Evolutionary Transitions

Darwin defined natural selection as the force driving biotic progress: good evolved traits are selected (worthwhile keeping); traits with negative utility are inevitably expunged. Once established, change provides new leaves on our tree of life, representing organismal progress. Here, progress means improved survivability in the host environment. The most useful selected phenotypes may extend survivability into additional environmental niches as well.

Earth’s tree of life has transitional nodes where significant new organism vectors became expressed. Here we examine such branching points in the history of our direct ancestral organisms, noting their differentiation from other branches of our tree of life.

Before we begin, it is instructive to reflect on the nature of animal progress over the last 3+ billion years. Change is the one constant of our dynamic tree of life. Change itself is random, where each change occurs in a single organism, usually in the single cell from which the organism grows.

Almost all change is deleted within the organism generation in which it arises. Evolutionary biology builds sensitively balanced chemical machines, where virtually any change will disrupt and destroy the organism before it can be fully developed. In particular, change that attempts to remove any part of the basal machine is almost always catastrophic to the organism, so as a general rule, only additive change will be retained. This may explain the near uniformly increasing complexity of evolved organisms.

If an organism can tolerate a change and develop fully, the change will either modify some ability/behavior, or have no effect on the organismal phenotype. Evolution continues to filter those very few changes an organism can tolerate and pass on, keeping useful or neutral ones over time, eventually deleting those that are deleterious to the organism’s ability to compete. Almost all changes are soon deleted from our tree.

Once a change is established, natural selection has the opportunity to find multiple uses for it. For instance, feathers may have been useful initially for thermal control. Later nature may have found a decorative display function for them, which was further developed via sexual selection. The ultimate use for them came considerably later when feathers enabled flight.

Thus, it is characteristic of random change to generate enhanced potential that can be focused in several directions and realized in different progress vectors. This is sometimes specifically referred to as evolutionary co-option, but it is not a separate process. Rather, it is the result of basic natural selection iterating over more available options, mixing and matching function in the search for enhanced utility.

The few most progressive changes establish significant evolutionary milestones, where an entire new mode of existence becomes possible. These evolutionary transitions will be the subject of this discussion. Such transitions generally signify advancement of organization and complexity.

In the most early and basal organisms, these advances tended to increase flexibility in resource usage or efficiency in energy production, providing a wider environmental range for increasingly robust organisms. Here, natural selection was aided by the cell’s ability to combine with other cells and to incorporate external material into itself to extend function.

In animals, the appearance of a nervous system and later a brain were milestones that provided enhanced control. Turchin suggests the following hierarchy of discrete evolutionary transitions in organization and control:

  • control of position -> motion: ability to randomly change position
  • control of motion -> irritability: purposeful motion responding to stimuli
  • control of irritability -> reflex: integrated and coordinated responsive behavior
  • control of reflex -> association: adaptive reflex behavior through learned associations
  • control of association -> thought: new behaviors from abstract, symbolic reasoning
  • control of thought -> culture: behaviors modified by cultural evolution

Evolutionary biologists continue periodic reorganization in the more basal regions of our tree of life, adding structural refinements as our knowledge growth provides increased resolution. New phylogenetic methods are particularly revealing at the very earliest segments of the tree where only soft-tissue and microscopic life existed and left little permanent record. Fossil discoveries continue to augment genomic research, providing physical form to illustrate abstract genomic relationship diagrams.

An example of this tendency to refinement is the identification of the basal animal life form from which all other animal life evolved. Jellies and sponges had long been debated regarding which held the more basal tree position, with sponges appearing in the lead. But genetic sequencing of current species reveals that the ancestor of the simple comb jelly is more basal than any sponge ancestor. Beyond this knowledge, uncertainty in the tree will remain, involving inference of earlier ancestral forms, as well as the definition of what it means to be an animal.

Sometimes, a fossil or animal appears that is difficult to classify. One such issue arises because rarely, evolution can go backward as well as forward in feature richness. Sometimes, organisms are found to have dropped features that had evolved in their ancestors, called a secondary simplicity. For example, snakes are tetrapoda that have lost their limb structures. (Thus, the rule of increasing complexity is not absolute, and we can distinguish the usual immutable primary features from occasionally removable secondary features.)

