BIOL0004 Life on Earth (All lecture notes) PDF

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Table of Contents:Lecture 2: Phylogeny and ClassificationThe Universe: OriginsLecture 3: Key Concepts in Embryology and Morphology for Understanding Animal EvolutionLecture 4: Origin of Animals, Diploblasts, Ediacarans and the Cambrian ExplosionLecture 5: Evolution of Bilaterally Symmetrical Animals...

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Table of Contents: Lecture 2: Phylogeny and Classification The Universe: Origins Lecture 3: Key Concepts in Embryology and Morphology for Understanding Animal Evolution Lecture 4: Origin of Animals, Diploblasts, Ediacarans and the Cambrian Explosion Lecture 5: Evolution of Bilaterally Symmetrical Animals Lecture 6: Urbilateria Lecture 7: Lophotrochozoa The Origin of Life The Evolution and Diversity of Eukaryotes Vertebrate Evolution I: From Water to Land; Early Vertebrates to Fishes to Early Tetrapods Vertebrate Evolution II: From Sails to Whales; The Evolution of Mammals Vertebrate Evolution III: Placental Mammal Evolution The Origin, Evolution and Extinction of Dinosaurs Lecture 8: Deuterostomes; Echinoderms, Hemichordates and Chordates Photosynthetic Organisms I (Aquatic) Photosynthetic Organisms II (Terrestrial) Sixth Mass Extinction Biodiversity in the Anthropocene

Lecture 2: Phylogeny and Classification

Monophyletic:

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Also known as clades Single common ancestor; - Included in group, all descendants of that last common ancestor (even if extinct) Ingroup - Outgroups; non-members of monophyletic group/clade - Two sister-groups (closest outgroup) form a monophyletic group

Paraphyletic: - Doesn’t include all descendants of the last common ancestor - E.g. Reptiles Polyphyletic: - Have more than one origin Cladogram: - Only shows branching pattern Phylogram: - Branch length shows branching pattern and relationships between organisms - Longer time leads to greater divergence

Cladistics and Occam’s Razor: - Cladistics: - Method of hypothesising relationships among organisms; reconstructing evolutionary trees - Principle of Parsimony - The simpler hypothesis is preferred; fewer assumptions - Shared derived characters (Synapomorphies) are informative - E.g change from cold to warm blood prefers one particular tree - Shared primitive characters (Symplesiomorphies) are uninformative - The characteristic shared with a more primitive animal is the primitive state - E.g. change in toe number does not prefer any tree - Same principle applies to nucleotides in gene sequence King & Carroll: - Gene fusion supports the close relationship between unicellular choanoflagellate and animals (metazoa) (Sponge choanocyte)

The Universe: Origins -

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Big Bang marks the beginning of the universe’s expansion Energy transformed into matter Basic building blocks: - Quarks - Combined in threes to form protons (+1) and neutrons (+0) - Electrons - Unknown dark matter Four different forces: - Strong force - Weak force - Electromagnetic force - Gravity

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Cooling process; approx. half a million years later - Fusion process of protons and neutrons via strong forces stops - Electromagnetic force sparks the electrons around the nuclei to form atoms - Hydrogen (75%), Helium (25%) - These numbers are evidence for the big bang; according to laws of thermodynamics and physics

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Universe enters a period of darkness for approx. 400 million years First stars formed at approx. 600 million years - Short lives; burn quickly - Supernova star death explosion - Increase in temp. allows for fusion of protons and neutrons again

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Lecture 3: Key Concepts in Embryology and Morphology for Understanding Animal Evolution -

Embryological cues can give us information about animal relationships - Embryos at early stages look almost identical between different animals

Gastrulation: 1. Hollow, single layer ball of cells; Blastula 2. Group of cells move inside/invaginates; Indentation 3. Forms 2 cell layers; Gastrula a. Inside: Endoderm (gut) b. Outside: Ectoderm (skin) Gastrulation of blastula to form gastrula:

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Lumen; hollow tube space within the gut is known as the archenteron - Opening of this gut to the outside world is the blastopore

Major Division of Animals: - Diploblasts and triploblasts - Triploblasts have an additional layer of tissue between the endoderm and ectoderm - Mesoderm - Makes muscles, blood, bone (in vertebrates) and connective tissues - Blind gut - Diploblasts have a single opening to gut - Food and waste pass through the same opening - Through gut - Triploblasts form an additional opening to the gut; separate mouth and anus Steinmetz et al. (2017): - Recent molecular data suggesting that cnidarians have 3 tissue layers Symmetry in diploblasts and triploblasts:

