1. Plant Classification and Nomenclature Spring 2014

2. Elements of Understanding Biological Diversity Description: requires observation and measurement of characters and their states and synthesis of this information Classification: requires hierarchical organization of taxa based on evolutionary relationships Naming (nomenclature): requires following nomenclatural conventions and enables communication Identification: requires tools such as keys that are based on previous description, classification, and naming of taxa

3. Elements of Understanding Biological Diversity Description of Diversity Classification of Diversity Naming of Diversity Observation & Organization Convention & Communication

4. Description Provides some basic identifiable set of characteristics to associate with the organism; also basis for characters and character states for phylogenetic analysis. Can be as general or as detailed as practicality dictates. Needs to contain enough data to provide adequate discrimination between similar organisms. Needs terminology. Descriptions are linked with a name when there is consistency in the set of observed characters for a given organism.

5. Classification A systematic arrangement in groups or categories according to established criteria; biological classification involves the delimitation, ordering and ranking of taxa. Classification provides ORDER to the group of entities. Relies on observations, many definable and comparable characters, and an ability to discern them. Completely effective classifications can be artificial, that is, not necessarily reflecting evolutionary relationships: i.e., trees vs. shrubs vs. herbs. But modern classifications are based on evolutionary history (phylogeny) because this provides predictive power and synthesis of many types of data is possible. Biological classifications are hierarchical (= information storage system).

6. Classification in Your Life… Do you classify things? Do you do it deliberately? Unconsciously?

7. Let’s go home...* In your room or apartment, think about what groups of items you automatically classify… What characteristics and criteria do you use to do this? Is the classification a continuous, ongoing thing, does it happen occasionally, or at very distinct times? WHY do you do this? *Mentally, that is – so just sit down and think…

8. Some examples: Kitchen: - Silverware [knives, forks, spoons], plates, bowls, pots, pans, cooking utensils, trays, etc. - Refrigerator – meats, vegetables, fruits, eggs, bottles, cans, salad dressings, frozen foods. Bedroom: - Closet & dresser [shoes, boots, shirts, slacks, etc.] - Jewelry Living room: - CDs, Video tapes/DVDs, books, magazines Study: - Textbooks, pens & pencils, paper, etc.

9. A basic fact of life: “Everyone is a Taxonomist”

10. Artificial taxonomy These classifications are based on use or similarity of shape. Generally based on one or few “characters”. Single character taxonomy may work in these situations, but…

11. Single character taxonomy is bad taxonomy for biological systems.

12. What makes a good classification? - Groups recognized according to overall similarity within groups (as seen by multiple characters) and discontinuities between groups and relatedness (evolutionary history). - The classification has predictive value – Characteristics of other related organisms can be predicted by the classification because of the evolutionary perspective. - The classification is practical and useful.

13. Why is biological classification possible? Because variation exists in nature. Four species of the bamboo genus Chusquea

14. Must be able to identify discrete “packages” of biological diversity: species.  Discontinuity is caused by: 1. evolution and speciation, or 2. extinction, or 3. a combination of 1. and 2. Discontinuity of Biological Diversity

15. To establish a classification, one must be able to use discontinuities to delimit groups at various hierarchical levels, e.g.: - How different are populations to warrant calling them distinct species? - How distinct are two groups to be able to recognize them as separate genera? Establishing ranks can be very subjective – the more objectivity we can impose on the process, the more reliable the classification. Assessing Biological Discontinuity

16. SpeciationPhylogeny Evolutionary Time

17. SpeciationPhylogeny Effects of Extinction

18. Speciation Apparent Phylogeny

19. Hierarchical (nested) categories and phylogeny PHYLUM CLASS ORDER FAMILY GENUS TIME

20. Phylogenetics and Classification

21. Principles of Biological Classification Should be based on a well established hypothesis of relationships (a phylogeny) whenever possible Ideally only recognizable (morphologically diagnosable) clades are formally named Ranks should represent more or less equivalent branching points (but this is often ignored)

22. Phylogenetics and Classification Branching order can be inferred from the written classification. Fig. 2.19A-C

23. Classification precedes nomenclature!

24. In terms of nomenclature, so far… We have been using names of plants to discuss their “position” in the plant kingdom, reflecting some level of evolutionary understanding. The names for plant species or genera have been used as a “given” – that is, we did not talk about how those names came into being or how they are correctly used. We need to understand how the accepted system of nomenclature works – how the giving of names to plants follows a specific set of guidelines and rules.

