Getting to the Roots of Plant Evolution Genomics and

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					    Getting to the Roots of Plant Evolution:
 Genomics and the Reconstruction of the Tree of

                                     Life




Sponsored by the National Science Foundation, the Deep Gene Research Coordination
               Group, CIPRES, and the Jepson Herbarium, UC Berkeley.
                            Introduction to the Green Plants

Land plants first appeared in the Ordovician
(~460 million years ago) but did not begin to
resemble modern plants until the Late
Silurian. By the close of the Devonian, about
360 million years ago, there were a wide
variety of shapes and sizes of plants,
including tiny creeping plants and tall forest
trees. Today, with more than 250,000
species, they are second in size only to the
insects.

We now know that plants, like all living
organisms, had aquatic ancestors. A
specific group of freshwater green algae are
the closest relatives to the land plants. The
story of plant evolution is therefore
inseparably linked with their progressive
occupation of the land and their increasing
independence from water for reproduction.




                                                 1. A comparison of conditions faced by algae and plants
      The origin of terrestrial plants from their aquatic ancestors

How did plants colonize land? What obstacles did they have to overcome? How did
  they cope, and eventually thrive in their new terrestrial environment? What were
 some of the key innovations that led to the diversification of the land plants? The
 land plants evolved slowly, and in stages. The fossil record chronicles four major

                            periods of plant evolution.



                   The first major period of plant evolution:
                             Plants move onto land

 The figure on the previous page provides a comparison of aquatic and terrestrial
environments. By understanding the differences, we can begin to think about some
       of the challenges faced by plants as they transitioned to life on land.
                             Introduction to the Green Algae


The Charophyceae, a group of fresh water green
algae, are the closest relatives to the land plants.
Like the land plants, green algae contain two
forms of chlorophyll (a and b), which they use to
capture light energy to make sugars that are
stored as starch inside plastids (specialized
organelles). Green algae differ from plants in
many ways. Because they live in the water, they
don't have a specialized transport or support
systems. Their bodies are supported by the water,
and almost all of the cells photosynthesize and
have access to the nutrients present in the water.
Therefore, transport of nutrients is not necessary.
Even though they photosynthesize, green algae
do not have true leaves (which are characterized
by the presence of vascular tissue). Additionally,
green algae lack cuticles (a waxy layer on the
outer wall of epidermal cells) and stomata
(specialized cells for gas exchange).
                                                       2. Chara, a green alga. The gametophyte is the
                                                       dominant life stage.
                        Early land plants

  The early land plants, represented today by the bryophytes
(mosses, liverworts, and hornworts), possessed two important
features that allowed them to live on land: 1) a waxy cuticle to
protect against desiccation (drying out) and 2) protection of gametes
and embryos in a protective jacket made of cells.

  Even with these adaptations, early land plants were still closely tied
to water, even if only in small amounts such as morning dew. They
had swimming sperm and required water to complete their life cycle.
Early land plants also lacked true vascular tissue to carry water from
the soil to the aerial parts of the plant. Water was imbibed as it
moved over the plant body (like a sponge) and distributed by
relatively slow processes like diffusion. This mode of hydration helps
explain why damp, shady places are the most common habitats for

the modern descendants of early land plants, the bryophytes.
                            Introduction to the Bryophyta

                      (The mosses, liverworts and hornworts)
   After flowering plants and ferns,
mosses are the most diverse group of
plants, with more than 10,000 species
in 700 genera. This makes mosses
almost twice as diverse as mammals.
Despite their diversity, bryophytes don't
receive as much attention as flowering
plants, ferns, or conifers because most
bryophytes are small and
inconspicuous. They have no vascular
tissue (no true xylem or phloem) to
lend them structural support, nor do
they have true leaves or showy
flowers. This does not mean that
bryophytes are not important; mosses
in particular, play important roles in
reducing erosion along streams, water
and nutrient cycling in tropical forests,   3. A moss.         4. A liverwort.
and insulating the arctic permafrost.
                       Introduction to the Bryophyta, continued

  The earliest land plants were probably very similar to modern-day bryophytes. In
bryophytes, the gametophytes are nutritionally independent of the sporophytes and
the sporophytes are either completely or partially dependent on the gametophytes.
Sperm are free swimming and require water to reach the egg. One key difference
between the mosses, hornworts, and liverworts is that liverworts have pores on their
surface but lack stomata. Mosses and hornworts (and all other land plants) have
stomata.