He et al. (2018): - However, jellyfish (cnidarians) has same Hox gene expression in humans - Questions whether cnidarians are really radially symmetrical - They are genetically bilaterally symmetrical Radial (Deuterostomes) vs. Spiral Cleavage (Protostomes) Patterns:

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Spiral division at a slight angle/orientation

Triploblast evolution seen as a progression in complexity: - Diploblast has no mesoderm - Acoelomate has solid mesoderm - Pseudocoelomate has cavity (coelom) - Coelomate (with smooth epithelium lined cavity; coelom) Ecdysis: - Process of cuticle moulting; required when arthropod wants to grow bigger, and new cuticle is secreted Segmentation: - Repeated units of construction along the antero-posterior axis (head to tail) Opisthokonts:

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Consists of animals, along w/ fungi, choanoflagellates etc. Rear-facing flagellum

Sister-group of all animals (most distant relatives) - Sponges: - Shares animal morphology: - Collagen, multicellularity, septate junctions, spermatozoa

Lecture 4: Origin of Animals, Diploblasts, Ediacarans and the Cambrian Explosion

Opisthokonts: - Rear facing flagellum Porifera (Sponges): - Share with other animals; - Collagen - Multicellularity - Septate junctions - Spermatozoa - Similarity of sponge collar cells to unicellular choanoflagellates - Zumberge et al. (2018) - Molecules found that are formed in the breakdown of sponges (biomarkers) - Existence of these molecules in rocks indicates the presence of sponges ~600 million years ago - Consists of chambers full of flagellated cells ( choanocytes); drives water currents

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Pulls water from outside through the sponge

Placozoa (plate): - Only 2 species were described until 2018 - Consists of functional upper and lower side, and cilia - Extracellular digestion; secretion of digestive enzymes - Possibly derived from a more complex ancestor; removed complexities due to a simple lifestyle - Evidence in genomes - Complex genetic pathways of humans and other animals found in Trichoplax - Chromosomes link many same genes that are linked in human chromosomes - Srivastava et al. (2008) Cnidarians: - Jellyfish, anemones/corals - Tissue around the mouth is equivalent to the gut; digestive cavity is genetically equivalent to mesoderm in triploblasts - Can reproduce sexually/asexually No Evidence for Cambrian animals before the explosions: - They were minute (extremely small) - Cryptic (rare/living in environments that don’t get fossilised) - Arose extremely rapidly from ediacaran lineage (period before Cambrian) - Some Ediacaran fossils may be Triploblasts - E.g. Kimbrella mollusc Explanations of the Cambrian Explosion: - Increase in oxygen levels - End of Snowball Earth; or genetic bottlenecks causing diversification due to Snowball Earth - Genetic/developmental inventions - E.g. Hox genes for patterning anterior-posterior axis - Predator-prey race leading to innovation/diversification - Invention of through-gut

Lecture 5: Evolution of Bilaterally Symmetrical Animals -

Divided into two large groups - Deuterostomes - Humans are part of this group - Protostomes - Ecdysozoa - Panarthropoda

- Insects and crustaceans; segmented body, jointed legs Introverta - Worms Lophotrochozoa - Annelids, molluscs, flatworm etc. -

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Differences between Protostomes and Deuterostomes are embryological: Protostomes (Mollusks, annelids, arthropods)

Deuterostomes (Echinoderms, chordates)

Cleavage

Eight-cell stage; spiral and determinate

Eight-cell stage; radial and indeterminate

Coelom formation

Schizocoelous; solid masses of mesoderm split to form coelom

Enterocoelous; folds of archenteron form coelom

Fate of blastopore

Mouth develops from blastopore

Anus develops from blastopore

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~ 76% of all animals are insects All animals within Ecdysozoa undergo periodic moulting of cuticle (ecdysis) as they grow; hence their name

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Introverta worms share a spiny introvert/proboscis - Muscles squish liquid out

Segmentation: - Repeated units of construction along the antero-posterior axis (head to tail) - Characteristic of the common ancestor of Ecdysozoans - 2 genes - engrailed and wingless regulate segmentation in all arthropods - Homologs of engrailed and wingless also seem to regulate segmentation in annelid

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Chelicerates have no pre-oral appendage - is it lost? Myriapod and insect heads are similar - are they sister groups?

