evolution

the beginning of life

organic molecules of polycyclic aromatic hydrocarbons (PAH) appear to form in molecular clouds which are very cold regions of gas in interstellar space and are present on comets and asteroids which bombarded earth. PAH constitutes a significant proportion of the carbon found on asteroids and comets.
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.
20 canonical amino acids “evolved” in two groups
- 10 'early' ones picked from the atmosphere and meteorite fragments of early Earth eventually formed “ancient proteins” and despite lacking basic residues, these early ones were remarkably adaptive at supporting protein folding
- 10 'later' ones added which were products of biosynthetic pathways and eventually formed “modern proteins” - the amino acids ending up in this group were the ones best at forming folding proteins ¹⁾
- unbranched aliphatic amino acids were purged from the proteinogenic groups despite their high prebiotic abundance because they generate polypeptides that are oversolubilized and have low packing efficiency
prebiotic peptides form 3.5-3.8 billion years ago, perhaps such as:
- 13 amino acid “nickleback” peptide capable of producing hydrogen - The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe] hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase, two ancient, extant proteins central to metabolism ²⁾
It is likely that RNA evolved before DNA and this primordial RNA could then start replicating 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
- in 2023, researches found that novel RNA genes can form via instantaneous generation of complete DNA palindromes and thus creation of new microRNA genes from previously noncoding DNA sequences ³⁾
- 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 ⁴⁾
  - 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) ⁵⁾
fresh water first appeared on earth c4,000mya - albeit as hot water several kilometres below Earth's surface while the rest of the earth was largely covered by ocean
the first bacteria
- bacteria life is thought to have started on earth 4,280 mya
  - see also evolution of bacteria
- these then evolved into:
  - archaea
  - Asgard archaea (2000mya)
    - one branch:
      - Lokiarchaeales
      - Helarchaeales
      - Thorarchaeia
      - Hermodchaeia
    - another branch:
      - Wukongarchaeia
      - etc
    - another branch:
      - Heimdallarchaeaceae
      - etc
    - common ancestor ⁶⁾
      - inclusion of mitochondria in a prokaryote (an archaebacterium) appears to have occurred only once in evolution - some time before 1800mya
        
        the ancestral mitochondrion was a metabolically versatile, facultative anaerobe
        
        the initial benefit of the symbiosis could have been the production of H₂ by the endosymbiont as a source of energy and electrons for the archaebacterial host, which is posited to have been H2 dependent ⁷⁾
        
        mechanism for cellular programmed death (apoptosis) was probably present in these early mitochondria ⁸⁾
        
        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 ⁹⁾
        
        anaerobic mitochondrial DNA
        
        aerobic mitochondrial DNA (>1450 mya - perhaps in a Rickettsial bacteria)
      - eukaryotes
        
        stem-group eukaryotic forms
        
        last eukaryotic common ancestor (LECA) (1800mya-1200mya)
        
        protosterol biota (1600mya - 800mya)
        
        protosterol-producing bacteria and deep-branching stem-group eukaryotes which were perhaps the 1st predators, hunting and eating bacteria; absence of steranes, the molecular fossils of eukaryotic membrane sterols; ¹⁰⁾
        
        Tonian Transformation (1000mya-720mya) - more advanced nucleated modern eukaryotes, such as fungi and algae, started to flourish
        
        red algae (rhodophytes) 800mya
      - Hodarchaeales - these “Hods” are found in marine sediments

evolution of Fungi

all Fungi descend from an organism that was single celled eucaryote and, at least at some point in its life cycle, able to swim with the use of posterior flagella.
NB. nearly all fungi are unicellular and grow via filamentous hyphae
NB. A gilled mushroom or toadstool is the fleshy, spore-bearing fruiting body of a fungus of the order Agaricales
- fungi (evolved 2400-1200mya)
  - zoosporic fungi
    - Chytridiomycota - free‐living saprobes and parasitoids; a zoosporic disemination stage and usually a growing non‐flagellated stage.
      - Chytridiomycetes
        
        by far the largest class of zoosporic fungi with around 1000 described species
      - Monoblepharidomycetes
        
