36. Rare Plants 2

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Rare Plants 2

Saturday, October 22 at 10:00-11:40 am, Donner Room

*note alternate instances of this session – Friday at 3pm and Saturday at 1pm

Session Description: Rare plants make up one-third of California’s native flora. They encompass nearly every habitat type and elevation range, are beautiful, and are important contributors to pollinators, ecosystem functions, and the rich biodiversity of the state. While great progress has been made at broader levels—families and genera—the California flora is still far from being understood at the species-level and it’s expected that hundreds of taxa have gone unnoticed by taxonomists; most of these will have narrow ranges and thus be more vulnerable to human impacts. Powerful tools are now available to describe and understand plant diversity in California, including a host of reduced representation sequencing methods, to understand fine-scale diversity and evolution.

Session Chairs: Aaron E. Sims (California Native Plant Society, Sacramento, CA, USA) and Israel Borokini (University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, USA)

*Session generously sponsored by Nomad Ecology, LLC

36.1    Conservation genetics of endangered Suisun Thistle and its congeners

Carly Mae Miranda (San Francisco State University, San Francisco, CA, USA), Jason Cantley (San Francisco State University, San Francisco, CA, USA), Michael Vasey (San Francisco State University, San Francisco, CA, USA), Colleen Ingram (San Francisco State University, San Francisco, CA, USA), Morgan Stickrod (San Francisco State University, San Francisco, CA, USA)

The native California thistle species Cirsium hydrophilum occurs endemically in serpentine wetlands and tidal salt marsh soils, surviving in edaphic conditions that prove toxic to most plants. The two varieties of C. hydrophilum are separately adapted to life in different stressful environments in Northern California. Cirsium hydrophilum var. hydrophilum, Suisun thistle, is restricted to the brackish tidal salt marsh of Rush Ranch in Solano County while C. hydrophilum var. vaseyi, Mt. Tamalpais thistle, sustains on the metallic serpentinite soils of Mt. Tamalpais fresh watershed in Marin. Both varieties of C. hydrophilum are recognized as endangered at the federal level due to their low total occurrences. Suisun thistle’s case of endemism is hypothesized to be a result of both environmental conditions and genetic factors. The paradigm we investigate is rooted in the understanding that small plant populations with limited distributions are prevented from expanding due in part to their own lack of alleles, or genetic diversity, making them inept to survive in distinctive neighboring habitats. Current genetic analysis of the species is limited to highly conserved nuclear ribosomal external transcribed spacers and internal transcribed spacers DNA. In this study we used genotype by sequencing (GBS) to develop a de novo reduced representation genome and cross analyze the geographic positions of individuals with their genetic content to investigate the genomic nature of this restricted endemic. Genetic analyses have substantiated the hypothesized inbreeding in Suisun thistle and our biogeographic analyses show that the individuals sampled from Rush Ranch thus far comprise a single population. This data ultimately guides our drafting of regional recommendations for out-planting of Suisun thistle to maintain native Cirsium in Northern California in the face of a rapidly changing climate and ecological conditions.

36.2    Population genomics of island mallow, Malva assurgentiflora (Malvaceae)

Kristen Hasenstab-Lehman (Santa Barbara Botanic Garden, Santa Barbara, CA, USA)

Malva assurgentiflora (Kellogg) M.F. Ray [Lavatera assurgentiflora] (Malvaceae) is a shrub endemic to four of the eight California Channel Islands: San Miguel, Anacapa, San Clemente, and Santa Catalina. Earlier population genetics and morphological study supported the recent recognition of subsp. glabra on San Clemente and Santa Catalina Islands. The northern island subsp. assurgentiflora is quite rare, originally documented on San Miguel and on two of the three islets of Anacapa Island. Both Middle and West Anacapa islets populations have been extirpated over the last two decades, although seed from Middle Anacapa Island has been used to generate plants that have been introduced on east Anacapa. San Miguel has two naturally occurring populations, with fewer than 300 plants total. Here we use population genomics techniques to 1) assess if genomic data continues to support taxonomic circumscription of northern island plants as differing from southern island plants, 2) investigate the within-island and between island genomic diversity of remaining plants on San Miguel and Anacapa, 3) investigate whether our data can identify the genetic provenance of plants in horticultural settings on the mainland and across the archipelago, and 4) identify the highest value seed banking targets. Our sampling includes 150 individuals from across the range of both currently recognized subspecies as well as horticultural settings. Our preliminary results suggest that populations of subsp. glabra on San Clemente and Santa Catalina samples are as genetically distinct from each other as from the northern Channel Island populations, and may merit taxonomic recognition. Samples from presumed horticultural settings all cluster with plants from Anacapa Island. Preliminary results also identify unique plants from Santa Rosa Island as genetically most similar to those on San Miguel.

