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Conservation genetics of Phlox hirsuta, a serpentine endemic

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A Correction to this article was published on 13 February 2023

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Abstract

Identifying units for appropriate management and conservation of rare species is an important and challenging process, and population genetics can inform this decision making. Using Phlox hirsuta, a rare species restricted to serpentine soils in Northern California and with a geographic range of less than 15 km, we examined genetic variation within and among populations, using tunable Genotyping-by-Sequencing (tGBS) to generate single nucleotide polymorphisms (SNPs) as well as 11 microsatellite loci, to identify population structure, patterns of migration and selection, and units for conservation. Multiple methods recognized three geographically structured population clusters. The species has undergone a recent genetic bottleneck, and the increase in population size may be influenced by the changing climate. Patterns of gene flow are greater from south to north than in the opposite direction. Some of the genes under selection are putatively involved in adaptation to edaphic conditions, and genes under selection differ among the populations. Four population units were identified as suitable for conservation purposes based on various partitions of the SNPs.

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Data availability

The VCF, microsatellite, and beagle data files that support the findings of this study are deposited and openly available at Dryad: https://doi.org/10.5061/dryad.gmsbcc2q4. Individual geographic coordinates are excluded because P. hirsuta is a rare species. The fastq files are available at the SRA at NCBI (BioProject PRJNA862075).

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Acknowledgements

The authors would like to thank Nadine Kanim (USFWS), Sheri Hagwood (USFWS), and Merissa Hanisko (California Department of Fish and Wildlife). Dana Shaw prepared the GIS map. Andrew Rotzin and Philip Congleton helped collect leaves and GPS coordinates in the field. The editor and four reviewers provided helpful comments on the manuscript. Funding for the project was made possible by a Traditional Section 6 Grant (#F16AP00010) from USFWS. tGBS sequencing was conducted by data2bio, and Eurofins amplified and sequenced the microsatellite loci. Lisa Coffey and Asgar Shir were quite helpful with these efforts. The KUHPC was from a National Science Foundation Major Research Instrumentation Program award (Award No. 1725938).

Funding

Funding for the project was made possible by a Traditional Section 6 Grant (#F16AP00010) from USFWS. The KUHPC was from a National Science Foundation Major Research Instrumentation Program award (Award No. 1725938).

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  1. Weber State University, Ogden, UT, USA

    James I. Cohen

  2. Christopher Newport University, Newport News, VA, USA

    Lauren R. Griffen

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  1. James I. Cohen
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JIC and LRG conceptualized the project, investigated the research question, and wrote the manuscript. JIC conducted the formal analyses on the data and undertook data curation. LGR obtained the resources for the project.

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Correspondence to James I. Cohen.

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The original online version of this article was revised due to the second author's given and family names were incorrectly structured. The author name has been corrected.

The author Lauren R. Griffen (formally Lauren G. Ruane).

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Cohen, J.I., Griffen, L.R. Conservation genetics of Phlox hirsuta, a serpentine endemic. Conserv Genet 24, 137–152 (2023). https://doi.org/10.1007/s10592-022-01478-y

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