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Hox genes in Chelicerates and other arthropod groups line up - Though mouth has moved relative to the appendages Suggests that appendages are the same (none lost)

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Changes in mitochondrial gene order supports insect/crustacean relationship

Ecdysozoa Summary: - Introvertan worms (introvert/proboscis) - Nematodes and nematomorphs - Priapulids, Kirnorhynchs and Loriciferans - Arthropoda (segmented body, jointed legs, tagmatisation) - Onychophorans (velvet worms) - Tardigrades (water bears) -

Chelicerates (arachnids and horseshoe crabs) Myriapods (centipedes and millipedes) Crustaceans (crabs) Insects

Lecture 6: Urbilateria

Urbilateria: - Common ancestor of all bilaterally-symmetrical Bilaterian animals; ‘Ur’ = ancient - Protostomes and Deuterostomes assumed as sister groups - How we can use their information to extrapolate about Urbilateria Homologous Characters: - Have similarities; common descent - Characteristics inherited from common ancestor and shared by two species - Determining when a character evolved is based on the principle of parsimony - Can be identified through extensive similarities; must be due to common ancestry, impossible to be convergently evolved - E.g. Pentadactyl limb - The probability that two genes are homologous can be statistically calculated - Opposed to amino acids being identical in sequence by chance - E.g. Mouse HOX4 gene and its Drosophila homolog, Deformed Analogous Characters: - Evolved independently - Convergent evolution HOX Genes: - Close correspondence between the various classes of HOX genes across the animal kingdom - HOX genes specify position in the body; anterior/posterior (A-P axis) - Expressing gene allows for cells to know where they are along the antero-posterior axis and what structures to be formed - Same HOX genes present in fruit fly and in mouse embryo - Homologous genes - Expressed in the same place in relevance to each other Development of eyes in vertebrates and fruit flies: - Eyeless (eyeless), Aniridia (human) and Smalleye (mice) results from mutations in the same homologous Pax 6 gene - Switching on Pax 6 gene from a vertebrate (mice) has the same effect on fruitfly, vice versa - Results in extra eyes formed in wrong places Dorso-ventral axis (D-V axis) in fruit fly and frog: - BMP 4 is expressed in belly of frog/vertebrate - Vertebrate originated from an inverted invertebrate - Gene expression chordates are upside down compared to all invertebrates - Conserved gene expression also suggests a CNS was present in urbilateria; common in both protostomes and deuterostomes - Dorso-ventral axis CNS patterned by SOG/Chordin in urbilateria -

Find other examples of homologous concepts between protostomes and deuterostomes to

characterize/extrapolate urbilateria

Evo-Devo: Variations on Ancestral Themes -

Most animals evolved from a common ancestor, Urbilateria - Had in place the developmental genetic networks for shaping body plans Comparative genomics show that many genes present in bilaterian animal ancestors have been lost by individual phyla during evolution Reconstruction of the archetypal developmental genomic tool-kit present in Urbilateria - Help to explain the contribution of gene loss and developmental constraints to the evolution of animal body plans

Introduction: - Last common ancestor shared by all bilaterians animals must have been a complex creature - Possessing most of the developmental gene pathways from which animals are built (Robertis and Sasai, 1996) - Urbilateria depicted as a segmented bottomdwelling (benthic) animal - With eyes, CNS, small appendage, open slit-like blastopore - Endoderm shown in red, CNS in dark blue, surface ectoderm in light blue The Genetic Tool-kit: - Sequencing of complete genomes allows powerful inferences to be made - If gene found in humans/chordate is also found in in either an Ecdysozoan or Lophotrochozoan animal, then gene was present in Urbilateria as well - If gene found in cnidarian/chordate, it must also have been present in Urbilateria - Until recently, it was believed that chordates had evolved new classes of genes serving as extracellular antagonists of growth factor signalling (since C. elegans and D. melanogaster lacked (Dkk) and secreted (sFRPs) and Noggin - However, BLAST search of mollusc genome - Reveals it contains several Dkks, sFRPs and Noggin - These Lophotrochozoan and chordate genes were present in Urbilateria genome, but secondarily lost in C. elegans and Drosophila (fruit fly) - Prominent role of gene loss; constitutes a powerful agent of rapid evolutionary change

Hox Complexes and the A-P Axis: - E.B. Lewis’ discovery that genes controlling the identity of abdominal segments (by repressing formation of legs and wings) of the fly were clustered in the genome and occupied the same order along the DNA as they were expressed along the A-P body axis - Cloning of vertebrate gene Hox-C6 (Carrasco et al., 1984) - Frog gene cloned turns out to have functions similar to fruit fly genes - First development-controlling gene identified in vertebrates

