San Marcos Vernal Pool Checklist
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San Marcos Vernal Pool Checklist
© W.P. Armstrong, 22 May 2011

Table Of Contents:
  1. A Plant Checklist For The San Marcos Vernal Pool Area
  2. A Federally Endangered Fairy Shrimp In The Vernal Pools
  3. Endangered Plants Of The San Marcos Vernal Pool Area
  4. Brodiaeas In San Marcos and On San Clemente Island
  5. Does Brodiaea jolonensis Occur In San Diego County?
  6. Other Interesting Species In San Marcos Vernal Pool Area (1)
  7. Other Interesting Species In San Marcos Vernal Pool Area (2)
  8. Other Interesting Species In San Marcos Vernal Pool Area (3)
  9. Isoetes & Pilularia In San Marcos Fry's Vernal Pool Area

Until a satisfactory name is applied to these populations, I will refer to southern California populations
previously called "Brodiaea jolonensis" as "Coastal BTK" and mountain populations previously called
"Brodiaea terrestris ssp. kernensis" as "Montane BTK."
The flower color for Brodiaea species on this page is blue-purple to violet. In the following images
I have attempted to match their true color;  however, they may appear different on your monitor.

Note: The Brodiaea, that I referred to as "Coastal BTK," is listed as a possible
undescribed taxon under B. jolonensis in the revised Jepson Manual II (2011)

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1. Checklist Of Plants In & Around The San Marcos Vernal Pools

Vernal pool during heavy rains of January 2005

This site comprises approximately 40 acres of vacant land northeast of the William R. Bradley Park and southwest of Palomar College. Like other vernal pool areas in San Diego County, it is composed of undulating topography with clay hardpan depressions and elevated "mima" mounds. Vernal pools are formed as the water from winter rains accumulates in these impervious clay depressions. The vernal pool area is bounded by S. Pacific Street on the west, S. Las Posas Drive on the east, La Mirada Drive on the north, and Linda Vista Drive on the south. Most of the names in this checklist follow the nomenclature of A Flora of San Diego County by R.M. Beauchamp (1986). They have not been updated with the Jepson Flora of Calif. (1993).
Plants with an asterisk * are considered rare or unusual.

Family Name

Scientific Name

Common Name


(Liliaceae In The Flora
of North America)

