Plants that are restricted to one or more specific localities within a region are termed endemic. For example, the Torrey pine is native as well as endemic to California. Although commonly cultivated, it only grows wild on the sandstone bluffs between Del Mar and La Jolla in San Diego County, and on Santa Rosa Island. Because of the many isolated mountain ranges and valleys in California, approximately 22 percent of the flora is endemic to the state. Some endemic plants in California include the California cypresses (Hesperocyparis), Santa Cruz Island ironwood (Lyonothamnus floribundus ssp. asplenifolius), Death valley sage (Salvia funerea), Death Valley locoweed (Astragalus funereus), Panamint daisy (Enceliopsis covillei), and Death Valley gilmania (Gilmania luteola). Death Valley is especially rich in endemics because of its isolation from other regions. It is surrounded by high mountain ranges and hundreds of miles of arid desert. In fact, one of the rarest endemic wildflowers in California is called "rock lady" (Maurandya petrophila syn. Holmgrenanthe petrophila), a member of the plantain family (Plantaginaceae). This unusual plant grows in crevices on vertical limestone walls in steep canyons of the Grapevine Mountains bordering Death Valley.

Naturalized: True naturalized plant species are introduced from another region (outside California). Because they are able to grow wild and reseed themselves, they are considered part of the California flora. Some naturalized species are considered very destructive to the natural environment because they are extremely invasive and may replace the native species. This is especially serious when the loss of native plants threatens the survival of native animals that depend on the plants for food. Naturalized plants that are considered undesirable are often referred to as weeds. It has been estimated that more than 16 percent of the California flora is composed of naturalized species. Naturalized "weeds" often have ingenious methods of dispersal, including hitchhiking on animals and airborne seeds. A single tumbleweed plant (Salsola tragus) may produce 20,000 to 50,000 seeds within numerous small fruits, each surrounded by a circular, papery border. Mature plants readily break off at the ground level and are pushed along by strong gusts of wind. As they roll along hillsides and valleys, the seeds are scattered across the landscape. The introduction of Saharan mustard (Brassica tournefortii) into the Anza-Borrego desert region is an ecological disaster. The South African shrub called boneseed (Chysanthemoides monilifera ssp. monilifera) was introduced into the Palomar College Arboretum in the 1970s and has become locally naturalized. It is listed for California in the Flora of North America but not in the Jepson Manual.

The Angiosperm Phylogeny Group (APG) has proposed some significant changes in the classification of many traditional angiosperm families, including the placement of all duckweeds in the Araceae rather than the Lemnaceae. Nomenclatural changes are cited under the APG II system (2003) and superceeded by APG III system (2009). These changes are based on computer-generated evolutionary trees or cladograms. Thousands of data characters have been used, including morphology, anatomy, flavonoids, allozymes, and DNA sequences from chloroplast genes and introns. The Jepson Manual Second Edition essentially follows the changes summerized in the following reference by W.T. Judd, et al. 2008. The incorporation of these changes into textbooks, floras, checklists and herbarium collections is a formidable task, not to mention relearning hundreds of new names.

Judd, W.S., Campbell, C.S., Kellogg, E.A., Stevens, P.F., and M.J. Donaghue. 2008. Plant Systematics: A Phylogenetic Approach (Third Edition). Sinauer Associates, Inc., Sunderland, Massachusetts. 611 p.   Angiosperm Phylogeny Group (2003). "An Update of the Angiosperm Phylogeny Group Classification for the Orders and Families of Flowering Plants: APG II." Botanical Journal of the Linnean Society 141 (4): 399-436.   Angiosperm Phylogeny Group (2009). "An Update of the Angiosperm Phylogeny Group Classification for the Orders and Families of Flowering Plants: APG III." Botanical Journal of the Linnean Society 161 (2): 105-121.

Based on derived characteristics over time, modern phylogenetic trees (cladograms) of animal and plant groupings show all taxa descending from a common ancestor. This grouping is termed monophyletic. Starting with a common ancestor all the branching is in 2's (dichotomous), with every new branch (clade) giving rise to a pair of closely related sister clades. Each of these clades in turn gives rise to another pair of sister clades, and so on. Evolutionary relationships displayed in cladograms are not always dichotomous. Three or more branches may arise from a node (polytomy) when closely-related taxa cannot be completely resolved into dichotomies. This is clearly seen in the cladogram for Acacia (see below). In monophyletic groupings all descendants have a common ancestor and share one or more derived characters. See the following simplified cladogram.