25. Naming and Nomenclature Plants did not evolve with a name! However, we need names to communicate about the plant Organized system of names enables fitting the plant into an accepted scheme Following formal naming rules = nomenclature The system must allow for changes as new information (and other species) are discovered It is helpful if names are descriptive

26. What about common names? Positives: - easily recognizable - easier to pronounce and spell (!) Negatives: - Name varies by language or region - Not specific (ironwood, bigleaf, ivy, etc.) - Conveys no evolutionary information - Does not include classificatory information Botanists rely on the ‘botanical’ or scientific name for accurate communication about the plant in question

27. Common name? Whitlow grass ‘Real’ name: Draba verna (Brassicaceae)

28. The International Code of Nomenclature for Algae, Fungi and Plants is the “legal” code for naming of plants. A new version is produced following each international botanical congress (ca. every six years).

29. Principles of Nomenclature Botanical and zoological classification systems are independent of one another Applying names to taxonomic groups is based on a system of nomenclatural types Names are based on the priority of publication – the earliest valid name is the one to use (later names for the same taxon are called synonyms); starting point for plants is Linnaeus’s Species Plantarum (1753) Each taxon can have only one correct name Scientific names are in Latin or are treated as Latinized words, regardless of origin Rules of nomenclature (ICN) are retroactive unless expressly limited

30. An exception to the rule that there is only ONE legitimate name per taxon: Eight angiosperm families have two acceptable names: (Arecaceae = Palmae; Apiaceae = Umbelliferae; Asteraceae = Compositae; Brassicaceae = Cruciferae; Clusiaceae = Guttiferae; Fabaceae = Leguminosae; Poaceae = Gramineae) Plant Names

31. Classification of Black Pepper Kingdom Viridiplantae (Chlorobionta) Division/Phylum Anthophyta (Embryophyta) Class Magnoliopsida Subclass Magnoliidae (often not used now) Order Piperales Family Piperaceae Genus Piper Species Piper nigrum Genus and species names are always italicized.

32. But all species names have three parts… Piper nigrum L. Scientific names are binomials!

33. Piper nigrum L. = Black Pepper Piper – Genus name or generic epithet – Member of the genus Piper nigrum – Species epithet – Latin for ‘black’ L. = Linnaeus – Author – Person who described plant Black Pepper – Common name

34. Naming a New Species These steps must be followed in naming a new species, according to the ICN: 1. The name (specific epithet) must be in Latin or Latinized (but Latin diagnoses or descriptions are no longer required) 2. The rank of the new name must be clearly indicated (in this case, species novum or new species) 3. A type specimen must be designated (including the herbarium where it is deposited) 4. All of this information and any additional material (e.g., illustrations) must be effectively published (presented in a publication that is widely available to other botanists) Following all of these steps results in valid publication of the name. The process of describing a new species can take a year or more, depending on what studies are needed to justify it as a new species, how long it takes to prepare illustrations and keys, and which journal or book it is published in.

35. Fig. 16.2 Latin no longer needed.

36. The Type System Each species name must be based on a type specimen, with which the name is permanently associated. Types are preserved as reference specimens, often kept separately from the remaining collections in the herbarium. The type specimen must fit within the concept of the species, but does not necessarily have to be representative of average variation (i.e., it may represent one of the extremes of variation in the species) The species name used for the type specimen is considered the basionym, or original name as described, and follows that specimen in perpetuity Names of higher ranks are based on typified names published validly and effectively

37. Types by Rank The type is one physical specimen deposited in an herbarium to which the name is attached and upon which the species description is based (holotype); the holotype can be an illustration although this is unusual. Every species has a type specimen. Every genus has a type species. Every family has a type genus (and so on): - Asteraceae -Aster; Poaceae – Poa; Lamiaceae - Lamium.

38. Type Specimen of Sobralia kerryae Dressler (Orchidaceae) Holotype

39. Botanical Types Holotype – The one specimen (or illustration) designated by the author that will serve as the nomenclatural type Isotype – A duplicate of the holotype (part of the same gathering); always a specimen Lectotype – The specimen designated as the nomenclatural type if no holotype is available or indicated by the author Syntype - Any specimen that is cited in the original description when no holotype was designated by the author Neotype – A ‘new’ type specimen designated when all material for the original type description is missing

40. Chusquea latifolia L. G. Clark (Colombia)

42. Also common to explain derivation of name and to highlight distinguishing features as well as to summarize distribution and habitat.

43. Illustrations, maps, and dichotomous keys distinguishing the new species from related ones are usually included.

44. Publication Names of new taxa must be published effectively and validly to have recognition in the systematics community under the ICN: - Effective Publication – The information must be published in a recognized botanical journal or book (…not a seed catalog or newspaper, internet, etc.); publication in electronic journals is now also approved. - Valid Publication – All of the conditions laid out in the ICN have been met, including effective publication. - The new name is considered to be a legitimate name if all of the correct publication conditions are met. Whether the name becomes accepted (or not) depends on how the botanical community agrees with the author.

