Genetics & Evolution (Lectures 7-13)

Front 1

Overproduction: Intrinsic rate of increase

Back 1

Intrinsic rate of increase - without limitation, the population would increase exponentially. Is limited by competition, predation & hostile environments.

Rate of increase is linear, populations must be bound by limiting factors

Front 2

Darwin: Theory & Arguments

Back 2

Assumes favourable conditions are preserved. Profitable variation means a stronger chance of survival & propagation of the modified characteristics.

Requires - overproduction, struggle for existence, variation and inheritance.

Arguments against - biology is too complex, nothing can arise by chance. Evidence of imperfect biology mutes this e.g. blind spot.

Front 3

Fitness: Variation & Inheritance

Back 3

Fitness - Measured by chance of leaving offspring (survival & fecundity).

Variation/Inheritance - Mendel introduced idea of discrete characters. Combined with Darwin's theory, resulted in population genetics.

Continuous variation - result of multiple genes having small effect, blurred by environmental factors. Individuals altar fitness due to genetics, natural selection encourages allele fixation.

Front 4

Hardy Weinberg Equilibrium

Back 4

Allele Frequency - P+q= 1

Phenotype Frequency - p^2 + 2pq + q^2 = 1

With Selection - p^2 + 2pq + (1-s)q^2 = 1

Recombination increases the rate of evolution,allowing beneficial mutations to combine from different lineages.

Front 5

Natural Selection: Neutral Drift

Back 5

In a small population, allele frequency varies slightly due to chance (genetic drift), where neutral alleles may become fixed.

oooOoo -(neutral drift)-> OOOooo -(fixation)-> OOOOOO or oooooo

Front 6

Sexual Selection: Handicap Principle & Red Queen Hypothesis

Back 6

Based on gene propagation (good for gene survival, not necessarily individual).

Handicap Principle - May lead to costly host signalling which decreases survival e.g. peacocks.

Red Queen Hypothesis - Improve and evolve at same rate as environment e.g. pathogenic resistance.

Front 7

Evidence of Ancestry: 3 factors

Back 7

Fossils - older more diverged, consecutive formations resemble each other, once extinct doesn't reappear. However, is incomplete.

Geographic Distribution - Barriers to migration, island species endemic e.g. Rhea in S.America. Related to nearest continent.

Classification - Hierarchy of organisms, unimportant features unadapted, vestigial organs now useless, homologous organs evolved different uses for same structure.

Front 8

Species & Speciation

Back 8

Species - interbreeding populations that are reproductively isolated form other groups, have a shared gene pool. Formed by splitting of existing species.

Allopatric - geographically isolated. Parapatric - adjacent but limited by environment. Sympatric - Host or time separated.

Speciation/Cladogenesis - formed by change over time. Anagenesis - cumulative change in lineage.

Front 9

Classification: Definitions

Back 9

Homologous - Inherited form common ancestor.

Analogous - similarity through convergence.

Taxon - unit of classification.

Cladogenesis - evolutionary division of lineages.

Monophyletic - Ancestor and all its decendants (forms a clade e.g. Reptiles & Birds).

Paraphyletic - Ancestor and some decendants (e.g. Reptiles).

Polyphyletic - Some species, no common ancestor, based on independent similarities (e.g. warm blooded).

Front 10

Classification: 4 Systematics, Advantages & Disadvantages.

Back 10

Evolutionary Systematics - Based on comparative analysis, geographic distribution and fossils. AD: uses all data, identifies common sense taxa. DIS: ambiguous criteria, evidence is random.

Phenetics - Grouped by similarity using numerical taxonomy. AD: most data used, no subjective judgement. DIS: No evolutionary model, many clustering methods, issues with convergent evolution and unequal evolution rates.

Cladistics - Grouped by evolutionary modified features from common ancestors. AD: reflects phylogeny, unambiguous. DIS: hard to determine ancestry, no account of anagenesis.

