AE notes for 199103 PDF

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L4: evolution of populationGenetic drift​: the change in allele frequency of a population due to chances.genetic drift: how allele frequencies change unpredictably from one generation to the next (more rapid in​ smaller population​).Gene flow​: the exchange of alleles from one population to the othe...

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L4: evolution of population Genetic drift: the change in allele frequency of a population due to chances. genetic drift: how allele frequencies change unpredictably from one generation to the next (more rapid in smaller population).

Gene flow: the exchange of alleles from one population to the other. Gene flow: ● consists of the movement of alleles among populations ● eliminate local difference between populations ● add new alleles to a population ● gene flow reduces variation among population over time

Bottleneck effect: when there is a sudden reduce in population size due to environmental events such as fire, earthquake or flood.

Founder effect: when a new population is established by a smaller number of population from a large population, the founder population is u  nrepresentative to the original population.

Evolution: the change in allele frequency over time within a population. Natural selection can only act on variations within a genetic component. 4 requiremtnes of evolution: c  ompetition, variation, inheritance, differential reproduction

Mutation: ● formation of new alleles ● alter gene number position ● new genetic combination produced frameshift mutation: mutation caused by the insertion/deletion  of bases in DNA sequence that change the reading frame of codons, resulting in completely different translation from the original, the earlier the insertion/deletion occur, the more altered the protein.

Sources of genetic variation: ● ● ● ●

formation of new alleles altering gene number or position rapid reproduction sexual reproduction

1. evolution can only act on germ-line mutation (mutations in germ cells, inheritable) 2. Neutral Theory: many change in genes and proteins have no effect on fitness so are not influenced by darwinian selection. 3. Alter gene number or position: chromosomal mutation can delete, disrupt or rearrange many loci. 4. Gene substitution has the least effect. 5. Gene duplication: increase the number of genes in the genome, duplicated genes can take on new functions by further mutations 6. Rapid reproduction: holding mutations rate constant, but have shorter generation and more offspring per generation, then increases and build up genetic variation over time. 7. Sexual reproduction: can shuffle existing alleles into new combinations by(3 ways): crossing over, independent assortment, fertilization. 8. Hardy-weinberg equation: alleles and genotypes frequencies in a population will remain constant if the evolutionary influences are absent. 9. Conditions of hardy weinberg equ.: extreme large population, no gene flow, no mutation, no natural selection, random mating. 10. If it is not ideal, the population may eolve. 11. p^2+2pq+q^2=1 12. p+q=1 13. p^2 is AA(dominant), 14. q^2 is aa(recessive) 15. 2pq is Aa heterozgous gene.

L5: natural selection ● ● ● ● ●

stabilizing disruptive directional artifical sexual: inter(different sex choice), intra(same sex competition)

Genetic drift, gene flow, mutation and NS can alter  allele frequencies in a population and cause evolution. Natural selection can not create variation, it only affects alleles that already exist in population. NS is the only mechanism that causes adaptive evolution. Relative fitness: the contribution an individual makes relatively compared to the others in the gene pool of future generation.

Individuals do not evolve, populations do. If environment changes, NS will result  in adaptations of the organisms to the new environment. Selections only act on inheritable  traits. Natural selection refers to survival advantages and reproductive success. Stabilizing selection: average favoured, extreme removed Disruptive selection: extreme favoured, average removed Directonal selection: one trait favoured Directional selection can change allele frequency in the population.

Artificial selection: human INTENTIONALLY select and breed animals or plants to develop desirable traits (bear little resemblance to their ancestral population)

Sexual selection: individuals with certain inherited traits are more successful at finding mates. Sexual selection refers to mating success, it can result in sexual DIMORPHISM. Intersexual selection: one sex choose mates of the other sex to mate with. Intrasexual selecton: same sex compete to have access for that mate of the other sex. In diploid organisms, recessive alleles are hidden from NS. Balancing selection: heterozygote advantage, frequency dependent selection. Heterozygote advantage: individuals who are heterozygous at a particular locus have greater fitness than other homozygous individuals. Frequency dependent selection: the fitness of a phenotype depends on how common it is in the population Positive FDS: fitness increases when frequency is high(very common) Negative FDS: fitness increases when frequency is low(less common) Fitness coefficient(w): the adaptive value of a phenotype. Individuals have produce the most offspring have a fitness of 1. Selection coefficient(s): a measure of selection pressure against that particular phenotype, 1-w=s.

