#michael g. simpson

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WHAT IS A PLANT?

This  question  can  be  answered  in  either  of  two  conceptual  ways.  One  way,  the  traditional  way,  is  to  define  groups  of  organisms such as plants by the characteristics they possess. Thus, historically, “plants” included those organisms that possess photosynthesis, cell walls, spores, and a more or less sedentary behavior. This traditional grouping of plants contained a variety of microscopic organisms, all of the “algae,” and the more familiar plants that live on land. A second way to answer the question “What is a plant?” is to evaluate the evolutionary history of life and to use that history to delimit the groups of life. We now know from repeated research studies that some of the photosynthetic organisms evolved independently of one another and are not closely related.Thus, the meaning or definition of the word plant can be ambiguous and can vary from person to person. Some still like to treat plants as a “polyphyletic”  assemblage (see later  discussion), defined by the common (but independently evolved) characteristic of photosynthesis. However, delimiting organismal groups based on evolutionary history has gained almost universal acceptance. This latter type of classification directly reflects the patterns of that evolutionary history and can be used to explicitly test evolutionary hypotheses (discussed later; see Chapter 2). An understanding of what plants are requires an explanation of the evolution of life in general.

Chapter One Plant Systematics Second Edition Michael G. Simpson

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Chapter One Exercises

1.  Obtain  definitions of the word plant by asking various people (lay persons or biologists) or looking in reference sources, such as  dictionaries  or  textbooks.  Tabulate  the  various  definitions  into  classes.  What  are  the  advantages  and  disadvantages  of  each?

2.  Take a day to note and list the uses and importance of plants in your everyday life.

3.  Pick a subject, such as history or astronomy, and cite how the principles of taxonomy are used in its study.

4.  Do a web search for a particular plant species (try common and scientific name) and note what aspect of plant biology each site covers.

5.  Peruse  five articles in a systematics journal and tabulate the different types of research questions that are addressed.

Chapter One  Plant Systematics Second Edition Michael G. Simpson

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CLADOGRAM CONSTRUCTION

RECENCY OF COMMON ANCESTRY

Cladistic analysis allows for a precise definition of biological relationship. Relationship  in  phylogenetic  systematics  is  a  measure of recency of common ancestry. Two taxa are more closely related to one another if they share a common ancestor that is more recent in time than the common ancestor they share with other taxa. For example, in Figure 2.7A taxon C is more closely related to taxon D than it is to taxon E or F. This is true because the common ancestor of taxa C and D is more recent  in  time  (closer  to  the  present)  than  is  the  common  ancestor of taxa C, D, E, and F (Figure 2.7A). In the earlier example of Figure 2.6E, it is evident that X. nigra and X. purpurea are more closely related to one another than either is to X. rubens.  This  is  because  the  first  two  species  together  share  a  common  ancestor  (S)  that  is  more  recent  in  time  than  the  common ancestor (R) that they share with X. rubens. Similarly X. rubens  is  more  closely  related  to  X.  nigra  and  X.  purpureathan it is to either X. lutea or X. alba because the first three taxa share a common ancestor (R) that is more recent in time than Q,  which  is  the  common  ancestor  shared  by  all  five  species.

The  fact  that  descent  is  assessed  by  means  of  recency  of  common  ancestry  gives  the  rationale  that  the  branches  of  a  given  cladogram  may  be  visually  rotated  around  their  junction point or “node” (at the common ancestor) with no change in  phylogenetic  relationships.  For  example,  the  cladograms  portrayed in Figure 2.8A, 2.8B, and 2.8C are all the same as that  in  Figure  2.6E,  differing  only  in  that  the  lineages  have  been rotated about their common ancestors. As discussed earlier, the topology of all these cladograms is exactly the same; only the visual structure of branches varies. (Again note that cladograms can be portrayed in different manners, with taxa at the top, bottom, or sides and with lineages drawn as vertical, horizontal, or angled lines, as in Figure 2.8A–C.)

Chapter Two  Plant Systematics Second Edition Michael G. Simpson

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CLADOGRAM CONSTRUCTION

APOMORPHY

A  primary  tenet  of  phylogenetic  systematics  is  that  derived  character  states,  or  apomorphies,  that  are  shared  between  two or more taxa (OTUs) constitute evidence that these taxa possess  them  because  of  common  ancestry.  These  shared  derived  character  states,  or  synapomorphies,  represent  the  products  of  unique  evolutionary  events  that  may  be  used to link two or more taxa in a common evolutionary history. Thus,  by  sequentially  linking  taxa  together  based  on  their  common possession of shared apomorphies, the evolutionary history of the study group can be inferred.

