The Web of Life – Life’s Diversity

Life’s Diversity

“Species in natural communities are interconnected.” ~ American environmental biologist Saran Twombly

The heritage of life is astoundingly rich in variety; a testament to Nature’s fondness for diversity and the ready versatility of adaptability. There are at least a billion distinct microbes – a number historically underestimated.

A conservative estimate of extant multicellular species is 8.7 million; some 90% of them undiscovered by humans. For multicellular eukaryotes over the course of the planet’s history, the number of species is easily 1,000 times that of those living today.

“The great Tree of Life, with its ever-branching and beautiful ramifications.” ~ Charles Darwin

From antiquity, the concept of a tree of life has been used in every realm of conceptualization: from mythology, religion, and natural philosophy to evolutionary biology.

“The tree of life is one of the most important organizing principles in biology.” ~ American planetary scientist Jill Banfield


Biology will relate every human gene to the genes of other animals and bacteria, to this great chain of being. ~ American molecular biologist Walter Gilbert

Biological classification is a facet of scientific taxonomy: naming everything according to some rule set. It fills biology books with hoary Latin words.

The living kingdom used to be divided into animals and plants. The division was based on the simple idea that all the interesting things moved and all the uninteresting ones did not. So, originally, both bacteria and fungi were classed as plants. Once it was realized that bacteria caused disease and plants did not, attitudes changed. ~ Anthony Trewavas

Coining the terms genus and species, 4th-century-BCE philosopher Aristotle classified animals by their method of reproduction. Aristotle’s system went the way of the dodo with additional knowledge and was long forgotten as others took up the classification cudgel.

17th-century English naturalist John Ray provided the first biological definition of species: as springing from the same seed, whether plant or animal. (Ray’s definition of species had no concept of evolution. But neither did his successor, Linnaeus. The exercise was merely cataloging.) By contrast, Aristotle’s definition was philosophical, in considering rationality and the hypothetical possession of a soul.

Ray also made a stab at biological classification. His work was overshadowed a half-century later by Swedish physician and biologist Carl Linnaeus (1707–1778).

If the names are unknown, knowledge of the things also perishes. ~ Carl Linnaeus

In laying the foundations for naming species (binomial nomenclature), Linnaeus is considered the father of taxonomy. (Linnaeus started the tradition of 2-part Latin names denoting genus and species. As his family spoke Latin at home, Linnaeus’ first language was Latin, learning (ostensibly native) Swedish later.) His 1735 book Systema Naturae held sway for centuries. (Linnaeus made no original advances. His classifying system and binomial nomenclature were anticipated by others. But Linnaeus created a well-esteemed presentation: clean-cut categories that made science alluring and accessible. His work inspired botanical gardens and a greater general interest in the wonders of Nature.)

Nature does not proceed by leaps and bounds. ~ Carl Linnaeus

By the time he died, Linnaeus was one of the most acclaimed scientists in Europe. Because of that, it took quite some time for his numerous mistakes to be cleared up.

Linnaeus labeled via physical characteristics. Based upon preconception, and in the spirit of animism, Linnaeus split the natural world into plants, animals, and stones. Abjuring the use of magnifying glasses, Linnaeus ensured that little life forms received little attention.

Linnaeus really lost the plot when it came to fungi. ~ English mycologist David Hawksworth

Linnaeus planted fungi in the plant realm. Fungi did not get their own kingdom until 1969. Confusion was doubled by the same fungus invariably getting at least 2 names based upon reproduction mode (asexual versus sexual). Meanwhile, with no protest, protists were thrown in as fungi.

Linnaeus’ 1753 book on plants described 6,000 species. It became the foundation of modern floral nomenclature, which has since ballooned to 1.05 million named species, of which only ~300,000 are unique – the others are redundant. The scientific moniker for the English oak has 314 synonyms, the common daisy 29, and the giant sequoia 18.

Linnaeus got numerous bad nomenclature balls rolling. As time marched on, new discoveries piled up like knowledge cordwood. Misnomers burgeoned.

Serial revisions were inevitable. Darwin introduced the notion of evolutionary descent and clades: a common ancestor to later speciation.

No one definition has satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species. ~ Charles Darwin

There has been a trend since the 1960s toward nomenclature based upon lineage (cladism), abetted by similarities at the genetic level. This evolutionary rationalization is still under development.

