Living Planet/ Diversity Of Life

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Directional selection

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Mode of natural selection in which an extreme phenotype is favoured over others causing the allele frequency to shift over time in the direction of that phenotype

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Diversifying selection

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Changes in population genetics where extreme values for a trait are favoured over intermediate values. The variance of the population increases and the population is divided into two distinct groups.

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Stabilising selection

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Natural selection where population mean stabilises on a particular non extreme trait value and thought to be most common mechanism of action for natural selection

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Fitness

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The fitness of a genotype is the average per capita lifetime contribution of individuals of that genotype to the population after one or more generations(measured same stage)

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Coefficient of selection

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The selective advantage of the fitter genotype or the intensity of selection against the less fit genotype in comparison to a 'reference' genotype

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Selective advantage

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Natural selection where the characteristic of an organism that enables it to survive/ reproduce better than other organisms in a population in a given environment.

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Allele frequencies

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The number of individual alleles of a certain type divided by the total number of alleles of all types in a population. Fraction of all chromosomes in the population that carry that allele

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Darwin's finches

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Galapagos colonised by ancestral finch species- DNA evidence one event after bad weather- small group 0.9 to 1.5 my ago- variation in beak form

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Geospiza fortis

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Variation in beak depth- differential survival- drought- population decreased- seeds increased in hardness-beak depth heritable trait- beak depth increased pick up harder seeds

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What is needed for Natural selection?

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1. Variable populations of animals

2. Differential survival/reproduction

3. Some variation that is heritable

4. The individuals who survive/reproduce the most are those with most favourable variations- not random

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Peppered moth

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Increase in number of the black form-natural selection by bird predation- melanics taken over population in 53 years after first sight- evolution can be fast- light/ dark moths suffer high predation on wrong backgrounds experiment

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Soapberry bug

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Introduction of flat padded golden rain tree with thinner fruit resulted in a rapid decrease in beak length

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Limitation of natural selection

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Natural selection can only act on the variation available historical/ new by mutation. It does not necessarily lead to perfection- can evolve other way from favourable if the genome is linked to something else

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Theory

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A well substantiated explanation of some aspect of the natural world that can incorporate fact, laws, inferences and tested hypotheses

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Decent with modification

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The passing on of traits from parent organisms to their offspring from a common ancestor

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Classifying animals

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Carl Linnaeus- hierarchical groups-from vertebrates with backbone/ limbs with 5 fingers to ruminants with specialized digestive system-evudence for decent with modification

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Lamarck

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Transformism-lineages persist indefinitely, underwent change through time but without extinction/branching-inheritance of acquired characteristics-the giraffes neck

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Darwin's evolution

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Lineages split and may become extinct-natural selection-tree diagrams-decent eith modification-relatedness of species- common ancestor-species in general diverge over thousands generations-some extinction those diversifying/not-lineages persist without diversification

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The beagle voyage

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5 years- a long time to be able to travel and observe-the galápagos- Spanish can tell from which island a tortoise is from based on shape/size-undermine the stability of species

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Plant evidence

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Careful labelled collections by island in galápigos- sent to botanist hooker-pattern of endemism-1/3 specific to galápigos, 1/3 specific to island, 1/3 found other areas-evidence divergence

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Darwin's observations

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Fossil seashells high above sea level/ results of earthquake land raised- local fossils resembled local flaura/fauna support continuity of decent- species in same area looked similar

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Marsupial evidence

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Recent evidence of marsupial fossil in Antarctica linking south american/ Australasian marsupials

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Wallace's line

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Divides distinct fauna and flora-now know is a deep water passage kept flanking land masses separate even when sea levels low

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Malthus essay on population

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argument from economics-because resources are finite/ reproduction can be exponential inevitable struggle for existence between individuals-idea/observations on beagle helped spark theory of evolution by natural selection 1858

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radiation

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A source of energy not forseen by kelvin that allowed reconcilliation of the descrepancy between physical/geolohical estimates of earths age-4.5 billion years-provides the time that would,ve been needed to support darwinism

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Mendel

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Inheritance resistant to blending or dilution-contempory of darwin-work not rediscovered until 1900's-support darwinism by supporting change through inheritance

