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Evolution of SPECIES


The first attempt to lay out evolutionary history as a progression based on anatomy  was Ernst Haeckel's Biogenetic Law (1866). His tree "Pedigree of Man" had the correct sequence of  Primitive - Invertebrate - Vertebrate - Mammals. 














We now have much more fossil history, biochemical information and DNA. A tree based on Mitochondrial DNA was recently compiled giving a more detailed view of relationships. The family tree drawing was inspired by a linear diagram of species differentiation in cytochrome C from  a biochemistry textbook, Lehninger. Cytochrome C is a genetic protein common in all living things. The organic curved branches is humans centered but not at the top of the tree. Canines evolved with better smell, whales with bigger brains, and eagles with better vision.

Personal communication from Mark Hom MD


I annotated the evolution tree with the key functions of metabolism, energy distribution, structure and reproduction, that enabled the different branches.  Life started with cyanobacteria and plants that use photosynthesis  to absorb CO2 fix carbon and produce oxygen, seeding earths atmosphere. Decomposers such as mushrooms then evolved that took plant proteins  and produce carbon dioxide and energy. The first oxygen users were the mollusks (insects, crustaceans, octopus) that had copper based blood that flowed through their body cavity. Octopus evolved a  closed blood distribution that  enabled oxygen to be delivered to key organs.  Iron based blood (hemoglobin) in a closed circulation system then became universal in vertebrates from lampreys and fish onwards. Warm blood evolved in dinosaurs on, enabling much faster metabolism. The final step increases the development of their young. Eggs provide a finite amount of energy to the developing fetus. Octopus' actively protect their eggs, sharks let them develop in their bodies for protection, and monotremes suckle their young after hatching. The placental mammals provide unlimited time and access to energy to maximize fetal development.

The key functions that appear as the species evolve can be overlayed on the Mitochondrial tree proving a much more detail of the expansion of functionality. 

It starts  with a bacteria  lipid walled, single cell with a ring of DNA.  Cloroplasts evolved that could absorb sunlight.  The first big branch is to plants with multiple cellulose walled cells with full DNA functionality in including Mitochondria. Mitochondria provide energy to the eukaryote cell by oxidizing sugars or fats and releasing energy as ATP. These two are responsible for the oxygen atmosphere.  Mitochondrial DNA is inherited only from the mother and contains only information needed for the mitochondria to work.

This evolution of species has progressed in bursts. The earth has  changed over time; through continental drift, volcanism, orbit changes, meteor impacts etc. Each change affects climate, and hence the vegetation, and all the life that feeds on the vegetation. A change that disrupts the local balance of between predators and prey, creates a new niche that provides an opportunity for new species to thrive. Large changes have led to mass extinctions and completely new classes of animals such as mammals. 

The ancestors of land plants evolved in water. An algal scum formed on the land 1,200 million years ago. Around 450 million years ago, the first land plants appeared. Around 420 million years ago, club mosses, ferns then appear. By the end of the 363 My ago, most of the basic features of plants today were present, including roots, leaves and secondary wood in trees.  The 358-298 My ago saw the development of forests in swampy environments dominated by clubmosses and horsetails, including some as large as trees, and the appearance of early gymnosperms, the first seed plants. In the time of the dinosaurs the world was covered by a hardy conifer forest, providing accessible food for very large herbivores. By the end of the Cretaceous 66 million years ago, over 50% of today's flowering plants "angiosperm"  had evolved,  accounting for 70% of global species. It was around this time that flowering trees became dominant over conifers, providing a new high calorie niche ready and waiting for the primates. 20 million years ago, grasslands took over from trees as the climate cooled and dried out providing a new niche for ruminants, the grass digesting herbivores, and their predators. 

Next up are the Fungi, which are the clean up crew as decomposers of protein and cellulose.  The users of oxygen starts with sponges which evolved as fixed growths in the water that filtered nutrients from the flowing water.  The genetic thread splits into the Bilatria with symmetrical eyes and limbs, and  Cnidaria  are predatory marine invertebrates including jellyfish, hydroids, sea anemones, corals and some of the smallest marine parasites. Corals are the most spectacular subgroup. Although some corals are able to catch plankton and small fish using stinging cells on their tentacles, most corals obtain the majority of their energy and nutrients from photosynthetic algae that live within their tissues.  Coral species include the important reef builders that inhabit tropical oceans and secrete calcium carbonate to form a hard skeleton. A coral "group" is a colony of very many genetically identical polyps. Each polyp is a sac-like animal typically only a few millimeters in diameter and a few centimeters in height. A set of tentacles surround a central mouth opening. Each polyp excretes an exoskeleton near the base. Over many generations, the colony thus creates a skeleton characteristic of the species which can measure up to several meters in size. Individual colonies grow by asexual reproduction of polyps. Corals also breed sexually by spawning: polyps of the same species release gametes simultaneously overnight, often around a full moon. Fertilized eggs form planulae, a mobile early form of the coral polyp which, when mature, settles to form a new colony.