L6: Darwin, the origin of species Reproductive isolation: the inability of a species to breed with related species due to geographical, behavioural, genetic barrier difference. There are 5 different reproductive isolation: ● ecological (live in different habitats) ● temporal (mate at different times) ● behavioural (birds prefer different songs) ● genetic/chemical  (genetic barriers prevent gametes from forming) ● geographical (physical barrier) Fossil records can be used to study speciation. individuals within a species can have extreme phenotypes Punctuated equilibrium: ● once a species appears in the fossil record, the population will be in stasis(stable), showing little evolutionary change for its geological history. ● Evolution occured rapidly with long period of non-change. ● Example: a sea animal species showed little change for thousands of years, then the sea level changed and they had to adapt.

Gradualism: a slow, steady change through time which leads to drastic morphological changes. 1. Most species that ever existed is now extinct. 2. The life time of a species is usually a few million years. 3. Rapid evolutionary changes might result from: speciation, adaptations, competitions, hybridisations and invasions. 4. Radiolarian fossil: the fossil of a single-cell organism. 5. Chromosome duplication can result in reproductive isolation and cause speciation for a single generation. Autopolyploidy: a type of polyploidy when the individuals have more than 2 copies of chromosomes from the same species. Allopolyploidy: a type of polyploidy when individuals have more than 2 copies of chromosomes from different species. Extinction is important: ● it stimulates the growth of others on the branches ● it reduces competition for limited resources. ● it leaves behinds niches (habitats+behaviours) Adaptive radiation: When 2 or more different species arise from the same ancestor in a short time, adaptive radiation can rapidly result in morphological diversity.

Heterochrony: an evolutionary change in the relative rate and timing of developmental events, it can have a huge impact on the body shape. Heterochrony can alter the timing of reproductive development relative to the timing of non-reproductive organs. Allometry: the relationship between an organism’s size and shape, it refers to the different rates at which different organs grow. Paedomorphosis: ● A type of heterochrony, when larval features of an organism are displaced to its adult offspring.（娃娃鱼的触角） ● The sexually mature species retain body features of larval structure. ● In paedomorphosis, the rate of reproductive development is higher than the somatic development. (性早熟） Change in spatial pattern(空间格局）: alterations in genes that control the placement and organization of body parts can cause evolutionary change. Homeotic genes: genes that control the pattern of body formation during embryonic development (e.g. where wings and head develop). Hox gene: a subset of homeotic genes that specify the head  to tail axis and segment identity of animals in early embryos. In vertebrate, Hox gene provide information in the development of fins in fishes and limb in tetrapods. HoxC6 gene: correlates with limbless region in embryos Ubx gene: a homeobox gene found in insects, control patterns in morphogenesis. A mutated Ubx gene can turn off leg development. Evolution is not goal oriented.

Why is hox gene important? Hox gene is important in the evolution of morphological forms because: hox genes lay out the body form of many organisms, they set up head to tail organization, small change in hox gene can lead to a big evolutionary change.

L3:phylogeny 1. Phylogeny: the evolutionary history of a species/group of related species. 2. Phylogenetic tree shows patterns  of descent, now phenotypic similarity.

3. 4. 5. 6. 7. 8. 9.

Hierarchy: a ranking system (dominant and submissive) A unit at any level of hierarchy: taxon Branch point represents divergence of two lineages. A phylogenetic tree is a hypothesis about evolutionary relationship. Sister taxa: groups that share an immediate common ancestor Clade: Homologous structure: structures that are similar in related  species due to common ancestor. 10. Analogous structure: structures that are similar in unrelated species due to similar selection pressure. 11. Convergent evolution: when unrelated species evolve to have similarities/similar adaptations due to natural selection. 12. Divergent evolution: when a group of related species evolve to accumulate differences, resulting in the formation of new species (due to NS/new niches). 13. A valid clade is monophyletic (single tribe) 14. Monophyletic: a group of organisms that are in the same taxon and share a most common recent ancestor. 15. Molecular clock: a technique to measure the timing of evolutionary change( can be corrected/proved with the fossil records) 16. Genetic mutation is random, but occur at a relatively constant rate. 17. Gene duplication: a type of mutation, increase the number of genes in the genome, provide opportunities for further evolutionary changes, duplicated genes can have new functions by further mutations. 18. Paralogous gene: result of gene duplication, the genes copied from duplication are paralogous to each other.

