Molecular Systematics Chapter 5

1
Molecular Systematics (Chapter 5)     Historically
, plant systematics has relied on morphological
characters for phylogenetic studies.   During
approximately the last ten years, use of
molecular data has become much more important in
constructing phylogenies.   molecular
systematics- use of DNA and RNA to infer
relationships among organisms     As with
morphological characters, molecular characters
are subject to convergence and parallelism,
making phylogenies more difficult to interpret.
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Benefits of using molecular data   - Many
more molecular characters are available.  
- Interpretation of molecular characters is
usually easier, because molecular characters
often are non-reducible.   Example An adenine
(molecular character) is always an adenine, but
compound leaves (morphological character) can
form in many different ways in different kinds of
plants.

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General results of using molecular data   -
Sometimes has supported phylogenies generated by
using morphological characters (example Poaceae,
Fabaceae, Rosaceae)   - Often has allowed
systematists to choose among competing hypotheses
of relationships (example helped to decide what
group is the sister group of the Asteraceae)  
- Occasionally has suggested novel relationships
(example documentation of cross-breeding between
groups that were thought to be intersterile)
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Plant Genomes   Plant cells contain three
genomes     Table 5.1 in Judd et al. Genome
Genome Size (kbp) Inheritance Chloro
plast 135-160 (circular) Generally
maternal (from the seed parent)   Mitochondr
ion 200-2500 (circular) Generally
maternal (from the seed parent)   Nucleus
1.1 x 106 to 110 x 109 Biparental    
 
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• How Molecular Data are Generated
•  
• Gene sequencing- determining precise sequence of
  nucleotides in a portion of DNA
•  
• 1. Production of DNA for sequencing
•        a.  DNA originally produced by cloning
  genes into bacteria to
• form genomic libraries
•         b. Polymerase chain reaction (PCR)
•         - Primers produced to match end
  points of DNA of interest
•         - Primers placed in tube with DNA
  from the organism, a
• DNA polymerase, and free
  nucleotides
•         - Heating and cooling of mixture
  allows DNA to denature, primers to bind, and
  polymerase to synthesize complementary strands
  of DNA
•  
• 2. Sequencing of genome done by one of several
  methods (e.g., gels, sequencer)

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Types of Molecular Data Used as Characters in
Constructing Phylogenies     1.    Genome
rearrangements - Restriction sites used
as genetic markers
Example Jansen and Palmer (1987) found
that most species in Asteraceae have a single
inversion in the DNA. Species in the sub- family
Barnedisiinae (right) are the only members of
Asteraceae with the ancestral arrangement of
DNA. So this is a sister group to the rest
of the family.
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•  
• DNA sequences- majority of molecular systematic
  studies have used these as characters
•  
•  
•  
• Most data are available on chloroplast DNA and on
  nuclear genes for ribosomal RNA.