        a group of freshwater, zoosporic fungi that can present either unicellular or mycelial growth
      - Hyaloraphidiomycetes
    - Blastocadiomycota
      - a relatively small group of zoosporic fungi with diverse morphological and ecological traits
    - Neocallimastigomycota
      - small group of flagellated, obligate anaerobic, non‐parasitic fungi
      - lack true mitochondria, harbouring mitochondria‐derived hydrogenosomes instead
    - Opisthosporidia
      - Microsporidia - intracellular parasites of metazoans
      - Rozellidea - parasitoids of diverse organisms
      - Aphelidea - parasitoids of photosynthetic unicellular eukaryotes
  - Zygomycetous fungi - terrestrial fungi (c635mya)
    - Loss of their flagellar apparatus and the development of hyphal growth allowed a particular group of Fungi to conquer emerged lands
    - Zoopagomycota
      - earliest diverging group of non‐flagellated fungi
      - Entomophthoromycotina
      - Zoopagomycotina
      - Kickxellomycotina
    - Glomeromycota
      - live as obligate symbionts of land plants, forming a particular type of symbiosis termed arbuscular mycorrhizae; mycelia grow inside the root of the plant, penetrating the cells of the host
    - Mucoromycota
      - the largest and best‐studied group of zygomycetous fungi. Most species grow as saprobes, with some species being non‐haustorial parasites of plants and other fungi, or ectomycorrhizal
      - Mortierellomycotina
      - Mucoromycotina
        
        Endogonales
        
        Mucorales
  - Dikarya
    - by far the most species‐rich and best‐studied group of Fungi
    - characterized for a sexual cycle that includes hyphal fusion uncoupled with meiosis, which in turn produces hyphae that contain two independent nuclear populations (dikaryotic hyphae)
    - Ascomycota
    - Basidiomycota
      - Agaricomycetes
        
        Agaricales (gilled mushrooms)
    - Entorrhizomycota

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. ¹¹⁾
sulphur oxidising and sulphate reducing bacteria
arsenic oxidising bacteria (these still live in the oxygen-deplete middle layer of tropical oceans)

Proterozoic eon (2500 - 540 mya)

Great Oxygenation Event (GOE) 2400 mya
mitosomes
hydrosomes
eukaryocytes presumably evolve from endosymbiosis of procaryocytes with mitochondrial DNA creating complex cells oxidative mitochondrial capacity as well as anaerobic pathways, although the role of viruses similar to the medusavirus which can create histones and thus chromosomes may have contributed (c1,800 mya)
- fungi (see above)
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.
- cyanobacteria (“blue-green algae”) photosynthetic, oxygen producing algae 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
  - plants
    - chloroplasts in plants evolved from an endosymbiotic relationship between a cyanobacterium, a photosynthesising prokaryote and a non-photosynthetic eukaryotic organism, producing a lineage of photosynthesizing eukaryotic organisms in marine and freshwater environments.
    - Rhodophytae - red algae - evolved with plastids lacking chlorophyll accessory pigments, rather, containing chlorophyll-a, phycocyanin, and phycoerytherin, so light is captured by phycobiliproteins
      - Rhodophytina
      - Cyanidiophytina
    - Glaucophyta
      - Cyanophora
    - Viridiplantae (>1000mya)
      - Prasinodermophyta
      - Chlorophyta - green algae (470mya?)
        
        Prasinophytes
      - Streptophyta
        
        Charophyta, a group of freshwater green algae
        
        Embryophyta - terrestrial plants c500mya?
- Choanozoa (950mya)
  - Choanoflagellata
    - choanoflagellate SOX2 genes, which were likely originally used to control basic cellular processes, were repurposed by multicellular organisms to drive stem cell formation and development.¹²⁾
  - 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 ¹³⁾
    - Porifera (sponges)
    - Eumetazoa
      - Ctenophora (comb jellies)
      - Parahoxozoa (680mya)
        
        Cnidaria (?741mya, but fossils dated to 580mya; corals, sea anemones, jellyfish)
        
        Ediacaran soft-bodied fauna (610mya)
        
        Quaestio simpsonorum c555mya - one of the earliest to show left-right assymetry; thin external membrane connecting more resilient tissues with anterior-posterior polarity, left-right asymmetry and tentative evidence for dorsoventral differentiation;
        