The Bilateria genetic thread led to insects and eventually mammals. Around 610 My ago, the Protostomes appeared  who developed mouth before anus in the embryo. They split into one branch (Arthropods) with a jointed exoskeleton  such as centipedes, millipedes, scorpions, spiders, woodlice, mites, and ticks, 6 legged insects and crustaceans. Another branch led to  mollusks and Cephalopods such as Squid and Octopus. Cameroceras with a 2m shell is an early cephalopod from 450 Mya.   The  Mollusks appeared with an shell and a whole body circulation of oxygen using "Hemolymph" and copper based blood. The snails evolved into squids and octopus with closed circulation of a copper containing blood, which enables oxygen to be delivered to key organs.


The octopus only have one cycle of reproduction in their lives. The female protects their eggs as they develop, one of the hallmarks of higher intelligence.  Octopuses, like other coleoid cephalopods but unlike more basal cephalopods or other molluscs, are capable of greater RNA editing, changing the nucleic acid sequence of the primary transcript of RNA molecules, than any other organisms. Editing is concentrated in the nervous system, and affects proteins involved in neural excitability and neuronal morphology. More than 60% of RNA transcripts for coleoid brains are recoded by editing, compared to less than 1% for a human or fruit fly. Coleoids rely mostly on ADAR enzymes for RNA editing, which requires large double-stranded RNA structures to flank the editing sites. Both the structures and editing sites are conserved in the coleoid genome and the mutation rates for the sites are severely hampered. Hence, greater transcriptome plasticity has come at the cost of slower genome evolution.  In addition, the octopus  evolved a genome as complex as humans with "jumping genes". In these, the DNA is  45% transposed (reorganized within the animal) a feature that has been linked to  intelligence in humans.  The octopus has demonstrated remarkable intelligence in problem solving  and ability to self camouflage in color and texture. The octopus seems be a real "alien" intelligence on this planet with completely different design, and biochemistry. What they found was a brain more complex than that of a rat or a mouse. In fact, its complexity was similar to that of a dog’s brain. Some cephalopods have more than 500 million neurons. In comparison, the resourceful rat has 200 million, and the ordinary mollusk has 20,000.   Their brain-to-body-mass ratio falls between that of cold and warm blooded vertebrates. They demonstrate tool use, recognition of humans, the ability to solve abstract problems for instance;  captive cephalopods have also been known to climb out of their aquaria, maneuver a distance of the lab floor, enter another aquarium to feed on captive crabs, and return to their own aquarium. They can unscrew the lids of bottles from the inside. These suggest an intelligence superior to dogs, on a par with primates.

There were no land based creatures so a huge niche was empty. The insects evolved from crustations as  pollinators of the  plants that appeared around 400 M years ago. Insects took over and  ruled the land until the amphibians showed up. Today, they probably represent 90% of the species on earth. They show some amazing collective capabilities. Butterfly's evolved around 50 M years ago post KT extinction. Butterflies have the unique migration from Mexico to Alaska, travelling north over 4-5 generations each lasting 2 months using the sun as a guide, following the flowering of milkweed.  They then fly south in a single 8 month generation. Bees have developed signals to show each other the direction to food. Ants are herbivores that  demonstrate large scale communication and cooperative action. 


In the ocean, lampreys were the first to evolve a closed circulation system with iron containing blood - hemoglobin. This enables oxygen to be delivered to key organs. 

The vertebrates first appeared with  lobe finned fish such as lungfish and celeocanth, as part of the Cambrian explosion 530 M years ago. In the Devonian 445 M years ago or the  "age of fishes"  ray finned fish (bony vertebrates) became easily the largest class of fish. The sharks with cartilage skeletons evolved keeping their eggs inside their bodies until they hatched to protect their young. Fish have a 2 chamber (atrium & ventricle)  heart.

The first major groups of amphibians developed in the Devonian period, around 370 million years ago, from lobe-finned fish which were similar to the modern coelacanth and lungfish. The amphibians, such as frogs, marked the transition onto land, while needing water for reproduction and their young. The amniotes evolved hard shelled eggs that no longer needed water emersion to develop. This lead them to spread all over Pangea. After the Carboniferous rainforest collapse 305M years ago, amphibian dominance gave way to reptiles, and amphibians were further devastated by the Permian–Triassic extinction event.

