An Introduction for Gardeners to the Eudicots and the New ‘Phylogeny’ of Angiosperms: Genetics and the APG, Part 1



While working on a blog posting over the spring of ’17, Palms, Bananas, All Monocots…Oh My! Their Similarities and the Differences that Distinguish Them From Dicots…and why this should matter to you! discussing Monocots, I necessarily said much about Dicots, those vascular, seed producing, Angiosperms (flowering plants) with two cotyledons or ‘seed leaves’.  These were the two major groups of Angiosperms that I grew up with in the gardening world…but, while I was working in my career, this began to change, beginning  some 25 years ago.  I’d been aware of the term Eudicots, or ‘true’ dicots, and knew that all Eudicots also fit within the older category of Dicots, while a small portion of the latter, are left outside.  I was unsure how these differentiated and so, ignorantly (not a bad word), blurred the two together as many have been doing since the concept of Eudicots was first put forward.  The differences between these two for me seemed very ‘arcane’ and fussy, focusing on the tiny pores or furrows, colpi, on pollen grains.  But it is more than just that.  To really understand what is going on in the esoteric world of taxonomy, the naming and organizing of plants and their relationships to one another, you need to look at the genetics, the DNA ‘fingerprints’ of a plant which allows us to follow evolutionary paths back from the plants of today through their ancestors to the earliest forms of life on Earth.  It is about the phylogeny, the ‘history’ and relationships that tie plants together.

Of course you don’t really need to know this stuff to garden, which name to put on a plant, what its relationships are to other plants, but it does enrich your experience and it brings with it an understanding of the wider living world, something the planet would benefit from.   The scales are so much larger than our individual lives and the details, innumerable and beyond our limited vision.  It is necessary to look at these scales to have any understanding of what the big ‘brouhaha’ is about, why science has been rearranging the ‘face’ of botany and taxonomy and how this relates to life on this planet, its evolution and our place on it today.  My previous post on Monocots takes a stab at this.  My two post preceding this one, Life Inside the Cell: Waking Up to the Miracle, part 1 and Evolution, Speciation and What it Means to the New Phylogeny: A Primer for Gardeners, Part 2, have set the stage and are part of this post and the next three posts in the series.  Both of these earlier pieces are long, so take them in bits.

These were always intended as a single larger piece.  The drafts were all written some time ago, but I became so mired down in them that i lost my perspective and have more recently returned to them to edit and ‘finish’.  My intention is to post them consecutively.  There are six parts in all…plus the earlier piece on Monocots.

For me the ‘why’ behind all of this taxonomic restructuring is important.  In our world today there seems to be a whole lot of rearranging of the deck chairs going on at a corporate and institutional levels of businesses and institutions, and much of it seems to be ego driven.  This rearranging of phylogeny isn’t.  It is an organized scientific effort to try to make more sense of the world, an acknowledgement that life on this planet is neither random nor a literal one time act of God.  If we are to continue living on this planet as a species it is becoming ever more important that we understand the ‘forces’ in play here and our appropriate role as a fellow species, of unprecedented power and ability,  If you have not read my previous post I encourage you to do so.

Since the study of botany began, it has relied upon the botanist’s eyes and what could be readily observed, the structure of a plant, it’s morphology and how it fits into the world.  This gave rise to the development of various classification systems since Linnaeus and before, when plants were first simply arranged into trees, shrubs and herbs.   ‘Keys’ were developed to help people with their identification and understanding of plants.  When Mendel first purposed the idea of genetics, botanists began to realize that there was an underlying structure or instruction, a code, that played a role in determining the structure and traits, even the purpose and function, of organisms.  They understood the general idea of heredity, but they were a long way from understanding DNA and the process of sexual reproduction through which it worked, it’s expression and the processes and forces whereby speciation and evolution happens.

