoRI-384-448_CcEiHyb.fasta: reference fasta sequences (R2SCO loci) used to map raw reads from loggerheads, hawksbills and their hybrids. Generated using the R2SCO pipeline described in Driller et al (2020)
  • R2SCO-MseI-EcoRI-384-448_CcEiLoCm.fasta: reference fasta sequences (R2SCO loci) used to map raw reads from loggerheads, hawksbills, olive ridleys, green turtles, and their hybrids. Generated using the R2SCO pipeline described in Driller et al (2020)
  • checkRestrictionSites.py: custom script that filters a fastq file to start and end with defined sequences

Structure folder

  • Create_Haplotype_Structure.py: python script used to convert the VCF output from Stacks populations into a Structure file based on haplotypes (instead of SNPs).
  • Hybrids_Haps_DP15.str: input structure file for haplotypes dataset
  • Hybrids_SNPs_DP15.stru input structure file for SNP dataset
  • ParallelStructure_HAPS.R: Command line used in parallel structure for haplotype dataset
  • ParallelStructure_SNPs.R: Command line used in parallel structure for SNP dataset

relatedness folder

  • populations.snps.vcf.gz: VCF file of SNP dataset with only loggerheads, hawksbills and their hybrids
  • run.sh: vcftools command line used to run relatedness analysis
  • relatednessmatrix.relatedness: square matrix with relatedness estimates
  • inds.txt: individuals included in the square matrix.
  • relatedness.R: plotting script in R for relatedness results (figure 3)

NewHybrids folder

  • Hybrids.NewHyb.input: input file for NewHybrids analysis.

Notes

Hybridization is known to be part of many species' evolutionary history. Sea turtles have a fascinating hybridization system in which species separated by as much as 43 million years are still capable of hybridizing. Indeed, the largest nesting populations in Brazil of loggerheads (Caretta caretta) and hawksbills (Eretmochelys imbricata) have a high incidence of hybrids between these two species. A third species, olive ridleys (Lepidochelys olivacea), is also known to hybridize although at a smaller scale. Here we used restriction site-associated DNA sequencing (RAD-Seq) markers, mitogenomes, and satellite-telemetry to investigate the patterns of hybridization and introgression in the Brazilian sea turtle population and their relationship with the migratory behaviors between feeding and nesting aggregations. We also explicitly test if the mixing of two divergent genomes in sea turtle hybrids causes mitochondrial paternal leakage. We developed a new species-specific PCR-assay capable of detecting mitochondrial DNA (mtDNA) inheritance from both parental species and performed ultra-deep sequencing to estimate the abundance of each mtDNA type. Our results show that all adult hybrids are first generation (F1) and most display a loggerhead migratory behavior. We detected paternal leakage in F1 hybrids and different proportions of mitochondria from maternal and paternal species. Although previous studies showed no significant fitness decrease in hatchlings, our results support genetically-related hybrid breakdown possibly caused by cytonuclear incompatibility. Further research on hybrids from other populations besides Brazil and between different species will show if backcross inviability and mitochondrial paternal leakage is observed across sea turtle species.

Files

Embargoed

The files will be made publicly available on August 31, 2032.

Additional details

References