        Placozoa
        
        Bilateria (bilaterally symmetric body plan arose c650mya; primitive eyes with c and r type opsins;)
        
        eg. Ikaria wariootia 555mya
        
        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)
        
        Eurypterida (“sea scorpions” some species growing to 8' long 432-418mya; now extinct)
        
        Arachnida
        
        Scorpiones
        
        earliest land scorpion dated to 437mya making it perhaps the earliest land animal
        
        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)
        
        millipede - the 414mya Pneumodesmus newmani and the 425mya Kampecaris obanensis is the earliest known terrestrial animal
        
        centipede - c430mya
        
        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
        
        Nautiloids (c415mya)
        
        Ammonites (479-66mya)
        
        Coleoids (c410mya)
        
        Decapodiformes
        
        squids and cuttlefish
        
        10 armed ancestral vampyropods (Syllipsimopodi bideni c328mya)
        
        octopodiformes
        
        vampyromorphida vampire squid with 8 arms and 2 long filaments
        
        octopus (oldest fossil 296mya)
        
        Annelida
        
        Deuterostomia (the first opening (the blastopore) becomes the anus) 558mya
        
        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)

there is a limit to individual cell size, hence larger organisms need to be multi-cellular with cells grouped together and usually with specialisation of cells (eg. structural support, digesting food and transporting substances such as oxygen and CO₂):
- bigger cells tend to have less surface area per unit of volume which means that the natural movement (diffusion) of molecules of gases, nutrients and wastes in and out of the cell isn't enough to keep things running without a transport system and these molecules also have further to travel in larger cells
- the alternative is to become flat or threadlike (like horsehair worms) or thin and flat (such as flatworms) -these animals don't need an internal transport system because none of their cells (or their contents) are far from the surrounding air or water
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 ancestor¹⁴⁾:
- 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) ¹⁵⁾
some vertebrate hormones may have had a role in neural tissues in invertebrates ¹⁶⁾
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 ¹⁷⁾
- 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) ¹⁸⁾
all animal species lines started out as small animals, some species evolved to become larger in size as this may make it easier to evade predators (elephants and whales have few enemies other than humans), hunt prey, out-compete rivals, better at conserving heat (because of their relatively smaller surface area) greater potential for intelligence, and have larger energy stores to endure temporary hardships but they are very specialized, reproduce more slowly and evolve more slowly so are unable to survive major environmental upheavals.
- small size allows animals to live in a greater diversity of niches, and to partition resources more finely, packing more species and individuals into the same habitat space
global mass extinction event of 65-66mya at the end of the Cretaceous Period when 75% of animal species died out including all the dinosaurs and anything larger than a domestic cat - this is now confirmed to be due to an asteroid hitting Mexico's Yucatan Peninsula where it created a 200km crater and it is thought the global winter event due to 2,000 gigatonnes of dust (11x weight of Mt Everest) being expelled into the atmosphere was the eventual cause of the mass extinction.

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 organs¹⁹⁾ 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 ²⁰⁾
only vertebrates have a locus coeruleus (a brainstem nucleus)
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 ²¹⁾
  - 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 ²²⁾
  - 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 ²³⁾
  - receptor genes GHR and PRLR arose through a local duplication in jawed vertebrates ²⁴⁾
  - 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 ²⁵⁾
  - this resulted in 6 types of IGFBPs have been designated IGFBP-1 through IGFBP-6 which are highly conserved in vertebrates ²⁶⁾
  - 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
a gene called SOX9 is key for male determination in all vertebrates, although it does not lie on sex chromosomes but is triggered by the SRY (sex region on the Y) which in most mammals including humans is on the Y chromosome (some rodents have lost the Y chromosome but still reproduce thanks to a small duplication of only 17,000 base pairs near the SOX9 gene in males but not in females)
a retrovirus-derived genetic element or “retrotransposon” (retrotransposons compose about 40% of our genomes) which has been named “RetroMyelin” is essential for myelin production in birds, mammals, amphibians, and fish ²⁷⁾
- it appears that retroviral infection and genome-invasion events occurred separately in each of the groups birds, mammals, amphibians, and fish and this myelin gene enabled more complex brains and allowed the vertebrate diversity to evolve as successfully as it has
- Myelin first appeared in evolution around the same time as jaws