In addition to secondary simplicities, considerations of parallel evolution complicate the analysis. Particularly in our basal tree, a feature could evolve independently in several lines, complicating our efforts to place the evolutionary path into a tree structure. While phylogenetic methods can sometimes resolve these issues, tree structure uncertainties remain as discontinuities early in our evolutionary path, where we have no unified hypothesis regarding how we got from stage A to stage B. These mysteries are annotated below as ‘Disconnects’.

In the following, we will examine the chronological sequence of major events leading to life on earth as we now know it. Dates are all in the ‘ma’ scale (million years ago).

4,500ma: Cataclysmic Birth of Earth

Over 4,500ma, a young (40 myo) proto-earth experienced a collision with a Mars-sized object. The impact turned Earth into a molten ball and ejected the material that would form our moon. This is the true birth of our current Earth-Moon system

It is assumed by the dating process that the impact removed any existing atmosphere of proto-earth. The time back to this null atmosphere is extrapolated from percentages of xenon gas found in air trapped in ancient quartz crystals, when compared to air today.
Earth’s first atmosphere, post-impact, was mainly helium and hydrogen. A lot of iron was vaporized, but it condensed out of the atmosphere as it cooled, the iron rain descending through the liquid mantle into the core. But with no internal core structure yet formed, there was no magnetosphere to protect the remaining atmospheric light gasses from solar wind, so they were largely lost.

As the earth cooled, the crust began to form and the core began to organize. Resulting volcanism replaced the minimal existing atmosphere with one beginning to resemble today’s, but without molecular oxygen. Volcanism released water vapor and most other molecules that are still emitted today through the earth’s crust, including methane and ammonia. The ammonia released its nitrogen into the new atmosphere, where it remains as 78% concentration. The cooling earth allowed the water vapor to liquify and begin to form our oceans. They were likely salty from the start as NaCl gas was abundant in the atmosphere.

4,200ma: Abiogenesis and the RNA World (Setting the Stage for Life on Earth)

Studies of zircon crystals help pinpoint the time of the earliest oceans. The formation of Zr crystals can be absolutely dated to within 1% via U-Pb radiometric dating. The conditions at the time of formation can be read from their δ18O/16O oxygen isotope ratio, a paleoclimate proxy. These two techniques suggest that Earth had a surface consistent with oceanic presence by 4,200ma, a brief 330my after its birth. The earliest known surviving sedimentary rock formation dates to 3,800ma, corroborating an earlier date for ocean formation.

Earth had an atmosphere essentially free from molecular oxygen for almost half of its existence. This is fortuitous, because the formation of the molecular precursors of life would have been inhibited in the presence of molecular oxygen. All early organisms utilized an anoxygenic metabolism, necessary until the first oxygen-generating metabolisms evolved. Elements necessary for cellular life include H, O, C, N, P, S, Mg, derived from water, carbon dioxide, phosphates, sulfates, magnesium, and ammonia.

It has been demonstrated that electric discharge in the presence of molecular hydrogen, methane, ammonia, and water can result in spontaneous synthesis of organic monomers such as amino acids, the building blocks of proteins. It has further been demonstrated that spontaneous polymerization of amino acids will occur when they are heated in a dry state, forming polypeptides.

Proto-life likely had only one function, the chemical replication of itself. It likely consisted of polymers in an anoxygenic environment. One such polymer, the ribozyme (an RNA molecule capable of enzymatic action), has been shown to catalyze the polymerization of nucleotides to make a copy of itself in a suitable environment, using complementary base pairing of its own template nucleic acids to self-replicate.

The original environment for primitive chemical replication is hypothesized to have been just such an RNA world. Interactions between RNA and amino acids would subsequently lead to RNA-directed synthesis of protein, and then DNA polymerization. DNA would then become the replication unit, synthesizing protein, the enzymes of the biotic world. There are complications for an RNA World hypothesis. Yet the hypothesis seems plausible, and it seems something like that had to have happened (if we exclude seeding via panspermia).