36.3    Genetic diversity of the rare and endangered vernal-pool grasses Orcuttia, Tuctoria, and Neostapfia — preliminary findings from population-level sampling and genomic sequencing (ddRADseq)

R. Doug Stone (California Native Plant Society, Sacramento, CA, USA), Bryana Olmeda (University of New Mexico, Albuquerque, NM, USA), J. Travis Columbus (California Botanic Garden, Claremont, CA, USA)

The Orcuttiinae (including Orcuttia, 5 species; Tuctoria, 3 species; and Neostapfia, 1 species) are annual grasses with an amphibious life-history. They are found only in vernal pools and similar habitats in the lowlands of California and Baja California. All members of the Orcuttiinae are listed under the federal Endangered Species Act and the California Endangered Species Act (except for the Baja Californian Tuctoria fragilis). In this study, we explore the genetic diversity of the Orcuttiinae using a genomic sequencing approach known as ddRADseq (double digest restriction-site associated DNA). Sampling is being done under permits issued to the California (formerly Rancho Santa Ana) Botanic Garden. Our preliminary results confirm that Tuctoria (as delimited by Reeder 1982) is an unnatural (i.e., paraphyletic) group with some of its species needing to be reclassified. At the population level, the resolving power of ddRADseq reveals past dispersal patterns within species on an evolutionary time-scale. Orcuttia tenuis populations in Sacramento County are distinct and should be formally recognized (although further study is needed of the populations identified as O. tenuis from Butte and southern Tehama counties). The same is true of an unusual Orcuttia inaequalis population in Solano County. Information on genetic diversity within and between populations will help to prioritize ongoing conservation efforts. Seed collections made during our study will be stored in the Garden’s seed conservation bank.

36.4    Population genetics, demographic, and evolutionary history of the Dudley’s lousewort (Pedicularis dudleyi), a rare redwood forest specialist

Tracy M. Misiewicz (University of Oklahoma, Norman, OK, USA; University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, USA), Christopher Hauser (Center for Natural Lands Management, Temecula, CA, USA), Benjamin E. Carter (San Jose State University, San Jose, CA, USA)

Pedicularis dudleyi (Dudley’s Lousewort, Orobanchaceae) is an extremely rare plant endemic to the redwood forests of Central California. Until recently, the species was known only from three extant natural populations. However, in 2019, one of those populations was described as a novel species (P. rigginsiae D.J. Keil) based on morphological and ecological data leaving only two populations described as P. dudleyi. While little is known about the past distribution of the species, historical records have led to speculation that the species was once more widespread and may have suffered from habitat destruction as a result of widespread logging during the early twentieth century. We utilized a combination of ddRAD SNP and Sanger sequencing data to: (1) test the morphological hypothesis that P. rigginsiae is distinct from P. dudleyi, (2) describe the genetic diversity and population structure of P. dudleyi, and (3) test the hypothesis that the species underwent a bottleneck corresponding with increased logging of redwood forests in the early twentieth century. Our results support the recognition of P. rigginsiae as distinct from P. dudleyi, increasing the conservation priority of both species. Genetic diversity statistics and analyses of genetic structure suggest that both populations of P. dudleyi are highly differentiated from each other with one population exhibiting unexpected substructure. Finally, demographic modeling supports a scenario where the contemporary rarity of the species is best explained by a recent bottleneck.

36.5    Pitcher sages in peril? A conservation genomics study of Lepechinia rossii (Ross’s pitcher sage)

Robert P. Comito Jr. (California Botanic Garden, Claremont Graduate University, Southern California Botanists, Claremont, CA, USA)

Lepechinia rossii (Ross’s pitcher sage) is a highly aromatic shrub narrowly endemic to southern California. It occurs in chaparral communities at two locations in the western Transverse Ranges of Los Angeles and Ventura counties. It is listed by the CNPS as California Rare Plant Rank 1B.2 (rare globally, fairly endangered in California). It faces several threats, including shifts in fire regimes and displacement by invasive species. Human activities, such as off highway vehicle use, power line maintenance, and petroleum exploration, also directly endanger both populations. Conservation actions include surveying known and potential occurrences, updating threat assessments, and studying the genetic structure of known populations. Field work was conducted on the Angeles National Forest (ANF) and Los Padres National Forest (LPNF) to sample L. rossii across its range (83 individuals from ANF, 45 from LPNF). DNA has been extracted from 88 samples of L. rossii and outgroups including: L. hastata, and California Lepechinia. The method ddRADseq was used to prepare libraries and sequence data from 96 samples. An alignment of 74,898 loci generated through an ipyrad pipeline and a maximum likelihood phylogeny has been estimated with 1,000 ultrafast bootstraps in IQtree. The preliminary phylogeny of sect. Calycinae of Lepechinia (Lamiaceae), with five sampled species from California (L. calycina, L. cardiophylla, L. fragrans, L. ganderi, and L. rossii) show a monophyletic group containing all sampled L. rossii as sister to a clade containing the remaining four California species. This finding supports the circumscription of L. rossii as a separate species, distinct from other Californian species of Lepechinia. Furthermore, specimens from the two sampled localities (Ventura and Los Angeles counties) form reciprocally monophyletic groups. The genetic structure of L. rossii populations in uncovered will inform future conservation management and restoration efforts.

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