Evolutionary relations are better represented by new classifications than by the traditional 2 kingdoms. ~ American plant ecologist Robert Whittaker in 1969

Robert Whittaker’s 5-kingdom classification (plant, fungi, animal, protist, and prokaryote) ruled in biology classrooms for decades; but it was based largely on nutritional habits, not evolution.

The basis for systematics has changed; classical phenotypic criteria are being replace by molecular criteria. ~ American microbiologist and physicist Carl Woese et al in 1990

Early attempts to see what genetics could say about the tree of life proved deceptive. Results seemed realistic, but were contradicted when researchers looked at different genes, and, later, mitochondrial development. Recent technological advances have allowed genetic analyses (phylogenetics) that were previously unavailable.

Molecular phylogenetics has revolutionized our knowledge of the eukaryotic tree of life. ~ Canadian biologist Fabien Burki

In 1967, American evolutionary biologist Lynn Margulis proposed that eukaryotes arose from one prokaryote engulfing another: a bacterium absorbed by an archaean host became the eukaryotic mitochondrial organelle; a good guess later confirmed. In the meantime, Margulis’s insight was ignored or dismissed.

To get a handle on evolution, biologists looked at the mitochondrial genes of parasites, specifically those supposed from pre-mitochondrial times. That approach fell apart when researchers realized some of the presumed parasitic relics were relatively modern. The little nippers had simply tucked away their mitochondrial DNA in hard-to-recognize bits. This was a case where the microsporidia under examination had simplified themselves: dropping genetic baggage they did not need. By the time parasites were performing it, such genetic streamlining was a well-worn stunt. The masters of life – viruses – had long before mastered the same trick while other prokaryotes were busy sprouting new traits with then-novel gene sets.

Genetic analysis improved considerably in the 2010s. Using a computer to determine speciation based upon genetically distinct lineages produces 5 to 13 times as many species as conventionally tallied. Species have traditionally been defined by mating behaviors and physical traits, not genetic similarity. The tentative take by biologists is that computers can’t count when it comes to species. The controversies over taxonomy continue, driven foremost by species being an ill-defined term.

(* Viruses are universally and inexplicably overlooked.

† Linnaeus ignored microbes, which were known in his day. Robert Hooke first wrote of microscopic cells in 1665, followed by Antonie van Leeuwenhoek beginning in 1673.

‡ Haeckel grouped all unicellular life as protists.

§ Monera are prokaryotes, which was a proposed phylum (under Protista) by Haeckel in 1866; adopted as a kingdom by Copeland in 1938.

** Eucarya are eukaryotes (Eukarya), misspelled as an affectation.)

Species concepts – a set of rules or characteristics used to define a species – abound in the literature and have been a subject of long-standing debate among evolutionary biologists. ~ American biologist Margaret Ptacek & American zoologist Shala Hankison

Although there is continuity between an ancestor and its descendants, and although taxonomy must take into account evolutionary relationships, schemes for assembling descendants into groups often seem mostly a mental construct. ~ Canadian biologist Brian Hall & Icelandic biologist Benedikt Hallgrímsson

The complexities of phylogenetic history emphasize that classification is a practical human enterprise where compromises must be made. All classifications should be regarded as interim. ~ American taxonomist Michael Ruggiero et al


Jellyfish illustrate the difficulties of classification. These marine creatures evolved ~580 million years ago.

All jellies were once in 1 phylum called Coelenterata. This made sense, as phylum is a high-level grouping based upon body plan. Coelenterata all had a radially symmetrical body plan, with sensory tentacles, and a single opening to capture prey. They share a common evolutionary ancestor, and so are in the same clade.

With a simple tissue organization, these aquatic creatures rely upon water flow through the body cavity for respiration and digestion. Coelenterata had a decentralized nerve network rather than a unified brain.

But then Coelenterata were bifurcated into cnidarians (Cnidaria) and ctenophores (Ctenophora), based upon differences that largely had nothing to do with body plan.

Ctenophores lack the stinging cells (nematocytes) that cnidarians have. Cnidarians have only 2 layers of cells, while ctenophores have 3. Embryonic development is different between the 2.