The  character  ×  taxon  matrix  supplies  the  data  for  constructing  a  phylogenetic  tree  or  cladogram.  For  example,  Figure  2.6  illustrates  construction  of  the  cladogram  for  the  five species of the hypothetical genus Xid from the character × taxon  matrix  at  Figure  2.6A,B.  First,  the  OTUs  are  grouped  together  as  lineages  arising  from  a  single  common  ancestor  above  the  point  of  attachment  of  the  outgroup  (Figure  2.6C).  This unresolved complex of lineages is known as a polytomy (see later discussion). Next, derived character states are identified and used to sequentially link sets of taxa (Figure 2.6D,E). In this example, synapomorphies include (1) the derived states of characters 1 and 3 that group together X. nigra, X. purpurea, and X. rubens; (2) the derived state of character 4 that groups together X.  alba  and X.  lutea;  (3)  the  derived  state  “four  stamens”  of  (ordered)  character  5,  which  is  found  in  all  ingroup  OTUs and constitutes an apomorphy for the entire ingroup and the  derived  state  “two  stamens”  of  character  5  that  groups  X. nigra  and  X.  purpurea.  The  derived  state  of  character  2  is  restricted to the taxon X. lutea and is therefore an autapomor-phy. Autapomorphies occur for a single OTU and are not informative in cladogram construction. Finally, the derived state of character 6 evolved twice, in the lineages leading to both  species X.  alba  and  X.  purpurea;  these  independent  evolutionary  changes constitute homoplasies due to convergence.

Chapter Two  Plant Systematics Second Edition Michael G. Simpson

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Figure 2.6

Chapter Two  Plant Systematics Second Edition Michael G. Simpson

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CHARACTER ANALYSIS

CHARACTER × TAXON MATRIX

Prior  to  cladogram  construction,  characters  and  character  states  for  each  taxon  are  tabulated  in  a  character ×  taxon  matrix, as illustrated in Figure 2.6A. In order to analyze the data using computer algorithms, the characters and character states must be assigned a numerical value. In doing so, character states are assigned nonnegative integer values, typically beginning with 0. Figure 2.6B shows the numerical coding of the matrix of Figure 2.6A. The states are numerically coded in sequence to correspond with the hypothesized transformation  series  for  that  character.  For  example,  for  the  ordered  transformation series “leaf type” of Figure 2.4D,F, the character  states  “simple,”  “ternately  compound,”  and  “unifoliolate”  could  be  enumerated  as  0,  1,  and  2.  In  the  character  ×  taxon  matrix, polarity is established by including one or more out-group   taxa   as   part   of   the   character   ×   taxon   matrix   (as in Figure 2.6A,B) and by subsequently “rooting” the tree by  placing  the  outgroups  at  the  extreme  base  of  the  final  cladogram (see later discussion).

Chapter Two  Plant Systematics Second Edition Michael G. Simpson

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CHARACTER ANALYSIS

CHARACTER STEP MATRIX

As reviewed earlier, assigning a character state transformation determines  the  number  of  steps  that  may  occur  when  going  from one character state to another. Computerized phylogeny reconstruction algorithms available today permit a more precise tabulation of the number of steps occurring between each pair of character states through a character step matrix. The matrix consists of a listing of character states in a top row and left  column;  intersecting  numbers  within  the  matrix  indicate  the  number  of  steps  required,  going  from  states  in  the  left  column  to  states  in  the  top  row.  For  example,  the  character  step  matrix  of  Figure  2.5A  illustrates  an  ordered  character  state transformation series, such that a single step is required when going from state 0 to state 1 (or state 1 to state 0), two steps are required when going from state 0 to state 2, etc. The character  step  matrix  of  Figure  2.5B  shows  an  unordered  transformation series, in which a single step is required when going   from   one   state   to   any   other   (nonidentical)  state.   Character  step  matrices  need  not  be  symmetrical;  that  of  Figure  2.5C  illustrates  an  ordered  transformation  series  but  one  that  is  irreversible,  disallowing  a  change  from  a  higher  state number to a lower state number (e.g., from state 2 to state 1) by requiring a large number of step changes (symbolized by “∞”). Character step matrices are most useful with specialized types  of  data.  For  example,  the  matrix  of  Figure  2.5D  could represent DNA sequence data, where 0 and 1 are the states for the  two purines  (adenine  and  guanine)  and  2  and  3  are  the  states  for  the  two pyrimidines  (cytosine  and  thymine;  see  Chapter  14).  Note  that  in  this matrix  the  change  from  one  purine to another purine or one pyrimidine to another pyrimidine (each of these known as a “transition”) requires only one step, being  biochemically more probable to occur, whereas a change from a purine to a pyrimidine or from a pyrimidine to a  purine  (termed  a “transversion”)  is  given  five  steps,  being  more  biochemically  less  likely. Thus,  in  a  cladistic  analysis,  the latter change will be given substantially more weight.

DNA sequence data may be transformed in a more complicated evolutionary model, based on a number of parameters, such  as  branch  length,  codon position,  base  frequency,  or  transition/transversion ratio. Such models of evolution are an integral  component  of  maximum  likelihood  and  Bayesian analyses (see later discussion).

Chapter Two  Plant Systematics Second Edition Michael G. Simpson

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Figure 2.5

Chapter Two  Plant Systematics Second Edition Michael G. Simpson