Such a dual function macro-molecule as the ribozyme, both enzyme and genome replicator, could explain the chicken-egg problem of life’s origins: which came first, the enzyme needed to produce the replicator, or the replicator needed to produce the enzyme. Yet the chemistry of the prebiotic world is not known, so the step for actually producing RNA from more primitive molecules was not explainable for a long time.

Researchers had been able to facilitate such a process in the presence of other compounds, such as borate and molybdate, but likely sources of such helper molecules in the primitive earth environment were not yet recognized. This persistent disconnect has perhaps now been eliminated, after our Rosetta spacecraft has identified glycine and phosphorus within a comet’s dust cloud.

In the lab, researchers further suggest that molecular building blocks of the first genetic material may have reached earth via water ice in comets.By placing a mixture of water, ammonia, and methane in a vacuum cooled to -328°F, then returning it to room temperature, a thin residue of cometary ice is deposited. Via multidimensional gas chromatography, the residue was found to contain ribose, as well as amino acids such as glycine, carboxylic acids, and alcohols. Of course, such a potential source of ribose bodes well for finding life on other worlds as well.

Prions, plasmids, and viruses may be direct descendants of this prebiotic world, but these primitive replicators seem to need protein synthesis and host cell metabolism to function, so it as yet hard to explain their existence prior to the first cellular forms.

Ur-life was based on enzymatic replication, but our notion of living organisms as chemical machines requires functions beyond mere replication. To fully qualify as ur-life, the organism needed a metabolic process and associated communicating processes. Naked replicating polymers would have had evolutionary incentive to internalize and expand metabolism modes, to lessen dependence on chance encounters with the free-floating molecules they would need for the energy to perform their functions.

The basic metabolic processes, common to all cellular life, produce a common energy molecule, adenosine 5′-triphosphate (ATP), enabling cell motility and other energy-consuming processes. ATP is the common intracellular energy currency, mediating between exothermal and endothermal cell processes. Production of ATP can be considered a defining characteristic of our biotic world.

Three fundamental cellular metabolic pathways evolved, each producing ATP (in order of evolutionary timing):

  • glycolysis, a form of anoxygenic homolactic fermentation (glucose -> lactic acid + ATP)
  • photosynthesis (two different electron donors)
    • anoxygenic in some bacteria (light + hydrogen sulfide -> sulphur + ATP)
    • oxygenic in plants, algae, and some bacteria (light + water + carbon dioxide -> molecular oxygen + ATP)
  • aerobic respiration (glucose + molecular oxygen -> carbon dioxide + water + ATP).

All cells today utilize a form of glycolysis, our hint that this is the ur-metabolism of cells. But aerobic respiration is nearly 20 times more energy productive than glycolysis, a strong selective advantage.

4,000ma: Bacteria and Archaea (In Search of the Ur-Cell)

All cell membranes are based on phospholipids, which are self-organizing in an aqueous environment. The individual molecules are amphipathic, having a hydrophilic ‘head’ (charged phosphate group) and hydrophobic ‘tail’ (fatty acid). They organize packed in a double row, aligned tail to tail and forming a lipid bilayer with the outward-directed heads attracted to water, providing the inner and outer membrane surfaces that come in contact with the aqueous inner and outer environments.

Disconnect: We do not know the precise chemistry, structure, or DNA of ur-life, so explaining the synthesis of the ur-cell is currently hypothetical. Such an ur-cell is likely to be the first complete metabolic life form, the common ancestor of living bacteria and archaea. The enclosure of the ur-cell by a phospholipid membrane, isolating and protecting the chemical processes from the environment, is a large step with only a rudimentary hypothesis offered in support. Also, one might ask whether the first cell used DNA or RNA replication.

