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Plant Evo-devo (Plant Evolutionary Development)

 
     
 

Evolutionary developmental biology (evo-devo) refers to the study of developmental programs and patterns from an evolutionary perspective. It seeks to understand the various influences shaping the form and nature of life on the planet. Evo-devo arose as a separate branch of science only in the last decade. Most of the synthesis in evo-devo has been in the field of animal evolution, one reason being the presence of elegant model systems like Drosophila, C.elegans, Zebrafish and Xenopus. However, in the past couple of decades, a wealth of information on plant morphology, coupled with modern molecular techniques has helped shed light on the conserved and unique developmental patterns in the plant kingdom also.


  Plants diversity
Contents

Historical perspective

 

Before 1900

 

1900 to the present

Organisms, databases and tools

Evolution of plant morphology

 

Overview of plant evolution

 

Evolution of meristems

 

 

Diversity in meristem architectures

 

 

Role of the KNOX-family genes

 

 

Evolution of the meristem architecture

 

Evolution of leaves

 

 

Origins of the leaf

 

 

Factors influencing leaf architectures

 

 

Genetic evidences for leaf evolution

 

Evolution of flowers

 

 

Origins of the flower

 

 

Evolution of the MADS-box family

 

 

Factors influencing floral diversity

 

 

Flowering time

 

 

Theories of flower evolution

 

Evolution of secondary metabolism

Mechanisms and players in evolution

See also

References



Historical perspective
Before 1900
Johann Wolfgang von Goethe  

The origin of the term "morphology" is generally attributed to Johann Wolfgang von Goethe. He was of the opinion that there is an underlying fundamental organisation (Bauplan) in the diversity of flowering plants. In his book titled The Metamorphosis of Plants, he proposed that the Bauplan enabled us to predict the forms of plants that had not yet been discovered. Goethe also was the first to make the perceptive suggestion that flowers consist of modified leaves.

In the middle centuries, several basic foundations of our current understanding of plant morphology were laid down. Nehemiah Grew, Marcello Malpighi, Robert Hooke, Antonie van Leeuwenhoek, Wilhelm von Nageli were just some of the people who helped build knowledge on plant morphology at various levels of organisation. It was the taxonomical classification of Carolus Linnaeus in the eighteenth century though, that generated a firm base for the knowledge to stand on and expand. The introduction of the concept of Darwinism in contemporary scientific discourse also had had an effect on the thinking on plant forms and their evolution.

Johann Wolfgang von Goethe
 

Wilhelm Hofmeister, one of the most brilliant botanists of his times, was the one to diverge away from the idealist way of pursuing botany. Over the course of his life, he brought an interdisciplinary outlook into botanical thinking. He came up with biophysical explanations on phenomena like phototaxis and geotaxis, and also discovered the alternation of generations in the plant life cycle.

1900 to the present

The past century witnessed a rapid progress in the study of plant anatomy. The focus shifted from the population level to more reductionist levels. While the first half of the century saw expansion in developmental knowledge at the tissue and the organ level, in the latter half, especially since the 1990s, there has also been a strong impetus on gaining molecular information.

Edward Charles Jeffrey was one of the early evo devo researchers of the 20th century. He performed a comparative analyses of the vasculatures of living and fossil Gymnosperms and came to the conclusion that the storage parenchyma has been derived from tracheids. His research focussed primarily on plant anatomy in the context of phylogeny. This tradition of evolutionary analyses of plant architectures was further advanced by Katherine Esau, best known for her book The Plant Anatomy. Her work focussed on the origin and development of various tissues in different plants. Working with Cheadle, she also explained the evolutionary specialization of the phloem tissue with respect to its function.

In the meantime, by the beginning of the latter half of 1900s, Arabidopsis thaliana had begun to be used in some developmental studies. The first collection of Arabidopsis thaliana mutants were made around 1945. However it formally became established as a model organism only in 1998.