Brodiaea now placed
in the Themidaceae

    1. Bloomeria crocea ssp. crocea
    2. Brodiaea filifolia *
    3. Coastal BTK (B. terrestris kernensis) *
         [Previously listed as B. jolonensis]
    4. Brodiaea filifolia x B. orcuttii *
    5. Brodiaea filifolia/B. orcuttii x BTK *
    6. Brodiaea orcuttii *
    7. Dichelostemma capitatum ssp. capitatum
    8. Muilla maritima
Golden Stars
Threadleaf Brodiaea
Coastal BTK
Mesa Brodiaea
Fertile Hybrid
Sterile Hybrid
Orcutt Brodiaea
Wild Hyacinth
Common Muilla
    9. Eryngium aristulatum var. parishii *
  10. Lomatium dasycarpum
  11. Sanicula bipinnatifida
Coyote Thistle
Lace Parsnip
Purple Sanicle
  12. Acroptilon repens
  13. Anthemia cotula
  14. Calycadenia (Osmadenia) tenella
  15. Carduus pyncnocephalus
  16. Centaurea melitensis
  17. Chaetopappa aurea
  18. Chamomilla suaveolens
  19. Corethrogyne filaginifolia virgata
  20. Cotula coronopifolia
  21. Cynara cardunculus
  22. Erigeron foliosus var. foliosus
  23. Filago gallica
  24. Gazania linearis
  25. Gnaphalium chilense
  26. Grindelia camporum bracteosum
  27. Hedypnois cretica
  28. Hesperevax sparsiflora sparsiflora *
  29. Hemizonia (Deinandra) fasciculata
  30. Holocarpha virgata ssp. elongata *
  31. Hypochoeris glabra
  32. Isocoma veneta vernonioides
  33. Lactuca sativa
  34. Lasthenia chrysostoma
  35. Layia platyglossa campestris
  36. Microseris douglasii ssp. platycarpha *
  37. Psilocarphus brevissimus *
  38. Senecio vulgaris
  39. Stebbinsoseris heterocarpa
  40. Stylocline gnaphalioides
Russian Knapweed
Mayweed Chamomile
Rosin Weed
Italian Thistle
Tocalote Thistle
Golden Daisy
Pineapple Weed
Sand Aster
Brass Buttons
Artichoke Thistle
Leafy Daisy
Narrow-Leaf Filago
Gazania Hybrid
Cotton-Batting Plant
Gum Plant
Erect Evax
Golden Tarweed
Graceful Tarweed
Smooth Cat's Ear
Prickly Lettuce
Small Flower Microseris
Dwarf Woollyheads
Common Groundsel
Brown Puffs
Everlasting Nest-Straw
  41. Plagiobothrys acanthocarpus
  42. Plagiobothrys bracteatus
  43. Plagiobothrys californicus
Spinefruited Popcorn
Popcorn Flower
Popcorn Flower
  44. Brassica geniculata (Hirschfeldia incana)
  45. Brassica nigra
  46. Brassica rapa sylvestris
  47. Lepidium lasiocarpum
  48. Lepidium nitidum
Perennial (Short-Pod) Mustard
Black Mustard
Field Mustard
  49. Callitriche longipedunculata *
Water Starwort
  50. Downingia cuspidata *
  51. Cerastium glomeratum
  52. Silene gallica
  53. Spergularia bocconii
Mouse-Ear Chickweed
Windmill Pink
Sand Spurrey
  54. Atriplex semibaccata
Australian Saltbush
  55. Calystegia macrostegia arida
  56. Convolvulus arvensis
  57. Convolvulus simulans *
  58. Cressa truxillensis
Clay Bindweed
Alkali Weed
  59. Crassula aquatica *
  60. Crassula connata
  61. Cyperus eragrostis
  62. Eleocharis macrostachya
Tall Flatsedge
Spike Rush
  63. Elatine brachysperma *
  64. Euphorbia spathulata *
Wart Spurge
  65. Lotus hamatus
  66. Lotus purshianus var. purshianus
  67. Lotus scoparius scoparius
  68. Lupinus bicolor microphyllus
  69. Lupinus densiflorus austrocollium
  70. Lupinus longifolius
  71. Lupinus succulentus
  72. Melilotus albus
  73. Melilotus indicus
  74. Trifolium amplectens
  75. Trifolium microcephalum
Grab Lotus
Spanish Clover
Dwarf Lupine
White Lupine
Bush Lupine
Succulent Lupine
White Sweet Clover
Yellow Sweet Clover
Bladder Clover
Maiden Clover
  76. Centaurium venustum
  77. Erodium botrys
  78. Erodium moschatum
  79. Erodium obtusiplicatum
Long-Beaked Filaree
Long-Beaked Filaree
  80. Sisyrinchium bellum
Blue-Eyed Grass
  81. Isoetes orcuttii *
  82. Juncus bufonius
  83. Juncus dubius
Toad Rush
Mariposa Rush
  84. Acanthomintha ilicifolia *
  85. Trichostema lanceolatum
Vinegar Weed
  86. Calochortus splendens
  87. Calochortus weedii var. weedii
  88. Chlorogalum parviflorum
  89. Zygadenus fremontii var. minor
Lilac Mariposa Lily
Weed's Mariposa Lily
Soap Lily
Star Lily
  90. Lythrum hyssopifolia
  91. Pilularia americana *
American Pillwort
  92. Clarkia purpurea quadrivulnera
  93. Gaura sinuata
Butterfly Weed
  94. Plantago elongata
  95. Plantago erecta
  96. Plantago pusilla
Alkali Plantain
California Plantain
  97. Aira caryophyllea (See note below)
  98. Avena barbata
  99. Avena fatua
100. Brachypodium distachyon
101. Bromus diandrus
102. Bromus mollis
103. Bromus rubens
104. Deschampsia danthonioides (See note below)
105. Distichlis spicata
106. Gastridium ventricosum
107. Hordeum intercedens *
108. Hordeum murinum leporinum
109. Lolium multiflorum
110. Nasella (Stipa) pulchra
111. Phalaris paradoxa praemorsa
112. Polypogon monspeliensis
113. Vulpia (Festuca) myuros
European Hairgrass
Slender Wild Oat
Wild Oat
Purple False-Brome
Ripgut Grass
Soft Chess
Foxtail Chess
Slender Hair Grass
Bobtail Barley
Foxtail Barley
Italian Rye Grass
Purple Needlegrass
Canary Grass
Rabbitfoot Grass
Foxtail Fescue
114. Navarretia fossalis *
115. Rumex crispus
Curly Dock
116. Anagallis arvensis
117. Centunculus minimus *
Scarlet Pimpernel
Common Chaffweed
118. Castilleja densiflora ssp. gracilis
119. Linaria canadensis
120. Veronica peregrina xalapensis
Owl's Clover
Blue Toadflax
121. Selaginella cinerascens *
Ashy Spike-Moss
122. Typha latifolia