                                                              Interesting note: Some
                                                              mosses have water
                                                              conducting tubes, but it is
                                                              not yet resolved what the
                                                              origin of those structures
                                                              are. So, for now, we refer
                                                              to mosses as
                                                              nonvascular plants.
  5. (left) pore on surface of a liverwort
     (right) stomate on land plant leaf
                            The second major period of plant evolution:
                                 The diversification of vascular plants
 Relatively early in the history of plants, the evolution of efficient fluid-conducting systems, consisting of xylem and phloem,
 solved the problem of water and food transport throughout the plant body. The ability to synthesize lignin (a plant polymer),
 which is incorporated into the cell wall of supporting and water conducting cells, was also a pivotal step in the evolution of
 plants. Lignin adds rigidity to cell walls, making it possible for vascularized plants to reach great heights. The shoot system of
 plants (stems and leaves) was well suited to the demands of life on land - namely, the acquisition of energy from the sun and
 carbon dioxide from the atmosphere.

 The reproductive systems of plants were also changing. The gametophytic stage remained free-living, requiring water for
 fertilization, but over time, the gametophytic generation underwent a progressive reduction in size - the sporophyte phase
 became the dominant phase of the life cycle. The earliest vascular plants lacked seeds, a condition still represented by ferns
 (and a few other groups not discussed here). Therefore, the second major lineage of land plants to evolve is referred to as
 the seedless, vascular plants.

 Seedless vascular plants dominated the landscape in shallow
 swamp like forests of the Carboniferous period about 300-350
 mya. Dead plants did not completely decay in the stagnant
 water, and organic rubble (called peat) accumulated. The
 swamps were later covered by the sea, and marine sediments
 piled on top of the peat. Heat and pressure gradually converted
 the peat to coal, thus the name of the geologic period
 (Carboniferous). Four divisions of seedless vascular plants are
 represented in the modern flora; Psilophyta (Psilotum),
 Lycophyta (lycopods), Sphenophyta (horsetails), and
 Pterophyta (ferns).



Interesting note: Seedless vascular plants grew along side
primitive seed plants but the seed plants were not dominant at
                                                                      6. Reconstruction of a Carbiniferous swamp (the coal age)
that time. The seed plant rose to prominence only after the
swamps began to dry up at the end of the Carboniferous.
                                         Introduction to the Lycophyta
                                         (Club mosses and scale trees)

                                The lycophytes are a small and inconspicuous group of plants today, but in the
                             Carboniferous some lycophytes were forest-forming trees more than 35 meters tall.
                             Lycophytes are the oldest extant group of vascular plants, and they dominated major
                             habitats for 40 million years.
                                The club mosses (Lycopodiales) are usually evergreen, and have been used as
                             Christmas decorations, though their flammable spores and increasing rarity has made
                             this illegal in some states. Other lycophytes, such as Selaginella, may form extensive
                             carpets in the understory of wet tropical forests.

7. Lycopodium, a lycophyte
with microphylls

The most significant feature of lycophytes is the
microphyll, a kind of leaf that has arisen and
evolved independently from the leaves of other
vascular plants (megaphylls). The microphyll
has only a single unbranched strand of vascular
tissue (xylem and phloem), whereas
megaphylls have multiple veins, usually
branching one or more times within the leaf.
According to one widely accepted theory
(diagrammed below), microphylls evolved as
outgrowths, called enations, of the main axis of
the plant. Megaphylls evolved by fusion of
branch systems. Microphylls cover the
sporophyte, the dominant life phase in
Lycophytes.
                                                                  8. Evolution of microphylls (showing enations) and megaphylls.
                                      Introduction to the Pterophyta

                                                 (The ferns)

                                   Even though ferns have free living gametophytes, the sporophyte
                                   is the dominant phase of the fern life cycle. Ferns produce spores
                                   (not seeds) that are borne on megaphylls (often called fronds). The
                                   pattern of spore distribution is often an important taxonomic
                                   character.