Many traditional phylogenetic groupings of species within families and genera are not monophyletic and are inconsistent with modern cladistical analyses based of DNA. In other words, the groupings are paraphyletic or polyphyletic, and do not show all species within a group descending from a common ancestor. Monophyly is the natural evolutionary pattern in which all species are descended from a common ancestor. In order to have consistent computer-generated, monophyletic cladograms, it is sometimes necessary to change paraphyletic and polyphyletic groupings by moving species into different genera, and by moving genera into different families. Many of the taxonomic revisions in the Jepson Manual 2nd Edition (2012) make more sense if you understand the terms monophyletic, paraphyletic and polyphyletic. For example, why was the duckweed family (Lemnaceae) reduced to a subfamily (Lemnoideae) within the arum family (Araceae)? Why were non-phyllode acacias with prickles (e.g. cat's claw acacia) removed from the genus Acacia and placed in a separate genus Senegalia? Hopefully, the following chart will shed some light on these significant changes.

Maintaining the duckweeds (Lemnaceae) and arums (Araceae) as distinct families would make the arum family paraphyletic, with a common ancestor but without all of its descendants (i.e. duckweeds are excluded). In order to have a monophyletc, computer-generated cladogram, the duckweeds are now placed in the family Araceae. Modern reptiles is also a paraphyletic grouping that contains a common ancestor, but does not contain all descendants (i.e. birds are excluded).

Morphological and genetic studies have shown that the genus Acacia is polyphyletic. As shown in the simplified diagram above, the most recent ancestor of "C" is not part of the grouping within the blue square. For example, it has derived traits that are not shared by the common ancestor. Therefore, it cannot be part of the group with A & B. In order to maintain Acacia as a monophyletic genus, "C" must be placed in a different clade. If "C" and "D" share the same derived traits and common ancestor, then "C" must be a sister clade with "D." This is essentially why some previous members of the genus Acacia, such as the "cats claw acacia" (Acacia greggii) are now placed in the genus Senegalia. A grouping of warm-blooded animals would include birds and mammals and is called polyphyletic because the members of this group do not include the most recent common ancestor.

Most members of the genus Senegalia differ from Acacia by the presence of prickles and the absence of phyllodes. A naturalized acacia in San Diego County called "sweet acacia" (A. farnesiana var. farnesiana) has been placed in the genus Vachellia. Members of the genus Senegalia can be distinguished from Vachellia by the absence of stipular spines and the presence of prickles. The origin of stipular spines vs. prickles is quite different, and molecular taxonomists have concluded that the separation of these species into separate groups is warranted.

Seigler, D.S., Ebinger, J.E., and J.T. Miller. 2006. "The Genus Sengalia (Fabaceae: Mimosoideae) Phytologia 88 (1): 38-94.  Maslin, B.R., Miller, J.T., and D.S. Seigler. 2003. "Overview of the Generic Status of Acacia (Leguminosae: Mimosoideae)." Australian Systematic Botany 16 (1): 1-18.

A. Prickles of cat's claw acacia (Senegalia greggii). B. Stipular spines of sweet acacia (Vachellia farnesiana var. farnesiana). Unlike stipular spines at the bases of leaves, prickles arise from the cortex and epidermis of plant stems. The classic thorns of roses are actually prickles.

This simplified dichotomous flow chart is not a computer-generated, monophyletc cladogram. It simply shows how the traditional genus Acacia was subdivided into groups in order to key out different species. Some of these species with prickles and stipular spines have been removed from the genus Acacia and placed in new genera. The original 1350 species now comprise 5 genera, with 960 (mostly Australian) spp. still retained in Acacia.

The five Acacia genera plus Faidherbia appear on the Kew Plant List at the following link. Most of the species have "Confidence Levels" of 2 (Medium) or 3 (High) according to Kew's Criteria For Taxonomic Integrity Of Source Data: Confidence Level Definition. You can easily look up the species placed in these genera.