L7: the tree of life Phylogeny: the study of relationships of different groups of organisms and their evolutionary development. Domain eukaryota: ● animals ● fungi ● protist (one celled) ● plantae(plants and green algae）

Prokarotes:

● bacteria ● archaea 3 domain of life: archaea, bacteria and eukarya Prokaryotes: ● single-cell organisms ● do not have nucleus or membrane-enclosed organelle ● can live in extreme conditions. Cell walls are found in all prokaryotes, plants, algae, fungi. Bacteria cells contain peptidoglycan in cell wall, polymer composed of sugar crosslinked by polypeptides. Cell walls can: ● maintain cell shape ● protect cells ● prevent cells from bursting in hypotonic(缺水) environment

Eukaryotes: ● ● ● ●

have membrane-enclosed organelle have nucleus have cytoskeleton most eukaryotes are sing-celled organisms call ‘protists’

charophytes (green algae): the closest living relatives of plants Plants are multicellular, eukaryotic, photosynthetic, autotrophs. Fungi are multicellular, eukaryotic, heterotrophs, they absorb nutrients from the environment Heterotrophs: organisms that cannot produce their own food but obtain energy/food from organic substances.(mainly fungi, animals and human) Animal cells are supported by protein. Animal’s unique characteristics: nervous  and muscle tissues. Tissues: groups of similar cells that act as functional groups. Most animals reproduce sexually. After fertilisation, the zygote undergoes rapid cell division called ‘cleavage’ that lead to the formation of multicellular blastula (an animal embryo at early development as a hollow sphere)

Eumetazoa: a clade of animals with real tissues. Most animals belong to the clade bilateria. Importance of invertebrate: ● make up biodiversity ● keep ecosystem to function ● many are parasites of domestic animals/human ● important for understanding evolution

Choanoflagellates: m  icroscopic aquatic organisms (flagellated protist) that can alternate between single-celled and multicellular states. choanoflagellates and animals are sister groups, closest single-celled relatives of animals.

Porifera sponges: a sister group to all other animals. sponges: basal animals that lack tissues (porifera) sponges do not have real tissues or nervous systems sponges are filter feeders they have a cell with a flagellum that draws water through a collar

Ctenophora ● comb jellyfish are radial symmetry and have real tissues （diploblastic） ● unique traits: 8 combs of cilia( ) that propel the animal through water ● some have specialised cells in tentacles that burst open and r elease sticky threads to prey Radial symmetry: a round shape that is symmetrical around the central axis, such as seastar, jellyfish, sea anemones and some flowers. Diploblastic: describe an animal with a body wall composed of 2 layers, ectoderm and endoderm. diploblastic animals have only endoderm and ectoderm layers.

Endoderm: the innermost germ layer, turns into inner lining of digestive/ internal organs and alimentary canal Ectoderm: the outer germ layer, those cells cover the embryo’s surface, give rise to skin, hair, nails neural tube and n  ervous systems

Mesoderm layer is the middle layer, give rise to bones, muscles, skeletons, tissues,  circulatory system and sex organs. Triploblastic: describe an animal with a body wall composed of 3  germ layers. endoderm, mesoderm and ectoderm. 1. 2. 3. 4. 5. 6.

sponges and other groups (that lack tissues) usually lack symmetry. all bilateral animals are triploblastic. all radial animals are diploblastic. only triploblastic o  rganisms can have a body cavity. diploblastic animals do not have organs Diploblastic/ Triploblastic animals have tissues and nervous system.

Cnidaria: jellyfish, coral, hydras ● ● ● ● ● ● ●

radial, diploblastic have true tissues gastrovascular cavity with a single opening can be sessile polyp(不能动) or motile medusa(能动). single opening as both mouth and anus sessile polyp: stick to the substrate by the absoral end of body motile medusa: not attach to substrate and move freely, have bell-shape body with mouth on the underside ● carnivores that use tentacles (armed with cnidocyte cells) to catch prey, n  ematocysts are organelles within cnidocytes that eject a stinging thread ● have nerve net with sensory organs ● lack brain

L8: lophotrochozoa ● platyhelminthes ● mollusc ● annelid Bilateral symmetry animals have : ● a top and a buttom side ● a left and a right side ● a front and a back side ● triploblastic

