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Historic DNA reveals genetic consequences of fragmentation in an endangered, endemic mustard

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Abstract

Understanding how anthropogenic disturbance affects genetic diversity is essential to appropriately incorporating genetic considerations into conservation plans. Unfortunately, we rarely have information about a population’s genetic diversity before it becomes imperiled. Here we reconstruct the historic range of the naturally rare annual mustard Streptanthus glandulosus subsp. niger (Sgn) and use herbarium specimens to quantify pre-disturbance genetic diversity. We compare this to the genetic diversity in the contemporary plant populations and to plants in the seed bank. We conclude that Sgn was recently a single, panmictic population composed of orders of magnitude more plants than exist today but experienced recent and abrupt declines following housing development. Today Sgn persists as two disjunct populations, the larger of which has retained historic levels of diversity although there is a downward trend in all measures. The smaller population has lost 21–28% of the diversity that was present only 50 years ago with an Ne ~ 5–16. The contemporary populations have differentiated from each other due to drift. The seed bank contained no novel alleles and had high levels of homozygosity, indicating that it is incapable of providing genetic rescue. This novel combination of hDNA, the aboveground plant population and the seed bank can be used to design high impact conservation plans that appropriately incorporate genetic diversity for this and other imperiled species.

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Fig. 1
Fig. 2
Fig. 3
Fig. 4

source for each sample: historic plants from the herbarium collected between 1909 and 1974, and each of the two contemporary populations (Old St. Hilary’s and Middle Ridge). OSH-SB = plants grown from the seed bank at Old St. Hilary’s; MR-SB = plants grown from the seed bank at Middle Ridge

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Data Availability

Data for this study will be available in the Dryad Digital Repository upon final manuscript acceptance. Prior to that, data are available from the corresponding author upon reasonable request.

Code availability

Not applicable. All data were analyzed using widely available and clearly cited freeware (GelAlEx, FSTAT, GENEPOP).

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Acknowledgements

We are especially grateful to the following herbaria for allowing us to destructively sample specimens: University and Jepson Herbaria (University of California, Berkeley), Hoover Herbarium (California Polytechnic State University, San Luis Obispo), J.M. Tucker and Beecher Crampton Herbaria (University of California, Davis), Southwest Environmental Information Network (Arizona), Harvard University Herbaria (Harvard University, Cambridge), Rancho Santa Ana Botanic Garden (Claremont, California), and the California Academy of Sciences Herbarium (San Francisco). Two anonymous reviewers offered thoughtful comments that improved this manuscript. Hannah Horten and Brittany Burnett assisted with lab work. We thank Dave Gotz and the Tiburon Landmark Society for access to historic photos. We thank Sam Abercrombie for creating the maps. This work was supported by a grant from Marin County Parks (14-6300-62) to SMS and Jill Barrett Foundation fellowships to TYS and NRKA. This work was conducted under a permit from the California Department of Fish and Wildlife (permit SEMP 2081(a)-14-004-RP) issued to SMS.

Funding

This work was supported by a grant from Marin County Parks (CA, USA) (award #: 14-6300-62) to SMS and Jill Barrett Foundation fellowships (through the Mills College Biology Dept.) to TYS and NRKA.

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  1. Tatyana Yazmine Soto

    Present address: Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA

Authors and Affiliations

  1. Biology Dept., Mills College, 5000 MacArthur Blvd., Oakland, CA, 94613, USA

    Sarah Macneil Swope, Tatyana Yazmine Soto & Nia Rahman-Khan Arana

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  1. Sarah Macneil Swope
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Contributions

SMS conceived of the study, collected leaf tissue in the field, acquired herbarium specimens and historical photographs, scored PCR results, analyzed data, conducted the literature search, wrote the manuscript. TYS and NRKA conducted the lab work, provided comments on drafts of the manuscripts, assisted with the literature search.

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Correspondence to Sarah Macneil Swope.

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Ethics approval not required. This work was conducted under a permit from the California Department of Fish and Wildlife (permit SEMP 2081(a)-14-004-RP) issued to SMS.

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Swope, S.M., Soto, T.Y. & Rahman-Khan Arana, N. Historic DNA reveals genetic consequences of fragmentation in an endangered, endemic mustard. Conserv Genet 23, 123–137 (2022). https://doi.org/10.1007/s10592-021-01406-6

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