Prior to this, in the Christian western world, life was often ascribed to the word of God.  That God created each life form and that was it.  Species, as they understood them then, were fixed and unchanging.  They were created in a single ‘burst’, constant, without later additions.  Ideas that questioned this ‘fact’ were considered blasphemous and were attacked and discredited.  The concepts of evolution and speciation have been coming together more clearly over recent decades supported by the development of new technologies and the instruments available to us to examine the biological and geologic records available to us.  Our understanding of biological life and its development has changed radically and this is what is all behind the changes in the world of taxonomy and phylogeny.  It is not just ‘hair splitting’, arguments between botanists who want to merge or split various groups of organisms.  It is reflective of a changed view or understanding of what life on this planet is, where it’s come from and where it is heading.  DNA has become a kind of measuring stick and guide in this work, augmented by our much more complex understanding of the geological and many bio-chemical processes at work in the cell, the soil, our water and atmosphere.  It is a grand and miraculous ‘puzzle’ that scientists have been working to ‘assemble’, in no way demeaned or lessened by their examination.

Most recently this has been the focus of the Angiosperm Phylogeny Group, or APG, an international group of botanists and researchers who have been collaborating, pooling the knowledge that has been accumulating as a result from the many thousands of scientists looking into various questions about life and its origins.  DNA has been central to their discussion.  Previously, classification systems were developed by remarkably talented and knowledgeable individuals and cooperating small groups of botanists.  Technology, especially the modern computer, has provided us with the ability to merge and analyze vast amounts of data rapidly while making it available to researchers around the world communicating in real time.  The ‘speed’ at which this incredibly complex work is carried out, the analysis of millions, even billions of ‘base pairs’ within a single species chromosomes, has enabled this work and opened up an entirely different and transforming approach.  Prior to the 1990’s name changes were limited primarily to the work of those reviewing previous work often largely of a ‘book-keeping’ type, clearing up redundancies and errors in precedence.  Today, with computers and DNA, recircumscription is possible, essentially redefining relationships between species that were previously only suggested by the available evidence.  This technology and capacity has enabled the ‘avalanche’ of change since its adoption.

DNA, Genetics, Botany and Phylogeny: The Evolution of a Science and a Rebirth of our World View

DNA consists of a very ordered structure of chromosomes, genes, ‘coded’, genetic ‘instructions’, which determine much of what any organism is or can become.  They exist within the cell’s nucleus in the form of the classic double helix structure, a spiraling ladder, with two ‘stringers’, long ‘bracketing’ strings of carbohydrate to which the rungs attach, each composed of a series of four different amino acids.  These are anything but random, passed from parent to offspring, displaying remarkable consistency, while creating unique individuals through the process of sexual reproduction, each displaying a consistency with slight, individual variations.  Each organism carrying within it these working copies, which links them back to its ancestors.  DNA goes a long way toward determining what we see when we measure, photograph and describe a particular organism, an individual…but, genetics do not tell the whole ‘story’.  Vanishingly small differences can result in recognizably different structures and forms.  In other cases remarkably similar forms have arisen despite less related genetics.

If DNA is the ‘plan’, the component bits of an organism, their proteins, carbohydrates, lipids, their countless ions, even and perhaps most critically, the water within and surrounding each and every cell, have specific chemical properties that when coordinated by DNA and the physical forces in play upon a place and organism, have over the Earth’s existence, resulted in the expression and dance of the countless individuals that populate the planet.  There is a tendency, a driving self-organizing ‘force’, toward ‘becoming’, moving structures, organisms, toward more efficient, complex, efficacious, ‘forms’, incorporating information in the very being of organisms and, in this increasing complexity develops a universal intelligence, a knowing universe.  Nothing forgotten.  Everything included.  We are somewhere along this path.

Two things worth noting here are that the ‘requirements’ of life, what constitutes it, what ‘defines’ it, what is common and shared between all organisms, is vital and animating.  Life is an intimate response to the conditions on Earth under which ‘we’ have all lived.  Our ‘structures’, our bodies, are the successful results of this over the course of many millions of years.  Because of this living organisms all share a huge portion of the same genetic material, amongst plants, amongst animals and even between them.  Much of any organism’s genetic footprint concerns life at the cellular level, its basic structures and tissues, biochemical processes that have evolved over many millions of years…that every individual still carries around in their DNA.