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macrosynteny

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conserved genomic regions containing the same genes but not necessarily same order/orientation-observed between human genome/more primitive(sponge, sea anemone)

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Bacteria are prokaryotes

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prokaryotes are organisms whose cells lack a true membrane enclosed nucleus

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Bacteria shapes/sizes

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spheres, rods, spirals-small- escherichia ecoli 0.5micrometres x 2 micrometres

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Bacteria binary fission

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most bacteria reproduce by binary fission-rod shaped: cell elongation, septum formation, completion of septum formation of walls cell seperation-chromosome replicated/cytoplasm divided up-doubling time under 3h

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bacteria spore formation

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form of reproduction when nutrients depletes/cells no longer grow(stationary phase)

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Bacterial structures

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cell wall-provides shape/protection from burst in hypotonic environment-composed from peptidoglycan-network sugar polymers cross linked by polypeptides

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peptidoglycan

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glycan strands with alternating B-1->4 linked N-acetylglucosamine / N-acelytylmuramic acid residues-NAM residues contain tetra peptide stem cross linked between strands give cell wall more stability

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gram positive bacteria

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simpler cell walls with a lot of peptidoglycan-peptidoglycan traps crystal violet that makes the safranin dye

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gram negative bacteria

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less peptidoglycan/ an outer membrane-crystal violet easily rinsed away showing the red safranin dye

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bacteria movement

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bacteria use a flagellum to move away/towards chemical stimuli in process called chemotaxis-a series of tumble/run cycles-direct when attractent/random when none

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horizontal gene transfer

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incorporation of genetic materia from one bacterium to another

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Transformation

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uptake/incorporation of DNA from surrounding environment-has to be competent-a complex apparatus required to do so- in lab artificially make bacteria competent using electricity/CaCI2 treatment

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Transduction

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movement of genes between bacteria/bacteriophages(viruses that infect bacteria)-phage infect bacteria with A+/B+ alleles, phage DNA replicated/proteins synthesised, fragment of DNA w A+ packaged in phage capsid, page w A+ infects recipient cell, incorporation of phage DNA created recombinant cell with A+ B-

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Conjugation

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process genetic material transferred between bacteria-plasmid DNA moves from donor to recipient via pillus

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bacteria gene transfer

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Important for speat of antibiotic resistance

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Cyanobacteria

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photoautotrophs that generate O2- plant chloroplasts likely evolved from by endosymbiosis

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fixation of N2 for plants

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Bacteria- rhizobium spp. form nitrogen fixing nodules on plant roots-leads to faster growing/ healthier plants

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Bacteria plant disease

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Tomato speck disease, potato scab, crown gall disease

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bacteria human disease

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cholera(vibrio cholerae) , food poisoning(escherichia ecoli), meningitis(neisseria meningitidis), STI's(neisseria gonorrhoeae), plague(yersinia pestis)

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Insect vector bacteria

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lyme disease is caused by a bacterium carried by ticks

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gut microbiome

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esophagus- prevotella streptococcus veillonella

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composition of gut microbiome

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obesity linked to composition of gut microbiome-mice-lean mice: high H2 reduces fermentation-obese mice:low H2 promotes fermentation-autism mouse model: low level bacteroides fragilis in gut-increased behaved more normal-linked increase blood levels of 4-ethylphenylsulphate

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Bacteria food production

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used in fermentation-glucose+2 lactic acid=yogurt-cheese,beer

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Bacteria bioremidation

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can be used to clean up pollution heavy metal contamination/oil spill-addition of microbes

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Bacteria biofuels

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important in biofuels industry-used produce bioethanol/biodiesle-important cellulose degrading enzymes

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Bacteria bioplastics

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bacteria engineered produce polyhydroxyalkanoate(PHA) starting material making plastics

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Virus structure

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nucleic acid surrounded by protein coat-largest known virus barely visible under light microsope

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Viral genome diversity

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viruses unique genetic info can encoded RNA/DNA ex. double/single strand rna, double/single strand dna

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viral genome size range

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poxvirus: virion up to 450nm long, double strand dna 270,000 nucleotide pairs-parovirus:less than 20nm diameter, single strand dna less than 5000 nucleotides