There is a modest body plan difference: ctenophores – such as sea anemones – have both bilateral and radial symmetry, while cnidarians may only be radially symmetrical. The Portuguese man o’ war is an exemplary marine cnidarian that lacks bilateral symmetry. But then, the man o’ war is not a single multicellular organism – it is instead a colonial creature, comprised of specialized zooids. (The inherent coordinated colonialism that comprises the man o’ war did not raise a classification issue, despite that being a defining characteristic. The discriminations which determine taxonomy involve a degree of arbitrary.)

Getting past the problem of Coelenterata, classification gets even trickier when considering a branch of cnidarians that degenerated into microscopic parasites. This group – Myxozoa – were originally considered protozoa: a diverse, catchall group of unicellular eukaryotes. Then genetic analysis revealed that myxozoans were in fact cnidarians that had shrunk and shed much of their genome, while retaining the most helpful genes, such as the ability to produce stingers.

The greatly reduced body plan included dumping genes considered hallmarks of animal multicellularity. Hence the understandable assumption that myxozoans were unicellular.

The confirmation that myxozoans are cnidarians demands the re-classification of myxozoa into the phylum cnidaria. ~ Israeli molecular phylogeneticist Dorothée Huchon

Tucking myxozoa into the cnidarian phylum may make some molecular sense but would ignore the notion that phylum is based upon body plan, not genetic lineage: physicality at odds with cladism. The problem with taxonomy begins with the methodology for defining taxa.


Kingdom has such gravitas. ~ English evolutionary biologist Alastair Simpson

In 2002, English evolutionary biologists Andrew Roger & Alastair Simpson blew away traditional classification, proposing instead cladistic supergroups for eukaryote: a small number of large groups that share a deep evolutionary history.

The classification caught on. Evolutionary biologists looking at the tree of life rarely use the word kingdom anymore, preferring supergroup instead.

Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the 4 eukaryotic groups within the 5-kingdom classification – plants, animals, fungi, and protists – have been transformed through numerous permutations into the current system of 6 “supergroups.” The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature, and is appearing in introductory biology textbooks. ~ Canadian bioscientist Laura Wegener Parfrey et al, in 2006

In that its lumps are so large, supergrouping is superficial and admittedly incomplete. There is an Orphans supergroup of evolutionary inscrutables, analogous to protist under traditional taxonomy.

Some supergroups are comprised of multiple supergroups. The term supergroup is meaningless as a hierarchical designation, and so is a super step into classification obfuscation. But then, Simpson wanted a term that no one would treat as a rank.

Supergroup taxonomies are unstable. The current classification scheme of eukaryotes is premature. ~ Laura Wegener Parfrey et al

Classification Confounded
Biological classification aims at conflicting goals which do not appear to conflict – identifiable distinctions which correspond with evolutionary descent. Life which looks or behaves similarly may be very distantly related at best, as is often the instance in cases of convergent evolution.

Genetic analysis shows traces which suggest heritage, but this too has often proven misleading or confusing – forensic evidence which wrongly convicts. The problem becomes especially acute with organisms which selectively pick up genes from the environment and incorporate them. This dilemma applies to all early life, when genetic expertise was de rigueur to surviving in an every-changing world. But it does not stop there. Cross-species genetic transfers have been a driver of evolution for all life forms. The likely culprit is viruses, which regularly infect their hosts with new genic material.

Horizontal transfer, differing from the normal parent-offspring transfer, has had an enormous impact on mammalian evolution. ~ Australian geneticist David Adelson

Setting aside the genetic perspective, categorizing is problematic when trying to make evolutionary sense. Consider those with backbones.

We are accustomed to consider vertebrates in commonly known and understood categories such as fish, amphibians and reptiles. But phylogenetic analyses demonstrate quite convincingly that these are not natural categories, if by natural we mean that each constitutes a group, all of whose members can be traced to a single ancestral lineage, that is, a group that is monophyletic. The recent elimination of birds as a group and the recognition of “birds” as flying dinosaurs, while fully justified, illustrates the shoals on the course we are navigating. “Fish” is a name for a polyphyletic group of animals that share many features, but a single evolutionary origin is not one of them. ~ Brian Hall and Benedikt Hallgrímsson

Amphibians arose from among a group of lobe-finned fish. How to distinguish the more-derived lobe-finned fish that gave rise to these first tetrapods? Because the most derived lobe-finned genus of fish is Panderichthys, some refer to an even more derived taxon as “postpanderichthyid stem tetrapods” – a breathtaking name for devotees only. “Fish-like amphibians” is at least somewhat memorable; but such labeling of descents into a new major group is less descriptive than it seems, as mammals-to-be illustrate.

