Notes & Commentary
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- ↑ Subject to major change, revision ,and/or retraction at any moment.
- ↑ Reconstructed by the maximum likelihood method for 78 protein-coding genes. Numbers beside the internal nodes are maximum likelihood bootstrap values obtained from RaxML and Bayesian MCMC posterior probabilities. Black circles indicate 100% bootstrap support and 1.00 posterior probability values.
- ↑ A: hedgehog and B: Notch homologues. The illustrated domains are some of those found by searches against the Conserved Domain Database. Numbers at the species names are accession numbers, protein IDs from the Joint Genome Institute (JGI) and references where annotation recently have been presented. Domain structure identified in Ministeria is compared with animals - Porifera (Amphimedon and Oscarella), Cnidaria (Nematostella) and Chordata (Homo) - and the choanoflagellate Monosiga. Abbreviations: Hh-signal domain, N-terminal hedgehog domain; Hint cleavage site, cleavage site of the C-terminal hedgehog domain; Hint domain, C-terminal hedgehog domain; Notch(DSL), Notch domain also called Delta Serrate Ligand; EGF, epidermal growth factor domain; NL, domain found in Notch and Lin-12; NOD, NOD region; NODP, NODP region; ANK, ankyrin reapeats; PTP, protein tyrosine phosphatase.
- ↑ The five choanozoan classes (bold) form at least four distinct clades, one probably related to fungi and the others to animals. Innovations in pseudopod character and their multiple losses with the origin of cell walls during nutritional shifts from engulfing prey (phagotrophy) to saprotrophy or parasitism are indicated by bars. In the common ancestor of animals and choanoflagellates a subset of the filozoan actin-supportd tentacles aggregated as a collar around the cilium (flagellum) for filter feeding. Epithelia and connective tissue made the first animals: the filter-feeding sponges.
- ↑ Cell structure divergence in phagotrophic non-amoeboid flagellates provided the basis for evolving animals, fungi, plants and chromists. Original description: "Cell structure divergence in phagotrophic non-amoeboid flagellates provided the basis for evolving animals, fungi, plants and chromists.
Pseudopodia evolved secondarily, myosin II providing the basis for pseudopodia in animals, Amoebozoa (and Percolozoa) and muscles.
Chloroplasts, originating when the plant ancestor enslaved and modified undigested cyanobacteria, were transferred laterally (red arrow) to make chromists (e.g. brown seaweeds, diatoms, dinoflagellates) whose ancestor modified an enslaved undigested red alga.
The most basic eukaryote structural dichotomy contrasts Euglenozoa (parallel centrioles; cilia with paraxonemal rods; cytopharynx for feeding) and excavates (Percolozoa, Eolouka, Neolouka: orthogonal centrioles: no paraxonemal rods; feeding by phagocytosing prey drawn into a ventral groove by posterior ciliary currents).
The pre-animal lineage lost excavate groove-feeding by evolving ventral ciliary gliding locomotion to generate Sulcozoa, protozoa with a dorsal proteinaceous pellicle (blue).
Irrespective of whether the eukaryote tree is rooted within the protozoan subkingdom Eozoa as shown (most likely) or beside Eolouka-like Reclinomonas with the most primitive mitochondria, the immediate ancestors of animals (Choanozoa) arose by loss of the anterior cilium and sulcozoan dorsal pellicle to make opisthokonts (in red) with a radically simplified, more radially symmetric, microtubular cytoskeleton.
Long actin-supported filodigits arose in the ancestor of Filosporidia and choanoflagellates and became a circlet of microvilli to make the choanoflagellate/sponge collar for catching bacteria. Filosporidia comprise Filasterea, Ichthyosporea, Corallochytrea.
The four derived kingdoms (e.g. ANIMALIA, PLANTAE) are shown in upper case; all taxa in lower case belong to the basal eukaryotic kingdom Protozoa." - Of interest to us on our journey towards animals are: myosin, integrins, catenins, cadherins, epithelia, gametes (sperm and egg), and extracellular matrix (ECM).
