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history:evolution

evolution

the beginning of life

  • organic molecules such amino acids and fatty acids spontaneously form in a hot hydrogen rich reducing environment perhaps resulting in the spontaneous formation of fatty acid membranes in water combined with self-replicating “genetic” molecules (the early ones may not have been DNA/RNA or protein) which then could randomly mutate in the copying process.
  • It is likely that RNA evolved before DNA and this primordial RNA could then start creating proteins
    • nucleobases can assemble spontaneously, in a series of steps, from cyanide, acetylene and water
    • sugar molecules are easily formed in warmed alkaline solutions of formaldehyde, the ribose could be created by interaction of two simple sugars but as it is unstable in alkaline solution, it needs to be stabilised unless it is formed already bound to a nucleobase as below
    • schreibersite, a mineral commonly found in certain meteors, releases a form of phosphorus that is more soluble in water than phosphate and far more reactive with carbon-based compounds
    • when cyanide, acetylene and formaldehyde are mixed with the phosphorus, a readily vaporizable small molecule called 2-aminooxazole, which can be viewed as a fragment of a sugar joined to a piece of a nucleobase and it is possible that when the water evaporated, these molecules too could have evaporated to be deposited in a more concentrated area in a more purified form where they can combine to form full sugar and nucleobases and solar UV destroys any “incorrect” nucleotides to leave just C and U nucleotides. Perhaps there is a similar mechanism for the production of the G and A nucleotides.
    • these nucleotides then form chains when in the presence of clay suggesting that life may have formed in the clay rich muds of hot springs and experiments suggest RNA has the raw catalytic power to catalyze its own replication
    • the simple RNA protocell evolves
      • simple fatty acid membrane vesicles enclosing RNA and immersed in a solution of nucleotides will allow these to migrate into the cell and combine with the RNA to form a complimentary version of the RNA and the osmotic effects of these then pull water into the vesicle and, if there are fatty acids nearby to incorporate into the membrane, make it expand into tubular shapes which then break off into daughter vesicles
      • if these vesicles moved from cool to hot areas of a water pool, the sudden heat could cause the double strands of RNA to separate and then be used as templates for new strands hence reproduction
      • mutations would then result in improved chemicals such as ribozymes which would speed up the replication process and synthesize nutrients and eventually synthesis of proteins which they amazing potential actions and then would “learn” to make the more robust DNA 1)
      • it is possible that the 1st forms of “life” may have been self-replicating RNA “virus” particles (although there are other ways viruses may have evolved) 2)
  • the first bacteria

Archeozoic eon: 3,900-2,500 mya

  • the “last” theoretical common ancestor of all life is called last universal common ancestor (LUCA) with an inferred set of 355 genes existed perhaps 3,500-3,800 mya which was anaerobic, CO2-fixing, H2-dependent with a Wood–Ljungdahl pathway (the reductive acetyl-coenzyme A pathway), N2-fixing and thermophilic. 3)
  • sulphur oxidising and sulphate reducing bacteria
  • arsenic oxidising bacteria (these still live in the oxygen-deplete middle layer of tropical oceans)
  • photosynthetic, oxygen producing cyanobacteria (“blue-green algae”) along with other microbes such as & archaens form microbial mats which over time become layered on a bed of calcium carbonates deposited from the carbon dioxide rich oceans (limestone) creating stromatolites start to oxygenate atmosphere

Proterozoic eon (2500 - 540 mya)