Amphibians have a skeletal system that is structurally homologous to other tetrapods, though with a number of variations. They all have four limbs except for the legless caecilians and a few species of salamander with reduced or no limbs. The bones are hollow and lightweight. The musculoskeletal system is strong to enable it to support the head and body. The bones are fully ossified and the vertebrae interlock with each other by means of overlapping processes.   In most amphibians, there are four digits on the fore foot and five on the hind foot, but no claws on either. They have lungs and a heart that consists of a single ventricle and two atria.

The origin of the reptiles lies about 310–320 million years ago, in the steaming swamps of the late Carboniferous period. The reptiles split into 2 genetic threads; one led to to todays reptiles and birds via the dinosaurs. The other became insect eating burrowers which led to todays mammals. It appears that by living in burrows, just like meercats, they survived predation by dinosaurs and extinction events for 200M years ! They slowly evolved into highly developed mammals that provided their growing offspring with unlimited energy through their placenta and milk.  Mammals and birds thrived after the K/T meteor and share about 80% of their DNA, and a similar number of mutations from their common root over the same time span. 


The first branch are called the sauropsids, led to dinosaurs and reptiles that are around today; Lizards, Snakes, Iguanas, Turtles, and Crocodiles. Along with lungs, the first 4 chamber heart appears in the reptile line, separating blood supply to the lungs and everything else. The second branch are the synapsids, Lystrosaurus was a key survivor until finished off by the dinosaurs, and the branch has no reptile survivors today but eventually evolved to mammals. 

The skeletal evolutions were first synapsids followed by 3 middle ear bones (including marsupials)  and then placentals. Synapsida[a] is one of the two major clades of vertebrate animals in the group Amniota, the other being the Sauropsida (which includes reptiles and birds). The synapsids were the dominant land animals in the late Paleozoic and early Mesozoic, but the only group that survived into the Cenozoic are mammals.[6] Unlike other amniotes, synapsids have a single temporal fenestra, an opening low in the skull roof behind each eye orbit, leaving a bony arch that provides anchor points for jaw muscles. The distinctive temporal fenestra developed about 318 million years ago during the Late Carboniferous period,[1] when synapsids and sauropsids diverged, but was subsequently merged with the orbit in early mammals. Originally, the openings in the skull left the inner cranium covered only by the jaw muscles, but in higher therapsids and mammals, the sphenoid bone has expanded to close the opening. This has left the lower margin of the opening as an arch extending from the lower edges of the braincase.

Mass extinction events cause an explosion of new species. Numerous ecological niches are suddenly empty of both competition and predators. New herbivores and insectivores can flourish, eventually leading to new predators, and new balanced ecosystems. 


The Permo-Triassic extinction event 251 My ago radically changed the structures of communities with a 60% marine extinction. Ocean acidification decimated any species with calcium carbonate shells. This may have set the scene for the evolution of flowering plants in the Triassic (~200 million years ago),  Conifers diversified from the Late Triassic onwards, and became a dominant part of floras in the Jurassic as a niche food source for huge herbivores.  On land, there was the largest known mass extinction of insects. Aridification induced by global warming was the chief culprit behind terrestrial vertebrate extinctions. There is enough evidence to indicate that over two thirds of terrestrial labyrinthodont amphibians, sauropsid ("reptile") and therapsid ("proto-mammal") taxa became extinct. Large herbivores suffered the heaviest losses.  Lystrosaurus  a pig-sized herbivorous proto-mammal, constituted as much as 90% of some earliest Triassic land vertebrate fauna.  

In the mid to late Triassic, the dinosaurs evolved from one group of archosaurs, and went on to dominate terrestrial ecosystems during the  Jurassic and Cretaceous. It appears that reptiles that were self sufficient straight out of the egg, did better than proto mammals that required parental support.  This "Triassic Takeover" may have contributed to the evolution of mammals by forcing the surviving  mammal successors to live as small, burrowing, mainly nocturnal insectivores.; nocturnal life probably forced at least the proto-mammals to develop fur, better hearing and higher metabolic rates,[284] while losing part of the differential color-sensitive retinal receptors reptilians and birds preserved. Archosaurs also experienced an increase in metabolic rates over time during the Early Triassic. 


