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Comparing inferences derived from microsatellite and RADseq datasets: a case study involving threatened bull trout

  • Justin BohlingEmail author
  • Maureen Small
  • Jennifer Von Bargen
  • Amelia Louden
  • Patrick DeHaan
Research Article

Abstract

Technological advancements have allowed geneticists to exploit an increasing array of molecular markers, many of which have different properties and may provide contrasting insights into the evolutionary history and structure of populations. This has important consequences for conservation managers attempting to identify units at which to conserve intraspecific diversity. In this study we compared the inferences derived from nuclear microsatellites and restriction-site associated DNA (RADseq) data for a threatened freshwater fish, the bull trout Salvelinus confluentus. For both marker types we generated data for the same suite of individuals collected from 24 populations distributed across the species range. The RADseq data were low coverage (mean site coverage < 3X), so we implemented a probabilistic genotyping approach. We performed a comparable suite of analyses for both datasets. Both datasets revealed similar broad patterns of subdivision that reflected primary evolutionary lineages (Coastal and Interior clades). However, the RADseq more clearly and consistently identified the hierarchical phylogenetic structure. Some populations had varying assignments to these lineages depending on the dataset. RADseq data also suggested admixture has shaped the genomic character of several populations. Such a signal was not apparent with the microsatellites, suggesting that the datasets are revealing different aspects of population history. Our study provides a valuable case study in how advances in molecular technology can enhance our understanding of a relatively well-studied species. It also underscores the importance of framing findings generated with high-throughput sequencing technology within the context of past research to enhance conservation decision making.

Keywords

Salmonidae Salvelinus confluentus Restriction-site associated DNA sequencing Conservation genomics Intraspecific diversity 

Notes

Acknowledgements

Funding for this project was provided by the US Fish and Wildlife Service Fish and Aquatic Conservation Program and Washington State general funds. We sincerely thank the numerous individual biologists and technicians from the different federal, state, tribal, and non-governmental agencies who collected tissue samples used in these analyses. We also thank Sewall Young and Ken Warheit (WDFW) for sharing scripts for running Stacks. The findings and conclusions in this paper are those of the authors and do not necessarily represent the views of the US Fish and Wildlife Service.

Supplementary material

10592_2018_1134_MOESM1_ESM.docx (111 kb)
Supplementary material 1 (DOCX 111 KB)
10592_2018_1134_MOESM2_ESM.docx (2.9 mb)
Supplementary material 2 (DOCX 2951 KB)

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Authors and Affiliations

  1. 1.Abernathy Fish Technology Center, US Fish and Wildlife ServiceLongviewUSA
  2. 2.Molecular Genetics Laboratory, Washington Department of Fish and WildlifeOlympiaUSA
  3. 3.Western Washington Fish and Wildlife Conservation Office, Fish and Wildlife ServiceLaceyUSA

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