  • Great Oxygenation Event (GOE) 2400 mya
  • bacterial precursor of mitochondria
    • oxidase assembly machinery critical for the development of the inner membrane of mitochondria was present in these bacteria and has been preserved in evolution. OXA-dependent proteins are synthesized in the cytoplasm and then imported into mitochondrial organelles where they play important functions in cellular respiration, the exchange of metal ions and biochemical reactions 4)
  • anaerobic mitochondrial DNA
  • aerobic mitochondrial DNA (>1450 mya - perhaps in a Rickettsial bacteria)
  • mitosomes
  • hydrosomes
  • eukaryocytes evolve from endosymbiosis of procaryocytes with mitochondrial DNA creating complex cells oxidative mitochondrial capacity as well as anaerobic pathways (1,450 mya)
  • multi-celled organisms
    • with the move to multicellular organisms comes the risk of cancer as the DNA from single celled organisms which allows for independent and infinite cellular reproduction is still present although multicellular organisms did have genes to keep this in check such as the TP53 tumour suppressor gene - some animals such as whales and elephants have multiple copies of this gene and this presumably accounts for their low cancer rates.
    • Choanozoa (950mya)
      • Choanoflagellata
      • Animals (760mya) - nearly all animals have a dramatically shrunken mitochondrial gene count of only 13 protein coding genes the other thousands have been relocated into the host nucleus DNA 5)
        • Porifera (sponges)
        • Eumetazoa
          • Ctenophora (comb jellies)
          • Parahoxozoa (680mya)
            • Cnidaria (?741mya, but fossils dated to 580mya; corals, sea anemones, jellyfish)
              • Ediacaran soft-bodied fauna (610mya)
            • Placozoa
            • Bilateria (bilaterally symmetric body plan arose c650mya)
              • Xenacoelomorpha (lack a typical stomatogastric system; nervous system is basiepidermal, ciliated epidermis)
              • Nephrozoa (650mya; excretory organs and nerve cords - eg. early marine worms)
                • Protostomia (610mya) (the first opening (the blastopore) becomes the mouth)
                  • Ecdysozoa (529mya, “animals that moult”)
                    • Arthropoda
                      • Trilobites (521mya but extinct due to Permian extinction 252mya)
                      • Chelicerates (“have fangs”; horseshoe crabs, spiders (?420mya), mites, scorpions)
                        • Arachnida
                          • Araneae (spiders)
                            • Mesothelae (only one extant family)
                            • Opisthothelae
                              • Araneomorphae (fangs slope towards each other; 200-250mya; most modern spiders, most live < 1yr )
                                • Hypochilidae (lampshade spiders)
                                • Austrochiloidea
                                  • Gradungulidae (eastern Aust and NZ)
                                  • Austrochilidae (Chile, Argentina, Tasmania)
                                • Araneoclada
                                  • Haplogynae
                                  • Entelegynae
                                    • Theridiidae (tangle web / cobweb spiders incl. Lactodectus)
                                    • many more spider families
                              • Mygalomorphae (downward parallel fangs; 200-250mya; tarantulas, funnel-web, trapdoor spiders; females can live 25-45yrs)
                      • Myriapods (millipedes, centipedes)
                      • Crustacea
                        • malacostraca
                          • pericarida - amphipoda, isopoda (300mya)
                          • eucarida - decapoda (shrimp, prawns, crayfish, lobsters, crabs, etc)
                      • Hexapods (insects; 400mya)
                        • rapid diversification of flying insects 299-251mya
                        • now account for 75% of named animal species
                    • Nematoda (worms)
                  • Spiralia
                    • Gnathifera
                      • Rotifera
                      • Chaetognatha
                    • Platytrochotozoa (580mya)
                      • Platyhelminthes
                      • Lophotrochozoa (550mya)
                        • Mollusca
                          • Cephalopoda
                            • octopus
                        • Annelida
                • Deuterostomia (the first opening (the blastopore) becomes the anus)
                  • Ambulacraria (starfish)
                    • Echinodermata
                    • Hemichordata
                  • Chordata (notochord, a dorsal nerve cord, pharyngeal slits, an endostyle, a post-anal tail)
                    • Tunicata, (salps and sea squirts)
                    • Cephalochordata (small, segmented marine animals)
                    • Vertebrata (525mya)

Cambrian explosion of life (541mya)

  • fossils from 518mya at Chengjiang formation in China
  • a massive fossil find in 518mya old rocks on the bank of the Danshui river in Hubei province in southern China in 2019 has unearthed 4,351 separate fossils so far represent 101 species, 53 of them new to science, where well preserved primitive forms of jellyfish, sponges, algae, anemones, worms and arthropods with thin whip-like feelers, including 4cm long mud dragons and numerous comb jellies were entombed in an ancient underwater mudslide that swept them into deeper, colder water where they were buried in fine sediment halting the usual process of decay
  • fossils from the Burgess Shale, a 508m-year-old rock formation in Canada
  • by now, a gene duplication event (400-1000mya and before vertebrates had evolved) had created the two growth hormone releasing factor peptide super-families from a common ancestor6):
    • GRF (GHRH); PRP/PACAP; VIP/PHI; secretin
    • Glucagon/GLP-1/GLP-2
  • the insulin and insulin-like growth factor (IGF) signaling pathway is highly conserved among the metazoans - many invertebrates have large numbers of insulin-like peptides (ILPs) 7)
  • some vertebrate hormones may have had a role in neural tissues in invertebrates 8)
  • the ancestral steroid receptor was likely present before the separation between protostomes and deuterostome, however, the oestrogen receptor may have been secondarily lost in taxa such as arthropod and nematode protostomes (Maglich et al. 2001), or the urochordate and echinoderm deuterostomes
    • adrenal and sex steroid receptors are not found in echinoderms and hemichordates 9)
    • the common octopus, Octopus vulgaris, is the first invertebrate species shown to possess representatives of three classes of sex-steroids found in vertebrates (progestins, androgens and estrogens) as well as binding proteins for these steroids
  • receptors for vertebrate oestrogens and 3-ketosteroids first appeared in basal chordates (cephalochordates: amphioxus)
  • an ancestral progesterone receptor and an ancestral corticoid receptor, the common ancestor of the glucocorticoid and mineralocorticoid receptors, evolved in jawless vertebrates (cyclostomes: lampreys, hagfish)
  • evolution of an androgen receptor and distinct glucocorticoid and mineralocorticoid receptors arose in cartilaginous fishes (gnathostomes: sharks) 10)