Seach Acacia, Acaciella, Vachellia, Senegalia & Mariosousa in Kew Plant List

See Legume (Fabaceae) Subfamilies at the Palomar College Arboretum Subfamilies:    Mimosoideae      Papilionoideae      Caesalpinioideae

From a purely morphological point of view, one of the most astonishing changes is the placement of members of the Nolinaceae and Dracaenaceae into the Ruscaceae. The type genus Ruscus includes a low-growing Eurasian shrub called butcher's broom (R. aculeata) that bears no resemblance to Nolina, Dracaena & Beaucarnea. See the following image:

Familiar genera such as Hyacinthus (hyacinth), Aspholelus (asphodel), Asparagus (asparagus), Allium (onion) and Iris (iris) belong to their own separate families, the Hyacinthaceae, Asphodelaceae, Asparagaceae, Alliaceae and Iridaceae. The latter family (Iridaceae) also includes the commonly cultivated Watsonia, Moraea (butterfly lily), Freesia (freesia), Sisyrinchium (blue-eyed grass), Crocus and Gladiolus. The genus Aloe, formerly of the Liliaceae, is now placed in the family Asphodelaceae, along with Kniphofia (red hot poker) and Haworthia.

Amaryllis (naked lady) still belongs to the Amaryllidaceae and also includes many genera that were once placed in the Liliaceae, including Crinum, Hippeastrum (amaryllis), Hymenocallis (spider lily), Haemanthus (blood lily), and Narcissus (daffodil). Agapanthus (lily of-the-Nile), Hemerocallis (day lily) and Colchicum (autumn crocus) belong to their own families, the Agapanthaceae, Hemerocallidaceae and Colchicaceae. Lilium (lily), Tulipa (tulip), Calochortus (Mariposa lily) and Fritillaria (chocolate lily) are still included in the lily family (Liliaceae). Chlorogalum (soap lily) is now placed in the agave family (Agavaceae) with Agave, Yucca, Hesperocallis (desert lily) and Camassia (camas). Death camas and star lilies (Zigadenus) are now placed in the Melanthiaceae along with Veratrum (corn lily), Trillium (trillium) and Xerophyllum (bear grass).

Computer generated monophyletic clades based on chloroplast DNA have resulted in major changes to the Scrophulariaceae. Plantago, Penstemon, Veronica, Linaria, Antirrhinum, Keckiella, & Digitalis are now placed in the Plantaginaceae. Mimulus with its thigmotrophic stigma is placed in the Phrymaceae. Traditional genera retained in the Scropulariaceae include Verbascum and Scrophularia. Other genera placed in the Scrophulariaceae include Buddleja and Myoporum. Indian paintbrush (Castilleja), Indian warrior (Pedicularis), and owl's clover (Orthocarpus) are placed in the parasitic family Orobanchaceae with the broomrapes (Orobanche). Other closely-related families representing separate clades are the Paulowniaceae, Lentibulariaceae, Acanthaceae and Bignoniaceae. Members of the Martyniaceae (Proboscidea, Martynia & Ibicella) are included in the Pedaliaceae with Uncarina, Harpagophytum & Sesamum.

Chocolate (Theobroma cacao)

7. Major Changes In The Mallow Family (Malvaceae)

DNA phylogenetic trees (cladograms) clearly show that the chocolate family (Sterculiaceae), basswood family (Tiliaceae), and bombax family (Bombacaceae) are not monophyletic. They are better treated as subfamilies within the mallow family (Malvaceae). This is similar to placing the duckweed subfamily Lemnoideae within the Arum family (Araceae).

Monophyletic: A taxonomic group that represents a single branch (clade) in a cladogram, and having a common ancestor. For example, all birds and reptiles are thought to have descended from a single common ancestor and are monophyletic. Humans (Homo) and chimpanzees (Pan) are also monophyletic.

The Genus Lotus Has Been Changed To Acmispon

Deerweed (Lotus scoparius var. scoparius), a native shrubby perennial found throughout the Palomar College Arboretum and adjacent coastal sage scrub. Much to the chagrin of botanists like myself, this genus has been renamed and the new scientific trinomial is Acmispon glaber var. glaber. In the desert var. brevialatus, the keel is longer than the wings.

Cactaceae: The Cholla Cactus Genus Opuntia Has Been Changed To Cylindropuntia
Cyperaceae: Naked Stem Bulrushes Scirpus Have Been Changed To Schoenoplectus
Asteraceae: The Genus For Cheesebush Hymenolcea Has Been Changed To Ambrosia

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10. Where To See Wildflowers In Southern California Favorite Anza-Borrego SD-Riverside Witch Creek Fire California Special Santa Rosa Plateau Brodiaea Joshua Tree Marine Parasite

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11. New Discoveries Continually Being Made: E.g. Brassica fruticulosa in San Diego County

Brassica fruticulosa In San Diego Couty

All text material & images on these pages copyright © W.P. Armstrong