45. Why (and how) do plant names change?

46. Plant names change when: The classification system has changed - By far the more typical and frequent cause of name changes - New data often support revision of concepts of generic, familial, or other circumscriptions, necessitating name changes Because of nomenclatural errors - Errors made in original descriptions or taxonomic revisions may need to be corrected by changing the names of plants due to improper format, invalid publication, etc.

47. Capsella bursa-pastoris (L.) Medik. Original Description - Described by Linnaeus as Thlaspi bursa pastoris L., because the species fit in his concept of Thlaspi - Placed as one species in genus Thlaspi, but was not the first species described in the genus (that was T. arvense L.) Subsequent Revision of Taxonomy - Friedrich Kasimir Medikus (Dir. Botanisches Garten Mannheim) thought the species should be placed in a separate genus, which he named Capsella in 1792 -The specific epithet must be retained in such a transfer and the original name becomes a synonym This is an example of a taxonomic transfer. The author names reflect the history of publication of the original species name (basionym) and the subsequent transfer to a new genus

48. Capsella bursa-pastoris (L). Medik. Syn.: Thlaspi bursa pastoris L. basionym The type specimen of the basionym (original name) stays the same and is the type of the currently accepted species name in Capsella. The concept of the species has not changed; only its generic placement has changed.

49. Synonyms - Priority If two (or more) different names are determined to be the same entity, the earliest validly and effectively published name has priority. –Malus pumila Miller, 1768 (invalid) –Malus domestica Borkh., 1803 –Malus communis Poiret, 1804 (SYNONYM) If the same name has been used for more than one taxon, these are considered HOMONYMS. –Platonia Raf. 1810 is a genus of Cistaceae (rock rose family) –Platonia Kunth 1829 is a genus of Poaceae (bamboo); this name was changed to Neurolepis Meisn. in 1843

50. Chusquea – 138 species Neurolepis – 21 species

51. Molecular phylogeny of the subtribe Chusqueinae C S R N1 N2 ▪Spikelet structure ▪Papillate subsidiary cells ▪Multiple, dimorphic buds ▪Connate lemma tips * *type species * Chusquea Neurolepis

52. What to do? Neurolepis is paraphyletic to Chusquea Neither N1 nor N2 has synapomorphies All clades share the same spikelet and flower structure Chusquea Kunth was published in 1822 and Neurolepis in 1843, so Chusquea is the older generic name So, we synonymized Neurolepis with Chusquea; all of the species formerly in Neurolepis received new combinations or new names in Chusquea

53. Neurolepis elata (Kunth) Pilg. (basionym Platonia elata Kunth) becomes Chusquea elata (Kunth) L. G. Clark Neurolepis pittieri McClure becomes Chusquea magnifolia L. G. Clark (a new name is needed because the combination C. pittieri Hack. already exists)

54. Are there similar examples at the family level?

55. Sapindaceae phylogeny (based on morphology; Judd et al. 1994) SAP HIPP ACER SAP Chemistry Appendaged petals Curved embryo w/ seed coat “pocket” 8 or fewer stamens Etc.

56. Sapindaceae (traditional) Aceraceae Hippocastanaceae Xanthoceraceae (X. sorbifolium) Sapindaceae molecular phylogeny (Buerki et al. 2010) ? Shares some but not all of the morphological synapomorphies shown on the previous slide. Sapindaceae in the broad sense

57. An example: Chusquea arachniforme L.G. Clark & Londoño was published in 1998 Subsequently corrected to Chusquea arachniformis L.G. Clark & Londoño because the original form of the specific epithet was not correct in Latin Nomenclatural Errors

58. Hybrid Taxa Hybrids are indicated with the "X" sign and may be given in two forms, the first where the parental taxa are indicated, the second where the hybrid taxon is given a new name: Quercus alba L. X Q. michauxii Nutt. or Quercus X beadlei Trelease Hybrid genera (a nothogenus) are indicated by an X before the name, which is composed of elements of the contributing parental genera: XDialaeliocattleya is an intergeneric hybrid of Diacrium, Laelia and Cattleya

59. Cultivar Names Cultivated plants follow a “related” code of horticultural nomenclature Examples of correct cultivar names of apple, Malus baccata Borkh.: –M. baccata cv. Columnaris –M. baccata 'Jackii' –Malus 'Barbara Ann' Cultivar Names: First letter capitalized, not Latinized (thus, not italic), preceded by cultivar abbreviation (cv.), or in single quotes (‘Jackii’).

60. Several databases help track all of this information http://www.tropicos.org/Home.aspx http://www.ipni.org/