Platyhelminthes ● include free-living  flatworms (planarians) that live in marine/freshwater ● many are parasites, such as flukes and tapeworms ● acoelomates, lack a body cavity, coelom, between digestive tract (endoderm) and outer body wall (ectoderm) ● have a central nervous system free-living flatworm: ● have a flatten body that is a few cells thick ● have high surface to volume ratio, allow them to exchange nutrients and products with their environment ● are predators and scavengers (eat  dead organisms) ● breath by diffusion, no circulatory/respiratory system ● have gastrovascular cavity with one opening Most platyhelminthes are parasitic. They have suckers to attach to the internal organ of the host. Two major groups of parasitic flatworms: flukes and tapeworms

(trematode

) flukes:

● have complex life cycle, can alter sexual and asexual stage (hermaphroditic) ● human parasites spend part of their life in snail hosts ● produce surface protein as their host and manipulate the host’s immune system

blood fluke: ● ● ● ●

mature fluke live in human’s blood vessels they reproduce sexually in the human host the fertilized eggs exit in host’s faece when the faece reach water, eggs develop into larvae, then the larvae infect snails, snails become intermediate host ● asexual reproduction occur in snails and another type of motile larvae produced, then they escape from the snail host ● the larvae penetrate skin and blood vessels of human that come into contact

(Cestode) tapeworm: ● parasites of vertebrates (pigs and cattle) ● have no mouth or gastrovascular cavity, they absorb nutrients directly  from host’s body ● have suckers and hookers for attaching to the host ● sexually produced fertilized eggs leave the host’s body through faece

● hermaphroditic

molluscs: ● snails, slugs, oysters, squids, clams….most are marine ● soft body, hard shell made of calcium carbonate (shells stop water from vaporating) ● squids, slugs have lost their shell completely during evolution ), mantle.(覆盖物) 1. Molluscs body plan: muscluar foot, visceral mass( 2. many mollusc also have water-filled mantle body cavity and feed with a strip-like radula(舌齿) 3. Most snails have separate sexes, but many are hermaphrodites. 雌雄同 体 4. Many molluscs have a ciliated larva stage called t rochophore ( ). (free-swimming marine larva with bands of cilia 纤毛) The four major classes of molluscs: ● polyplacophora (chiton) ● bivalvia (clam, oyster) ● cephalopoda (squid) ● gastropoda (land snails, sea slugs)

polyplacophora (chitons): 椭圆形oval-shaped marina animals, they use foot to grip rock and use radula(齿舌) to scrape algae off the rock surface.

gastropoda(snails, slugs): ● ● ● ● ●

(

75% of molluscs are gastropods. gastropods move slowly by rippling motion of their foot or cilia most gastropods have a shell for protection, dehydration. most gastropods are herbivores musclar foot, visceral mass, mantle

) Bivalvia (clam, oyster): ● ● ● ●

bivalves are aquatic, such as clams, oysters, mussels have a shell divided into halves joint together by muscles some have eyes and sensory tentacles along their mantle mantle cavity is used fo both feeding and gas exchange

● most cannot move, but some have some limited motility

cephalopoda (squids): ● they are active predators with beaks surrounded by tentacles (触手) ● able to immobilize prey with poison from their saliva(唾液) ● foot is motified into a muscular  excurrent siphon(延伸的虹吸管) and part of the tentacles ● the shell is lost in most species, except the chambered nautiluses( ) ● have a closed circulatory system(循环系统), well developed sense organs and a complex brain ● cephalopod with shell called ammonites were common but extinct at the end of Cretaceous Period(白垩纪) 1. The most threatened groups are: freshwater bivalves (pearl mussels), land gastropods (snails). 2. They are threatened by habitat loss, pollution, non-native species and overharvesting by human. 3. Mollusc are the group of animals with the largest number of extinction.

annelida:(earthworm) ● ● ● ● ● ●

body system in repeating segments bodies composed of a series of fused rings use setae(刚毛) for swimming are coelomate segments divided internally by a s  eptum (隔膜) (not in leech) have chitinous bristles called setae (or chaetae) that provide anchorage or used for swimming (not in leech)

Annelida can be divided into 2 major clades: errantia and sedentaria.

Sedentatian: ● ● ● ●

less motile than errantia include leeches and earthworm some live in susbrates, some in live protective tube Tube-dwelling(居住) sedentarians often have elaborate gills or tentacles used for filter feeding

Erratian: ● most are motile marine predators ● have paddle-like structure called parapodia on each segment for motion ● each parapo...