The old term “mammal-like reptiles” was once used for those reptiles recognized as having given rise to mammals. It is no longer considered appropriate because: 1) these creatures (therapsids) consist of multiple independent evolutionary lines, only a few which bequeathed mammals; 2) the term confuses a crown group (the culmination of an lineage) with a stem group (a lineage that gave rise to another group); and 3) the attribution makes it sound like some reptiles were trying to become mammals, and so struck a mammalian pose.

Many long-standing taxonomic groups are paraphyletic: they do not include all descendants of a common ancestor. A famous example is reptiles, which cladistically includes both birds and mammals. Among humanity’s closest relatives, the family of “great apes” is paraphyletic in excluding humans.

Conversely, paleoanthropologists go through some pains to delineate between those humanoid creatures that supposedly did not beget humanity, such as Neanderthals, and those that did: hominins. Considering the crossbreeding that went on (including with Neanderthals), the exercise is quaint.

In the finale, the problem is that you can’t square the circle of identifying groups of organisms with an eye toward descent, as the reality of evolution is seldom so simple as to be simply labeled. Humans are considered a single species, but not by any reasonable definition of what a species is. The attribution is political, and an acknowledgement that biological classification is a social convention, not a scientific discovery.

It is really laughable to see what different ideas are prominent in various naturalists minds, when they speak of ‘species’. It all comes from trying to define the undefinable. ~ Charles Darwin

Evolution is a messy business, defiant to easy tagging. Forgetting heritage for the moment, there is any even more fundamental problem inherent in classifying extant groups in a world with biological diversity beyond imagination: where do you draw the lines? To even begin, you have to have some consistent concept of species. There isn’t one.

There are n+1 definitions of ‘species’ in a room of n biologists. ~ Australian science philosopher John Wilkins

 Linnaeus’ Curse

No matter how hard we try, there cannot be a robust, all-inclusive, objective species concept. ~ Dutch geneticist Peter de Knijff

Linnaeus introduced a dilemma that has plagued biologists ever since. His insistence on a stringent hierarchical species classification has thwarted defining species in an inclusive manner. The sting of this conundrum was felt by Darwin a century after Linnaeus created his curse.

To discuss whether they are rightly called species or varieties, before any definition of these terms has been generally accepted, is vainly to beat the air. ~ Charles Darwin

 Classifying Crows

Ever since the hooded crow (Corvus cornix) and carrion crow (Corvus corone) were described by Linnaeus in 1758 as separate species, their taxonomic status has been debated.

The 2 crows look different. The carrion crow is solid black, its plumage giving off a green or purple sheen. The hooded crow (pictured) has a gray body, albeit with a black hood, throat, wings, thigh, and tail feathers.

The 2 crows generally prefer their own kind. But there is gene flow between the 2 species. Hybrids are common in a narrow geographical band in central Europe where ranges overlap.

Despite different coloration, the genomes of the German carrion crow and hooded are undifferentiated (this ignores epigenetic differences); much more selfsame than the genic distinctions between the carrion crows that live in Germany and those that reside in Spain.

German carrion crows could be considered to represent hooded crows with a black (carrion crow) phenotype. ~ Peter de Knijff


Specimens in museums are the primary source of verifiable information about organisms. The world’s collections more than doubled from 1970 to 2010. But half of the specimens in museums are misidentified. The curse of classification is more than conceptual.


Species generally have a fixed number of chromosomes in the cell nuclei, while between-species differences are common and often pronounced. These differences could have evolved through multiple speciation events, each involving the fixation of a single chromosomal rearrangement. ~ Russian zoologist Vladimir Lukhtanov et al

Species may be most precisely defined at the cellular level; or not.

A karyotype is the number and arrangement of chromosomes in the nucleus of a eukaryotic cell. Karyotype is usually stable within species, as chromosomal changes contribute to forming barriers between populations, thereby establishing reproductive isolation and speciation.

Rapid karyotypic diversification is how the prolific butterfly genus Agrodiaetus managed to cover the vast Palearctic ecozone of Eurasia and beyond with its kind. Interspecific diversity in chromosome number among Agrodiaetus is broader than any other known genus.