This is intimately connected to the fact that our living conditions fit within a very narrow band of what is possible in the universe.  Life on Earth can only exist within a very narrow temperature range that averages somewhere above freezing to 80ºF or so, much above that and plant metabolism can become severely compromised, below that and water freezes eliminating the possibility of carbon based life which is absolutely dependent upon liquid water.  Tilt the mix of atmospheric gases even slightly and life will have to adjust to it.  Land based plants are completely dependent upon their soil, dirt is not just dirt.  Organisms depend upon a particular mix of organisms to help maintain the very conditions upon which they depend.  When modern horticulture attempts to grow things outside of this community it must account for every single variable itself.  In a sense life on Earth has figured this out, it ‘knows’ the rules and has adopted roles that will work toward sustaining them.  This is true all of the way down to the cellular level.  Living cells, whether they themselves are an entire organism or comprise a single cell within a tissue of a larger organism, share more with one another than than they do points of divergence.

With so much ‘shared’, systematic botanists examine a relatively minute portion of an organism’s DNA to differentiate one from another….They look primarily at that within the nucleus, the chromoplasts within the ‘plastids’ and the ribosomes within the mitochondria, which are unique to plants.  (Several of these organelles within a given cell contain at least remnants of their own DNA, independent of the larger cell.  Cell biologists believe that these organelles, along with their particular functions were once independent cells themselves and were long ago incorporated into eukaryote cells that make up complex organisms today.) These DNA sequences contain the code that enables plants to convert solar energy to carbohydrate and power their growth, determine their nucleus and a plant’s ribosomes, those organelles within the cell’s mitochondria are responsible for the biological synthesis of proteins, the many metabolites and so directly effect the growth of plants.  Obviously, this ‘selective’ analysis gives these scientists an ‘incomplete’ record of any plant’s genome, however, the certainty that a complete analysis would require, would be an extremely ponderous task, there are many million, even billions, of ‘base pairs’ within each individual’s chromosomes, and they aren’t really necessary to parse one species from another…especially when a portion of it seems ‘unnecessary’.  A large portion of any organism’s DNA is of indeterminate purpose.  For example in humans only 2% of ours codes our protein synthesis, the building blocks of our bodies.  The remainder seems to be ‘copies’, redundancies, stitched together in different ways and positions throughout the chromosomes. One geneticist coined the term ‘junk DNA’ for this and it stuck…but the name is deceiving.  Modern research and thinking indicates that these aren’t ‘junk’ at all and are repositories from which a plant can draw upon in it process of adaptation, transforming itself and taking on previously unused possibilities and functions, and maybe central to the process of evolution.  There are many mysteries still within DNA.

The second thing to note is that these genetic patterns can be traced back through the pre-historic record and direct links can be made between species over time, morphological and hereditary links.  Because of this we can link organisms together in lines of development over time…we can create histories of the species and their development.  The outer form and structure, the morphology, of an organism may change over the course of millions of years.  Researchers have described, for example, the ‘cone like’, more spiral structure in the center of a Magnolia flower, and have determined how it is related to similar structures in the older, non-flowering structures of Conifers, as well as other structural similarities in other Gymnosperms, that do not possess what we today define as ‘flowers’.  There is an almost limitless ‘catalog’ of structures that plants have drawn on.  These structures can reappear in different combinations, possibly performing different functions, linked to unique gene sequences.  More ‘primitive’ plant forms can resurface in species that have evolved more contemporarily.  Magnolias share these genetic patterns amongst themselves patterns that aren’t shared by the core Eudicots.   It is this genetic work that has driven this redefining and structuring of plant taxonomy, separating the old dicots from the Eudicots and reordering much of what we once ‘knew’.