Molecular Phylogenetics - Use DNA sequences, quantitative analysis & cladistics. AD: large data set, all organisms, neutral characters, complex trees. DIS: not fossils, rooting , difficult with paralogs & parrallels.

Front 11

Phylogeny: Constructing Trees

Back 11

Tree representation of evolutionary relationships, history at molecular level. Branching is a divergent event, node is last common ancestor. Outgroup not related. Sister group at last node.

Rooting - use the outgroup; distance, parsimony (number of mutations), likelihood (of tree being true). Boostrapping works out reliability by replicating sequences with one gene mutation ( 70%< significance).

Front 12

Molecular Evolution: Mutations & Sequence Divergence

Back 12

Assumes sequences have descended from a common ancestor & differentiated by point mutation, insertion or deletion. Types of subsitution - synonymous makes same codon, missense makes different codon, nonsense makes stop codon. 1st mutation - 96% change a.a., 2nd- 100%, 3rd - 31%.

4-fold substitutions have more substitutions have 2-fold or nonsynonymous, evolve at same rate at introns. Pseudogenes highest rate, no selection. Flanking regions more conserved.

As genetic distance increases, difference increases then levels as only 4 base pairs (1/4 same by chance).

Front 13

Tree of Life: Construction with 3 domains

Back 13

Uses molecular data/ gene sequences from ssRNA, is conserved, universal, large and slow evolving. Discovered 3 domains.

Root discovered using sister groups and "outgroups". Use duplicated genes (with ATPase and elongation factors), will begin where two duplicates split. Sister group was Eukarya, root between bacteria and archaea.

Front 14

Mitochondria & Chloroplasts

Back 14

Mitochondria - out and convoluted inner membranes produce 2 compartments with charge separation, makes ATP. Site of respiration.

Chloroplast - outer and inner membrane, thylakoids for light and cytosol for dark reactions, makes O2. Site of photosynthesis.

Front 15

Endosymbiosis Theory & Organelle proteins

Back 15

Mitochondria once alpha proteobacteria, chloroplasts once cyanobacteria. Early eukaryotes was a bacterial predator, engulfed bacteria, enclosed in vacuole, kept as an ATP source, lost cell wall, shrank, genes moved into nucleus/lost. Few genes in own nucleus.

Organelle proteins - transcribed in nucleus, translated at ribosome. Half from endosmbiont transfer, half new Eukaryotic origin. Photosynthesis transferred as plastids between phyla (Kleptoplastidy)

Front 16

Human Ancestry

Back 16

Studied using fossils and some molecular evidence.

Apes closer to humans than thought. Human-chimp split shown to be 5-7m years ago. 1.23% subs, 3% ins/del and 27% duplications, some genes differ or are less evolved.

Comparison of synonymous (quick) and non-synonymous (slow) DNA differences found rapid evolution at 9% loci.

Front 17

Hominins: Neandertal & Denisovan Ancestors

Back 17

Hominins - Evolved from Africa repeatedly (migration & interbreeding).

Neandertals - Ancestors to Europeans, split 500-700k ago, estimated from nuclear genome sequence.

Denisovans - DNA shows to be closer to Neandertals, trace in humans (Asians).

Front 18

Genome Sequencing: Mitochondrial Eve

Back 18

Lower mutation rate estimated from genome sequencing, variants spread faster, splits earlier than predicted.

Mitochondrial Eve - Earliest mitochondria branch in Africa, traced back to one of severn women for most Europeans (15,000-17,000 years ago). Same technique mapped history of men's Y chromosome.

Front 19

Humans: Selection & Evolution

Back 19

Evolved many unique advantages e.g. walking, large brain, speech. May be due to a.a. changes or regulation.

e.g. Speech - evolution of FOXP2 gene, has 2 a.a substitutions, low variation, strong selection.

e.g. Lactose Tolerance - change in gene regulation, leaves lactase on, due to single base change upstream of intron regulatory sequence.

Medicine has eliminated death form infection,but reduced selection against genetic disorders. Increased mobility has reduced inbreeding of deleterious recessive homozygotes.

Front 20

Genetic Disorders & Eugenics

Back 20

Common heterozygotes confer advantages e.g. Sickle-cell anemia & malaria resistance. Infectious disease is a major selective force. Low fecundity & small families encourage less variance.

Germline Therapy - May allow for selective traits in humans.

Eugenics - sterilising undesirables to increase preferred traits.

Front 21

Eras

Back 21

4600-->4000 Hadean Era (no surviving rock)

4000-->2500 Archaean Era (first cells)

2500-->541 Proterozoic Era (free O2, Euk)

541-->252 Palaeozoic Era (land colonised)

252-->66 Mesozoic Era (reptiles, gynosperms)

66-->0 Cenozoic Era (mammals, angiosperms)

Front 22

Hadean Era

Back 22

Solar system formed by accretion, earth became hot. Iron melted and formed core, silicates formed geosphere. Hydrosphere of water formed (high iron levels). Atmosphere very reducing, oxidised gas increased slowly (98% CO2).

Front 23

Life: Requirements & Prebiotic Organic Synthesis

Back 23

Life - requires multiplication, variation and heredity, by natural selection and self-regulating.

The chemoton model - that life needs 3 properties: metabolism, self-replication, and a bilipid membrane. Membrane vesicles spontaneously replicate, cause hypercycles (each replicate catalyses next replication).

Organic synthesis from primordial soup, clay, aerosol or water droplets.

Front 24

RNA World: Theory & Evidence

Back 24

RNA before DNA.

DNA is synthesised from RNA monomers, RNA is key for DNA/protein synthesis. RNA is catalytic and informational.

Many enzymes use ribonucleotide cofactors. Peptide bonds formed by ribozymes. Ribosome is a ribozyme.

It high mutation rate limits genome size, so it is less stable and holds little information, causing selection towards DNA.

Front 25

Archaean Era: Stromatolites and O2

Back 25

Appearance of stromatolites - structured sediments around gelatinous mats of cyanobateria in shallow seas. Fossils similar to cyanobacteria filament, O2 absorbed by Iron. However, may have been chloroflexi, which is less evolved (only one photosystem), which doesn't use O2 but H2.

O2 - rose briefly, too cold. Increase later due to algae. Snowball Earth.

Front 26

Proterozoic Era: Ediacaran

Palaeozoic Era: Cambrian Explosion & Post-Cambrian

Back 26

Ediacaran Period - (635m) quilt-like animals fossilised, now extinct.

Cambrian Explosion - (541m), dip in c13 levels, increase in Eukaryotes, new recognisable fossils (soft bodied organisms at Burgess Shale).

Post Cambrian - Modern animal phyla, many fossils. Ordovician (485m, life in ocean), Silurian (443m, plants on land, issues with water loss) and Devonian (419m, Rhynie Churt- silaceous sinters in silica).

Front 27

Continental Drift: Pangea, Drift &Climatic Zones

Back 27

Pangea - one land mass, supported by continental fit, climate belts & biotic species disjunctions. Plate tectonics - crust formed in centre of oceans, moves to continent and forms land features e.g. volcanoes.

Drift - species barriers and isolationism, phylogeny shows evolution e.g. N&S.America. Climatic zones - changes in location, caused land features e.g. coal in GB. Ocean circulation altars climate patterns. Volcanic islands occur at margins.

Front 28

Mass Extinctions & Cenozoic Era: Glaciations.

Back 28

Mass Extinctions - Correspond with changes of periods, global change. Cretaceous-Paleogene (66m) extinction of dinosaurs from asteroid, spread iridium, caused dust, darkness, cooling etc.

Cenezoic - mammals and flowering plants. Glaciations - linked to clustering of land masses in one hemisphere. Quaternary Ice Age (2.4m) regulated by earth's orbit, brief cool periods, long glacial, altars rainfall, land expands/contracts.