It is thought that warm blooded dinosaurs evolved to better survive the volcanic created extinctions 250 and 205 M years ago. A new study of thigh bones from Plesiosaurus, Stegosaurus, Diplodocus, Allosaurus, and modern hummingbirds  posits that the extinct animals were warm blooded,   Imaging the bones with infrared spectroscopy, scientists found an abundance of molecules produced as waste during oxygen inhalation,  The molecules are a sure sign of a high-powered metabolism, which warm-blooded animals use to keep their body temperatures constant.

Studying the minuscule tubes of the inner ear, places the evolution of mammalian warm-bloodedness at around 233 million years ago

Based on an analysis of the relationships among Tawa and other early dinosaurs, the researchers hypothesize that dinosaurs originated in a part of Pangea that is now South America, diverging into theropods (like Tyrannosaurus rex), sauropodomorphs (like Apatosaurus) and ornithischians (like Triceratops); and then dispersed more than 220 million years ago across parts of Pangea that later became separate continents.

The dinosaur era lasted 200M years and was the cradle of most of todays species. The feathered birds evolved from warm blooded dinosaurs, the first is Anchiornis. “It seems like birds had happened upon a very successful new body plan and new type of ecology—flying at small size—and this led to an evolutionary explosion,”

In the proto-mammal genetic thread, the monotremes were the first mammals who laid eggs but suckled their young, duck billed platypus is the best known. DNA evidence supports a South American origin for marsupials, with Australian marsupials arising from a single Gondwanan migration of marsupials from South America, across Antarctica, to Australia, 100-120 My ago. The Marsupials thrived in Australia, Wallacea and the Americas now  include kangaroos, koalas,  Tasmanian devils, wombats, wallabies, possum and bandicoots. The Opossum is a close relative, a marsupial that originated in S America, and now live in N America.  

By 70 My ago (Creataceous), the continents had started to move apart. N America was the home of the widest variety of dinosaurs, with a land bridge to the other continents.  The first placental mammals were shrew - like and  small enough to be ignored by the dinosaurs. To this point all species of animals used eggs for reproduction with a limited  energy supply  before the fetus had to be viable.  The placenta  allowed much longer time for the fetus to develop with unlimited energy supply. This enabled much more complex species.  However,  dominant dinosaur predators blocked any chance for the mammals, birds and reptiles to thrive.

The KT meteor impact 65 My ago produced a combination of blast, tsunami, firestorm from re-entering impact debris, dust that blocked the sun for years and acidified the oceans. As a result, there was a  mass extinction of  anything over 50 lbs which included all large herbivore and their predator carnivore dinosaurs, presumably the little guys could hide underground. Marine invertebrates were also decimated. In these new uninhabited niches new species of mammals, reptiles, and birds had a better chance of survival.


Over the next 65 M years, plate tectonics created all the young mountain features such as Himalayas, Alps, and Rockies which were eroded back creating new ecological niches filled by new mammal and bird species. The humans evolved over the last 7M years with volcanic activity and ice ages creating another set of niches for species to thrive.

After the KT impact, the small dinosaurs that were left evolved as warm blooded birds and cold blooded reptiles. Once the plant life recovered, all the resource niches occupied by large dinosaurs become available such as grasslands and tree tops accessed from land and air. The small dinosaurs that survived, evolved into the birds. The corvids (ravens, crows, jays, magpies, etc.) and psittacine (parrots, macaws, and cockatoos) are often considered the most intelligent. They demonstrate tools use. Cormorants have been shown to count to 7.  Kea's also show malicious destruction including letting air out  of tires. After the extinction, lobe finned fish disappeared and were replaced by ray finned fish. The "perch like" ray finned fish (Percomorpha) and the "perching" song birds (Passeriformes)  thrived into tens of thousands of variants.  Passeriformes feed on insects and in some cases nuts and fruits as well. Apparently they were particularly adapted to exploit the new environment after the KT impact. 

A number of birds reverted to flightless including penguins, emus, and ostrich. Dodos (relative of doves)  unique to Mauritius located just off of Madagascar were made extinct by humans. Moa in New Zealand met a similar fate. 

Phorusrhacids, colloquially known as terror birds, are an extinct family of large carnivorous flightless birds that were among the largest apex predators in South America   from 53 to 0.1 million years (Ma) ago. Red-legged seriema in Southern S America are the closest survivors.

Starting from the shrews, a huge range of new mammal herbivores and their predator carnivores evolved rapidly to replace the dinosaurs that had dominated over the land. The huge variety evolved to fit different climate, food, and competitor niches.  Mammals also returned back to the water evolving into hippos and eventually marine mammals such as whales, a relation confirmed by DNA. Marine mammals have a up down spinal motion like galloping mammals another indication of their land mammal ancestors. This is a contrast to reptiles such as crocodiles and snakes retain the side to side spinal motion as they move just like fish.