Mechanisms of Segmentation: - Body plans of vertebrates and invertebrates are metameric - Comprised of repeated segments - Arthropod segments and mammalian vertebrae; examples of a unity of plan in animal design (Appel, 1987) - Insect and vertebrate metamerism share striking similarities in mode of development - Drosophila first forms parasegments, which are subsequently subdivided so each one forms the posterior and anterior half of the adjoining definitive segments (Carroll et al., 2001) - In mammals, vertebrae develop from a portion of the somite - sclerotome - Undergoes resegmentation, so that the posterior half of one sclerotome and the anterior half of the next one fuse to form the vertebral bodies (Bagnall et al., 1988) - Ensures that muscles and tendons generated by each somite span adjoining vertebrae; facilitating movement coordination - Deep homology may exist in the mechanisms of animal segmentation (De Robertis, 1997) - Despite profound anatomical differences in resegmentation - Vertebrate segmentation clock driven by Notch signalling (Dale et al., 2003) - But, Notch does not appear to play a main role in Drosophila segmentation - However, Drosophila represents a minority of the insects in which the embryo develops rapidly, with all segments developing simultaneously (long germ-band development) - Most insects/arthropods form segments by short germ-band development (Damen, 2007) - Although still premature to conclude that Urbilateria was segmented, the plot has thickened over the past decade (De Robertis, 1997) - Search literature on Urbilateria segmentation The Chordin-BMP Pathway and the D-V Axis: - Gradient of D-V positional information regulates subdivision of the embryo into tissue types - Chordate body plan; ectoderm is subdivided into CNS, neural crest and epidermis; mesoderm into notochord, somite and intermediate (kidney) and lateral (body wall) mesoderm - Xenopus and zebrafish; cell differentiation decisions mediated by conserved extracellular pathway involving ventral BMPs (bone morphogenetic proteins) and their antagonist Chordin

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expressed in the dorsal organiser region Same molecular machinery is utilised, except the homologs are Dpp (Decapentaplegic) and Sog (Short gastrulation); inversion of axis takes place (O’Connor et al., 2006) Chordin-BMP developmental gene network controls D-V pattern in spiders (Akiyama-Oda & Oda, 2006), hemichordates (Lowe et al., 2006) and amphioxus (Yu et al., 2007) - Ancestral to bilateral animals

The Ancestry of the Bilaterian CNS: - CNS forms dorsally in chordates and ventrally in protostomes in regions in which the BMP gradient is low - Suggests that Urbilateria had differentiated CNS that was inverted during evolution (De Robertis & Sasai, 1996) - However - Questions whether bilaterian ancestor had a centralised CNS separate from the epidermis or a diffuse one (Lowe et al., 2006) - Arendt group subsequently revealed that annelids share deep homologies with vertebrates - Entire molecular fingerprints have been conserved in D-V CNS neuronal cell type patterning (Denes et al., 2007) - Annelids have neurosecretory cells that secrete Vasopressin, Oxytocin, Neurophysin prohormone - homologous to cells in zebrafish hypothalamus - Overall D-V arrangement of neuronal cell types in the CNs is regulated by BMP gradient in Drosophila (Mizutani et al., 2006) and zebrafish (LIttle & Mullins, 2006) - Pax6 gene is an upstream regulator of eye development (Gehring, 1998; Arendt & Wittbrodt, 2001) - These results support the view that hemichordates lost neural centralisation secondarily, and that Urbilateria had an organised CNS with elaborate neuronal cell types inherited by its descendants The Genetics of Evolutionary Adaptation: - Identifying actual mutations that provided variation; selective pressure acted upon in natural animal populations

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cis-Regulatory Mutations: - Provide the variation for most of the novelties in body form in animal species (Carroll et al., 2001; Davidson, 2006). - Achieved by bringing together combinations of transcription factors on DNA regulatory regions - enhancers; control spatial and temporal expression of genes - Tissue-specific enhancer modules can be added/deleted; avoiding pleiotropic effects on other regions

Historical Constraints: - Dilemma between homology and convergence in evolution - Homology; two structures arising from an ancestral structure by the action of natural selection/common ancestors - Convergence; driven by functional needs - E.g. pentadactyl limb evolved at different times, similar adaptations - Constraints in evolutionary biology should also be considered a positive influence - Facilitates effective adaptive responses to the strictures of natural selections - Designated parallelism (Gould, 2002) - Reflections on how Urbilateria was constructed - Did it contain complete genetic tool-kit animals now use? - Segmented? - Were the D-V and A-P axes patterned by BMP/Chordin - Wnt and Hox genes? - Did the gene machinery that generates works into similar morphological solutions

Lecture 7: Lophotrochozoa Distinction between Deuterostomes and Protostomes is becoming fuzzy: - Protostomes, Ecdysozoa and Lophotrochozoa are clearly a monophyletic group - Protostomes are not all spiral cleavers; only Lophotrochozoa are - Protostomes are not all protostomes - Chaetognaths and priapulids make their mouths secondarily - Deuterostomes being monophyletic is questionable Annelids: - Segmented worms - Coelomic cavity - Spiral cleavage (formed during embryogenesis; specific to Lophotrochozoa) - Trochophore larva -

Annelids which lost their segmentation; once thought to be independent animal groups

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