  Arabidopsis thaliana. This flowering plant has been a model system for most of plant molecular studies
 
Arabidopsis thaliana. This flowering plant has been a model system for most of plant molecular studies


The recent spurt in information on various plant-related processes has largely been a result of the revolution in molecular biology. Powerful techniques like mutagenesis and complementation were made possible in Arabidopsis via generation of T-DNA containing mutant lines, recombinant plasmids, techniques like Transposon Tagging etc. Availability of complete physical and genetic maps, RNAi vectors, rapid transformation protocols are some of the technologies that have significantly altered the scope of the field. Recently, there has also been a massive increase in the genome and EST sequences of various non-model species, which, coupled with the Bioinformatics tools existing today, generate interesting opportunities in the field of plant evo devo research.


Organisms, databases and tools
The sampling of the Floral Genome Project  

The most important model systems in plant development have been Arabidopsis and Maize. Maize has traditionally been the favorite of plant geneticists, while extensive resources in almost every area of plant physiology and development are available for Arabidopsis. Apart from these, Rice, Antirrhinum, Brassica, Tomato are also being used in a variety of studies. The genomes of Arabidopsis and Rice have been completely sequenced, while the others are in process.. It must be emphasized here that the information from these "model" organisms form the basis of our developmental knowledge. While Brassica has been used primarily because of its convenient location in the phylogenetic tree in the mustard family, Antirrhinum is a convenient system for studying leaf architecture. Rice has been traditionally used for studying responses to hormones like abscissic acid and gibberelin as well as responses to stress. However, recently, not just the domesticated rice strain, but also the wild strains have been studied for their underlying genetic architectures.

The sampling of the Floral Genome Project
 

Some people have objected against extending the results of model organisms to the plant world.


One argument is that the effect of gene knockouts in lab conditions wouldn't truly reflect even the same plant's response in the natural world. Also, these supposedly crucial genes might not be responsible for the evolutionary origin of that character. For these reasons, a comparative study of plant traits has been proposed as the way to go now.

Since the past few years, researchers have indeed begun looking at non-model, "non-conventional" organisms using modern genetic tools. One example of this is the Floral Genome Project, which envisages to study the evolution of the current patterns in the genetic architecture of the flower through comparative genetic analyses, with a focus on EST sequences. Like the FGP, there are several such ongoing projects that aim to find out conserved and diverse patterns in evolution of the plant shape. Expressed sequence tag (EST) sequences of quite a few non-model plants like Sugarcane, Apple, Lotus, Barley, Cycas, Coffee, to name a few, are available freely online. The Cycad Genomics Project, for example, aims to understand the differences in structure and function of genes between gymnosperms and angiosperms through sampling in the order Cycadales. In the process, it intends to make available information for the study of evolution of structures like seeds, cones and evolution of life cycle patterns. Presently the most important sequenced genomes from an evo-devo point of view include those of A.thaliana (a flowering plant), Poplar (a woody plant), Physcomitrella patens (a bryophyte), Maize (extensive genetic information), and Chlamydomonas reinhardtii (a green alga). The impact of such a vast amount of information on understanding common underlying developmental mechanisms can easily be realised.

Apart from EST and genome sequences, several other tools like PCR, Yeast two hybrid system, microarrays, RNA Interference, SAGE, QTL mapping etc. permit the rapid study of plant developmental patterns. Recently, cross-species hybridization has begun to be employed on microarray chips, to study the conservation and divergence in mRNA expression patterns between closely related species. Techniques for analyzing this kind of data have also progressed over the past decade. We now have better models for molecular evolution, more refined analysis algorithms and better computing power as a result of advances in computer sciences.