Peach-potato aphids have a jumble of karyotypes, even within a single individual. Despite this, they have preserved their morphological identity over time and across a broad geography. The wood white butterfly also has karyotypic polymorphism, with geographically dispersed populations that may interbreed, despite different numbers of chromosomes. Such karyotypical cacophony illustrates how little we know of genetics.


There were 8 major biological taxonomic ranks generally recognized before supergroups showed up: life, domain, kingdom, phylum, class, order, family, genus, and species. The disciplines of zoology and botany have their own schemas, including subdivisions, such as tribe. Other outliers exist, as do numerous proposed taxonomic systems. Ironically, the 2 things that classification has lacked are consistency and consensus.

Bizarrely, all major biological classification systems ignore viruses, which have been a major driver of evolution in all other life. This omission is inexcusably thoughtless.

If we accept that viruses are alive, we must radically reassess the tree of life as it is currently accepted. ~ American biologist Peter Ward & American geobiologist Joe Kirschvink


As Margulis first suggested, eukaryotes arose as archaea absorbed bacterial endosymbionts which gave rise to the mitochondrion found in all eukaryotic cells. (Archaea and bacteria were long confused as variants of the same life form, as they look and act a lot alike.)

Carl Woese proposed archaea, bacteria, and eukaryotes as domains in 1977 after discovering archaea.

The iconic rooted 3-domains tree of life shows eukaryotes and archaebacteria as separate groups that share a common ancestor to the exclusion of eubacteria. By contrast, the eocyte hypothesis has eukaryotes originating within the archaebacteria, and sharing a common ancestor with a particular group called the Crenarchaeota or eocytes. ~ English evolutionary biologist Cymon Cox et al

In 1984, American evolutionary biologist James Lake and his colleagues proposed that eukaryotes descended from an archaean kingdom called eocytes (aka Crenarchaeota). Follow-on research showed this to be the case.

Bacteria are by far the most diverse domain, with 92 named phyla. There are 26 known archaeal phyla, and 6 eukaryotic supergroups. Classification of eukaryotes is a mess.

The placement of Eukarya relative to Bacteria and Archaea is controversial. ~ Canadian microbiologist Laura Hug et al

There are 3 domains of life: viruses, archaea, and bacteria. Viruses descended from ancient cells which genetically slimmed down to a pathogenic lifestyle: their presence more energetic than molecular. Eukaryotes descended from archaea, in endosymbiotic partnership with bacteria, and so nominally comprise a kingdom, not a domain (if one leaves the current taxonomic stratification intact).

Adjusting yet adhering to familiarity, Spokes refers to 4 eukaryotic kingdoms: plants, protists, fungi, and animals, which are descended from the domain of archaea. Prokaryotes refers to the domains of archaea and bacteria, with eukaryotes herein stated as kingdoms.

Eukaryotic supergroups may be the new fashion for evolutionary biologists (despite remaining unsettled), but the terminology is awkward and not yet publicly well-known: hence, not arguably superior. Further, supergroups break down into conventional phyla. Phylum is the level below kingdom, generally based upon body plan (shades of Linnaeus).

Nomenclature Overload

What’s in a name? ~ English playwright and poet William Shakespeare

The goal of biological classification has been ubiquitous uniqueness of name by convention. The failure of botanical and zoological societies to agree built a tower of taxonomic babble.

Some 5,000 duplicate ambiguities are known. The genus of golden peas and night monkeys is Anura. (The monkeys don’t eat those peas or vice versa.) The water dropwort, a poisonous swamp plant, and the wheatear, in the flycatcher bird family, are both of the genus Oenanthe.

Proboscidea is the genus of flowering unicorn plant and the order of elephants. They both at least have a long beezer.

Life forms are scientifically termed by genus and species. Genus is the generic name; always capitalized. Species is specific, but what exactly that means remains controversial (Linnaeus’ curse). In short, despite scientific bestowal, common names are preferable, if only to avoid mouthfuls of ersatz Latin gibber. In the unlikely event that the naming mess is ever sorted out, scientific names will change, but the commoners will remain constant.

Even then, the redundancy and confusion offered in common names are tremendous. One typical abhorrent tendency is to name plants after animals, thus requiring separate identification as flora, not fauna (e.g., spider plant).


The assumption that species are fixed entities underpins biology. Yet for a discipline aiming to impose order on the natural world, taxonomy (the classification of organisms) is remarkably anarchic. ~ Australian zoologist Stephen Garnett & Australian ornithologist Les Christidis