The date of  the ur-cell, precursor to archaea and bacteria, can be roughly estimated as approaching 4,000ma. The oldest sandstone formations in Western Australia show evidence of microbial mats (colonies of cells) dated to 3,480ma, the oldest physical evidence of life on Earth. Other carbon isotope readings from Greenland allow us to infer that life was present over 3,800ma.

Archaea are in many ways bacteria-like, with most commonality between archaea and gram-positive bacteria. Which is ancestral remains to be determined, although bacteria seem to get the nod. Archaea tend to inhabit extreme anaerobic environments and to metabolize inorganic compounds, its modus from the beginning. Its extreme environments may have caused its chemistry to change significantly from bacteria early on.

Initial bacteria and archaea metabolized by internal fermentation such as glycolysis, breaking down complex molecules into simpler ones, utilizing the energy released during replacement of weak bonds by strong bonds. A large variety of bacteria and archaea then evolved, pursuing every chemically feasible metabolism and thus every habitable niche in the environment, from great pressure in deep oceans, to great heat around hydrothermal vents, to the cold of ice sheets, adapting to all the available chemistries provided in these environments.

3,000ma: Cyanobacteria

Before there could be cells energized by aerobic respiration, there had to be atmospheric oxygen. Cyanobacteria are the putative source of the early atmospheric oxygen via anoxygenic photosynthesis. They seem to have been well established by 2,900ma, dated from a rock sample containing their residue. There are both single- and multi-celled (colonial) cyanobacteria.

Initial atmospheric oxygen was consumed as rapidly as it was produced, used up via oxidization of earth’s surface minerals. After that binding process completed, the oxygen content of our atmosphere began to rise.

2,000ma: Eukaryota

All life that is not bacteria or archaea is based on eukaryotic cells. Eukaryotes began as single cell organisms likely evolved from bacteria, but also have identifiable characteristics of archaea. Eukaryotic cells can be a thousand times larger than bacteria.

Eukaryotes are encased in a membrane and supported by a cytoskeleton. Its membrane adds the lipid sterol to the phospholipid bilayer. Within is a nucleus enclosed in its own membrane and containing nuclear DNA. Single cell eukaryotes still exist. They were once grouped together as protista, but now are understood to represent several distinct phyla.

Disconnect: The evolution of a eukaryote from archaea and bacteria is not yet well-understood or agreed. The recent eocyte hypothesis proposes an archaea such as Crenarchaeota was enfolded by a proteobacteria. There was likely a mutual benefit to this arrangement. The bacteria would have shielded the eocyte from hostile environments for which the bacteria was tolerant, such as oxygen presence. The eocyte may have provided antibiotic protection to the host bacterium. The eocyte was enclosed and protected by folds in the bacterial membrane that engulfed it. One hypothesis has this internal folded membrane eventually detaching from the rest of the bacterial membrane, becoming the internal nuclear membrane.

The following chart shows five subclades of Eukaroyota.

F1.large

From American Journal of Botany Vol. 91, October 2004

Differentiating these clades are cells of type unikont, bikont, and heterokont, referring to cells whose motive power is supplied by one or two flagella. Unikonts are basal to all animal life and fungi. Bikonts are basal to plants and algae. Heterokonts are a subset of bikonts consisting of the brown algae and related groups, whose cells have two flagella like the bikonts, but whose flagella differ in structure and function from each other.

Via the eocyte hypothesis above, ur-Eukaryotes had primitive metabolism capabilities of their host bacterium. To augment these, a primordial eukaryote ‘ingested’ bacteria having more diversified metabolisms, then used the metabolized products and energy. Endosymbiosis is a process by which an eukaryote engulfs a beneficial bacterium into its cytoplasm.

All eukaryotes contain mitochondria, hypothetical remnants of endosymbiosis in which ancestral eukaryotes encapsulated α-proteobacteria into themselves. Significant support for this hypothesis comes from the mitochondrial DNA, which has many affinities to DNA of proteobacteria. Such endosymbiosis probably was repeated multiple times in early eukaryotes. Oxygen respiration was likely provided via endosymbiosis.

