Distribution, Abundance, and Genomic Diversity of the Endangered Antioch Dunes Evening Primrose (Oenothera deltoides subsp. howellii) Surveyed in 2019

Open-File Report 2021-1017
Prepared in cooperation with the U.S. Fish and Wildlife Service and the Friends of San Pablo Bay National Wildlife Refuge
Edited by: Karen M. Thorne and Amy G. Vandergast

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Abstract

Sand dune ecosystems are highly dynamic landforms found along coastlines and riverine deltas where a supply of sand-sized material is available to be delivered by aquatic and wind environments. These unique ecosystems provide habitat for a variety of endemic and rare plant and animal species. Sand dunes have been affected by human development, sand mining, and shoreline stabilization from invasive weeds. This report provides a summary of a comprehensive literature review, field survey, and genomic analysis for the Antioch Dunes evening primrose (Oenothera deltoides subsp. howellii, hereafter howellii), an endemic species to the San Francisco Bay-Delta, California, which was listed as a federally endangered subspecies in 1978. Howellii is found on a historic dune sheet (the Antioch sand sheet) near the confluence of the Sacramento and San Joaquin Rivers. The Antioch sand sheet has been greatly altered by sand mining and land conversion into agriculture and urban development. In chapter A, we describe results of the literature review and field survey. We found howellii at eight locations with over 90 percent of the adult population and nearly 99 percent of juveniles observed on the Antioch Dunes National Wildlife Refuge. We measured a negative relationship between howellii numbers and invasive weed cover, illustrating the importance of mobilized open sand for this species. In chapter B, we describe the genomic study results. We surveyed genomic diversity by using double-digest restriction-site associated sequencing to estimate population genetic structure and levels of diversity across all surveyed occurrences. The genomic analyses included outgroup samples of the closely related Oenothera deltoides subsp. cognata and three occurrences of an unknown taxon with intermediate morphology to cognata and howellii, which also occurs on the Antioch sand sheet, east of the Antioch Dunes National Wildlife Refuge. These three morphologically distinctive groups formed genetically distinctive clusters and well-supported monophyletic clades in clustering and phylogenetic analyses, respectively. There was no indication of recent hybridization among any of the groups. Among howellii occurrences, the Antioch Dunes National Wildlife Refuge contained the greatest genetic diversity. Our approach, which combined field surveys, habitat assessments, and genetic analyses, can provide useful information for the conservation and management of rare and at-risk plant species and highlights the uniqueness of the Antioch sand sheet floral diversity through the discovery of a putative new taxon within the bird-cage evening primrose species complex.

Suggested Citation

Thorne, K.M., and Vandergast, A.G., 2021, Distribution, abundance, and genomic diversity of the endangered Antioch Dunes evening-primrose (Oenothera deltoides subsp. howellii) surveyed in 2019: U.S. Geological Survey Open-File Report 2021–1017, 40 p., https://doi.org/10.3133/ofr20211017.

ISSN: 2331-1258 (online)

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Table of Contents

  • Abstract
  • Chapter A. Distribution and Abundance of the Endangered Antioch Dunes Evening-Primrose (Oenothera deltoides subsp. howellii)
    • Acknowledgments
    • Executive Summary
    • Introduction
    • Methods
    • Results
    • Discussion
    • References Cited
    • Appendixes
  • Chapter B. Population Genomic Structure of the Endangered Antioch Dunes Evening-Primrose (Oenothera deltoides subsp. howellii) and Detection of a Potentially New Oenothera deltoides Taxon in Contra Costa County, California
    • Acknowledgments
    • Executive Summary
    • Introduction
    • Methods
    • Results
    • Discussion
    • References Cited
    • Appendixes
Publication type Report
Publication Subtype USGS Numbered Series
Title Distribution, abundance, and genomic diversity of the endangered antioch dunes evening primrose (Oenothera deltoides subsp. howellii) surveyed in 2019
Series title Open-File Report
Series number 2021-1017
DOI 10.3133/ofr20211017
Year Published 2021
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) Western Ecological Research Center
Description vi, 40 p.
Country United States
State California
Online Only (Y/N) Y
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