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; development of vertebrate dentition c430mya;)
    - Chondrichthyes / Acanthodians (cartilaginous fish, no swim bladders or lungs; sharks, rays, skates and the extinct spiny sharks)
      - shark teeth have been found from around 400mya, many became extinct in the Permian period and the remaining sharks underwent a second burst of adaptive radiation during the Jurassic.
      - Elasmobranchii (c450mya; sharks and the rays and skates)
        
        Galeomorphii (c200mya modern sharks except dogfish sharks)
        
        seems that after thriving for 40 million years, 90% were wiped out 19 mya and modern shark forms then began to diversify within 2-5 million years of this extinction event ²⁸⁾
        
        Squalomorphii (c145mya dogfish sharks)
        
        Batoidea (c145mya rays and skates) evolved in the Jurassic period
      - Holocephali (c490mya)
        
        Chimaeriformes
        
        rat fishes (e.g., Chimaera)
        
        rabbit-fishes (e.g., Hydrolagus)
        
        elephant-fishes (Callorhynchus)
    - Osteichthyes (c420mya common ancestor of bony fish and developed a primitive air-breathing lung)
      - lampreys (developed a cough reflex to expel excess CO₂, and perhaps the 1st auditory hair cells), 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.
    - tetrapod-like fish, Elpistostege with articulating digits in the pectoral fin which are like the finger bones found in the hands of most animals and fin contains a humerus, radius and ulna, rows of carpus and phalanges organized in digits
    - amphibia (c370mya)
      - In the early Carboniferous (360 to 345 million years ago), the climate became wet and warm. Extensive swamps developed with mosses, ferns, horsetails and calamites which allowed amphibia to access the land.
      - tetrapod amphibia (c367mya) Devonian mass extinction 360mya appears to be due to a temporary loss of the ozone layer²⁹⁾
        
        salamanders grow limbs preaxially due to repressor effects of the Gli3 gene
        
        all other tetrapods grow limbs postaxially due to repressor effects of the Gli3 gene being disabled but are able to revert to preaxial development if GLi3 gene activity is permitted by gene manipulation ³⁰⁾
        
        Batrachomorpha (frog-like)
        
        Lissamphibia
        
        extinct orders Temnospondyli, Temnospondyli, Nectridea, Microsauria, Allocaudata (became extinct 2.5mya)
        
        Anura (without tails)
        
        Salientia (frogs, toads, and their extinct relatives)
        
        Urodela (lizard-like)
        
        Caudata (salamanders, newts, and their extinct relatives)
        
        Gymnophiona (the limbless caecilians and their extinct relatives)
        
        appear to have venom glands associated with teeth
        
        Diadectomorpha (c330mya - large reptile-like amphibians - perhaps the 1st to walk on 4 legs)
        
        Reptiliomorpha
        
        after the Carboniferous rainforest collapse (305mya) amphibian dominance gave way to reptiles, and amphibians were further devastated by the Permian–Triassic extinction event 252mya
        
        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 250mya eg. tuatara (NZ)³¹⁾
        
        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)
        
        Najash rionegrina (95mya) - Argentinian terrestrial snake with rear legs³²⁾
        
        Alethinophidia
        
        Madtsoiidae (extinct Gondwanian such as Australian Wonambi and Yurlunggur)
        
        includes the extinct Vasuki indicus (~47mya, perhaps grew to 10.9-15.2m long - the longest snake on record)
        
        Pythonoidea (4-chambered hearts)
        
        Boidae (4-chambered hearts; ovoviviparous snakes including boas, anaconda)
        
        Titanoboa (evolved following the extinction of all non-avian dinosaurs 60-58mya and grew to perhaps 12.8-14.3m long and weighed 730-1,135kg in Egypt)
        
        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) / Ornithodira
        
        Pterosauromorpha
        
        Dinosauromorpha
        
        Lagerpetidae
        
        Kongonaphon (Middle to Late Triassic in Madagascar)
        
        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)
        
        eg. the feathered dinosaur, Caudipteryx had 9 primary feathers, but those feathers are almost symmetrical, and the proportions of its wings would have made flight impossible.
        