Phylogeny is the study and classification, of life in a way that shows clear and direct lines of inheritance and development for the hundreds of thousands of species over time, both those extant, or alive today, as well as those now extinct, in an effort to create a  ‘history’ of life on Earth.  It utilizes the study of the fossil record, genetics and morphology.  With morphology they make connections between current species and those from the fossil record.  While physical structure can be strongly influenced by growing conditions over time, genetics serves as a more accurate measure to gauge the actual relationship.  Morphology, appearance, can be either supportive or not in terms of establishing clear links.  Most of us have at one time confused certain Populus and Platanus species with Maples because of their common palmate, lobed leaf shape. When we do this we are looking at the ‘wrong’ structures, less consequential structures than dominant or even important, genetic links.  Life ‘recycles’ itself over time.  ‘Primitive’ structures resurface in new species.  Successful structures are encoded in the DNA, the ‘memory’ of life.  There are reasons for their previous success.  Structures can return, despite an increasingly complex genome, often with slightly modified functioning and internal structural differences.  Sometimes species can exhibit morphological ‘quirks’ because some of these are so ancient, so basal, common to countless species, remaining latent in some, but more strongly expressed in others.

What the APG is doing is no easy task and agreement is found by consensus…it is not unanimous. Agreement can be expressed in probabilities, the likelihood that species are linked or not.  We can’t go back to previous ages to examine the ‘living’ plants.  Sometimes agreement is not found at all and they agree to disagree, leaving certain groups in a kind of limbo, a transitional placement.  Experienced botanists know where to look and how to ‘read’ various morphological signs, physical differences, as well as those ‘apomorphies’, those traits shared within a phyletic group back through a common ancestor, that reinforce this still evolving genetic picture.  These are often very small and difficult to discern for the layperson, sometimes including a plant’s metabolites, the products of its own functions, compounds used in their internal processes and growth.  Many signs are microscopic and are found in the examination of an organism’s ultrastructure, such as in the structure of the tiny vessels and tissues within xylem.

Historically, plant collectors have done exhaustive field work, methodically noting everything they can observe in the field, while collecting what they believe to be a range of forms of a species in an attempt to define it.  All of this is sent ‘home’ for study by other botanists and horticulturists to grow and examine more intensively.  Papers are written, conclaves held and a consensus position is taken including the assigning of an appropriate name and how a species is related to others already determined.  It is an exhaustive and comprehensive effort in which the most accurate assessment is chosen.  Like all bonafide science it is an intensive peer reviewed process,  Genetics provides a more precise determination, than ‘mere’ visual observation.   It is in the nature of knowledge itself that it is never complete and the process of life itself is never ending.  Not every species fits easily into the structures that we apply to the world.

In their attempt to establish a consensus around the taxonomy of flowering plants, the Angiosperms, many systematic botanists, have collaborated to define their relationships to one another.  Others have been working on the much older and the much less numerous Gymnosperms.  To do this they have adopted the same techniques and approach used by the APG, the results of which continue to evolve.  These are the people ‘causing’ such consternation amongst many of us, splitting families, joining others, assigning species to different lines, ‘whining’ about paraphyletic groups and ‘confusing’ how many of us once looked at plants….Their approach is not random. These systematic botanists are as methodical as their predecessors.  Their goal is to better understand life and its evolution.

Many scientists are studying the ‘ultra-structure’ of plants, the architecture of their cells and the structure of the various tissues within plants, stems, leaves, phloem, xylem and seeds.  What they have found is that these tiny structures that makeup plants today are themselves evolving, that through the fossil record and various methods of genetic analysis, the ‘tiny’ changes in these structures and tissues often reflect the genetic changes and underlie the more ‘gross’ structures that we all are more likely to recognize. In other cases changes to a plant’s genetics don’t seem to directly correlate to any discernible physical change.