Mammals DNA subdivide into:

  • Primates - Monkeys, Apes, Humans

  • ​Rodents - Mouse, Rabbits, Capybara, Beaver, Nutria, Squirrels

  • Herbivores - Megacerops evolved into  Horses, Deer, Giraffes, Rhinos. Hippos are the nearest land relatives to Marine Mammals. 

  • Predators  - Cats including civets, dogs, hyenas.

  • "Xenarthra" Insect eaters - Sloths, Anteaters, Hedgehogs, Armadillos 

  • "Afrotheria" Trunked - Elephants, Aardvark, Elephant Screw, Hyrax, Dudong (Manatee or sea cow).

There are key bone signatures of species. There is a large vertical fin on the vertebrae of quadrupedal walking mammals that anchors the big muscles that support galloping .  There is a bone dome behind the ears of whales that hear underwater. Pelvis shape and hip socket show if the animal is quad or bi-pedal. Tooth shape indicate the preferred food. Ungulate herbivores have hooves. Ruminants have multiple stomachs who thrived on the grass that replaced forest 20 M years ago as the earth cooled and dried. 

Rodents and primates diverged 80-55 My ago, 53 My ago is the date of the earliest primate fossil.  There is a very patchy fossil record for early primates.  The first primate-like mammals are referred to as proto-primates. They were roughly similar to squirrels and tree shrews in size and appearance. The existing fossil evidence (mostly from North Africa) is very fragmented. These proto-primates remain largely mysterious creatures until more fossil evidence becomes available. Although genetic evidence suggests that primates diverged from other mammals about 85 Mya.

Fossils of Purgatorius, the oldest genus in a group of the earliest-known primates called plesiadapiforms are 65M years old. These ancient mammals were small-bodied and ate specialized diets of insects and fruits that varied by species.  The first remains (P. unio and P. ceratops) were reported in 1965,[5] from what is now eastern Montana's Tullock Formation (early Paleocene, Puercan), specifically at Purgatory Hill (hence the animal's name) in deposits believed to be about 63 million years old, and at Harbicht Hill in the lower Paleocene section of the Hell Creek Formation. Both locations are in McCone County, Montana. They have also been found in the Ravenscrag Formation and widely discovered in the early Paleocene Bug Creek Group, along with leptictids.[6] These deposits were once thought to be late Cretaceous, but it is now clear that they are Paleocene channels with time-averaged fossil assemblages. It is thought to have been rat-sized (6 in (15 cm) long and 1.3 ounces (about 37 grams)) and a diurnal insectivore, which burrowed through small holes in the ground. In life, it would have resembled a squirrel or a tree shrew (most likely the latter, given that tree shrews are one of the closest living relatives of primates, and Purgatorius is considered to be the progenitor to primates). The youngest remains of Purgatorius date back to ~65.921 mya, or between 105 thousand to 139 thousand years after the K-Pg boundary

Fossils like the proto-primate  Plesiadapis is one of the oldest known primate-like mammal genera which existed about 58–55 million years ago in North America and Europe had some features of the teeth and skeleton in common with true primates. They were found in North America and Europe after 65Mya and went extinct by the end of the 33Mya. There was a Thulean Land bridge connecting Europe to N America until  around 57 M years ago that could have been the path to populate Africa.

Primates are adapted for tree climbing;  1) a rotating shoulder joint, 2) a big toe that is widely separated from the other toes and thumbs, which are widely separated from fingers (except humans), which allow for gripping branches, 3) stereoscopic vision, two overlapping fields of vision from the eyes, which allows for the perception of depth and gauging distance. Other characteristics of primates are brains that are larger than those of most other mammals, claws that have been modified into flattened nails, typically only one offspring per pregnancy, and a trend toward holding the body upright.

The first true primates date to about 55 MYA. They were found in North America, Europe, Asia, and Africa. As the climate cooled, tropical forests and their occupants were pushed down to the tropics. Fruiting trees that emerged after the KT extinction provided a new niche with high calorie food for tree dwellers, that is filled by the primates. It helped that  primates are really the only tree based predators for other primates.  These early primates resembled present-day prosimians such as lemurs. Evolutionary changes continued in these early primates, with larger brains and eyes, and smaller muzzles being the trend. By the end of the Eocene epoch, many of the early prosimian species went extinct due either to cooler temperatures or competition from the first monkeys.