Around 1,500ma, a bikont eukaryote captured a cyanobacteria via endosymbiosis. Thus began a subclade of multicellular bikont eukaryotes called Archaeplastida that comprise the algae and all plants. The resulting Plantae organisms continued to increase Earth’s atmospheric oxygen via the photosynthesis reactions in the encapsulated plastids. This endosymbiosis completed the great Earth life cycle of plants consuming carbon dioxide and producing oxygen, and animals completing the reverse process.

Initially, there were far more oxygen producers than oxygen consumers, so the atmosphere became oxygen-rich. Atmospheric methane, a strong greenhouse gas abundant in our early atmosphere, had been further augmented by methanogenesis of certain archaea and bacteria. Methane together with the increasing insolation from our new sun, kept early Earth’s temperature warm, likely facilitating the rapid chemical evolution leading to the first cell.

With the rising levels of molecular oxygen, atmospheric methane became converted to carbon dioxide, a weaker greenhouse gas. This had a hypothetical cooling effect sufficient to outweigh the early sun’s increasing insolation, which may explain several great freezes that covered the early earth’s land masses with ice, periods referred to as ‘snowball earth’.

700ma: Metazoa, The Basal Animals

Multicellular eukaryotes are basal to all plant and animal life on earth. Brown algae (e.g. kelp) are a further form of multicellular eukaryote. Multi-celled eukaryotes comprised of unikont cells are called metazoa, and are the basal stage for all animal life and fungi. We have now arrived at the branch of our life that is separate from all plants and algae.

Disconnect: The transition from unicellular to multicellular is thought to have occurred multiple times. Some instances may have involved a form of colonization, for example by aggregation, as with slime molds. Another may be by incomplete mitosis, where cells do not completely divide, producing an organism with two identical cells.

By basal animal, we mean the creation (branching from the root organism type) of a new phylum whose descendants are still existent. DNA analysis and rare fossil evidence may add earlier suspected phyla by hypothesis, which may help us to further understand and substantiate our basal phylum claims. Some attach importance to which phylum was earliest to branch, but such sister clades can be studied successfully without a correct sequencing model. And doing so will avoid confusions with the many suspected instances of co-evolution in the most primitive forms of animal existence.

[Disconnect: The question of which metazoa subclade is most basal has persisted. Initially, it was thought that a sponge (porifera) was the ur-metazoan. Current genomic analysis suggests the ur-metazoan was a primordial comb jelly (ctenophora). Placozoa, cnidaria, and bilateria are now considered sister clades of ctenophora. Porifera and ctenophora are the only known animal phyla lacking Hox genes, so we can infer they were either 1/2 or 2/1 in order.

Further analysis may yet be needed to completely decide the matter, if it is decidable. As with every essential discovery, more questions are raised than are answered. Porifera have less structure and complexity than current ctenophora. To account for ctenophora being basal to porifera, either porifera lost features or early ctenophora had a simpler genome than current forms.

Current ctenophora have evolved muscle tissue and a neural net, absent in porifera. Yet these features do not seem basal to all other animal muscle and neural cell functioning, for both features arise differently in embryonic development from that of later animal forms. Further, ctenophora neural cell chemistry is different from all other animal nerve tissue, being absent the standard neurotransmitters.

These questions seem to imply that evolution may have a very big recipe book to read from in its early phases of organismal development. The more we learn about our most basal life forms, the more we may encounter early alternatives to what have become the standard life forms. Ctenophora may be somewhat unique in bringing forward over hundreds of millions of years different answers to what is muscle and what is nerve tissue.]

In the evolutionarily-fast-paced first 100 million years after the appearance of metazoa, the complete basal structure for vertebrates had evolved. In the subsequent 500+ million years, changes in the basal development process were less significant. One can speculate that it could only have happened in one way, and once completed, was essentially immutable. Evolutionary development since the vertebrate baseline has consisted of mere tweaking at the periphery, punctuated by the notable transitional adaptations below.