Note: The San Marcos vernal pools contain native hairgrass (Deschampsia danthonioides) and the similar European hairgrass (Aira caryophyllea). When comparing the dried inflorescences of both species in the field, Aira has smaller spikelets (see following image):

Comparison of the dried spikelets of Aira caryophyllea and Deschampsia danthonioides
in August. Spikelets of Aira caryophyllea are generally less than 4 mm long and narrower.

Poaceae: Hordeum intercedens (Bobtail Barley)

Bobtail barley (Hordeum intercedens), a native species in the vernal pool preserve adjacent to Fry's Electronics in San Marcos. The dense spikes are more slender than other naturalized (weedy) species. The spikelets are three per node like other species; however, the sterile lemma of lateral spikelets is 1.7-4.4 mm long with a short awn less than 1.2 mm. This species is similar to H. depressum which also grows in vernal pool areas and has been reported from San Diego County.

Bobtail barley (Hordeum intercedens), a native annual in vernal pools of San Marcos.

The status of these vernal pools and lovely wildflowers is rather dismal. They are surrounded by buildings in a rapidly growing area zoned for industry. Many of the vernal pools have been intentionally damaged by deep tire ruts and the dumping of debris. Raised topography (mounds) near the vernal pools once supported burrowing owls, but they haven't been seen in this field for years.

Burrowing Owl (Speotyto cunicularia) photographed in May 1979.

2. A Federally Endangered Animal In The San Marcos Vernal Pools

Fairy Shrimp Belong To The Arthropod Class Crustacea Order Anostraca

San Diego Fairy Shrimp (Branchinecta sandiegonenis). Discovered in the San Marcos Vernal Pools by Tom Chester during a Palomar College Botany 110 field trip on 8 Mar 2003. Identified by U.S. Fish & Wildlife certified biologist Megan Enright using the taxonomic key: Eriksen, C.H. and D. Belk. 1999. Fairy Shrimps of California's Puddles, Pools, and Playas. Mad River Press, Eureka, California.

San Diego Fairy Shrimp In Spring 2008
  Swimming Fairy Shrimp (4 MB MPEG File)  

The San Diego fairy shrimp (Branchinecta sandiegoensis) is endemic to vernal pools of coastal San Diego County. They have also been recorded from a few localities in Orange County and Baja California. Since most of the vernal pool habitats have been destroyed in southern California due to urbanization and pollution, these tiny crustaceans have been added to the U.S. Fish & Wildlife Service Endangered List in accordance with the Endangered Species Act. Their plight in the San Marcos area is uncertain due to the dumping of debris in the few remaining pools within a rapidly developing industrial zone.

This minute crustacean belongs to the order Anostraca, along with brine shrimp (Artemia). Other related orders of microscopic crustaceans include Cladocera (water fleas), Copepoda (copepods), Ostracoda (seed shrimp), Notostraca (tadpole shrimp), and Conchostraca (clam shrimp). All of these crustaceans are visible to the naked eye, although magnification is required to see details of their body structure. San Diego fairy shrimp are small and transparent, about 5 to 8 mm long.

A Massive Colony Of Brine Shimp In Mono Lake
Ostracods In A Vernal Pool On The Santa Rosa Plateau
Nostoc Balls In A Vernal Pool On The Santa Rosa Plateau

During winter and early spring, when the ponds collect water, fairy shrimp mature quickly, live as adults, and reproduce. During their mating cycle the male attaches to the female with his clasping antennae. Each female lays hundreds of eggs, which settle into the soft bottom mud and silt as the pool dries out. At this time the adult fairy shrimp die, and plants bordering the pools bloom and set seed for the next winter wet season. During the dormant stage, fairy shrimp survive as embryos within resistant eggs called cysts which are embedded in the desiccated mud sediment. They can remain here for years until sufficient winter rains once again fill the shallow depressions with water. As the vernal pools refill, the mud imbibes water and the cysts hatch, thus releasing a new generation of fairy shrimp into the shallow ponds. Clay hardpan depressions that fill with water during the winter and early spring provide the essential requirements for the survival and perpetuation of fairy shrimp. If vernal pool habitats are destroyed by land developers, the fairy shrimp will not emerge from their dormant cysts and will disappear forever. Unlike many other aquatic crustaceans, they cannot survive in permanent ponds or lakes. They must have the specific requirements of a vernal pool.