- ↑ The cytoskeleton is a dynamic structure and microtubules play an important role in determining the architectural state of differentiation for specialized cells. In many ways, the dynamic action of microtubules manifests one of the first, and most easily observable, indications in cells of what we would recognize as life - flagellar motility and/or the amoeboid exploration of the environment through process extension and retraction - all processes determined by the adaptive dynamics of microtubule formation and dissolution.
- ↑ Multicellular lifecycle diagrams in terms of soma and germ line populations in A.) Plants, B.) Animals, C.) Fungi - (1) Meiosis, leading to the production of germ, (2) Mitosis, leading to production of soma and amplifying germ line populations (3) Sexual Recombination of germ lines within the species population
- ↑ Induction of the Neural crest during neuralation. Once the neural tube has successfully formed and the neural crest cells delaminate from the neural tube and ectoderm by down regulating their CAMs.
- ↑ Description: 1) Degeneracy is the source of Robustness. 2) Degeneracy is positively correlated with Complexity. 3) Degeneracy increases Evolvability. 4) Evolvability is a prerequisite for Complexity. 5) Complexity increases to improve Robustness. 6) Evolvability emerges from Robustness.
- ↑ The ingenuous 1964 Nirenberg and Leder experiment would identify the mRNA codons, a triplet sequence of ribonucleotides, that coded for each amino acid; thus elucidating the universal genetic code within the DNA when the transcription process was taken into account. Changes in the third position of the codon, the wobble position, often result in the same amino acid, and oftentimes the choice comes down to purine or pyrimidine only when a choice must be made. Similar, but variant, codon sequences tend to yield similar classes of amino acid - polar to polar, non-polar to non-polar, acidic to acidic, and basic to basic residues.
- ↑ The twenty biological amino acids breakdown into four major classes of biological amino acids - polar (hydrophilic), nonpolar (hydrophobic), acidic, and basic side chain residues. The amino acid backbone is an amino group linked to an α-carbon, on which resides the side chain residue and a hydrogen atom, that is connected to a terminal carboxylate group.
- ↑ Description: Scanning Electron Microscope (SEM) image of leukocytes, red blood cells platelets circulating in the human bloodstream.
- ↑ Description: Illustration of disulfide bridges (red) linking the light (L, green) and heavy (H, purple) chains of Immunoglobulin G (IgG) antibody. The variable (V) regions are located at the antigen-binding end; and, the constant (C) domains form the primary frame of the IgG molecule. Another disulfide bridge holds the two symmetrical units made up of a light chain (VL+CL) and a heavy chain (VH+CH1+CH2+CH3) together to form the completed antibody. Work by Rodney Porter with the enzyme papain resulted in cleavage of the antibody into Fab and Fc fragments, while work by Gerald Edelman lead to the reduction of the disulfide bridges so as to separate the molecule into light- and heavy-chain fragments. Together, this work allowed the antibody structure to be sequenced and reconstructed, resulting in the awarding of the Nobel Prize in Physiology or Medicine in 1972.
- ↑ Description: The immune system has an ancient history within animals. All animals have an innate immune system, but only vertebrates have an "active" antibody-based immune system. The innate (left branch) immune system is ancient and anchored around the phagocytic white blood cells discovered by the pioneering biologist, embryologist, zoologist, immunologist, gerantologist Élie Metchnikoff (May 15, 1845–July 15, 1916).. The antibody-based system (right branch) arose at the origin of vertebrates and is associated with the genome duplication events that provided the duplicate copies of NCAM which eventually resulted in the emergence of genetically recombinant antibodies. Paul Ehrlich (March 14, 1854–August 20, 1915)) was the discoverer of antibodies - and, along with Elie Metchnikoff, is considered to be one of the founders of Immunology. In 1908, they would share the first Nobel Prize in Physiology or Medicine. 64 years later, Edelman and Porter would share this very same prize.