Evolution of plant morphology
Overview of plant evolution

Evidence suggests that an algal scum formed on the land 1,200 million years ago, but it was not until the Ordovician period, around 500 million years ago, that land plants appeared. These begun to diversify in the late Silurian period, around 420 million years ago, and the fruits of their diversification are displayed in remarkable detail in an early Devonian fossil assemblage known as the Rhynie chert. This chert preserved early plants in cellular detail, petrified in volcanic springs. By the middle of the Devonian period most of the features recognised in plants today are present, including roots, leaves and seeds. By the late Devonian, plants had reached a degree of sophistication that allowed them to form forests of tall trees. Evolutionary innovation continued after the Devonian period. Most plant groups were relatively unscathed by the Permo-Triassic extinction event, although the structures of communities changed. This may have set the scene for the evolution of flowering plants in the Triassic (~200 million years ago), which exploded the Cretaceous and Tertiary. The latest major group of plants to evolve were the grasses, which became important in the mid Tertiary, from around 40 million years ago. The grasses, as well as many other groups, evolved new mechanisms of metabolism to survive the low CO2 and warm, dry conditions of the tropics over the last 10 million years.


Evolution of meristems
The meristematic cells give rise to various organs of the plant, and keep the plant growing. The Shoot Apical Meristem (SAM) gives rise to organs like the leaves and flowers. The cells of the apical meristems - SAM and RAM (Root Apical Meristem)- divide rapidly and are considered to be indeterminate, in that they do not possess any defined end fate. In that sense, the meristematic cells are frequently compared to the stem cells in animals, that have an analogous behavior and function.

Diversity in meristem architectures
Is the mechanism of being indeterminate conserved in the SAM's of the plant world? The SAM contains a population of stem cells that also produce the lateral meristems while the stem elongates. It turns out that the mechanism of regulation of the stem cell number might indeed be evolutionarily conserved. The CLAVATA gene CLV2 responsible for maintaining the stem cell population in Arabidopsis is very closely related to the Maize gene FASCIATED EAR 2(FEA2) also involved in the same function. Similarly, in Rice, the FON1-FON2 system seems to bear a close relationship with the CLV signaling system in Arabidopsis. These studies suggest that the regulation of stem cell number, identity and differentiation might be an evolutionarily conserved mechanism in monocots, if not in angiosperms. Rice also contains another genetic system distinct from FON1-FON2, that is involved in regulating stem cell number. This example underlines the innovation that goes about in the living world all the time.

Role of the KNOX-family genes

Genetic screens have identified genes belonging to the KNOX family in this function. These genes essentially maintain the stem cells in an undifferentiated state. The KNOX family has undergone quite a bit of evolutionary diversification, while keeping the overall mechanism more or less similar. Members of the KNOX family have been found in plants as diverse as Arabidopsis, rice, barley and tomato. KNOX-like genes are also present in some algae, mosses, ferns and gymnosperms. Misexpression of these genes leads to formation of interesting morphological features. For example, among members of Antirrhinae, only the species of genus Antirrhinum lack a structure called spur in the floral region. A spur is considered an evolutionary innovation because it defines pollinator specificity and attraction. Researchers carried out transposon mutagenesis in Antirrhinum, and saw that some insertions led to formation of spurs that were very similar to the other members of Antirrhinae, indicating that the loss of spur in wild Antirrhinum populations could probably be an evolutionary innovation.

The KNOX family has also been implicated in leaf shape evolution (See below for a more detailed discussion). One study looked at the pattern of KNOX gene expression in A.thaliana, that has simple leaves and Cardamine hirsuta, a plant having complex leaves. In A.thaliana, the KNOX genes are completely turned off in leaves, but in C.hirsuta, the expression continued, generating complex leaves. Also, it has been proposed that the mechanism of KNOX gene action is conserved across all vascular plants, because there is a tight correlation between KNOX expression and a complex leaf morphology.

Evolution of the meristem architecture
The meristem architectures do differ between angiosperms, gymnosperms and pteridophytes. The gymnosperm vegetative meristem lacks organization into distinct tunica and corpus layers. They possess large cells called Central Mother Cells in the meristem. In angiosperms, the outermost layer of cells divides anticlinally to generate the new cells, while in gymnosperms, the plane of division in the meristem differs for different cells. However, the apical cells do contain organelles like large vacuoles and starch grains, like the angiosperm meristematic cells.
  Complex leaves of C.hirsuta are a result of KNOX gene expression
 
Complex leaves of C.hirsuta are a result of KNOX gene expression
   
  Note the long spur of the above flower. Spurs attract pollinators and confer pollinator specificity. (Flower:Linaria dalmatica)
 
Note the long spur of the above flower. Spurs attract pollinators and confer pollinator specificity. (Flower:Linaria dalmatica)

Pteridophytes, like fern, on the other hand, do not possess a multicellular apical meristem. They possess a tetrahedral apical cell, which goes on to form the plant body. Any somatic mutation in this cell can lead to hereditary transmission of that mutation.