625ma: Eumetazoa (Metazoa with Tissue Differentiation)

On the ending of the final ‘snowball earth’ glaciation stage, multicellular life exploded on earth, resulting in the evolution of most of the body plans of succeeding organisms. Eumetazoa are distinguished as the metazoa (animals) with tissues. Other metazoa (e.g. sponges and placozoa) have no such differentiated cellular organizations.

590ma: Bilateria

The bilateral eumetazoa constitute the basal body plan for the majority of eumetazoa. They have a front and back (ventral and dorsal), and a top and bottom (anterior and posterior). The other major animalia body plan has radial symmetry, as in jellyfish. Almost all bilateria have three embryonic germ layers, endoderm, mesoderm, and ectoderm. Almost all have a digestive tract with mouth and anus at opposite ends.

560ma: Deuterostomia

Deuterostomes are bilateria in which the embryonic blastophore first becomes the anus via radial cleavage during gastrulation. These are our ancestors. Excluded from deuterostomia are other phyla where the blastophore first forms the mouth via spiral cleavage during gastrulation. These latter are classified as protostomia and include all arthropods, molluscs, annelids, and platyhelminthes.

545ma: Chordata

The chordates are deuterostomes having a notocord, a primitive, cartilaginous, flexible unsegmented backbone. Chordates further possess a hollow, dorsal nerve tube and a post-anal tail. Other differentiating characteristics relate to the structure of the pharynx.

Pharyngeal slits appear that will become gills in fish, and in our lineage will become the pharyngeal pouches in the throat between the mouth and larynx, corresponding to the branchial arches. Pouch-I contributes to the eustachion tube and middle ear structures. Pouch-II further develops the middle ear and provides the tonsils. Pouch-III contributes the thyroid glands and thymus. Pouch-IV, along with the derivative final two pouches, further contribute to thyroid function and provide the structure of the larynx.

An endostyle appears, a ciliated, mucus-filled groove in the ventral pharynx that serves to capture food particles and guide them to the esophagus. It is considered homologous to the thyroid of more evolved descendants.

A sequence of further development marks the chordata as they evolved closer to our lineage. A proposed subclade of Craniata arose that encased the frontal nerve canal bulge with a bony case. This head then began to evolve sensory organs.

542ma: Cambrian ‘Explosion’

[Disconnect: A great radiation of apparent new phyla are documented at the start of the Cambrian period. Darwin considered this event, if scientifically established, as the potentially most challenging contra-indication to his theory of gradual selection. The theory of punctuated equilibrium arose subsequently to modify Darwinian theory in hopes of better explaining such an ‘explosion’.

But it is perhaps not necessary to panic and formulate new theories. First, we should examine the assumption behind a Cambrian event, that it was sudden. It is at least as likely that it was a gradual development for which past evidence is too scanty to demonstrate the developmental history in true perspective. The organisms of this time mostly had soft tissue bodies that leave only traces of their existence unless a shale formation can be found for the earlier period that has preserved such organisms.

There are many external environmental factors which could accelerate and diversify new evolutionary growth: temperature, climate, ocean chemistry, terrestrial fauna. Perhaps plate tectonics had reached a sweet spot configuration that made earth significantly more habitable.

It is also plausible that the developmental process for metazoa had reached a similar sweet spot, where tissue differentiation was accelerated by new DNA processes, driving enhanced  availability of novel phenotypes. Specialization would have become more common, enabling better defenses against predation and more efficient food access. All the basic animal body plans existent today originate from this period.

Such an inflationary period in evolution is not unique to metazoa. It happened also for terrestrial flora around 400ma, and again later for the angiosperms.  The causes of evolutionary inflation periods seem most likely to be rooted in DNA process advancements, which at critical developmental stages produce organismal potential for a rapid period of advancement. When these inflationary pressures coincide with a period of environmental encouragement, an ‘explosion’ may be evident.]

525ma: Vertebrata

Basal vertebrata were fish-like filter feeding craniata with gills; they developed in a marine environment from more primitive chordata (e.g. tunicates). All vertebrates have a nervous system, cranium with brain, segmented backbone, paired appendages, and a tail. The notocord persists only in embryonic states, then is transformed into the cartilage disks separating the vertebrae.