Many mammal species monkeys, bears, cats, large herbivores  are common to both S America and Africa however they evolved after KT event 65M years ago long AFTER the tectonic split 120M years ago. Apes evolved around 25M years ago.  Therefore there must have been a much later path but before 25M.  Around 50M years ago, temperatures were +8C from today, heavily forested, with no land ice and sea levels 100m higher.  The consensus view is that most were "lucky arrivals" from a combination of island hopping in the north and riding vegetation rafts. The accepted view is that Madagascar, Galapagos and other islands were also populated using rafts.

Monkeys originated in Africa and the first group known to have reached South America are thought to have migrated there on vegetation rafts up to 40 million years ago, when the land masses were probably between 1500 and 2000 kilometres apart, around a quarter of the distance now. Videos of pieces of land floating down the Panama Canal after a storm, show natural rafts that could have sustained upright trees that might have borne fruit. Monkey fossils in S. America date from 36M years ago.

In Columbia, "While travelling across a vast expanse of wetland, he passed an enormous floating island complete with tall trees and a resident colony of howler monkeys". As vegetarian fruit eaters, they could easily survive on an island with just trees for many months.

Floating islands  form during floods of the great tropical rivers when large masses of aquatic vegetation or chunks of their banks are torn away and carried downriver. The Congo in Africa is one such river, and floating islands that came down the Congo were reported 240 km out to sea from the river's mouth. Floating islands are also common in the Sepik river in Papua New Guinea following the monsoon rains. The islands are called "Lik Lik Aislans" in pidgin English, and can be up to 100 metres across with living trees on them. The Ro Paran and Ro de la Plata in South America also generate floating islands -- when they flood they are filled with floating islands called camalotes , which are matted masses of water hyacinth. A famous episode at Convento de San Francisco in Santa Fe, Argentina, which is located on the Ro Paran, involved the killing of two friars at the Convento by a jaguar that arrived on a camalote during a flood of the Paran on April 18, 1825. An example from Loktak lake, Manipur, India. In 2019 a pumice island 150 ​odd square kilometres in area was found in the Coral Sea.


Compared to rodents, the primates are much larger tree dwellers, with all sorts of enabling adaptations such as grip, strength, and prehensile tails. As large tree dwellers they were safe from most predators. There was little competition for  high calorie food.  The result was they thrived and developed much larger brains.


Early Primates - mostly nocturnal and very small

      Lemurs in Madagascar,

      Tarsiers SE Asia Islands, 

      Loris in SE Asia,

      Galagos or Bushbabies in Africa

Monkeys - tails, walking through trees;

      Macaques including Rhesus & Japanese, Proboscis, Langur (India)  in Asia

      Baboons, Ververt, Colobus, Mandrill, Gelada (Ethiopia) in Africa

      Howler, Squirrel, Tamarin, Capuchin, Marmoset  in S America with prehensile              tails

Apes - no tails, swinging through trees;

     Gibbons in Asia

     Orangutans in Asia

     Gorillas in Africa

     Chimpanzees, Bonobos in Africa

Humans in Africa


N and S America were connected only 3M years ago accounting for the species differences between them. Around 200 K years ago humans appeared and are now for better or worse are the dominant species.

A species of primate "Giantopithecus blacki" grew to 10 ft tall ! but went extinct 250,000 years ago during a period of grassland domination possibly due to the loss access to fruit. Closely related to Orangutans,  


Many more animals in South America have prehensile tails than in Africa and Southeast Asia. It has been argued that animals with prehensile tails are more common in South America because the forest there is denser than in Africa or Southeast Asia.[3] In contrast, less dense forests such as in Southeast Asia have been observed to have more abundant gliding animals such as colugos or flying snakes; few gliding vertebrates are found in South America. South American rainforests also differ by having more lianas, as there are fewer large animals to eat them than in Africa and Asia; the presence of lianas may aid climbers but obstruct gliders.[4] Curiously, Australia-New Guinea contains many mammals with prehensile tails and also many mammals which can glide; in fact, all Australian mammalian gliders have tails that are prehensile to an extent.

During the early Miocene, 23.03 to 5.333 million years ago, a wave of mammalian immigration from Eurasia over the Bering land bridge brought bear-dogs (early ancestors of modern canines of the genus Amphicyon), European rhinocerosesweasels, and a variety of deerlike mammals to North America. Also during this time, mastodons escaped from their isolation in Africa and reached North America by the middle of the Miocene

Many large animals disappeared 13–11,000 years ago, "Quaternary extinction event", possibly due to climate, habitat and sea level change at the end of the last ice age, or human predation as communities get established. In North America ​the last camel  vanished along with horses, short-faced bears, mammoths and mastodons, ground and unicorn sloths, sabertooth cats, and many other megafauna.   In New Zealand the arrival of the Polynesians led to the extinction of the Dodo and other flightless birds. 

Borneo is situated on the Asian side of the "Wallace Line", which is another example of the effect of geographic isolation  on evolution. The Wallace  Line that separates the biogeographical realms of Asia with elephants and tigers, and 'Wallacea', a transitional zone between Asia and Australia also called the Malay Archipelago and the Indo-Australian Archipelago with marsupials.   The line runs through Indonesia, such as Makassar Strait between Borneo and Sulawesi (Celebes), and through the Lombok Strait between Bali and Lombok, where the distance is strikingly small, only about 35 kilometers (22 mi), but enough for a contrast in species present on each island. The complex biogeography of the Indo-Australian Archipelago is a result of its location at the merging point of four major tectonic plates and other semi-isolated microplates in combination with ancient sea levels. 

Function evolution 


Metabolism started with bacteria and plants evolving photosynthesis that used light energy to combine carbon dioxide and water to fix carbon produce oxygen  and  grow the full range of biomoleculescatalyzed by enzymes.

Next digesters such as fungi evolved that use oxygen and enzymes to breakdown carbohydrates into carbon dioxide and energy using the citric acid cycle.

Animals evolved to combine these 2 steps using sugars as the energy source in the citric acid cycle to generate ATP energy and use ATP energy to grow and live. 

In bio systems, energy is stored and released in the exchange between ADT "diphosphate" and ATP "triphosphate". Cyanobacteria use  photosynthesis as an energy source to  support replication leading to stromatolites and  oxygen. This includes creating a wide range of molecules in their cells such as DNA, lipids, proteins.  In photosynthesis, plants use the energy of sunlight to make ATP and then the Calvin cycle fixes carbon to create glucose, and a full range of biomolecules. There are also nitrogen fixing bacteria.

The Calvin cycle uses CO2 and energy from ATP in a process of taking a 5 carbon bi-phosphate, making two 3 carbon phosphates one of which is used and the other recycled. The key enzyme of the cycle is called RuBisCO, another bi-phosphate. After 5 cycles, the five 3 carbon phosphates are reorganized into three more of the  5 carbon bi phosphates, completing the cycle.

Plants expanded their metabolism to grow cellulose shells for huge multicellular structures, and added more efficient  energy generation from  chloroplasts to become prolific oxygen generators.

Fungi were the first "digesters" that could breakdown carbohydrates into heat, carbon dioxide and water.  Fungi use the citric acid  (Krebs) cycle to break down biomolecules and release the energy as heat. The citric acid cycle is found in species as diverse as the unicellular bacterium Escherichia coli, fungi, and huge multicellular organisms like elephants. They breath in oxygen and breath out carbon dioxide. 

The citric acid energy cycle starts with citric acid (5 carbon, 3 acid ,1 ketone molecule). It gets oxidized to remove 2 carbons leaving succinic acid, (4 carbon 2 acid molecule) plus energy as ATP. The succinic acid then combines with acetyl (2 carbon 1 acid molecule) to regenerate citric acid. The acetyl molecules are peeled off glucose. Additional byproducts of the cycle are a number of bio precursors.


Fungi also fabricate new biomolecules to grow. The engine for building sequences is the ribosome that uses messenger RNA to provide the template, and the t-RNA bound to amino acids to build a peptide chain.  

Animals  evolve ways convert the biomolecules in plants and animals in  food to glucose using their new specialized organs. They use the glucose  in the citric acid (Krebs) cycle to produce usable energy in the form of ATP.  Animals expanded their metabolism to include  oxygen supply using blood,  in using energy to trigger molecular reconfiguration in muscles, and electrical transfer in nerves and  neurons, and the growth of biomolecules. These reactions combine monosaccharides to form polysaccharides, fatty acids to form triglycerides, amino acids to form proteins, and nucleotides to form nucleic acids. These processes require energy in the form of ATP molecules generated by catabolic reactions. Anabolic reactions, also called biosynthesis reactions, create new molecules that form new cells and tissues, and revitalize organs.

The first animals were all cold blooded. The evolution of warm blood  enables higher metabolic rates with enhanced unloading of oxygen by hemoglobin. This relationship is helpful as metabolically-active peripheral tissues such as exercising skeletal muscle which often display supra-normal temperatures. Because of this increased temperature, oxygen unloading by hemoglobin is enhanced in these metabolically-active tissues, thus improving oxygen transport to areas which require it most.


The animals use blood to concentrate and deliver oxygen.  Copper blood carries 1/4 of the oxygen as iron blood (haemoglobin), but works better at low temperature and may have less tendency to clot. 

Copper blood first  appeared in mollusks with open circulation throughout their body cavity.


Closed circulation with arteries and veins evolved to better deliver oxygen and nutrients to key organs in vertebrates and cephalopods like octopus.  


The vertebrates then evolved with more efficient iron based blood.

Finally amphibians evolved lungs that enabled complex air breathing life.  


Bacteria started with dual lipid based cell walls. 

Plants added a cellulose superstructure that enabled large trees. 

Exoskeletons appeared  with the first mollusks that provided physical protection and a structure for load bearing and locomotion. The big limitation was that the skeleton does not grow, it must be shed and regrow for the animal to grow larger. 

The evolution of vertebrates with an internal support structure started with fish and continues today. The basic bone architecture has been retained for hundreds of millions of years. The internal structure  allows growth and training changes. 


It starts with cell division in bacteria. Plants use seeds usually spread annually. 

The first animals reproduced through large numbers of fertilized eggs, that were left to fend for themselves. Eggs provide a limited energy supply and when it is used the fetus must be self supporting. 

An improved survival strategy appeared where eggs are  protected by parents (octopus) before birth. Warm blooded animals had to keep the eggs warm as well (birds). After birth, the infants are often fed by parents until self-supporting. 

Another survival strategy appeared in monotremes. After eggs are hatched, the infants are supported by mothers milk   

One  way to improve survival appeared when eggs were allowed to develop protected inside the mothers body, for example in sharks. 

The final evolution occurred in placental mammals, where the fetus develops with unlimited energy and time, with energy supplied by the placenta inside the mother, and then is supported after birth by mothers milk. 

It appears that the recipe  for intelligence is a creature with locomotion, a  closed circulation oxygen deliver system for key organs, and a complex gene structure that can be locally reorganized. 

The most intelligent species seem to track the brain to body weight ratio, but requires a long time to reach maturation. 

Primates are large tree dwellers which protects them from predation.

Elephants have great size which protects them.  

Octopuses have remarkable camouflage for protection.

Cetaceans (whales & dolphins) are the largest water dwellers. 
Crows show remarkable adaptability and the ability to problem solve. 

Small mammals, such as rodents, were prey for many larger species. Survival requires mobility with little time for maturation. This would block evolution of greater intelligence. 

Cats actually have 90.2% of the DNA in common with us! You read that right! Cats are genetically surprisingly closer to us than dogs, who share about 84% of the genes with us (Pontius et al, 2007).

Match to Human DNA 

             Plants (18%)  1.5 B years for 82% change                    18 My/%

                             Insects (44%)  500M years  66%                      9 My/%

                                    Birds (80%)  200 M years  for 20%         10 My/%

                                        Dogs 84%

                                          Cats (90.2%)

                                              Rodents (93%)  80 M years for 7% 11 My/%                                                                                  Apes (99%)  7 M years for 1%   7 My/%

                                                        Humans (100%)

It took 1.5 By for plants to evolve to  Dinosaurs (80% human DNA), who then lasted for 200My. Insects have 60% human DNA. It took 60My for Shrews (93% human DNA)  to evolve to Apes (99.5% human DNA). It took 7M years for Apes to evolve to Humans. The DNA differences represent a "round trip", so the mutation rate is around 20M years for 1% DNA change in gene location. 

Bacteria  - ring DNA - converts CO2 to O2

       Plants (18%)  - Mitochondria - cellulose multi-cell walls,  uses light to converts CO2 to O2 in chloroplasts 

                      Yeasts (26%)  - Unicellular - digests sugar to alcohol !

                      Mushrooms - multicellular - breaks down cellulose.

                           Sponges - fixed structures that use water flow to feed, 

                               Jelly fish - locomotion,  basic sensors, no dedicated respiration or digestion

                                   Mollusks  - Soft Exoskeleton

                                           Snail - Shell


                                           Octopus - Closed circulation, copper based blood, brain, jumping genes.

                                   Crustacians - Hymolph - Hard Exoskeleton  

                                   Insects (44%) (Millipedes, Flies, Moths) -   

                                         Starfish -  

                                             Lampreys - cartilage skeleton - closed circulation Haemoglobin



                                                     Fish (Carp & Tuna)


                                                              Birds (80%) , Crocodiles, Snakes, Lizards


                                                                       Rodents (93%)

                                                                             Dogs, Cows, Marine Mammals

                                                                                Apes (99%) & Humans

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