The earliest meristem-like organization is seen in an algal organism from group Charales that has a single dividing cell at the tip, much like the pteridophytes, yet more simpler. One can thus see a clear pattern in evolution of the meristematic tissue, from pteridophytes to angiosperms. Pteridophytes, with a single meristematic cell; gymnosperms with a multicellular, but less defined organization and finally, angiosperms, with the highest degree of organization. The genetic innovations that contributed to this evolution are yet not clearly known.


Evolution of leaves
For a discussion on Evolution of Photosynthesis, see Photosynthesis.

Origins of the leaf

Leaves are the primary photosynthetic organs of a plant. Based on their structure, they are classified into two types - microphylls, that lack complex venation patterns and megaphylls, that are large and with a complex venation. It has been proposed that these structures arose independently. Megaphylls, according to the Telome hypothesis, have evolved from plants that showed a three dimensional branching architecture, through three transformations - planation, which involved formation of a planar architecture, webbing, or formation of the outgrowths between the planar branches and fusion, where these webbed outgrowths fused to form a proper leaf lamina. Studies have revealed that these three steps happened multiple times in the evolution of today's leaves.

It has been proposed that the before the evolution of leaves, plants had the photosynthetic apparatus on the stems. Today's megaphyll leaves probably became commonplace some 360mya, about 40my after the simple leafless plants had colonized the land in the early Devonian period.

 
A leaf with laminar structure and pinnate venation
 
Leaf lamina. The leaf architecture probably arose multiple times in the plant lineage
 


This spread has been linked to the fall in the atmospheric carbon dioxide concentrations in the Late Paleozoic era associated with a rise in density of stomata on leaf surface. This must have allowed for better transpiration rates and gas exchange. Large leaves with less stomata would have gotten heated up in the sun's heat, but an increased stomatal density allowed for a better-cooled leaf, thus making its spread feasible.


Spiny leaves of Aciphylla squarrosa. It is thought that these leaves evolved as an adaptation against the now extinct Moas  
Factors influencing leaf architectures
Various physical and physiological forces like light intensity, humidity, temperature, wind speeds etc. are thought to have influenced evolution of leaf shape and size. It is observed that high trees rarely have large leaves, owing to the obstruction they generate for winds. This obstruction can eventually lead to the tearing of leaves, if they are large. Similarly, trees that grow in temperate or taiga regions have pointed leaves, presumably to prevent nucleation of ice onto the leaf surface and reduce water loss due to transpiration. Herbivory, not only by large mammals, but also small insects has been implicated as a driving force in leaf evolution, an example being plants of the genus Aciphylla, that are commonly found in New Zealand. The now extinct Moas fed upon these plants, and its seen that the leaves have spines on their bodies, which probably functioned to discourage the moas from feeding on them. Other members of Aciphylla that did not co-exist with the moas, do not have these spines.
Spiny leaves of Aciphylla squarrosa. It is thought that these leaves evolved as an adaptation against the now extinct Moas
 

Genetic evidences for leaf evolution
At the genetic level, developmental studies have shown that repression of the KNOX genes is required for initiation of the leaf primordium. This is brought about by ARP genes, which encode transcription factors. Genes of this type have been found in many plants studied till now, and the mechanism i.e. repression of KNOX genes in leaf primordia, seems to be quite conserved. Interestingly, expression of KNOX genes in leaves produces complex leaves. It is speculated that the ARP function arose quite early in vascular plant evolution, because members of the primitive group Lycophytes also have a functionally similar gene. Other players that have a conserved role in defining leaf primordia are the phytohormone auxin, gibberelin and cytokinin.