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An example of work on chloroplast DNA is a
community-wide effort to generate a large
database of sequences of the chloroplast gene
rbcL.   - Encodes the large subunit of the
photosynthetic enzyme RuBisCO, that is the major
carbon acceptor in all photosynthetic eukaryotes
and cyanobacteria. - Selected for study
because it is nearly universal among plants, it
is long, relatively easy to analyze, and is
present in many copies in the cell.
- Limitation is that it is a slowly-changing
gene, so is not very useful in analyzing
relationships among closely-related groups of
plants. Other chloroplast genes have been used
to study closely related taxa.   Nuclear
ribosomal RNA has been used extensively in
molecular systematics because many copies
(several hundred to several thousand) exist in
the cells.
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Nuclear DNA is increasingly being used in
molecular systematics   - Low copy number
nuclear genes are being used as phylogenetic
markers. - High copy number, noncoding
nuclear sequences are used for research
in systematics at the within-species, or
population level. - The random amplified
polymorphic DNA (RAPD) method also is
used in research at the population
level.   Although molecular data has led to
many advances in systematics, Alanysis of
morphological data still has to be done as well.
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Evolution of Plant Systematic Diversity (Chapter
6)     Systematists analyze, classify, and try to
understand the diversity of plants. Diversity of
plants is tremendous (260,000 species of
vascular plants on Earth), and is influenced
primarily by evolution.   Evolution source of
plant diversity   - Speciation part of
the process of evolution, and of central
interest to systematists  
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  Evolution   Evidence for evolution by natural
selection as a source of diversity among
plants   1)     Fossil record- records
evolution of structures such as flowers, fruits,
and leaves and the origin and extinction of
taxa   2)     Homologies- fundamental
structural similarities among species that are
not dependent on function           - Genetic
code - Other homologous structures and organs
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Example of a homologous structure the orchid lip
Pogonia ophioglossoides
Cypripedium calceolus
Habenaria flava
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  3)     Adaptations- close correspondence
between organisms and their environment.
Adaptations increase fitness, or ability to
survive and reproduce.   4) Geographic
variation within groups of plants, that varies
with physical or biotic features
anagenesis- evolution within lineages
(species)   cladogenesis- evolution that leads to
the formation of new species, by splitting one
species in two    Mutation and recombination
introduce new variation into plant
taxa.   mutation- alteration in DNA (point
mutations, insertions, duplications, deletions,
inversions)   recombination- rearrangement of
genes that occurs mostly during meiosis (crossing
over, independent assortment of chromosomes)
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Mechanisms of evolution   -   Natural selection
Organisms with higher fitness leave more
descendents   -   Gene flow (migration) may
introduce new genetic variation into a
population   - Random genetic drift chance
fixation of genes in small populations
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• Speciation
•  
• speciation- Permanent severing of population
  systems so that migrants from one system would be
  at a disadvantage when entering another. Could
  be due to difficulty finding mates, or difficulty
  competing for pollinators, fruit dispersers, etc.
•  
• Types of speciation
•  
• 1)     Allopatric (geographic) speciation-
  Geographic isolation
• prevents gene flow, and allows divergence
  of the isolated
• populations.
•  
• Is probably not common in plants, because often
  neither of the mechanisms required to form
  distinct species is operating
•  
• - Gene flow throughout all individuals of a
  geographic race over a large region could
  require thousands of generations.
•  

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  - Natural selection (due to biotic,
physical, and/or climatic
characteristics of the environment) usually does
not operate uniformly on all
individuals of a geographic race over a large
region. 2)     Local speciation- Small
populations at the edge of a species
range may be affected by random genetic drift,
natural selection due to extreme
environmental conditions at the edge of the
range, or a combination of both factors.
Changes induced by these factors could
create a new lineage (species).   - This
mechanism does not require that gene flow or
natural selection operate over large
regions.   3) Sympatric speciation-
Occurs without geographic separation.
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Example of possible sympatric speciation
Mimulus lewisii (left) and Mimulus cardinalis
(right)
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Reproductive Isolating Barriers All of these
barriers operate when two species are sympatric
(in contact).   Table 6.1 in Judd et
al. Premating Postmating, prezygotic
 1.   Temporal 5. Incompatibility a.
Seasonal a. Pollen-pistil b.
Diurnal Postmating,
postzygotic 2.  Ecological b.
Seed 3. Floral a. Behavioral 6.
Hybrid inviability, including b.
Structural ecological isolation 4.
Self-fertilization 7. Hybrid floral
isolation 8. Hybrid
sterility 9. Hybrid breakdown
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  1.     Temporal isolation Flowering at
different times of the year (seasonal), or at
different times of the day (diurnal).   2.
Ecological isolation Ecological differences
(habitat, etc.) are strong enough to reduce
fitness of hybrids.
Example of Ecological isolation White and
yellow ladys slippers
Cypripedium candidum
Cypripedium calceolus
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  3.     Floral isolation Flower adaptations to
attract different pollinators           a. 
Behavioral- Influences behavior of pollinators
that can distinguish floral signals
(e.g., color, shape, fragrance). Some
pollinators exhibit floral constancy, or
limitation to one species of flower
even though flowers of other species
are available.
Example Bees exhibit floral constancy in two
closely-related species of Ophrys in he
Mediterranean region.
Ophrys fusca
Ophrys scolopax
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•  
• Structural- Pollination is dependent on
  structure of the flower.
• Example Asclepias flowers