3. Endangered Plants Of The San Marcos Vernal Pool Area

Left: Navarretia fossalis (Polemoniaceae), a fragile vernal pool endemic described by Dr. Reid Moran of the San Diego Natural History Museum in 1977 (Madroño 24: 141-159). Right: San Diego thornmint (Acanthomintha ilicifolia), a rare herb in the mint family (Lamiaceae) found in clay soils near the San Marcos vernal pools. This endemic species has been extirpated from many areas of northern San Diego County during the past two decades, mostly due to the construction of extensive housing developments on Las Posas soils. Both species are on the CNPS List 1B: Rare, threatened and endangered. They are also on the U.S. Fish & Wildlife List of Endangered Species.
See Another Image Of The Rare Thornmint

Navarretia fossalis (Polemoniaceae)

Navarretia prostrata at the Santa Rosa Plateau Ecological Reserve

San Diego coyote thistle or button-celery (Eryngium aristulatum var.parishii), a rare member of the carrot family (Apiaceae) that appears in dry vernal pol depressions during late spring. This California endemic is on the CNPS List 1B: Rare, threatened and endangered. It is also on the U.S. Fish & Wildlife List of Endangered Species. The globose flower heads resembling rabbit droppings (red arrow) are dwarf woollyheads (Psilocarphus brevissimus).

4. Brodiaeas In San Marcos & San Clemente Island

Abstract: Coastal populations of Brodiaea in San Diego County with prominent hooded staminodes (with incurved apex) have been previously called B. jolonensis. Using the Jepson Manual (1996) which is based on A Biosystematic Study of the Genus Brodiaea (Amaryllidaceae) by T.F. Niehaus (1971), they key out to B. terrestris ssp. kernensis. This species has a green ovary, unlike the purple ovary of B. jolonensis. The term "dentate connective" used in the Jepson key ideally applies to B. terrestris ssp. terrestris of central and northern California. In this subspecies, the apex of the anther connective extends into a prominent dentate lobe. In southern California populations of Coastal BTK and Montane BTK, the connective apex has a U-shaped or V-shaped notch. At the base of this notch there may be a minute, dentate lobe, although it is absent in most southern California populations. With a dentate appendage at the base, the notch appears W-shaped. B. jolonensis also has a V-shaped notch without a dentate appendage. These subtle differences are difficult to observe in pressed herbarium specimens. Floral dimensions of Coastal BTK and Montane BTK are significantly larger than populations of B. jolonensis in Monterey County, and the scapes are generally shorter. In addition, vascular strand patterns of the inner perianth match those of B. terrestris kernensis.

Populations of Coastal BTK throughout San Diego County generally have staminodes that are incurved at the apex (hooded), while populations of Montane BTK generally have erect staminodes that are inrolled along the upper margins, but not hooded or slightly hooded. Both Munz (A Flora of Southern California, 1974) and Beauchamp (A Flora of San Diego County, California, 1986) recognized a difference between the coastal and mountain populations. These authors called the mountain populations B. terrestris ssp. kernensis and the coastal populations "B. jolonensis." Brodiaeas resembling both the coastal and montane forms of BTK grow together on the Santa Rosa Plateau of Riverside County. There is also staminode variation at Cuyamaca Lake in San Diego County. Perhaps this is a single variable species in southern California. This is an ongoing research project with Tom Chester to understand the Brodiaea populations in southern California. W.P. Armstrong, May 2005.

Left: Downingia cuspidata, a lovely vernal pool endemic in the San Marcos Vernal Pools. This species belongs to the bellflower family (Campanulaceae). Right: A variant of Coastal BTK with strap-shaped staminodes.