One interesting feature of a plant is its phyllotaxy. The arrangement of leaves on the plant body is such that the plant can maximally harvest light under the given constraints, and hence, one might expect the trait to be genetically robust. However, it may not be so. In maize, a mutation in only one gene called abphyl (ABNORMAL PHYLLOTAXY) was enough to change the phyllotaxy of the leaves. It implies that sometimes, mutational tweaking of a single locus on the genome is enough to generate diversity. The abphyl gene was later on shown to encode a cytokinin response regulator protein.

Once the leaf primordial cells are established from the SAM cells, the new axes for leaf growth are defined, one important (and more studied) among them being the abaxial-adaxial (lower-upper surface) axes. The genes involved in defining this, and the other axes seem to be more or less conserved among higher plants. Proteins of the HD-ZIPIII family have been implicated in defining the adaxial identity. These proteins deviate some cells in the leaf primordium from the default abaxial state, and make them adaxial. It is believed that in early plants with leaves, the leaves just had one type of surface - the abaxial one. This is the underside of today's leaves. The definition of the adaxial identity occurred some 200 million years after the abaxial identity was established. One can thus imagine the early leaves as an intermediate stage in evolution of today's leaves, having just arisen from spiny stem-like outgrowths of their leafless ancestors, covered with stomata all over, and not optimized as much for light harvesting.

  The diversity of leaves
 
The diversity of leaves
 

How the infinite variety of plant leaves is generated is a subject of intense research. Some common themes have emerged. One of the most significant is the involvement of KNOX genes in generating compound leaves, as in tomato. But this again is not universal.

For example, pea uses a different mechanism for doing the same thing. Mutations in genes affecting leaf curvature can also change leaf form, by changing the leaf from flat, to a crinky shape, like the shape of cabbage leaves. There also exist different morphogen gradients in a developing leaf which define the leaf's axis. Changes in these morphogen gradients may also affect the leaf form. Another very important class of regulators of leaf development are the microRNAs, whose role in this process has just begun to be documented. The coming years should see a rapid development in comparative studies on leaf development, with many EST sequences involved in the process coming online.

Evolution of flowers
For a more ecological discussion on the evolution of flowers, go to Flower or Evolutionary history of plants

A flower is, arguably, one of the most beautiful products of evolution. Flower-like structures first appear in the fossil records some ~130 mya, in the Cretaceous era.

The flowering plants have long been assumed to have evolved from within the gymnosperms; according to the traditional morphological view, they are closely allied to the gnetales. However, recent molecular evidence is at odds to this hypothesis, and further suggests that gnetales are more closely related to some gymnosperm groups than angiosperms, and that gymnosperms form a distinct clade to the angiosperms. Molecular clock analysis predicts the divergence of flowering plants (anthophytes) and gymnosperms to ~300 mya.

  The pollen bearing organs of the early flower Crossotheca
 
The pollen bearing organs of the early flower Crossotheca


Phylogeny of anthophytes and gymnosperms, from
 

 

Cycads

 

 

 

 

Ginkgo

 

 

 

 

 

 

 

 

 

Conifers

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Bennettitales

 

 

 

 

 

 

Anthophytes

 

Gnetales

 

 

 

 

 

 

 

 

Angiosperms

 

 

 

 

 

 

Angiosperms

 

 

 

 

 

 

 

 

 

 

Cycads

 

 

 

 

 

 

 

 

Bennettitales

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Ginkgo

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Conifers

 

 

 

 

 

 

Gnetales

 

 

 

 

 

 
 
Traditional view
 
Modern view
 

The main function of a flower is reproduction, which, before the evolution of the flower and angiosperms, was the job of microsporophylls and megasporophylls. A flower can be considered a powerful evolutionary innovation, because its presence allowed the plant world to access new means and mechanisms for reproduction.

Origins of the flower
The family Amborellaceae is regarded as the sister family of all living flowering plants. That means members of this family were most likely the first flowering plants.