The origin of the vertebrates

  • development of the embryonic neural crest allowed evolution from being filter feeders to having a predatory lifestyle courtesy of the new, distinct anatomical head with a distinct brain and paired sensory organs11) and appears to evolved with the early lampreys and gnathosomes 500-550mya which had the following types of neural crest genes:
    • patterning signalling genes
    • neural plate border specifiers
    • neural crest specifiers - transcription factors that render the cells bona fideneural crest progenitors conveying the ability to delaminate and migrate
    • neural crest effector genes
  • invertebrates have a ventral nerve cord but vertebrates developed a dorsal nerve cord and this 180deg “somatic twist” relative to the brain resulted in the neural fibres crossing or decusatting 12)
  • lampreys lack the commissural sympathetic chain that all gnathostomes possess, but did have preganglionic sympathetic fibres, noradrenaline and two G-protein coupled adrenergic receptors, a beta-adrenoreceptor A and a beta-adrenoreceptor B.
  • hearts of hagfish lack neural inputs, while hearts of lampreys are innervated by the vagus but it does so in a stimulatory manner perhaps as their cardiac muscle is more like striated muscle unlike in gnathosomes which have vagal inhibitor and synpathetic stimulatory inputs to the heart
  • jawed vertebrates have a peripheral nervous system divided into somatic and autonomic or visceral nervous system which can be divided into parasympathetic, sympathetic and enteric systems.
  • two basal vertebrate tetraploidization events 1R/2R duplicating the genome
    • it is thought the 1st and 2nd of the basal vertebrate tetraploidization events 1R/2R (cells gaining a duplicate number of chromosomes) occurred around this period of the evolution of lampreys and jawed fish
      • the vertebrate opioid receptor gene family arose by quadruplication of a large chromosomal block containing at least 14 other gene families 13)
      • this expanded the ancestral set of 10 nicotinic acetylcholine receptors (nAChR) to a set to 19 genes - 3 of these have been lost in mammals 14)
      • expanded the two ancestral genes for muscarinic acetylcholine receptors (mAChRs) to 5 (birds subsequently lost one of these)
      • it seems PRL and PRL2 genes arose from a common ancestor of GH gene in 1R/2R 15)
      • receptor genes GHR and PRLR arose through a local duplication in jawed vertebrates 16)
      • the ancestral insulin-like gene has diverged during the evolution of vertebrates into insulin, IGFs-1 and -2, and several ILPs including relaxin and relaxin-like peptide 17)
      • this resulted in 6 types of IGFBPs have been designated IGFBP-1 through IGFBP-6 which are highly conserved in vertebrates 18)
      • presumably the common ancestral gene for “vasotocin” was duplicated and became the genes for vasopressin and oxytocin with oxytocin being critical to maternal behaviours such as nursing and nurturing while vasopressin has been implicated in aggressive paternal defence behaviours, mate guarding and aggression towards strangers, while both have a role in pair bonding
      • most duplicated genes are eliminated in the genome over millions of years in a process called diploidization, but in the interim, the duplication allows for a much greater diversity of life forms as one copy will be mutated differently to the other copy for better or worse