460ma: Gnathostomata (Jawed Vertebrates)

99% of living vertebrata have jaws. Such evolutionary selection evidence seems to indicate that jaws provide significant survival benefit. The lamprey is a descendant of a vertebrata subclade that missed out on jaw development.

The jaw originates from the mandibular arch, the anterior of the branchial arches. This first arch was gradually modified to support the mouth opening wide and closing to pump more water over the gills. An intermediate form of this development was recently discovered in the Burgess Shale. Metaspriggina is a fish fossil dating from 505ma. It shows the branchial arches in early vertebrata occurred in pairs, and already the anterior arch was specializing, appearing slightly thicker in the fossil.

Other evolutionary advances in Gnathostomata include myelin sheaths on neurons, and our adaptive, VDJ immune system.

395ma: Fish to Amphibian, First Vertebrates on Land

The fishapod, Tiktaalik, resembled a fish with four leg-fins that could support much of its weight. It had both lungs and gills to enable it to complete the transition. A fossil dated to 375ma was discovered in 2004 in northern Canada. Surviving amphibians include the frogs, toads, and salamanders.

330ma: Amniota, Reptilians

The earliest amphibians likely still reproduced in the water. Some subset of these adapted to reproduction on land. These are called the amniotes, for the special membranes developed to protect the egg.

230ma: Reptile to Mammal (and Bird)

The walking whale, Thrinaxodon, had scales and laid eggs, but was warm-blooded, had whiskers, and perhaps some body fur. Fossils have been found in Antarctica and South Africa. This suggests that internal temperature control adaptations preceded the reproductive adaptations of mammals.

Once vertebrates left the marine environment for the terrestrial one, they became more susceptible to significant temperature changes, requiring an enhanced ability to control internal temperature independent of environment. Since different organs and processes had to adapt, it must have taken a long span to accomplish the change. This might suggest that the cold-warm blood difference is not like an on-off switch, but like a dimmer switch, with various intermediate stages of internal temperature control corresponding to symbiotic genetic mutations, reinforced by cold temperature regimes.

The transition from cold-blooded to warm-blooded is not yet completely characterized. The basic mechanism consists of adaptations for maintenance of an elevated basal metabolism. Supporting cold adaptations are insulating fur and feathers, and a shivering response for temporary bursts of metabolic activity. Supporting heat adaptations are an evaporative cooling (sweating) response, and a panting response.

We see some remnants of hypothetical intermediate thermal control stages today. Bats and small birds can reduce their resting metabolism far below typical levels (daily torpor), allowing them to survive cold nights and the scarcity of winter food sources. The hibernating mammals can further extend periods of torpor for an entire season of down-regulated metabolism, accompanied by various supportive adaptations. Even in the marine environment, thermal regulation processes are evident. Swordfish and some sharks are able to maintain temperatures above ambient levels in their brains and eyes, enhancing performance of these critical organs.

Mammals were not the only reptilian descendants to adopt internal temperature controls. The dinosaurs did also. The only current descendants of dinosaurs are the birds. Birds and mammals have essentially shared the earth during their contemporaneous evolutions.

The earliest transitional bird was identified in 1868 to be Archaeopteryx, from a 150myo fossil found in Germany. It was a feathered dinosaur, with teeth, claws, and bony tail. In 2013, an earlier fossil from China, named Aurornis xui, or ‘dawn bird’, was suggested as the node species. It is thought to have lived 10my earlier than Archaeopteryx. It was the size of a pheasant with long tail and downy feathers, but was not yet able to fly.

80ma: Mammal to Primate

Primates are thought to have originated in Asia. The 55ma Chinese fossil Archicebus is the size of a small mouse with long legs and tail. It is unequivocally a primate and is thought to be ancestral to tarsiers and very close to the branch node between the tarsiers and other primates.

The primate transition is not yet in clear focus. Our earliest primate-like fossils date to ~60ma, but genetic dating of the most recent common ancestor of all primates is estimated to be 80+ma. The earliest fossils reveal a tiny mouse-like mammal whose ancestors spawned both tree shrews and primates.