9. Fiddle head of new fern frond

The ferns are an ancient lineage of plants, dating back to
at least the Devonian. Today, there are approximately
11,000 species of ferns; they are the second largest group
of plants and are the most diverse in both form and habit.
Only about 380 species of ferns occur in the United States,
most of the diversity is found in tropical areas.
Approximately 1/3 of all species of tropical ferns grow on
the trunks or branches of trees as epiphytes.                          10. Spores on the back of a fern frond
             The third major period of plant evolution:
                       The origin of the seed

   The seed, a specialized unit of reproduction, advanced the colonization of
land by further providing a food source for the plant embryo and protecting it
from harsh conditions. Seeds are also an important unit of dispersal
(replacing the spore as the stage of the life cycle that disperses offspring).
The seeds of gymnosperms are not enclosed in any special chambers (or
ovary, as they are in the flowering plants); the name gymnosperm means,
literally, “naked seed”.

  The gametophytes of seed plants became even more reduced than
the gametophytes of ferns and other vascular plants. The reduction of
the gametophyte set the stage for another major innovation - pollination.
Pollination replaced swimming as the mechanism for delivering sperm (in
the male gametophyte) to the egg (on the female gametophyte). Water
was no longer needed to disseminate sperm cells. Wind, insects, or other
animals could do the job. This became increasingly important because as
the gymnosperms diversified, the climate was becoming drier.
                               Introduction to the Gymnosperms
                                     The gymnosperms descended from a group of Devonian plants, the
                                     progymnosperms. They coexisted with the bryophytes, ferns, and other
                                     seedless vascular plants, but their adaptive radiation occurred during
                                     the Carboniferous and early Permian when the climate became warmer
                                     and drier. The gymnosperms formed vast forests that dominated the
                                     landscape for more than 200 million years.


                                     There are four divisions of gymnosperms; Cycadophyta (the cycads),
                                     Ginkgophyta (Ginkgo), Gnetophyta, and Coniferophyta (the conifers).
                                     The largest division, the conifers, are almost all large trees, and include
                                     pines, firs, spruce, junipers, and redwoods. Although there are only
                                     about 550 species, conifers dominate vast forested regions of the
11. A pine with female cones
                                     Northern Hemisphere.

The pine tree, a representative gymnosperm, is a sporophyte. The
gametophyte generation develops from spores that are produced in              Interesting note: The bluish-
male and female cones. The pollen (male gametophyte) is transferred to        white structures of the juniper
the ovule (female gametophyte) via wind. After fertilization, the seed        are often referred to as
begins to develop. The entire process, from cone production to seed           "juniper berries." Berries are a
production, can take up to three years.                                       type of fruit and because fruit
                                                                              develops from the ovary of a
All gymnosperm leaves, including the needle like leaves of conifers, are      flower, angiosperms are the
megaphylls. Most gymnosperms are evergreen but some, like Ginkgo,             only plants that have fruit.
are deciduous. We get most of lumber and paper pulp from the wood of
conifers. What we call wood is actually an accumulation of lignified
xylem tissue. Tracheids, special conducting cells, are the primary
components of xylem in gymnosperms.
                The fourth major episode in the evolutionary history of plants:
                                The emergence of the flower

The angiosperms arose during the early Cretaceous period about 130 mya. The main feature that led to their success was the
evolution of flowers and fruits. The flower is a complex reproductive structure that bears seeds within protective chambers
called ovaries. The presence of the ovary is one of the major differences between angiosperms (the flowering plants) and the
gymnosperms (the naked seed plants). The ovary develops into the fruit, which is an important structure for seed dispersal.
Flowers also allow for specialized pollination by attracting and rewarding pollinators.


Vascular tissue also became more refined during angiosperm evolution.
Vessel elements, present in almost all angiosperms, are shorter and wider
than trachieds (the xylem tissue in ferns and gymnosperms), and allow
for more efficient water transport. Leaves (megaphylls) also became
more diverse and specialized. While these changes in the plant body were
important, it was really the evolution of the flower that contributed most
significantly to the success of the angiosperms.



                                                                             12. The parts of a flower
                                     Today, the flowering plants are by far the most diverse and geographically widespread of all
                                     plants. They are important in many ways above and beyond their aesthetic appeal. Not a
                                     day goes by in which our lives are not affected by a flowering plant. Nearly all of our food
                                     comes from flowering plants; grains, beans, nuts, fruits, vegetables, herbs, and spices
                                     almost entirely come from plants with flowers, as do tea, coffee, chocolate, wine, beer,
                                     tequila, and cola. Much of our clothing comes from them as well; cotton and linen are made
                                     from "fibers" of flowering plants, as are rope and burlap, and many commercial dyes are
                                     extracted from other flowering plants. We owe flowering plants credit for a large number of
                                     our drugs, including over-the-counter medicines such as aspirin and prescribed drugs such
                                     as digitalis and atropine.



13. A bee pollinating a flower
              Getting to the Roots of Plant Evolution - Exercises

Now that you know all about the characteristics of plants and how they made their move from fresh water
to land, you can use this knowledge to reconstruct the evolutionary relationships of some plant groups
that are alive today.

In addition to the morphological characteristics, such as the cuticle and seeds, there are other types of
characters, present in the genomes of plants, that can also help us understand their evolutionary
relationships. While molecular characters such as these used to be very difficult to obtain, recent
advances in fast, high volume DNA sequencing has made it possible to get large amounts of genetic
sequence data. One useful source of this sort of data is the circular genome of the plant chloroplast,
because it is smaller, more easily sequenced, and as a plant organelle (having been derived from a
bacterial endosymbiont) its genome does not undergo recombination (like nuclear DNA). This makes
reconstructing evolutionary relationships much less complicated, because each genetic trait in the
chloroplast can be traced directly back (in time) through a lineage of mothers and daughters.

On the next page, you’ll find a selection of schematics representing various chloroplast genomes and
their arrangements for several groups of plants. These representations of the chloroplast genome show
the positions of several genes (A-E) as well as the position of a distinctive region known as the inverted
repeat. Genome-level characters such as gene position and structural rearrangements are very useful
for reconstructing deep evolutionary relationships, because they are believed to occur fairly infrequently.
It is unlikely that two groups of plants would have the same unique gene rearrangement due to chance
alone.

With this genomic information and all you learned about land plants in the previous section,
please do the following:
(1) fill in the land plant data matrix,
(2) construct a cladogram,
(3) answer the discussion questions.
                    Phylogenetic Analysis of the Green Plants
                                  Data Matrix

              1.        2.         3.        4.           5.           6.            7.           8.        9.
              inv.      inv.       cuticle   stomata      xylem &      megaphyll     sporophyte   seed      flower
              repeat    gene       absent    absent (0)   phloem       absent (0)    domin.       absent    absent (0)
              absent    position   (0)       present      absent (0)   present (1)   no (0)       (0)       present (1)
              (0)       no (0)     present   (1)          present                    yes (1)      present
              present   yes (1)    (1)                    (1)                                     (1)
              (1)
Green algae
(outgroup)

Liverworts


Mosses


Lycophytes


Ferns


Gymnosperms


Angiosperms
                                     Questions for discussion

1) Contrast a seed plant to an alga in terms of adaptation for life on land versus water.

2) What evidence is there to support a charophyte ancestry for plants?

3) Bryophytes and vascular plants share a number of characteristics that distinguish them from
charophytes and that adapt them for existence on land. What are those characteristics?

4) What is coal? How was it formed? What plants were involved in its formation?

5) What is a seed, and why was the evolution of the seed such an important innovation for plants?

6) How do the mechanisms by which sperm reach the egg differ between gymnosperms and seedless
vascular plants?

7) Why was the flower such an important innovation?

8) What role do insects, animals and wind play in plant reproduction?
                        Acknowledgments


Biology of Plants. P. H. Raven, R. F. Evert, and S. E. Eichorn. W.
   H. Freeman and Company, New York, New York.

Biology. N. A. Campbell. The Benjamin/Cummings Publishing
   Company, Inc. Menlo Park, California.

Introductory Plant Biology. K. R. Stern. Wm. C. Brown
    Communications, Inc. Dubuque, Iowa.

The Museum of Paleontology, UC Berkeley.
  http://www.ucmp.berkeley.edu/