Vertebrata

  • anamniotes (eggs laid in water)
    • cartilaginous marine vertebrates (fish the Devonian period is The Age of fish))
      • Jawless Fish (Agnatha)
        • all became extinct by the end of the Devonian
      • Placoderms (armoured fish) all became extinct by the of the Permian
      • gnathostomes (jawed fish - evolved ability to convert nitrogen waste into urea which helped raise their blood osmolarity to that of sea water allowing migration to marine waters; development of the sympathetic nervous system)
        • Chondrichthyes / Acanthodians (cartilaginous fish, no swim bladders or lungs; sharks, rays, skates and the extinct spiny sharks)
        • Osteichthyes (c420mya common ancestor of bony fish and developed a primitive air-breathing lung)
          • lampreys (developed a cough reflex to expel excess CO2), hagfish
          • Actinopterygii (bony fish)
      • Sarcopterygii (lobe-finned fish), air-breathing fish (ancient lobe-finned fish evolved multi-jointed leg-like fins with digits that enabled them to crawl along the sea bottom. Some fish developed primitive lungs with new paired pulmonary arteries to help them breathe air when the stagnant pools of the Devonian swamps were low in oxygen)
        • a small lobe-finned fish called Kenichthys (c395mya) evolved the beginnings of the internal nares / choanae which would allow air to move from the external nares to the lungs - the maxilla and premaxilla separated and an aperture—the incipient choana—on the lip in between the two bones. The paired fins had a build with bones distinctly homologous to the humerus, ulna, and radius in the fore-fins and to the femur, tibia, and fibula in the pelvic fins. These bony fish became the most numerous of all bony fish in the Devonian and most of the Carboniferous, although most were open-water fish, one group, the Elpistostegalians, adapted to life in the shallows. They evolved flat bodies for movement in very shallow water, and the pectoral and pelvic fins took over as the main propulsion organs, while they lost their median fins but the spiracle became large and prominent, enabling these fishes to draw air.
        • amphibia (c370mya)
          • tetrapod amphibia (c367mya) Devonian mass extinction 360mya
            • Diadectomorpha (c330mya - large reptile-like amphibians - perhaps the 1st to walk on 4 legs)
            • Reptiliomorpha
              • Casineria kiddi (340mya)
              • basal amniotes (c312mya eggs fertilized within the mother or laid on ground)
                • sauropsids / reptilia (c320mya)
                  • Archelosauria
                    • Archosaurs
                      • Pseudosuchia (crocodilian)
                    • Testudeans (turtles)
                  • Lepidosauria
                    • sphenodon lizards (NZ)
                    • squamata / reptiles
                      • lizards
                        • Toxicofera (toxin venom producing reptiles evolved 200mya)
                          • Anguimorpha
                            • Varanus monitor lizards (112-65mya; 4-chambered hearts) eg. Megalania
                              • Mosasaurs (extinct marine reptiles 100-65mya)
                            • Anguidae (75mya; alligator lizards, glass lizards, etc.)
                            • Helodermatidae (Gila monster and Mexican beaded lizard)
                            • Shinisauridae (Chinese crocodile lizard)
                            • Xenosauridae (knob-scaled lizards)
                          • Iguanomorpha (190mya in India)
                            • Acrodonta including chameleons
                            • Pleurodonta – American arboreal lizards, chuckwallas, iguanas
                          • Ophidia
                            • Serpentes (snakes 120-150mya initially with legs but a trio of mutations in the enhancer of a gene known as Sonic hedgehog disrupt a genetic circuit that drives limb growth in snakes)
                              • Alethinophidia
                                • Madtsoiidae (extinct Gondwanian such as Australian Wonambi and Yurlunggur)
                                • Pythonoidea (4-chambered hearts)
                                • Boidae (4-chambered hearts; ovoviviparous snakes including boas, anaconda)
                                • Henophidia
                                • Caenophidia
                                  • “colubroid” snakes
                                    • colubrids
                                    • vipers
                                    • elapids 38mya
                                      • coral snakes (30-25mya)
                                      • Afro-Asian clade of cobras and mambas (30-25mya)
                                      • Australasian clade (Hydrophiinae) 25mya
                                        • Sea Kraits (Laticauda) 25mya
                                        • Australian terrestrial Elapids 20-25mya
                                          • viviparous sea snakes 16mya
                                            • hydrophiids 8mya
                                    • atractaspids
                                  • Acrochordids
                              • Scolecophidia (blind snakes)
                  • Avemetatarsalia (avian-like)
                    • Pterosauromorpha
                    • Dinosauromorpha
                      • dinosaurs (243mya)
                        • Sauropodomorpha (long-necked herbivore dinosaurs)
                        • Ornithischia (bird-hipped dinosaurs eg. Stegosaurus)
                        • Theropoda (hollow bones and three-toed limbs c231mya)
                          • Megalosauroidea (early group of large carnivores)
                          • Carnosauria (Allosaurus and close relatives)
                          • Coelurosauria (feathered theropods, with a range of body sizes and niches)
                            • Maniraptora (“hand snatchers”; had long, slender arms and fingers)
                                • includes small membrane-winged gliding dinosaurs with ribbon like feathers on the tail such as Yi qi and Ambopteryx longibrachium (c160mya)