Primates are thought to have co-evolved with the angiosperms as arboreal insectivores who expanded their diets to include fruits, seeds, and other products of flowering plants. Their hands and feet adapted nails to replace claws and developed grasping capabilities. They evolved leaping ability to enable a flexible arboreal lifestyle. Their eyes migrated forward in the skull to enable 3D, stereo vision. Visual acuity replaced olefaction as the primary sensory capability. Their brains evolved ever larger, as their gestational and developmental periods lengthened. We primates have a long and dependent relationship with trees.

Other Notable Transitions Recorded in the Animal Fossil Record

Amphistium is a 50ma fossil fish exhibiting a unique evolutionary adaptation. Flatfish lie on the seabed, so have by adaptation moved both eyes to the same side of their head. Amphistium is a transitional flatfish fossil. Its eyes have started to migrate to one side of its head, but the transition is incomplete.

Ambulocetus is a 50ma fossil resembling a walking whale. Sometime after primates first evolved, some mammals returned to the sea. Darwin had trouble explaining the return of mammals to a marine environment. Our eureka moment came via the 1993 discovery of Ambulocetus, having four legs for walking in both land and water. Its hind feet were already partially adapted for efficient swimming. Its hearing was via vibrations in its jaw bone, just as with modern whales. Its teeth resemble those of modern cetaceans, and its nose was adapted to enable it to swallow under water. In size, it resembled a 3m long crocodile, but with straightened legs. It may have hunted like a crocodile in both fresh and salt water. There was not to be a happy amphibious middle ground for these reverse adaptations, however. As the marine adaptations to hearing and feeding and limb structure progressed, they were forced to adopt the ocean as their sole environment.

A Brief Timeline of Plantae and its Subclades

As noted above, eukaryotes began around 2,000ma. Plantae sensu lato are the bikont eukaryotes, aka Archaeplastida, which includes the land plants and algae. Clades within Archaeplastida are Viridiplantae (land plants, green algae), Rhodophyta (red algae), and Glaucophyta. Much research to date suggests that Archaeplastida is monophyletic and that the various plastids in this group have a common source (although paraphyly arguments persist).

Green plants (1,200ma): Plantae sensu stricto are the Viridiplantae or green plants. All possess chlorophyll a and b, have plastids that are bound by only two membranes, are capable of storing starch, and have cellulose in their cell walls. Subclades include Chlorophyta and Streptophyta, two clades of green algae.

Streptophyta: Streptophyta is the clade of green algae within Viridiplantae from which all land plants evolved.

Land plants (540ma): Embryophyta is a clade within Streptophyta that includes all the plants except green algae. Embryophyta likely evolved from a species of complex green algae. Today’s descendants include fresh water pond weeds such as stonewort. They differ from algae by internalizing the early fertilization and embryonic development, and by a growth process based on metamers, groups of cells generated by a specific cell type that get repeated. Metamers are analogous to animal tissue, giving rise to the alternate name for this group, Metaphyta. All land plants are further distinguished by utilizing a phragmoplast during mitosis, a complex scaffold of microtubules to assist in forming new cellular walls.

Spore-producing plants (380ma): The sporophytes are a clade of Embryophyta that reproduce via spores, either homosporous or heterosporous (two spore types produced). The gymnosperms likely evolved from such heterospores.

Naked seed plants (320ma): The gymnosperms are the naked seed bearers, including today’s conifers and ginkgo. Both gymnosperms and their subclade the angiosperms are collectively referred to as the Spermatophyta or seed-bearing plants. Gymnosperms are a clade of the Sporophyta and likely evolved via a whole genome duplication event from the progymnosperm branch of the spore producing plants.

Flowering plants (250ma): Our most familiar land plants are the flowering plants whose seeds are enclosed in ovaries. These are called the angiosperms or Magnoliophyta, which evolved from the naked seed plants. Angiosperm origins are dated based on fossilized seed species identified from core drillings.

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