Brodiaea kinkiensis, an endemic species on San Clemente Island, off the coast of San Diego County. It has strap-shaped staminodia like the San Marcos variant brodiaea; however it also has a mucronate or cuspidate apex (with a minute, abrupt tip). There is a gradual reduction in staminodia in these three species (B. kinkiensis--B. filifolia--B. orcuttii), culminating in B. orcuttii with no staminodia. Chromosome size also decreases in the same sequence. According to T.F. Niehaus ("A Biosytematic Study of the Genus Brodiaea (Amaryllidaceae)." Univ. of Calif. Publications in Botany Vol. 60, 1971), B. kinkiensis and B. filifolia are closely related and may have evolved from the same ancestral species.

This rare and beautiful brodiaea (Brodiaea filifolia) grows in and around the San Marcos vernal pools, along with several other endangered wildflowers. It can readily be distinguished from other brodiaeas by the spreading perianth and threadlike (filiform) staminodia. This California endemic is on the CNPS List 1B: Rare, threatened and endangered. It is also on the U.S. Fish & Wildlife List of Endangered Species. Populations of this endemic wildflower were once abundant in the San Marcos area, but most of them have been destroyed due to rapid urbanization in this region during the past 30 years.

This rare and beautiful brodiaea (Brodiaea orcuttii) grows in the San Marcos vernal pools, along with several other endangered wildflowers. It can readily be distinguished from other brodiaeas by the lack of sterile stamens called staminodia. This California endemic is on the CNPS List 1B: Rare, threatened and endangered. The following image shows another rare species of Brodiaea with distinctive staminodia.

The normal flower of Brodiaea orcuttii (left) has 3 stamens and no staminodes. The abnormal flower (right) has 6 stamens rather than the normal 3. Additional stamens (red arrows) have developed where staminodes normally appear in other species. Apparently an ancestral gene for stamens has been expressed in this unusual individual.

Coastal BTK (previously labeled B. jolonensis), a spectacular brodiaea with incurved petaloid staminodia. Unlike the other species of Brodiaea on this property, this species has a shorter scape that is generally less than 8 inches (2 dm). The scapes of other species may be 12 inches (3 dm) or taller. For many years this species was listed in Wayne's Word as B. jolonensis, but recent observations by the author and Tom Chester indicate that the identity of this species may be questionable.

Does Brodiaea jolonensis Occur In San Diego County?

Three rare brodiaeas in the San Marcos vernal pool area with distinctive staminodia. A. Coastal BTK, previously labeled B. jolonensis; B. San Marcos variant brodiaea; and C. Thread-leaf brodiaea (B. filifolia).

The San Marcos variant brodiaea has intermediate characteristics between two other species. One of the most obvious characteristics that indicate possible hybridization is a structure called a staminodium which represents a sterile, nonfunctional stamen. All three species (A, B & C) have three staminodia in the center of the flower, just outside the three yellow stamens. The three staminodia of the variant are intermediate between the conspicuous, petaloid staminodia of Coastal BTK (A) and the slender (filiform), inconspicuous staminodia of B. filifolia (C). The three staminodia of the variant appear strap-shaped and are visible in the center of the flower, just outside the three yellowish stamens. The variant occurs throughout several acres of the property and may have reproduced asexually through cormlets. In May 2005 I visited this same site but did not observe any variants. Instead I found numerous B. filifolia and Coastal BTK. The previous winter and spring was an exceptional year for rainfall in San Diego County and brodiaea populations were plentiful. Unfortunately, the fate of this 40 acre field of brodiaeas is dismal because of the rapid (uncontrolled) urbanization of northern San Diego County. The field is within an industrial zone and is surrounded by buildings.

On the Santa Rosa Plateau of Riverside County populations of BTK exhibit a wide range of variation, including strap-shaped staminodes similar to the San Marcos "variant." Could it be that the San Marcos variant brodiaea is simply a variation within the BTK population?

Staminode Variation On The Santa Rosa Plateau

Coastal BTK and the San Diego endemic mesa mint (Pogogyne abramsii) in a dried vernal pool on Kearny Mesa. The scapes are very short, barely extending above the population of mesa mint. Photograph taken in May 1982 on Kearny Mesa, San Diego County.

Pteridophytes Of The
    San Marcos Vernal Pools    

Selaginella cinerascens
Pillularia americana
Isoetes orcuttii

8. Vernal Pools Adjacent To Fry's In San Marcos (8 April 2013)

A: Isoetes orcuttii (Quillwort). B: Pilularia americana (American pillwort).

Vernal pool popcorn flower (Plagiobothrys bracteatus).

Brodiaea terrestris vs. Brodiaea jolonensis
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