Transcript Systematic Implications of DNA variation in subfamily

Plant Classification and
Nomenclature
Spring 2014
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
Elements of Understanding
Biological Diversity
Description of Diversity
Observation & Organization
Classification of Diversity
Convention & Communication
Naming of Diversity
Description
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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.
Classification
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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).
Classification in Your Life…
• Do you classify things?
• Do you do it deliberately?
Unconsciously?
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…
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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.
A basic fact of life:
“Everyone is a Taxonomist”
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…
Single character taxonomy is bad
taxonomy for biological systems.
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.
Why is biological classification
possible?
Because variation exists in nature.
Four species of the bamboo genus Chusquea
Discontinuity of Biological Diversity
• 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.
Assessing Biological Discontinuity
• 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.
Evolutionary Time
Speciation
Phylogeny
Effects of
Extinction
Speciation
Phylogeny
Speciation
Apparent Phylogeny
Hierarchical (nested) categories
and phylogeny
GENUS
TIME
FAMILY
ORDER
CLASS
PHYLUM
Phylogenetics and Classification
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)
Phylogenetics and Classification
Fig. 2.19A-C
Branching order can be
inferred from the written
classification.
Classification
precedes
nomenclature!
In terms of nomenclature, so far…
• We have been using names of plants to
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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.
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
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information (and other species) are
discovered
It is helpful if names are descriptive
What about common names?
• Positives:
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- 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
Common name?
Whitlow grass
‘Real’ name:
Draba verna
(Brassicaceae)
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).
Principles of Nomenclature
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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
Plant Names
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)
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.
Scientific names are binomials!
But all species names have
three parts…
Piper nigrum L.
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
Naming a New Species
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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.
Fig. 16.2
Latin no
longer needed.
The Type System
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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
Types by Rank
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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.
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Every species has a type specimen.
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Every genus has a type species.
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Every family has a type genus (and so on):
- Asteraceae -Aster; Poaceae – Poa; Lamiaceae Lamium.
Type Specimen of
Sobralia kerryae Dressler
(Orchidaceae)
Holotype
Botanical Types
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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
Chusquea latifolia L. G. Clark (Colombia)
Also common to
explain derivation
of name and to highlight
distinguishing
features as well as to
summarize distribution
and habitat.
Illustrations, maps,
and dichotomous
keys distinguishing
the new species from
related ones are
usually included.
Publication
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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.
Why (and how) do
plant names change?
Plant names change when:
• The classification system has changed
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- 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.
Capsella bursa-pastoris (L.) Medik.
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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
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.
Synonyms - Priority
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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)
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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
Chusquea – 138 species
Neurolepis – 21 species
Molecular phylogeny of the subtribe Chusqueinae
Chusquea
▪Multiple, dimorphic
buds
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C
S
R
▪Connate lemma
tips
▪Spikelet structure
▪Papillate
subsidiary cells
N1
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N2
*type species
Neurolepis
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
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)
Are there similar examples
at the family level?
Sapindaceae phylogeny
(based on morphology; Judd et al. 1994)
SAP
HIPP
SAP
SAP
SAP
SAP
Chemistry
Appendaged petals
Curved embryo w/
seed coat “pocket”
8 or fewer stamens
Etc.
SAP
ACER
Sapindaceae molecular phylogeny
(Buerki et al. 2010)
Sapindaceae
in the broad
sense
Sapindaceae (traditional)
Aceraceae
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Hippocastanaceae
Xanthoceraceae
(X. sorbifolium)
Shares some but not all of the morphological synapomorphies
shown on the previous slide.
Nomenclatural Errors
An example:
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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
Hybrid Taxa
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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
Cultivar Names
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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’).
Several databases help track
all of this information
http://www.tropicos.org/Home.aspx
http://www.ipni.org/