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Diversity of viral morphology

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tobacco mosaic: RNA-capsid, 18x250 nanometres- adenoviruses:glycoprotein dna-capsid, 70-90nm diameter-influenza viruses: membranous envelope-rna-capsid-glycoproteins, 80-200nm

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DNA virus

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small(5kbp)/v large(1.2mb) genomes-mainly double stranded-one family animal viruses single-linear(adenoviruses)/circular(papovaviruses)

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Human DNA viruses

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nonenveloped: adenoviridae(common cold)-enveloped:poxviridae(smallpox)-non enveloped:parvoviridae(fifth disease)

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Human RNA viruses

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Positive strand: Coronavirus 2(SARS-CoV-2),hepatovirus A- Negative strand: Influenza viruses, paramyxoviruses

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Features DNA Viruses

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replicate host cell nucleus- exceptions pox/hepadnaviradae use host polymerase to replicate genomes-capsids enveloped/non-enveloped- viral mrna's spliced-genomes overlapping genes

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RNA Viruses

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generally small genomes(3-32kb)/ replicate quick-polymerase error prone/ lack proof reading-mostly single strand-one family double-positive/negative sense

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Features of RNA viruses

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ssrna/dsrna genome-many replicated directl- retroviruses indirectly through virally encoded reverse transcriptase-capsids enveloped/ non-enveloped- positive sense(mrna/directly translated)/ negative(complemetary mrna not directly translated)-smaller/depend host cell for replication-error prone

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obligate intracellular parasites

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viruses-can only replicate in host cells

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host range

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limited number host cells virus can infect

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Viral replicative cycles

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cell manufactures the viral proteins-use host enzymes, ribosomes, trna, amino acid, ATP/others-viral nucleic acid/capsomeres spontaneously self assemble new viruses-exit by budding/lysing cell

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Double stranded DNA replication

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entry/uncoating-replication-transcription/ manufacture capsid proteins-self assembly new virus particles/exit cell

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Positive RNA virus replication

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Relies on host's mechanisms to replicate viral genome-viral genome broken down/used as template-mrna-capsid proteins-glycoproteins formed in ER-buds off

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Viral envelopes

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Viral envelopes/associated glycoproteins used enter host cell, protects capsid/ hide from host immune factors-envelope derived from plasma membrane of host cell-some molecules(glycoproteins) encoded by virus genome

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Aquisition of viral envelope

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capsid containing viral chromosome(nucleocapsid)->capsid protein->viral chromosome-transmembrane viral envelope proteins-nucleocapsid induced assembly of envelope proteins-budding-progeny virus

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Viral Host range/tropism

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host range broad/ narrow:rabies infects all mammals, measles only humans- cell type specific tropism: human cold upper respitory tract-controlled by:cell surface receptors, viral protein recepetors, intracellular conditions(affect availability)

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Cellular receptors

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proteins, glycoproteins, carbohydrates/ lipids-essential components of host-some use single type others require co receptor

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efficency of viral attachemt

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density of receptors host cell, density ligands viral surface, conc virus/ host cell, temp, ph, presence/absence specific ions

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Cell lysis

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mature virions release by destruction of infected cell/ membrane-acute infection-ex.SARS/ Influenza

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Budding

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virions released by budding from infected membrane-cell membrane intact-can still damage(cytopathic effect)-acute/persistent infection-ex. HIV, dengue virus

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emerging viruses

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novel/unknown agen/pathogen whose incident increased considerably in susceptible population

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contributions to emerging viruses

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mutation of existing(common RNA), dissemination viral disease small isolated human population go unoticed before begin spread, spread existing virus from animal(zoonosis) 3/4 new disease originate

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Dengue virus

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100 million infections anually -increasing-severity incidence/geographic spread increase-transmission: sylvatic cycle mosquito to monkey in west africa, zone of emergence rural areas, mosquito to humans city human cycle-factors favouring: population growth/urban migration

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Evolution of viruses

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evolved after first cells-candidated for source plasmid/transposons(mobile genetic elements)-recombination/reassortment-error prone replication: retroviral average 1 point mutation per replication