- ↑ Description: Clonal selection theory (CST) - hematopoietic stem cells (1) differentiate and undergo genetic rearrangement to produce a population of cells possessing a wide range of pre-existing diversity with respect to antibody expression (2). Lymphocytes expressing antibodies that would lead to autoimmunity are filtered from the population (3), while the rest of the population represents a degenerate pool of diversity (4) where antigen-selected variants (5) can be differentially amplified in response (6). Once the antigen has been cleared, the responding population will decrease, but not by as much as it was amplified, leaving behind a boosted capacity to respond to future incursions by the antigen - a form of enhanced recognition and memory within the system.
- ↑ Neuron counts of cerebral cortex and cerebellum - The cerebellum is a key player in integrating the output of the thalamocortical system with the subcortical system. Notice the greater than four-fold abundance of neurons in the cerebellum relative to the neocortex.
- ↑ Superior-pattern-processing-is-the-essence-of-the-evolved-human-brain-fnins-08-00265-g0002 - Structural features of the brains of mammals are conserved from rodents to humans. The upper drawings show the hippocampal formation of an adult human, a kitten and a young mouse. The lower two drawings show the cellular organization of the cerebral cortex of an adult human and an adult mouse, both of which exhibit six cell layers. All of the drawings are adapted from Santiago Ramon y Cajal (DeFelipe and Jones, 1988). CA, cornu ammonis; DG, dentate gyrus; SUB, subiculum.
- ↑ Subject to major change, revision ,and/or retraction at any moment.
- ↑ Original description: "Figure 1. Phylogenetic classification of animals and their unicellular relatives.
(a) A timeline of different events during early animal evolution. The transition to animal multicellularity, and therefore the origin of the first animals, occurred sometime at the end of the Tonian period, according to molecular clock estimates. The oldest fossil or geological evidence of recognizable animals dates back to the Ediacaran period, with molecular clocks extending the emergence of different animal phyla back to the Cryogenian. Time units are million years ago (Ma).
(b) Cladogram representing the major clades of the tree of animals and the major groups of unicellular relatives of animals: choanoflagellates, filastereans, ichthyosporeans and corallochytreans-pluriformeans.
Coloured nodes indicate different ancestors that we can reconstruct and that are important to understand the transition to animal multicellularity; the highlighted internal branch (from the Urchoanozoan to the animal LCA) indicates the animal stem. Uncertain positions within the animal tree and within Holozoa are represented with polytomies."
- ↑ The three domains being:
- Eubacteria
- Archea
- Eukarya
- ↑ The seven kingdoms being:
- Eubacteria
- Archea
- Protozoa
- Chromista
- Plants
- Fungi
- Animals
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![Multicellular lifecycle diagrams[g] Plants (A), Animals (B) and Fungi (C)](/https/en.wikiversity.org/wiki/File:Lifecycle_diagram.svg)
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![Relationships between degeneracy, complexity, robustness, and evolvability.[i]](/https/en.wikiversity.org/wiki/File:Relationships_between_degeneracy,_complexity,_robustness,_and_evolvability.png)
![The degeneracy of the genetic code buffers biological systems from the effects of random mutation.[j]](/https/en.wikiversity.org/wiki/File:06_chart_pu3.png)
![A large number of degenerate sidechain residue combinations form the tertiary structures that make the protein globular.[k]](/https/en.wikiversity.org/wiki/File:Overview_proteinogenic_amino_acids-ENG.svg)
![Cells in the Bloodstream[l]](/https/en.wikiversity.org/wiki/File:SEM_blood_cells.jpg)
![Immunoglobin Antibody[m]](/https/en.wikiversity.org/wiki/File:AntibodyChains.svg)
![Vertebrate Immunity[n]](/https/en.wikiversity.org/wiki/File:Hematopoiesis_simple.svg)
![Clonal Selection Theory[o]](/https/en.wikiversity.org/wiki/File:Clonal_selection.svg){kind=small}