It seems that on the level of the organ, the leaf may be the ancestor of the flower, or at least some floral organs. When we mutate some crucial genes involved in flower development, we end up with a cluster of leaf-like structures. Thus, sometime in history, the developmental program leading to formation of a leaf must have been altered to generate a flower. There probably also exists an overall robust framework within which the floral diversity has been generated. A example of that is a gene called LEAFY (LFY), which is involved in flower development in Arabidopsis. The homologs of this gene are found in angiosperms as diverse as tomato, snapdragon, pea, maize and even gymnosperms. Interestingly, expression of Arabidopsis LFY in distant plants like poplar and citrus also results in flower-production in these plants. The LFY gene regulates the expression of some gene belonging to the MADS-box family. These genes, in turn, act as direct controllers of flower development.

  Amborella trichopoda : Amborellaceae is considered the sister family of all flowering plants (magnified image)
 
Amborella trichopoda : Amborellaceae is considered the sister family of all flowering plants (magnified image)
 


Evolution of the MADS-box family

The members of the MADS-box family of transcription factors play a very important and evolutionarily conserved role in flower development. According to the ABC Model of flower development, three zones - A,B and C - are generated within the developing flower primordium, by the action of some transcription factors, that are members of the MADS-box family. Among these, the functions of the B and C domain genes have been evolutionarily more conserved than the A domain gene. Many of these genes have arisen through gene duplications of ancestral members of this family. Quite a few of them show redundant functions.

The evolution of the MADS-box family has been extensively studied. These genes are present even in pteridophytes, but the spread and diversity is many times higher in angiosperms. There appears to be quite a bit of pattern into how this family has evolved. Consider the evolution of the C-region gene AGAMOUS (AG). It is expressed in today's flowers in the stamens, and the carpel, which are reproductive organs. It's ancestor in gymnosperms also has the same expression pattern. Here, it is expressed in the strobili, an organ that produces pollens or ovules. Similarly, the B-genes' (AP3 and PI) ancestors are expressed only in the male organs in gymnosperms. Their descendants in the modern angiosperms also are expressed only in the stamens, the male reproductive organ. Thus, the same, then-existing components were used by the plants in a novel manner to generate the first flower. This is a recurring pattern in evolution.

Factors influencing floral diversity
How is the enormous diversity in the shape, color and sizes of flowers established? There is enormous variation in the developmental program in different plants. For example, monocots possess structures like lodicules and palea, that were believed to be analogous to the dicot petals and carpels respectively.It turns out that this is true, and the variation is due to slight changes in the MADS-box genes and their expression pattern in the monocots. Another example is that of a plant called Linaria vulgaris, which has two kinds of flower symmetries-radial and bilateral. These symmetries are due to epigenetic changes in just one gene called CYCLOIDEA.

Arabidopsis has a gene called AGAMOUS that plays an important role in defining how many petals and sepals and other organs are generated. Mutations in this gene give rise to the floral meristem obtaining an indeterminate fate, and many floral organs keep on getting produced. We have flowers like roses, carnations and morning glory, for example, that have very dense floral organs.
  The various shapes and colors of flowers
 
The various shapes and colors of flowers
 

These flowers have been selected by horticulturists since long for increased number of petals. Researchers have found that the morphology of these flowers is because of strong mutations in the AGAMOUS homolog in these plants, which leads to them making a large number of petals and sepals. Several studies on diverse plants like petunia, tomato, Impatiens, maize etc have suggested that the enormous diversity of flowers is a result of small changes in genes controlling their development.

Some of these changes also cause changes in expression patterns of the developmental genes, resulting in different phenotypes. The Floral Genome Project looked at the EST data from various tissues of many flowering plants. The researchers confirmed that the ABC Model of flower development is not conserved across all angiosperms. Sometimes expression domains change, as in the case of many monocots, and also in some basal angiosperms like Amborella. Different models of flower development like the The fading boundaries model, or the Overlapping-boundaries model which propose non-rigid domains of expression, may explain these architectures. There is a possibility that from the basal to the modern angiosperms, the domains of floral architecture have gotten more and more fixed through evolution.
  Large number of petals in roses has probably been a result of human selection
 
Large number of petals in roses has probably been a result of human selection

Flowering time
Another floral feature that has been a subject of natural selection is flowering time.

Some plants flower early in their life cycle, others require a period of vernalization before flowering. This decision is based on factors like temperature, light intensity, presence of pollinators and other environmental signals. We know that genes like CONSTANS (CO), Flowering Locus C (FLC) and FRIGIDA regulate integration of environmental signals into the pathway for flower development. Variations in these loci have been associated with flowering time variations between plants. For example, Arabidopsis thaliana ecotypes that grow in the cold, temperate regions require prolonged vernalization before they flower, while the tropical varieties, and the most common lab strains, don't. We now know that this variation is due to mutations in the FLC and FRIGIDA genes, rendering them non-functional.

Quite a few players in this process are conserved across all the plants studied. Sometimes though, despite genetic conservation, the mechanism of action turns out to be different. For example, rice is a short-day plant, while Arabidopsis is a long-day plant. Now, in both plants, the proteins CO and FLOWERING LOCUS T (FT) are present. But in Arabidopsis, CO enhances FT production, while in rice, the CO homolog represses FT production, resulting in completely opposite downstream effects.



Theories of flower evolution
See also : Evolutionary history of plants
There are many theories that propose how flowers evolved. Some of them are described below.

The Anthophyte Theory was based upon the observation that a gymnospermic group Gnetales has a flower-like ovule. It has partially developed vessels as found in the angiosperms, and the megasporangium is covered by three envelopes, like the ovary structure of angiosperm flowers. However, many other lines of evidence show that Gnetales is not related to angiosperms.

The Mostly Male Theory has a more genetic basis. Proponents of this theory point out that the gymnosperms have two very similar copies of the gene LFY while angiosperms just one. Molecular clock analysis has shown that the other LFY paralog was lost in angiosperms around the same time as flower fossils become abundant, suggesting that this event might have led to floral evolution. According to this theory, loss of one of the LFY paralog led to flowers that were more male, with the ovules being expressed ectopically. These ovules initially performed the function of attracting pollinators, but sometime later, may have been integrated into the core flower.

One theory also suggests that humans have been one of the reasons for the diversity of flowers. This theory suggests that since the early settlers found flowers beautiful, they may have started selecting for them artificially. The flowers may have evolved to exploit the ecological niche being opened because of humans finding them attractive. The validity of this theory, however, is debatable, not least because flowers started diversifying long before they came into contact with humans.

Evolution of secondary metabolism

Although we know a lot of secondary metabolites produced by plants, the extent of the same is still unfathomable. Secondary metabolites are essentially low molecular weight compounds, sometimes having complex structures. They function in processes as diverse as immunity, anti-herbivory, pollinator attraction, communication between plants, maintaining symbiotic associations with soil flora, enhancing the rate of fertilization etc, and hence are significant from the evo-devo perspective. The structural and functional diversity of these secondary metabolites across the plant kingdom is so huge that it is estimated that hundreds of thousands of enzymes might be involved in this process in the entire of the plant kingdom, with about 15-25% of the coding genome coding for these enzymes. Despite this, every species has its unique arsenal of secondary metabolites. Many of these metabolites are of enormous medical significance to humans.

What is the purpose of having so many secondary metabolites being produced, with a significant chunk of the metabolome devoted to this activity? It is hypothesized that most of these chemicals help in generating immunity, and in consequence, the diversity of these metabolites is a result of a constant war between plants and their parasites. There is evidence that this may be true in many cases. The big question here is the reproductive cost involved in maintaining such an impressive inventory.

  Structure of Azadirachtin, a terpenoid produced by the Neem plant, which helps ward off microbes and insects. Many secondary metabolites have complex structures
 
Structure of Azadirachtin, a terpenoid produced by the Neem plant, which helps ward off microbes and insects. Many secondary metabolites have complex structures
 


Various models have been suggested that probe into this aspect of the question, but a consensus on the extent of the cost is lacking. We still cannot predict whether a plant with more secondary metabolites would be better-off than other plants in its vicinity.

Secondary metabolite production seems to have arose quite early during evolution. Even bacteria possess the ability to make these compounds. But they assume more significant roles in life from fungi onwards to plants. In plants they seem to have spread out using different mechanisms like gene duplications, evolution of novel genes etc. Furthermore, studies have shown that diversity in some of these compounds may be positively selected for.

Although the role of novel gene evolution in the evolution of secondary metabolism cannot be denied, there are several examples where new metabolites have been formed by small changes in the reaction. For example, cyanogen glycosides have been proposed to have evolved multiple times in different plant lineages. There are several such instances of convergent evolution. For example, we now know that enzymes for synthesis of limonene - a terpene - are more similar between angiosperms and gymnosperms than to their own terpene synthesis enzymes. This suggests independent evolution of the limonene biosynthetic pathway in these two lineages.


Mechanisms and players in evolution
While environmental factors are significantly responsible for evolutionary change, they act merely as agents for natural selection. Change is inherently brought about via phenomena at the genetic level - mutations, chromosomal rearrangements and epigenetic changes. While the general types of mutations hold true across the living world, in plants, some other mechanisms have been implicated as highly significant.

Polyploidy is a very common feature in plants. It is believed that at least half (and probably all) plants are or have been polyploids. Polyploidy leads to genome doubling, thus generating functional redundancy in most genes. The duplicated genes may attain new function, either by changes in expression pattern or changes in activity. Polyploidy and gene duplication are believed to be among the most powerful forces in evolution of plant form. It is not know though, why genome doubling is such a frequent process in plants. One probable reason is the production of large amounts of secondary metabolites in plant cells. Some of them might interfere in the normal process of chromosomal segregation, leading to polypoidy.

In recent times, plants have been shown to possess significant microRNA families, which are conserved across many plant lineages. In comparison to animals, while the number of plant miRNA families are lesser than animals, the size of each family is much larger. The miRNA genes are also much more spread out in the genome than those in animals, where we find them clustered. It has been proposed that these miRNA families have expanded by duplications of chromosomal regions. Many miRNA genes involved in regulation of plant development have been found to be quite conserved between plants studied.

Domestication of plants like maize, rice, barley, wheat etc has also been a significant driving force in their evolution. Some studies have tried to look at the origins of the maize plant and it turns out that maize is a domesticated derivative of a wild plant from Mexico called teosinte. Teosinte belongs to the genus Zea, just as maize, but bears very small inflorescence, 5-10 hard cobs and a highly branched and spread out stem.

Interestingly, crosses between a particular teosinte variety and maize yields fertile offsprings that are intermediate in phenotype between maize and teosinte. QTL analysis has also revealed some loci that when mutated in maize yield a teosinte-like stem or teosinte-like cobs. Molecular clock analysis of these genes estimates their origins to some 9000 years ago, well in accordance with other records of maize domestication. It is believed that a small group of farmers must have selected some maize-like natural mutant of teosinte some 9000 years ago in Mexico, and subjected it to continuous selection to yield the maize plant as we know today.

  The stem-loop secondary structure of a pre-microRNA from Brassica oleracea
 
The stem-loop secondary structure of a pre-microRNA from Brassica oleracea
   
  Extreme left: teosinte, Extreme right: maize, middle: maize-teosinte hybrid
 
Extreme left: teosinte, Extreme right: maize, middle: maize-teosinte hybrid
   
  Cauliflower : Brassica oleracea var botrytis
 
Cauliflower : Brassica oleracea var botrytis

Another interesting case is that of cauliflower. The edible cauliflower is a domesticated version of the wild plant Brassica oleracea, which does not possess the dense undifferentiated inflorescence called the curd, that cauliflower possesses. Cauliflower possesses a single mutation in a gene called CAL, controlling meristem differentiation into inflorescence. This causes the cells at the floral meristem to gain an undifferentiated identity, and instead of growing into a flower, they grow into a lump of undifferentiated cells. This mutation has been selected through domestication at least since the Greek empire.

See also
Plant morphology
Evolutionary history of plants


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