Asclepias flower
pollinia
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4.     Self-fertilization Outcrossing shifts to
self-fertilization (selfing).
Self-incompatibility changes to
self-compatibility. Some species have
cleistogamous flowers, in which self-
pollination occurs in unopened flowers, and no
cross-pollination occurs at
all.   Example Some subpopulations of grass
species that have developed a tolerance for heavy
metals around mines have self-fertilization, that
reduces cross-pollination with other,
non-tolerant individuals.
  5.     Incompatibility  
a.  Pollen-pistil- If pollen from one species
reaches the stigma of another species, the
stigma and style often will prevent germination
and/or growth of the foreign pollen tube to the
ovule.   b.  Seed- Even if a hybrid
embryo forms, it may not develop fully,
due to incompatibility between the parental
genomes, or incompatibility between the embryo
and the maternal endosperm.
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• 6.     Hybrid inviability If a hybrid is
  inviable, it will not reach
• reproductive maturity. Another cause of
  hybrid inviability is
• ecological isolation.
•  
• Hybrid floral isolation If two species that
  hybridize have very
• different pollinators, flowers of the
  hybrids may have no effective pollinators.

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  8. Hybrid sterility Although hybrid
plants reach reproductive maturity, they are
sterile, because parental chromosomes from the
two original species cannot pair during meiosis,
and nonfunctional gametes are formed.
BB
AA
Diploid plant
Diploid plant
Meiosis
Gametes
B
A
Sterile hybrid
AB
  9. Hybrid breakdown- Hybrid plants are
vigorous and fertile, but later generations are
either inviable or sterile.
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• Origins of Reproductive Isolating Barriers
• Hybridization- Most often means matings between
  different species. May reduce diversity by
  merging species, or may lead to formation of new
  species.
•  
• Often associated with habitat disturbance.
•  
• Example White and yellow lady's slippers, that
  usually do not hybridize due to ecological
  isolation. In Lake County, IN near Gary, many
  hybrids of the two species have been found after
  controlled burning.
•  
• Very prevalent among plants- an estimated
  70,000 naturally-
• occurring, interspecific plant hybrids exist
  worldwide.

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Evolutionary Consequences of Hybridization 1.
Reinforcement of reproductive isolating
mechanisms. An example of this is character
displacement, in which characters of two species
are more divergent when the species are sympatric
(share the same range) than when they are
allopatric (do not share the same range).
Example Phlox drummondii and Phlox cuspidata in
Texas
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  2.  Formation of a hybrid swarm through
reproduction of hybrids at a site- A hybrid
swarm occurs as a result of hybrids of two
species backcrossing with both parental species
at a site. Sometimes called local
introgression.   3. Introgression, or transfer of
genetic material from one species to another
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  4.     Increase in genetic diversity and
adaptation   5.     Evolution of new
species   Sometimes a new diploid hybrid species
is produced. More often, however, allopolyploid
speciation occurs.
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BB
AA
Allopolyploid speciation- Two species first
hybridize. Polyploidy (adding one or more sets
of chromosomes) then occurs in the hybrid
offspring. The hybrids are interfertile amongst
themselves, but no longer able to form viable
gametes with the parental species. A new species
is formed.
Diploid plant
Diploid plant
Meiosis
Gametes
B
A
Sterile hybrid
AB
Fertile polyloid
AABB
AB
Gamete
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•  
• Breeding Systems uniparental reproduction can
  lead to
• higher numbers of species (higher
  diversity)
•  
•   Biparental- Most common breeding system.
•   Self-fertilization- Populations with
  self-fertilization tend to have less genetic
  variability (lower heterozygosity) and more
  variation between populations than those with
  biparental reproduction.
• Agamospermy- Egg becomes an embryo without
  fertilization. Especially common in Asteraceae,
  Poaceae and Rosaceae.

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Species Concepts   The Biological Species
Concept (BSC) is the most traditional species
concept, used mostly for delineating species of
animals. According to the BSC, a species is a
group of interbreeding individuals, and
speciation is primarily allopatric.   This
concept does not work very well for plants,
because interbreeding, or gene flow, varies
widely among plant groups. Reproductive
communities range from one or a few individuals
(in selfing or clonal plants) to very large
hybridizing assemblages.
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Other species concepts sometimes used for
plants   -  Recognition Gene flow maintains
similarity among individuals in a species. Does
not work for species such as giant reed
(Phragmites australis), with individuals very
similar that are found on different
continents.   -  Phenetic Members of the same
species are similar, and there is a gap in
similarity between species.   -  Evolutionary
Members of a species share an evolutionary
lineage.   -  Autapomorphy Species are
monophyletic groups.   -  Diagnosability Member
of a species share a unique combination of fixed
character states. -  Geneological Members of
the same species are closer genetically than
members of different species.    No consensus
exists on which species concept to use for
plants.