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Sibship reconstruction with SNPs illuminates the scope of a cryptic invasion of Asian Swamp Eels (Monotperus albus) in Georgia, USA

Citation

Taylor, Andrew; Bangs, Max; Long, James (2020), Sibship reconstruction with SNPs illuminates the scope of a cryptic invasion of Asian Swamp Eels (Monotperus albus) in Georgia, USA, Dryad, Dataset, https://doi.org/10.5061/dryad.zcrjdfn92

Abstract

Cryptic invasive species are particularly problematic to study, manage, and control because of the difficulty detecting these species within their invaded habitats. Such is the case of the Asian Swamp Eel (Monopterus albus; ASE) where it is established in vegetated marshes along the Chattahoochee River, Georgia. Adult eels have been nearly impossible to detect or quantify with traditional sampling, although leaf-litter trapping of juvenile ASEs has been somewhat successful.In this study, we leveraged a collection of juveniles from the 2015 cohort and used single-nucleotide polymorphisms (SNPs) to reconstruct sibship among these juveniles in COLONY. Sibship reconstruction allowed us to learn about adult breeding behaviors and provided the first quantified estimates of breeder abundance. Pedigree reconstruction revealed that adults of both sexes were polygamous and likely traveled up to 0.5 km among marsh habitats during a single breeding season. Estimates of the number of breeding adults contributing to offspring (Ns) and the effective number of breeders (Nb) indicated an approximate minimum bound of 100 breeding adults in the marshes in 2015. Our study updated the invasion status of a cryptic population formerly riddled with uncertainty, highlighting that low captures of adult eels in the study area have been the result of low detectability, not low abundance. Given that low detectability would likely hinder removal efforts, our results suggest that future efforts could focus on suppression of ASE abundance when they are most vulnerable to capture and containing the spatial extent of the invasion.

Methods

Please see our full Methods in Taylor et al. - Biological Invasions. Briefly, we used GBS to generate de novo SNPs for an introduced population of Asian Swamp Eels (Monopterus albus) in marshes of the Chattahoochee River, Georgia. We collected n = 67 juvenile eels from the 2015 cohort and extracted genomic DNA. We used GBS and then used Stacks v. 2.4 to filter, cluster, and align reads. We estimated full- and half-sib relationships with maximum likelihood pedigree reconstruction in COLONY v. 2.0.6.5 .

Usage Notes

Curated files include a compressed folder containing the following numbered subfolders: 1) the GBS reads splits by sample, filtered, and trimmed (pTages_trim output) used in this study; 2) relevantStacksoutput (populations.snps.vcf, populations.haplotypes.tsv, and catalog.fa.gz files); and 3) the final SNP genotypes formatted for input into COLONY.

Funding

National Park Service through the Great Plains Cooperative Ecosystems Studies Unit, Award: task order P14AC0183