Most of us ‘know’ a plant when we see one.  With nearly 300,000 ‘variations’ on the plant theme within the Angiosperms, the differences between them can appear to be very small.  With so much shared between plants, systematic botanist focus on the often tiny differences to help them parse them out and trace back their origins and relationships.  These things often don’t show in obvious ways.

By doing all of this they have been able to order plants into monophyletic groups, genetic lines of descent, that are continuous back to a single ancestor.  This was not possible when classification was based on morphology alone.  ‘Like’ structures were once  considered to be indicators of shared ancestry.  Now they can see the genetics shared between species, note changes, and see the links between larger groups,  based directly on genetics and generational descent.  Many of these old morphologically based relationships have been found to be ‘paraphyletic’, meaning that the group derives from different ancestors.  Botanical and ecological study have long established that species can share outward physical characteristics while possessing different genetics, through the process of convergent evolution, or convergence.  It is relatively common for changes to arise independently amongst different species, scattered around the world.  It is also true that species can share very similar genetics while their physical expression of them, their structure or morphology, significantly diverge…as some genes may be recessive or held essentially dormant.  Our older morphological systems of classification sometimes suggested links between plants that were genetically absent while in other cases offered little morphologically that might have us link otherwise related species. These differences have lead us to the ongoing conflicts and corrections that have been taking place since the APG system began its work.

A Necessary Note on Nomenclature

It is practice in the biological sciences to identify species by both their genus and species name, such as Rosa glauca, creating its ‘binomial’.  All of the species Roses share the genus name Rosa. As you go ‘up’ the classification ladder, the class becomes more broad and general.  The name of each of these groups is taken from one of the members that comprise it with the change of a suffix that denotes the grouping.  They are agreed to by the responsible taxonomists.  They are assigned and once assigned they take on a kind of weight that gives them precedence when groups are reconfigured.  This can result in groupings with confounding names as a genera or family now finds itself a member of one whose name we once associated with a different group.  The suffix ‘ales’ will always denote the Order, ‘aceae’ will denote the Family and so on down the line.  Larger classes may be further divided into Subfamily, Tribe and Subtribe and will have an identifying suffix.  A more recent acquisition in my garden is a Rose relative, Sanguisorba hakusanensis.  If you were to do a casual examination of the flower and its inflorescence, you likely won’t see the connection, unless under magnification.  This example leads to one of the difficulties gardeners and amateur botanists may have with taxonomy and their various phylogenetic and monophyletic charts.  Those of us who garden may look to such things to better understand the links between plants when these are not intended to be plant keys or aids to the field identification of plants.  They are ‘historical documents’, charts tracing lineage back over time, aids to our understanding of life on this planet.  We need to get over our heavy reliance on outward appearances, because what is important to the botanist or evolutionary scientist may be ‘invisible’ to casual observation.  When our non-gardening friends casually comment about how plants look the same to them…they are to some extent right.  Plants share far more between species than those of us infatuated by them will readily admit.  This is what makes them plants, their shared characteristics.


This is Sanguisorba hakusanensis. If you zoom in you can see the small, crowded, 4 petalled flowers in the inflorescence. The ‘show’ portion are the bright lavender stamen of each flower.

‘The ‘list’ below is an example.  It names the classes within which Sanguisorba hakusanensis has been assigned, each lower, more specific class, subsumed within the one above it.  Each lower ‘class’ recognizes a point of divergence.  Kingdom Plantae is the broadest and most inclusive, including every single species of plant.

Kingdom: Plantae
(unranked): Angiosperms
(unranked): Eudicots
(unranked): Rosids
Order: Rosales
Family: Rosaceae
Subfamily: Rosoideae
Tribe: Sanguisorbeae
Subtribe: Sanguisorbinae
Genus: Sanguisorba
Species: hakusanensis

Several of the tiers toward the top are ‘unranked’.  It is the practice within the APG system to do this, to leave their ‘titles’ on their own.  Older systems named the general tiers above Order and remain in the record, still being used, to confuse things further.  These include Phyla or Division,  Class and, sometimes, Domain.  The APG has dropped these.





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