                              • Avialae (birds and extinct relatives; 160mya)
                                • Ornithothoraces (bird thoraces for flight including a large, keeled breastbone)
                                  • Enantiornithes - (145mya) became extinct with the dinosaurs
                                  • Euornithes (advanced flying birds “true birds”)
                                    • Aves (modern, beaked birds and their extinct relatives)
                                      • Palaeognathae ⇒ Pachystruthio dmanisensis (1.8mya), ostrich, emu, cassowary, kiwi bird, moa, etc
                                      • Neognathae
                                        • Galloanserae (fowl) - the predominant group of modern birds by the end of the Cretaceous
                                        • Neoaves (other modern birds)
                • synapsids
                  • mammals (201-227mya; females have breasts which produce milk, brain has a neocortex, middle ear has 3 bones and skin has fur or hair)
                    • monotremes c110mya (egg laying mammals)
                      • platypus
                      • echidna
                    • theria (not egg laying, retrovirus enabled syncytins proteins which allowed placentae, and lost the coracoid bone)
                      • eutherian mammals c161mya (amniotic sac surrounds the fetus, lack epipubic bones)
                        • atlantogenata (105mya)
                          • afrotheria: aardvarks, elephants, sea cows, dugongs
                          • xenarthra: anteaters, armadillos in the Americas 59mya
                        • boreoeutheria (most males have external testes; 80-100mya)
                          • Laurasiatheria
                            • Eulipotyphla (hedgehogs, shrews, moles)
                            • Scrotifera
                              • Chiroptera: bats
                              • Ferungulata
                                • Ungulates
                                  • Cetartiodactyla (even-toed ungulates)
                                  • suinea (pigs, hippopotamus)
                                    • Cetacea (45-53mya): 4 legged aquatic whale-like species
                                      • toothed whales (40mya - mass extinction toothed baleen whales 23mya19))
                                        • dolphins, porpoises
                                      • baleen whales (25mya)
                                  • Selenodont (camels, giraffe, deer, antelope, cattle)
                                    • Giraffoidea (giraffes)
                                    • cervoidea (deer)
                                    • caprinae
                                      • sheep
                                      • goats
                                      • ibex
                                    • bovinae
                                      • antelopes (16-18mya)
                                      • African buffalo
                                      • Bubalina genus (13,7mya)
                                        • water buffalo (India)
                                      • Bovina genus (13.7mya)
                                        • steppe bison Bison priscus (2-5mya)
                                        • Eurasian auroch (2mya)
                                          • modern cattle
                                  • Perissodactyla: odd-toed ungulates, including horses, donkeys, zebras, rhinoceros
                                • Ferae:
                                  • Hyaenodontidae (c66mya extinct) the 1st mammalian carnivores in Africa and lacked post-carnassial crushing molar teeth which limited foods to meat - the 22mya Simbakubwa kutokaafrika was a hyena-like apex predator in Africa larger than a polar bear
                                  • Oxyaenids (c55mya now extinct) - specialized climbing carnivores with teeth designed for crushing and preyed on other terrestrial vertebrates, eggs and insects, and may be related to pangolins
                                  • Pholidota (pangolins)
                                  • Carnivora (42mya; evolved in Eurasia and moved south to Africa; cats, hyenas, dogs, bears, seals)
                                    • Felinae
                                      • Panthera the big cats (6.37mya) eg. Panthera blytheae 4.1−5.95mya in
                                      • Acinonyx (cheetah)
                                      • Puma
                          • euarchontoglires (supraprimates including rodents)
                            • glires (rabbits, rodents)
                            • euarchonta (excludes rabbits, rodents)
                              • Scandentia or treeshrews
                              • Dermoptera or colugos
                              • Plesiadapiformes (extinct)
                              • primatomorpha
                                • primates - 80mya
                                  • Strepsirrhini
                                  • haplorhines (dry nosed) - 63mya
                      • metatherians c125mya in Asia (give birth to relatively undeveloped young)
                        • marsupials (?100mya in Utah) 65mya (young are carried in a pouch)
                          • Laurasian possums ⇒ North America ⇒ South America (connected to Nth America until 65mya)
                            • Ameridelphia (American marsupials - oppossums)
                            • Australidelphia (arose in Sth America, there is one species in Sth America, then migrated across a temperate Antarctica to Australia c55mya)
                              • Australian megafauna (now mostly extinct)
                              • kangaroos, wombats, Tasmanian devil, Tasmania tiger, etc

NB. In all animals, limbs are regulated by Hox genes, switch-boxes that control the expression of entire modules of genes at specified domains along the body axis.

history/evolution.txt · Last modified: 2019/08/03 02:22 by gary1