        Maniraptora (“hand snatchers”; had long, slender arms and fingers)
        
        Scansoriopterygids
        
        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)
        
        in addition to asymmetrical feathers, all flighted birds have between 9 and 11 primary feathers in contrast, flightless birds have variable numbers — penguins have more than 40, while emus have none.
        
        Ornithothoraces (bird thoraces for flight including a large, keeled breastbone)
        
        Enantiornithes - (145mya) became extinct with the dinosaurs
        
        Euornithes (advanced flying birds “true birds”)
        
        oldest bird footprints in Gondwana: 120-128mya Wonthaggi, Victoria
        
        earliest unequivocal example of secondary flightlessness is Patagopteryx 80mya Argentina ³³⁾
        
        Aves (modern, beaked birds and their extinct relatives)
        
        Palaeognathae c177mya based on genomics
        
        Pachystruthio dmanisensis (1.8mya), ostrich, emu, cassowary, kiwi bird, moa, etc
        
        Neognathae c177mya based on genomics³⁴⁾
        
        Galloanserae (fowl) - the predominant group of modern birds by the end of the Cretaceous
        
        Odontoanserae
        
        Pelagornithidae (pseudo-tooth birds) extinct
        
        Anserimorphae
        
        Gastornithidae extinct
        
        Dromornithidae extinct
        
        Anseriformes (screamers and waterfowl)
        
        Pangalliformes (all birds more closely related to chickens than to ducks, and includes all modern chickens, turkeys, pheasants, and megapodes)
        
        Neoaves (other modern birds) - c75mya
        
        Coronaves diurnal birds
        
        diversified around or soon after the K/T boundary 65mya
        
        terrestrial and arboreal birds
        
        Psittacopasserae
        
        Passeriformes (passerines, a large group of perching birds, songbirds)
        
        Psittaciformes (parrots)
        
        Columbimorphae
        
        Columbiformes (pigeons and doves, dodo)
        
        Columbinae (typical pigeons and doves)
        
        Claravinae (American ground doves)
        
        Raphinae
        
        Phabini (bronzewings and relatives)
        
        Turturini (other doves)
        
        Treronini (green pigeons)
        
        Ptilinopini (fruit doves and imperial pigeons)
        
        Pterocliformes (sandgrouse)
        
        Mesitornithiformes (mesites)
        
        aquatic and semi-aquatic birds
        
        shorebirds
        
        Metaves - nocturnal bird ancestors c75mya ³⁵⁾
        
        diversified around or soon after the K/T boundary 65mya
        
        ‘caprimulgiforms’ nightbirds (except owls)
        
        apodiform birds (swifts and hummingbirds)
        
        synapsids (earliest known is 318mya)
        
        caseids
        
        eupelycosaurian synapsids
        
        sphenacodontia
        
        pantherapsida
        
        sphenacodontoidea
        
        therapsida
        
        eutherapsida
        
        neotherapsida
        
        anomodontia
        
        lystrosaurus (250mya) able to hibernate (go into torpor)
        
        theriodontia
        
        eutheriodontia
        
        cynodontia
        
        mammals (201-227mya; females have breasts which produce milk, brain has a neocortex, middle ear has 3 bones and skin has fur or hair)

mammals

mammals (201-227mya; females have breasts which produce milk, brain has a neocortex, middle ear has 3 bones and skin has fur or hair)
- see also: evolution of mammals
  - 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 23mya³⁶⁾)
        
        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
        
        anthropoidea - 58mya
        
        catarrhini (Old World Monkeys) - 40 mya
        
        see also Evolution of Humans
    - 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.

¹⁾

https://pubs.acs.org/doi/full/10.1021/jacs.2c12987

²⁾

https://www.science.org/doi/10.1126/sciadv.abq1990

³⁾

https://www.helsinki.fi/en/hilife-helsinki-institute-life-science/news/new-genes-can-arise-nothing

⁴⁾

https://www.mcb.ucdavis.edu/faculty-labs/scholey/journal%20papers/ricardo-szostak-sa2009.pdf

⁵⁾

https://www.nature.com/scitable/topicpage/the-origins-of-viruses-14398218

⁶⁾

Nature June 2023: Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes