Evolutionary biology

decent with modification - all species descended without interuption from an original form. Natural selection - casual agent of adaptive evolutionary change, more offspring produced than survive, less well adapted animals contribute less to next generation. non adaptive evolutionary changes: genetic drift. 

evidence: fossils, living organisms- traits form and function, experimental evolution- view microevolution. fossils - structures, trace, chemical and unaltered remains. oldest - filamentous cyanobacteria 3.6bya. world - 4.6bya. first humans 0.4mya. fossils tell us morphology and behaviour, ancestors of living organisms e.g bacteria, sycamore and coelocanth. fossil intermediates = archaeopteryx and S.freyi. problems - fossilization unlikely, record very incomplete. many species not represent because - not suitable fossil material, organism was rare, sediments not always solidified, rock must persist, radiometric dating of igneous rock as cant date sedimentary. also doesnt tell us the processes that created the organisms. 

living organisms  e.g morphology, ecology, behabiour and genes. charactors must be homologous not analagous having evolved indepdantly e.g whale (whale) and shark (fish). limb structure of tetrapods - pentadactyly is homologous. 

morphology - inter and intra specific. genes - diff in DNA, better as correct analogous morphology and missinterpretations, can also add timeline to events. can get DNA from ancient samples found in amber and ice. however, DNA is acid - hydolyses over time. oldest DNA sequence 400,000ya. 

mutation in DNA happens on a long time scale, changes in frequency of alleles can occur quickly e.g peppered moth (micro-evolutionary scale processes). experimental evolution - E.coli or flys, each generation select for a specific phenotype. over many generations compare physiological and genetic changes. macro-evolution - infered from fossils, large evolutionary changes e.g origin of new organisms, body plans. micro - smaller scale, alterations to gene frequences. 

non-synonymous mutation changes the amino acid sequence coded for by a codon. 45% human genome is repeated sequences. 1% exons. 3rd position in codon most degenerate. 

changes during replication or unrepaired DNA damage - point mutation, recombination, duplication or chromosome rearrangments. C->T A->G transition, pyrimidine-purine transversions. protein truncation (stop codon). substitutions - changes in DNA that have been passed on. synonomous changes accumlate faster than non-synonomous as they are selected against. with time sites become more saturated i.e multiple mutations on same site. transitions occur more than transversions. 

low rate of substitutions on non-degenerate sites as not normally passed on. most substitutions in degenerate sites and psudogenes. asexual organims cant do recombination. alleles that are always inherited together are in complete linkage disequilibrium.

unequal crossing over caused by mispairing, transposons and non chromo segregation results in gene duplication = gene families. polyploidy - usually plants as self-fertilise. diploid cell undergoes failed meiosis producing diploid gamets which self-fertlise producing tetraploids. 'odd' sterile. polyploids cant breeed with original diploids - speciation. higher levels of proteins, duplicated genomes give new gain of function allows for genetic innovation. 

chromo rearrangements - translocation of a small piece of one chromo to another, leukemia between chromo 8 and 22, philadelphia chromo. Fission, fusion - whole chromos bind to each other. inversions - mean at meiosis no recombination so chunks get inherited. 

gene conversion - not recombination, repair mechanism gone wrong, alleles being changed across diff chromos, proof reading enzymes 'repair' one chromo by copying the other. not always random, if repair is biased all alleles will eventually be same e.g ribosomal RNA genes are repeated - concerted evolution keeping the alleles the same and multiple copies so more protein made

aquisition of new DNA - transposition -  leave copy behind which encodes 'transposase enzyme', . class I - retrotransposons  product of mRNA being reverse transcribed, leave copy behind, LINE elements in humans chromo 22 has 14,000. retrorvirus can cross cell boundries. class II - transposons - no RNA intermediate, some leave copy behind, most common in bacteria. can knock out genes and cause recombination between diff chromos as the transposons match so can pair up. can cause inversions, deletions and translocations

horizontal gene transfer - virogene - derived by reverse transcription of a virus gene similar strain found in baboons and cats, suggest HGT. transformation - neutral taking up of external DNA e..g in plasmid form, can be beneficial as could contain antibiotic resistance. Bacteriophagee infection - virus-like particles that infect bacteria and pass on bacterial DNA as well to next target. HGT also in endosymbiont bacteria i.e mitochondria and chloroplasts. they are broken down a lot so DNA floats around and incorporates in host's nucleus. hybridisation - new DNA from sex of diff species. 

mutations only have evolutionary consequences if passed on to next gen. most occur in cell division not germiline cells. 5X more mutations in spermatogenesis than eggs as more cell division. if mutation beomces fixed in population = substituition.

neutral theory (kimura) - genetic drift, most neutral muations eliminated by selection, benefitial ones fixed by natural selection, most neutral fixed by random processes (drift). slelection - purifying, positive directional selection and balancing. can also reduce variation at closely linked sites even is this variation is neutral = background selection. 

pleitropy - single gene affects many traits. epistasis - effect of one gene modified by another. microsatalite variation between pops used. variation in non-coding repeats for between individuals e.g paternity tests - EPP superb fairy-wrens 76% EPP. good gene theory

numt - copy of mitochondrial DNA broken up and inserted into nuclear DNA, used to date evolutionary history as mutates faster. 

darwin 4 postulates: individuals within species are variable to nearly all traits because of mutations creating new alleles and recombination with independant assortment. variations are heritable intact. more offspring produced than survive. survival and reproduction not random, ones that survive have most favourable variations. natural selection based on heritable variation not blending variation as genes retain their identity when passed on. combination of mutation and natural slection: adaptive evolution, not neutral.

homogenous populations cant evolve. macroevolution is explained by microevolution. natural selection acts on individuals but causes adaptive evolution in the pop. balance school: large amounts of genetic variation are maintained in pop (going against natural selection): natural selection e.g hetrozygous advantage, gene flow and neutral processes. 

'standing genetic variation' lots of varients in pop causes lots of varients with diff niches. discrete variation: polymorphism in phenotype bcs a single gene with 2 or more alleles lead to distinct phenotypes in pop, shows bimodal distribution. continous variation: predominant variation, polygenic inheritance, additive effect of each gene, shows normal distribution curve. 

to measure variation need to know : fraction of loci are polymorphic. how many alleles at each loci, frequencies of each allele at a locus. use to see how pop will evolve and its' adaptive potential. 

DNA sequecing. sanger sequencing - uses chemically altered bases in PCR to stop replication at diff points, fragments then put together to see the DNA sequence, bases labelled diff colours. next generation sequencing illumina: acoustic waves fragemnt DNA,illumina adaptors bound to ends of DNA, these gel electrophoresed, fragment 200-300bp is taken, templates then amplified, flourescently labeled deoxybases added. 454: amplifys DNA templates inside water droplets in oil, (emulsion PCR), DNA has has primers and luciferase lights up each base. 

a locus is polymorphic if dominant allele frequency is less than 95%. average nucleotide diversity per site = differing sites/base seq. observed genotype frequency = dominant homozygotes/ total population, etc. allele frequency, homozygotes x 2 + hetrozygous x 1 / total pop. p = D + H/2, q = R + H/2. use p2 + 2PQ + q2 = 1 to get expected frequencies. allele frequencies the same but distribution is diff. 

hardy weinburg principles - no selection, infinite population, mating is random, no gene flow, no mutation. if allele distribution is diff shows that evolution is happening! few species live in panmictic pops, most species subdivided into pops, pops may differ in genetic composition, may diverge into subspecies with diff areas, pops and a hybrid zone sometimes. 

horizontal gene transfer: transduction: vectors/viruses, conjugation: pilus, plasmids, transformation: takes DNA up from surroundings. means get new genetic info, allows phylogenetically diff species to mix, dont have to wait millions of years for mutations can just get a antibiotic resistant gene, operational genes more easily taken up than informational. 

mitochondrial pseudogenes: numts - copies of mito genes that have broken up and incorporated into nuclear dna. more common in plants. useful: can see when species diverged as numts dont mutate but mt genes do. can see when numpt happened to use as marker in phylo tree. 

transposons: RNA mediated, reverse transcriptase used. they transcribe own transposase enzyme which makes own transcription molecule so can move and insert. good - increase genetic diversity, maintain telomeres, T cells made form transposons. bad - allows replicates of same DNA chunks - uneven chromo corssing over,insert into functional gene or btwn promoters. 

polypoloidy caused split in seed and angiosperms. whole genome duplication and gene/chromo. estimated time scales showed whole genome dupl. good - causes divergance of groups.

movement of mimicry gene btwn species means can ward off predators. mimicry gene same in diff species, other genes very diff, would create 2 diff phylo trees. humans adapted when migrated from africa to europe through hybridisation with neanderthals to get disease resist etc.

change of allele freq over time - evolution. No pop is infintely large so stochastic changes - genetic drift. Genetic drift acts more on smaller populations. is a fundamental evolutionary force with selection, mutation, migration and recombination. natural selection not random - adaptive evolution. genetic drift - random fluctuations in allele freq as a result of sampling error between generations of limited size - non-adaptive evolution. all alleles subject to genetic drift but not natural selection. genetic drift - null hypothesis to explain evolutionary change

V=p(1-p)/2N, more varience with less sample size. loss of hetrozygocity - freq of hetro highest when p=0.5, as it moves to 0 or 1 hetrozygosity falls. expected freq of hetrozygosity in next generation is always less that the freq in current. bottleneck - rapid decrease in pop size - limited alleles, can lead to divergance from ancestor. if new pop is formed called founder effect due to loss of genetic variation, level of hetro not reduced much in first generation.

humans originated in africa and diverged out, multiple founder effects, highest hetro in africa. phenotypes affected by genetic drift e.g skull shape, 40% variation in humans due to drift, additional variation due to selection e.g from pathogens, e.g of drift as null hypothesis. amish pop - 200 settlers, 1 carrier for ellis-van crevald, 7% amish have it

genetic drift cna be stronger than evolution. berthelots pipit bird colonised north to canary islands, 60% genetypic variation between islands and 30% phenotypic. bottlenecks better predictor of morphological distance between islands than georgraphical or ecological distance.

effective pop size - not all individuals in population breed. all individuals = consesus size. genetic drift proceeds at same rate of effective pop size. factors influencing Ne = variation in progeny number,  overlapping generations - offspring mate with parents, effective number of genes reduced. unequal numbers of males and females - elephant seals, 1 alpha 1 beta male breed with all females, small variation of genes passed on. fluctuations in pop size - use harmonic mean 2/(1/n + 1/n). 

small Ne leads to loss of hetrozygocity and hetrozygosity advantage causing loss of genetic diversity - loss of adaptive potential - lower levels survive - less reproduce - smaller population - extinction. inbreeding - inevitable in smaller pops. probability that two alleles in an individual are identical by descent. inbreeding depression - reduces hetro, exposes rare deleterious recessive alleles as homozygotes, loss of genetic diversity. e.g pigs mated over 2 generations - average litter reduced from 7.15-4.26.  

genetic rescue - increases hz, only needs single immigrant to breed - swedish wolf. population structure - most structured, very few panmictic. due to natural aggregations and fragmented habitats. causes pop subdivisions and genetic difference among subpops. evolution makes them diff, genetic drift also makes them diff, can cause speciation and diversification. selection on diff habitats for diff traits. 

pop substructure changes allele frequencies to less hzs, called wahlund effect. pop structure can be quantified using wrights F stats. F = loss of hz relative to expected if all populations were mating. F=(Hexp - Hobs)/Hexp. lower Hobs is due to subdivision into smaller pops. Total F can be Fis - in individuals compared to subpops. Fit - indivuduals relative to total pop. Fst - subpops compared to total pop (Ht-Hs)/Ht. genetic structure quicker in smaller pops Fst= 1-(1-1/2N)t. 

gene flow and genetic drift important for pop structure. gene flow = movement of gametes or individuals among pops. island model - pops with individuals migrate form one to another with equal probability. stepping stone model - defined prob that differs according to distance etc. isolation-by-distance model - even dist of continous overlapping pops, less likely to migrate to further sites, neighboroughing pops are genetically similar. 

changes in allele freq due to migration are determined by - allele freq difference between populations (p2-p1) and the level of gene flow (m). expected change per generation - m(p2-p1). gene flow can homogenise allele freqs. change is rapid initially as gene freq get closer between pops the rate of change slows. high migration over few generations can have huge effect. genetic drift and migration are opposing forces. pop differentiation depends on pop size and effective migration rate. given enough time they will reach migration-drift equilibrium

estimating gene flow - direct short term - mark and recapture. track marker alleles over short no. generations. doesnt take into account what proportion of migrants contribute to gene flow. indirect long term methods - stastics from allele frequences. directly reflect gene flow. Nm = amount of migration, high number = lots. Fst = pop subdivision, high = significant pop division. Fst estimates gene flow. Fst - directly linked to migration. Nb- neighbourhood size. high Nm = Low Fst. Nm = no. migrants each generation. 1/(4Nm+1). 

isolation by adaption or physical barrier- individuals cant survive in other pops enviroment, decreasein gene flow, increase in genetic drift, increase neutral difference. selection can have diff effects on diff genes due to recombination e.g divergant selection on genes coding for colour patterns. colour polymorphism maintained in the face of gene flow high Fst. 

natural selection - if phenotype trait is heritable the alleles will increace in freq over generations. fitness - the average lifetime contribution of indiviuduals to a given genotype to the pop after one generation (reproductive success). viability selection, sexual selection, fecundity and gametic selection, compatibility. adaptation - a character that has evolved by natural selection, selection causes adaptation, natural selection is random, selects for whatever turns up.

darwins finches -lots of diff niches in gallapogous. adaptive radiation - evolution of diversity within a rapidly multiplying lineage, includes both speciation and pheotypic adaption to divergent enviros. natural selec - acts of phenotypes, selects for genotypes. directional selection - favours one extreme, e.g cliff swallows diversifying - favours diff extremes, feed on small or large seeds, diff beaks. stabilising - selects against extremes, reduced phenotypic variation, e.g birth weight. purifying selection - removal of mutations that change phenotype.

selection against recessive alleles still get recessive alleles hidden in Hz. pop mean fitness increases rapidly then slows as reaches maximum. when select for recessive it rises slowly due to genetic drift by chance then more rapidly when reaches max, will become fixated.

selection eliminates variation and so does genetic drift. variation maintained by mutations, gene flow and balancing selection. Hetro advantage e.g sickle cell. frequency dependant selection - fitness of genotype is not constant. negative FD - rarer form is advantageous. positive - common form. negative leads to oscillations in mean phenotype, positive quickly causes fixation of allele. rare allele advantage - new alleles, relative fitness of allele declines when frequency is high, e.g competition for food in cichlid parasites left handed and right handed feeding on fish and individuals with new/rare MHC alleles.

fluctuating selection - RPW8 gene gives plants resistance to pathogen, but grows less so cost of resisitance. depends on temporal and spatial variation in pathogen presence - maintains polymorphism. if directional selection on homos it will be fixed, if on hetros - hetro advantage.

factors that explain adaption - genetic drift, correlated evolution, ancesteral character e.g appendix. and natural select. methods to infer - observation, experiemtns and the comparative method - patterns across species, correlations among traits and the enviro, if a certain relationship between traits evolved repeatedly then it is likely to be adaptive.

components of fitness - survival, mating and reproductive sucess. variation in demographic traits - no and size of offspring, life span, age distribution of reproduction, alternative mating strategies, disperal and mode of repro. differences determine diff fitness, fitness = measured as r, per capita rate of birth-rate of death, so higher r - genotype is growing. evolutionary change in demographic feature e.g repro lifespan causes change in components of fitness, evolutionary change in feature e.g body size, occur because they affect  one of the demographic traits. 

r increased by - higher survival up to and through reproductive ages, earlier age of first repro, higher fecundity, hiher fecundity early in life, longer reproductive lifespan. constraints and trade offs - phylogenetic constaints - arise from evolutionary history e.g silkworms have no mouths to eat. genetic constraints - lack of genetic variation. Trade-offs - advantage of a change in character causes disadvantage someweher else. e.g genotype that increases signalling for mates results in increased predation. antagonistic pleitropy - negative genetic correlation between traits e.g allocation trade-offs - how to spend energy budget. 

genotypes differ in investment in repro or maintenance and growth. positive genetic correation - genetic variation in amount of resources aquired e.g good at getting food so get bigger lots more mates. cost of repro - tradeoff between repro effort at one age and components of fitness at other ages. 

selection of lab flies for age at repro - those selected to repro when old had lower mortalilty at older ages, however had lower egg production when young. aging or senescnece - physiological degernation with age. selective advantage of enhanced survival decreases with age - medewar 1952 - accumulation of deleterious mutations affect later age classes accumulate in population because selection for survival against them is weak. williams 1957 - antagonistic pleitropy - greater contribution of earlier age classes to fitness, alleles that provide an advantage in early life have a selective advantage even if deletirious later. senescence is cost of earlier repro. 

effect of fecundity decreases with age, advantageous to repreoduce as early as poss and max effort at this stage, no energy left for growth and maintance. semelparity - reproduce once then die. iteroparity - reproduce repeatedly, advantageous if: early age repro causes high mortality, extra investment in growth reduces mortality, allows indivusals to go on to higher later fecundity, individuals survive long enough to repro repeatidly and if pop growth is low. repro effort lower in iteroparous then semelparous organisms e.g annual grasses. the lower the annnual adult mortaliity the later repro begins. 

optimal no. offspring - maximises no. of surving offspring. trade off btwn no and size of offpsinr. finite resources to invest in egg/ embryo/ young. instantanous rate of increase - reduced by density dependace. 

B - less offspring invests more - lower rate of increase at low densities but a selective advantage at higher density nearing carry capacity (k). At high densities dead indivudals are more frequenctly replaced by B rather than A. r-selected organisms - in unstable or unpredictable enviros with low density dependance r-selection predominates - ability to reproduce quickly is crucial, traits e.g high fecundity, small size, short life, dispersal. K-selected - stable enviros strong density dependace - ability to compete for limited resources critical, long life span, produce fewer well cared for kids. 

sex selection - anisogamy - diff size of sperm and egg, females limiting sex, males limited sex, males compete, females choose. male repro sucess affected by no. mates - intense compeition, lots of energy e.g lekking. alternative mating tactics in males - sneaker male. sequential hermaphroditism associated with change in relative repro success of 2 sexes. when initial phase males and femal bluehead wrasses get to certain size can choose to become terminal phase male. 

dispersal - not same as migration. selected against as - dangerous, offspring less adapted to new enviro, selection against dispersal alleles as remove themselves immediately. advanatges - colonisation of new empty habitat, inbreeding avoidance, find better enviro to avoid succession and density regulation. 

old world monkeys - trichromatic. 1 allele on autosome, 2 on X. new world monkey can get tri and di. one on autsome but can get one locus and 3 diff alleles on X. definite link between being tri and distinguishing orange food. evolutionary adaptive explanation for tri. advantage to being di as can see in dark. blackcap birds migrate from germany to meditteranian, increase in overwintering in britain. adults from meditteranian migrate there. adults from UK migrate to Uk and their offspring did aswell not meditteranian so must be genetic. due to recent climate improvement. 

nature vs nurture. some under more genetic control e.g migration. other enviro control. genotype x enviro = phenotype. certain phenotypes only arise due to enviro conditions act on genes. can measure heritability of behaviour. H2 - proportion of total phenotypic variance due to additive genetic effects. variabilityin host plant choice in checkerspot butterflies - use parent offspring regression. offspring is identical to parent preference h=1 slope is angled. offpspring and parent diff, h = 0, gradient is flat. 

selection differential is diff between mean of the whole pop and those leaving offspring, causes response to selection. diff tbetween selection diff and response is due to host preference not being entirely genetic (h=0.9). lay eggs on C.parviflora, but prefer plantago lanceolata. 

diff in phenotype value of the parent population after selection will be the same as the response to selection in the offspring if gradient is 1. gene not destiny, enviro has effect. high IQ rents have high IQ kids but kids are 20 points higher. even if heritability is high it can even be erased by enviro. if heritability e.g 0.3 then response will be much lower than selection diff. 

COMT enzyme in brain. get valine allele and Methionine allele. v/v - fast dopamine breakdown - less dopamine, lower IQ, better under pressue, fewer affective disorders. opposite in m/m. low stress m/m does better, high stress v/v does better but not as good as m/m with no pressure. if repeated exposure to high stress, m/m does better. 

use Dna sequences that evolve neutrally through time, i.e purely by chance no selection on them so doesnt change phenotype. intron, non-coding DNA and 3rd position of codon are all neutral. will accumulate in genome through time due to mutation and genetic drift. shared derived mutation reveal common ancestry. private mutations only on one species. homology: shared derivived. homoplasy: non-shared derived mutations, so 2 species can look the same but not be realted. homoplasy: random, homology: co-occuring. use maximum parisomony: the tree requiring the least amount of evolutionary change. 

use a closest living relative as an outgroup to root the tree. can use algarithms to search: shortest tree mutation number used, if bound exceeded it moves to next possible tree. bootstrap resampling: sampling with replacement from the empirical sequence data. do it 1000 times and count how often particular trees occur. 

use phylogeny to hypothesise the history of species. can see community assembly. shows that two species can mutate seperately to produce the same species on diff islands. conflict btwn nuclear and mt DNA evidence, however, mt DNA can travel across species barrier easily. gene trees can be diff to species trees. nuclear dna supports multiple invasion theory of cersina and pacifica - diversification happened on diff islands then groups co-invaded islands. 

coevolution: evolution of one species is affected by its interaction wtih another. Antagonistic coevolution: when interactions are harmful to one of them e.g predators. e.g rabbit myxoma virus - spread rapidly using mosquitos, effective biocontrol agen killing 99.8% of infected rabbits. however, rabbits evolved to confer resistance due to strong selection by virus. Less virulent strains of virus became more prevalent as ones that didnt immediately kill host were more readily dispersed to new hosts. left along the system would probs evolve into equilibrium state. contagious diseases spread through atmospher or water less likely to evolve hypvirulence as not dependant on host. 

coevolution and brood parasitism: think naturla selection will favour host: recognising parasite eggs and brood parasite: increased trickery/mimicry. e.g cuckoos, give eggs to another nest, huge energy save. they lay mimetic eggs, individual females specialise in on one particular host. cross-mating by males maintains one species. when hatched cuckoo chicks eject rest of eggs in nest to maximise resources to that cuckoo. 

host brood ejects eggs that dont look like own, ability to detect them is adaptive, dunnocks dont eject eggs that arent similar, suggests through evolutionary time cuckoos switch hosts when currrent host egg search pattern is too strong. dunnocks havent evolved yet .  

red queen hypo - continuing adaption is needed to maitin relative fitness amongst the systmes being co=eveolved, with constant probabilities of extinction within families. probability of ability to survive and avoid extinction doesnt improve over time. linear distribution of number of genera and survivial time, length of time they've been around for doesnt mean they will survive longest. red queen - describes dynamic equilibrium for coevolution. takes lots of coevolutionary adaptive responses to stay in the same place. 

need antagonism for this to persist - responses of each organism to the other results in a continula cycling of virulent/avirulent pathogens and susceptible/resisitant hosts. coevolutionary arms race. molluscs developed to have increasing prevalance of protecive mechanisms as molluscivores have developed to be more specialised shell breakers. beetles: high species diversity associated with feeding on angiosperms. 

we are naked because a naked ape would have fewer parasites. fire = warm at night = no need for fur. still have small parts of 'fur'. body and head louse same genus, pubic louse diff. humans and chimps split 6mya and took diff lice species with them and they speciated - co-speciation. humans and chimps already diverged - chimp lice jumped to humans, host switching. clothing made new habitat so head and body louse speciated 72,000ya. pubic lice speciated around 3mya due to diff separation of hair creating new habitits, duplication and speciation on host

- increases another individuals fitness at a cost to ones own. e.g - alarm calls, nest helpers, sterile bee, ant, wasp, slime molds and in humans - charity etc. mutualistic - bee carrying pollen btwn plants, fish cleaning parasite off other, bacterium making antibodies to protect host. mutualism - many live together in symbiosis but only some are mutually benefiical. parasitism and commensalism also. trophic mutualism - partners specialised at getting food and energy e.g rhizobium on plant roots fixing nitrogen. Defensive mutualism - get food in return for protection e.g cleaner fish removing parasites from client fish. Dispersal mutualism - e.g pollen in return for necter reward. 

get bacteria one syntrophy that digests fatty acids the other easts waste H2 if it builds up. millions of bacteria in our gut. leafcutter ants - cut leaves and feed to fungus, this digests plant and makes ant food, fungus is vertically transmitted - clonally propogated. escovapsis mold kills ant fungus. ants also host actinomycete bacteria which produce antibacteria, found in glands on ants. many other bacteria in the ant which also kill the mold.

vertcal transmission model - one coevolved species - pseudonocardia evolving in arms race against mold, other bacteria just contaminants. Horizontal - ants recruit many useful species from soil. phylogeny shows that pseudo have been regularly recruited from soil as species of bacteria from loads of diff groups and classes of genera. 

however, phylogeny also shows that ant clades have same groups of bacteria which suggestss one of few recruitments and mainly co-diversification via vertical transmission. however, pseudo creates new antifungal compound nystatin that is new to science which supports coevolution arms race theory. ants also have steptomyces which shows that some bacteria is recruited from soil. coexisting models of symbiosis. 

switching from on commmunity to another - bistability, e.g in coral bleaching. due to change in substrate, beneficial bacteria, antibiotics and pathogenic bacteria. two types of compeition - scramble and interference. scramble - faster growth = winner so chace resources. interference - better fighter = winner. antibiotic production is inter, better fighter wins. on the ants pathogenic bacteria grows faster and beneficial bacteria make antibiotics against them. depends on who starts growing first. start with more beneficials and theres lots of food they win. start with more pathogens they win. 

vertical transmission theory in ants starts with more beneficial bacteria as they innoculate new ants with good bacteria so pathogenic bacteria loses. antibiotic resistance bacteria resistant to many other antibiotic bs so many are recruited from soil e.g pseudo recruits strepto. so get spatial variation in pathogenic b. microbiomes e.g human gut, are a kind of ecology but the enviro evolves and is selected to favour some communities over others. 

study of distribution of organisms. result of ecology (can it live here now?) and history (did it have a chance in first place or did something make it impossible to live here in the past). factors - ecological - species absent: unsuitable lving conditions (fundamental niche), competition, predation (realised niche). climatic history - repeated glacial cycles e.g C.parallellus grasshopper, restricted to southern low regions to get heat, pushed down by ice, then moved north and up mountains as it got hotter. vicariance events - moutain, tectonic plate separation, river, volcano, landslide etc. dispersal - life history e.g seed release, flight by insects or chance - such as rafts. 

krakatau - volcano erupted entire island dead. spider found a year later, then grass (seeds came on on bird feet), 15y later lizards found due to raft of vegetation. now lots of species. all animals came from populations somewhere else, now geneticallyy isolated so can speciate. not textbook sequence of plants - herbivores - carnivores. vicariance - pop gets separated, dispersal subpop separates itself. continental drift - explanation for why same species seen in entirely diff places. gondwana 200Myr. 

diamond (ecology) - island species rich equilibrium - large island near mainland will have more species as higher rate of immigration and low extinction as more resources. small island far away - less species. more immigration on island with less species as less comp and predators

diamond - islands above net equilibrium line as returning to equilibrium due to a reduction in island size. islands below have been defaunated recently and are undergoing recolonisation. e.g new guinea avifauna. current ecological factors e.g compeition, resources etc explain the primary patterns whereas historical forces e.g sea levels rising explain the secondary deviations from these patterns. 

croizat - panbiogeography - uses line of minimal distance to link all known species - track. plot tracks for many groups get generalised track patterns which relate to historical geological events. major factor affecting distribution of fauna dates back 40-60mya when australia and melanesia landmasses crumbled away. 

vicariance vs dispersal - previously thought speciation was due to historical change dispersal events/ vicariance biogeogrpahy - emphasis on barriers subdiving previously continous ranges. how to distinguish between them = both scenarios have same phylogeny. repeat patterns across multiple groups is evidence for vicariance. use phylogenetic tracks to see if  monophyletic species dispersed across country. phylogenetics: traditional morphological: ancesteral or dervived features (subjective). Cladisitc: uses molecules and morphology. Distance: uses similarity of molecules. Maximum liklihood method uses molecules combines cladistic and distance. 

drastic intercontinental vicariance patterns around antarctica. very old family. split due to vicariance due to tectonic splits. southern hemisphere. phylogenetics showed that african genera diverged first, africa split first from gondwana. Then New zealand. Then southe america and Australia. multiple parallel splits along many diff groups. chironomid distribution in southern hemisphere due to break up of gondwana. 

biographic time scale - paleobiogeogrpahy( old history) -> phylogeography (recent) . divergance among freshwater fish - changes in pleistocene climate and landscape generated genetic divisons between them due to florida separating atlantic and gulf coast waters. pattern of intraspecific mtDNA of many diff freshwater fish species show diff populations either side of florida. due to galacial advance so enlarged florida peninsula. 8 of 10 showed subdivision 

evolution of reproductive isolation within an ancesteral species resulting in 2 or more descendant species. caldogenesis = speciation occurs at fork, all descendants from one ancester. anagenesis - species a evolves over time into species b in fossils, one population lineage. importance: generate biodiversity, shows how new species form, can create phylogenetic trees, see role of genetic processes e.g genetic drift and natural selection.

are species real? common sense: everyone recognises they are real. but do humans want to put everything in groups. folk vs linnean - compare indiginous peoples' species list with linnean species list. one-one correspondance evidence for species. folk are undifferentiated - evidence for. folk are overdifferentatied - against. assumes linnean is correct. remarkable concordance between them. statistics - DNA barcoding identifies >7% diff between species and <1% within species. doesnt work with some groups i.e ones that diverged mroe recently and ones that hybridise and are asexual.

biological species concept - species are reproductively isolated from others. pros - genetic independance of speices, interbreeding can be tested, widely adopted. cons - not to asexual or fossils. in practise hard to test, reproductive isolation not all or nothing e.g plant hybrids.

morphological - by morphological features. pros - widely applicable for extinct and asexual. cons - subjective and arbitrary, some may be subdivided into species that dont differ much (crytic species) e.g pipistrelle bat only differ in kHz of sound made - genotyped to find diff. biological species concept - incomplete reproductive isolation - ring species,. connected series of neighbouring populations which interbreed with close neighbourhoods causing 2 'end' populations that are distinct from each other that cant interbreed. also get geographically variable degree of hybridisation in non-ring species.

phylogenetic species concept - species is smallest monophyletic group of common ancestory. pros- ever-increasing phylogenetic data, reflects genetic isolation, used for fossils and asexual. cons - phylogenys always changing, not clear what charactors can be used for phylogeny, robust phylogeny not always available.

genotypic cluster SC : groups that remain recognisable due to morphological and genotypic gaps. pros - combines both elements. separates definiion of species from hypotheses about how speciation occurs, doesnt assume reproductive isolation. cons - still subjectivity, not used much as cant really test it.

species created by hybridisation has different genome and are reproductively isolated to parents. red wolf is species by MSC but not under BSC as it hybridises with coyotes. PSC - red wolves result from hybrids of gray wolf and coyote. no actual species concept - BSC most widely followed, most agree on evolutionary independance as key criteria. speciation in lab - flys 4 pops reared of starch 4 on maltose. got diff bacteria in gut and so became differentiated and only mated with ones of own new species. when treated with antibiotics though they mated with everyone. repro isolation due to positive assortive mating. 

a few polycheate worms were selected (bottleneck) and grown into population of 1000. 4 of these selected and then grown into new 1000 population. reproductive isolation between the 2 pops due to bottlenecking and/or adaption to lab enviro. however, lab population was derived from P1 or P2 and they were already differentiated. pre-mating worms reluctant to mate with lab-field cross. post mating - 0% survived compared to 75-95% in lab-lab or field-field. 

intrinsic or phenomenon that forms a barrier between gene flow between pops. excludes geographic barriers. can be products of selection or by-products of other differences. premating barriers: by-products or products of selection for avoidance of hybridisation (reinforcement) if if hybrids have reduced fitness. post mating barriers: by products since there cant be selection for greater degree of sterility in hybrids. 

premating, prezygotic isolating barriers: features that impede transfer of gametes to members of other pops e.g temporal - breed at diff times of year or habitiat isolation. potential mates meet but do not mate due to behavioural isolation - diff looks or song etc. pollinater isolation in plants. 

postmating prezygotic isolating barriers - mating or gamete transger occurs but zygotes are not formed: mechanical mismatch/copulatory failure. gamete incompatibilty. when flys live together they evolve pre zygotic baarrier so they dont hybridise. 

postzygotic isolating barriers: hybrid zygotes are formed but have reduced fitness: hybrid inviability - die during development. hybrid sterility e.g mule. F2 hyrbrid breakdown - F1 hybrids common but F2 are rare as die during embryonic development. extrinsic postzygotic isolation increased predation on hybrid. 

mutiple barriers - apple maggot fly put larvae on apples and hawthorns. differ in 6 out of 13 allozyme loci proving isolation. no prezygotic isolation - 6% gene flow too much for allozyme differentiation. no postzygotic isoation - no intrinsic inviability or sterility of larvae. fitness similar on apple and hawthorn so no isolation between races. hawthorn race is 'fast' apple is 'slow' - apples available 3 weeks earlier and apple race pupate 16 days earlier so dont break diapause bfore overwintering. 

hybrid zone - result in at least some offspring of mixed ancestry. primary - pop genetic differentiation correlate with enviro discontinuites. secondary - 2 formerly separate pops expand meet and interbreed. coincidence of clines in genetic and morphological features. maintenance of stability - balance of dispersal, hybridisation brining about gene flow, selection against hybrids preventing gene flow. introgression - introduction of an allele into pop. steepness of cline determined by balance of amount of gene flow and selection against hybrids. 

fate of hybrid zone - fitness of hybrid lower than rents - zone low short lived - reinforcement. fitness same as rents - wide long lived - differentiation between parent pops decreases. hybrids fitter than parents - stable hybrid zone or speciation. 

allopatric - geographically separated pops become reproductively isolated. vicariance - existing pop is subdivided into one or more smaller pops. peripatric - larger parental pop gives rise to a smaller pop by subdivision or dispersal. parapatric - geographcally neighborouing pops become reproductively isolate. sympatric - geogrpahically overlapping pops become reproductively isolated. these modes differ from the causes of speciation. 

low reproductive compatibility if not very related. peripatric could be due to founder events, isolation of peripheral pop, non-peripheral pop could become isolated from rest (rare). gentic drift more important in small pops. parapatric - 2 pops exchanging genes 'clinal models involves single species distributed across a variable enviro e.g in temperature so extremities become adapted to local enviro. sympatric - not caused by geography or distance but by some biological feature of organisms. 

4 criteria for sympatric - species must be largely sympatric, species must have substantial repro isolation, sympatric taxa must be sister groups, biogeogrpahic and evolutionary hisory must make existance of an allopatric phase very unlikely. e.g cichlids. 

snapping shrimps acorss isthmus of panama 1% interspecific matings yeild fertile offspring c.f 60%. diff sides of isthmus have diff salinity, clarity, temp. 

1. macromutation - e.g polyploidy. e.g in T.mirus - tetraploid hybrid of T.dubius and T.porrifolius. 2. genetic drift - occurs under peripatric speciation, also known as founder effect speciation. small subpop becomes geographically isolated from parent pop and becomes reproductively isolated with it by genetic drift, reproductive isolation may also be aided by indirect effects of natural selection. 

e.g of speciation via peripatric mode - neighbouring islands more closely related, age of island corresponds to age of branching off of new species. peripatric speciation through island hopping. use bottlenecking experiemtns in lab. gradual decline in genetic variation with successive colonisations; implies founder effects unimportant in this system.

natural selection: directly - reinforcement = selection for prezygotic isolation arising from reduced fitness of hybrids. indirect - in allopatry - Dodd fly experiment. assortative mating leads to partial reproductive isolation. in sympatry - ecological character displacement  (natural selection for habitat specialisation). indirect natural selection has caused sepciation to occur sympatrically.

sexual selection - e.g cichlid fish. 99% of species in each lake evolved there. feeding biology evolved with diff pharyngeal jaws for diff niches. most morphological diff found occurs in male colouration. 

habitat choice (e.g water column, rock, sand) - ecological diversification - colour diversification through sexual selection via female choice of male colour differences. could have occured via allopatric micro-allopatric or sympatric modes. microallopatry - water levels may hall of rise so lakes may be formerly subdivided, few species have lake-wide distribution. patchy within lake habitiat distribution. genetic evidence shows fine-scale pop differentiation. if sex selection drives speciation, expect allopatric related colour forms to show assortative mating. 

evidence - females given choice of males from each colour form, 62% of broods were fathered by the male from the same colour as female. consitant with colour forms representing incipient species diverging under sexual selection bought about by female preferences for diff male sexual colouration. 

long term stasis e.g horseshoe crabs little morphological change since 230mya. vertebrate e.g pangolins havent changed much in 35mya and sturgeons 80mya. phyletic gradulaism - speciation events not associated with increased rates of evolutionary change within lineage, slow divergance at lineages or spliting points. punctuated equilibrium model - not much change long periods of stasis then rapid formation of new species, all character change is associated with cladogenesis. gradual - all character change is within lineages (anagenesis).

stasis hypothesises. 1) genetic or developmental constraints e.g no genetic variation or strong correlated evolution. 2) stabilising selection for a constant phenotype e.g variable optimum for enviro. 3) empherical local divergance - occur in local pops but dont spread to full species due to extinction or introgression of initial morphology. lineages that show high stasis also show very little diversification by speciation either by anagenesis or cladogenesis. however, morphologically stasis horseshoe crabs have same level of genetic variation as morphologically diverse king-hermit crabs.

speciation rate: time for speciation- time required for reproductive isolation to occur, still get movement of genes between groups (hybrids) after speciation event for a while. biological speciation interval - average time between speciation events, can work out from amount of time between present no. species and the common ancestor 

however, extinction messes this up. diversitification rate = speciation - extinction. molecular trees only have knowledge of living species. use phylogenetic trees to investigate speciation intervals, patterns of clade richnees and temporal chanegs in diversification. biological speciation rate - average rate at which one species branches to produce 2 groups that are repro isolated. inverse gives mean waiting time for speciation = BSI - interval between branching.

comb tree e.g mainlaing species splits to island then another island splits etc. balanced - 2-2-2-2. high speciation number e.g 21.7my dont speciate rapidly e.g horses. cichlids have 0.03my so new species form rapdily. trees can give topological distribution of species e.g high or low imbalance of species clades. temporal distribution can be early or late diversification timings. adaptive radiation would be expected to have high rates of diversification early on and declining through time.

can calibrate trees to find timings. lineages through time plot to study speciation rates. can be declining as speciation declines and extinction increases or vice versa. factors that promote diversification: new niches to invade, new key innovations. Eg. 1 all vertebrates had 9 exceptional radiationss + high turnover explains species diversity in jawed vertebrates.

link between speciation rate and morphological change? eg.2 yes, high level of morphological change when rapid speciation occuring. Eg.3. no latitudinal change of diversification with birds over last 50mya. large increase over last 50mya. occured all over world.

genome duplication in teleosts and fish - teleosts underwent 3 rounds of whole genome duplication wheras non-teleosts only did 2. 28,000 species of teleosts because of this WGD. increased diversification rapidly, biggest increase.  

accelerating lineage of time - actual increase of speciation or illusory increase caaused by constant background extinction rate. evolutionary opportuntiy evolutionary potential - success. extrinsic opportunity e.g varied environs of hawaii and intrisic potential eg hybrid genome in hawaiian silverswords. 

variety of ecosystems, species, population within species and genetic diversity within spceies. genetic variation, slection, genetic drift, phlogeny, macroevolution, biogeogrpahy and speciation. erratic rise in biodiversity increasing through mesozoic and cenozoic. mass extinctions - climate change usually, 65mya wiped out dionsaurs. mass extinctions selective - entire groups lost while some survive, patterns differed between events, survival greatest for species with wider geographical and ecological distributions and species richness. random - with respect to many characteristics, superbly evolved species went extinct, e.g oyster drills.

3rd tier or evolution - physical and biotic conditions differ before and after mass extinct, wipe slate clean allow new evolutionary radiations. micro - change within pop e.g mutations. macro - e.g speciation. shaping of biota by mass extinctions. resistance to extinc - rates of mutation suppling gentic variation, pop size, dispersal ability. overall background rate of extinct is decreasing. 

rates of origination highest in early history peaks - cambrian explosion due to evolution of eye or o2 in water. new ecological opportunites after mass exctint. origination/ diversification: 1) release from competition so can expand into new ncihes  caused by finding new habitat or extinct of another group. 2) ecological divergance - evolution of key adaptation, can exploit new niches e.g flight in bats. 

3) co-evolution- species interactions promote evolution of diversity, species serve as resources for others e.g parasites. 4) provinciality/vicariance - partitioning of biota among geogrpahical regions e.g plate tectonic processes, distinct land masses and oceans. 5) environmental stability/variability - ice ages etc, species pump, range expansion/contraction. 6) genome duplication - polypoloidy, haploid and diploid gametes not compatible. 

human impact reducing biodiversity. caused extinctions. massive pop growth. causing 6th extinction. important of biod - food e.g fruit and veg, pollination, aesthetics, genetic manipulation, medicines, genetic diversity. conserve genes - genetic diversity enables species to adapt. species - which species to conserve? ecosystems - best but is it practical how to prevent loss of keystone species? regions - which regions important. 

measuring biod - count species - do all species contribute equally to biod? taxonomic distinctiveness or degree of independant evolutionary history to assign value to species. use phylogeny to maximise genetic and character diversity, choose most diverse set that are least related. e.g tuatara, sole survivor of group from triassic similarly related to repltiles as croc and birds = 20% IEH. but is it a 'dead end', rare becasue lack ability to adapt. 

species richeness - estimates biod value of an area, species richness within family is reasonable surrogate for gene/character richeness. relationshop between no of families and no of species among areas. indicator species - can species richeness of one group predict the spcies richness of another as an indicator group? cannot always be assumed, indicator and target organisms may differ in habitat associations because different factors govern their distributions. 

rarity - rarity of occupancy among areas (range-size), rarity of individuals within an are (density). species with restricted geographical ranges do not always have low local abduncances. endemism - condition of being restricted to particular area e.g blubells - restricted range in europe but common in britain. 

conserving genetic diversity - intra specific genetic variation through mutations subject to selection is foundation of evolution which biod is created. genetic diversity - lowest level of hierachy, but for species to evolve they need genetic diversity so preservation of genetic diversity should be high priority. new molecular tools for measuring genetic diversity. 

most related to chimps and bonobo, gorillas split from us before. separation from chimps around 5.4mya. within hominidae there are chimps, orangutans, gorillas and hominini = humans, extinct ancestors and related races. all hominins are extinct apart from humans. homo genus split around 2.5mya. first discovered west africa 6mya. homo branched out from africa 1.8mya. homo erectus spread across world. reproductive isolation between forms is controversial.

human definition - use of tools, increased cognitive abilities and brain size, bipedalism. footprints 3.3mya. to free hands for fine manipulations, huntin, greater stamina, carry food better. genetic differences - gorillas and chimps 24 chromos, humans 23, 2 chromos fused. 1% diff in coding sequences, 5% in non. 80 genes in chimps switched off in humans, protein diff in immunology, sensory perception and spermatogenesis. lots more brain gene expression in humans.

homo sapians - originated 200,000ya, left africa 100,000ya. lone survivors, long periods of coexisance with erectus and lived near neanerthals 20-30,000ya. origin 1) emerged from africa and spread and replaced archaics. 2) mult-regional - hominin pops evolved in situ into modern pop with gene flow between. more evidence show expansion/replacement. 3) hybridisation and assimilation - integression from non african archaics.

genetic origin - some genes may be from archaics, but estimaed serparated times against genetic difference shows not much diff from expected curve when no intregression, reutes multi-reion evolutiion. hybridisation and assimilation model assumes that modern and archaics from same region will be more similar than modern and archaics from diff regions. analysis of ancient mtDNA sows european neanderthal same divergance from european and non - european humans. but when genomes of neaqnderthals were compared to humans 1-4% genome is from neanderthals e.g MHC genes. green et al, 2010. shows after humans left africa some neanderthals and h.sapians interbred.

humans demographically young, only 200,000ya, recent expansion. bottleneck event around 120,000ya, lost lots of variation, all humans very closely related only around 3% diff between 2 random people. much more diff in other apes. worldwide fst -0.15, 80% variation found within pops, only 20% among pops, most variation in peeps from africa. subtle differences in allele freqs. genetic and linguistic boundaries across europe. linguistic barriers possible boundries to gene flow.

0.15 fst shows low levels of gene flow since human expansion, no obsticle to changes caused by selection. some loci have very high fst 0.5 so are under lots of selection and are very diff between pops. e.g 70% humans cant digest lactose. persistance of lactase enzyme into older age in nortern european pops, polymorphism of LCT gene associated with lactase persistance, freqeuncy of it matces distribution of dairy products. mutation found in haplotypes as recombination hasnt had time to break up ancesteral sequence, length of haplotpe consitant with origin 100,000ya when dairy cattle farming happened in eurpe.

skin colour - dark skin protects against UV, but need UV for vitimin D synthesis. Pail skin evolved at higher latitudes. HIV - people with more resistance to the onset of AIDS have 50% more offspring than those that are suceptable. strong selective advantage. countries with higher incidences of HIV have even stronger selection against suceptible genotype.

entire hereditary info. collect DNA, break into frags, read with illumina, piece together, recognise genes. locate regulatory sequences and ORF. Buchnera - pea aphids. buchnera bacteria produce nutrients for aphid and recieve them from it. genes for essential amino acids, phospholipids, enviro defense and regulatory response missing. 6/7's missing compared to E.coli. vertically transmitted. 'candidate gene approach'. 

genes in echolation - sequence prestin gene, convergant molecular evolution of prestin in dolphins and bats. compare genomes of them found 2,326 coding sequences in all 22 species. made phylogeny. fake tree groups them all together. 400-800 genes support echolators together tree. those genes are candidate genes to allow echolation, found many hearing and vision related genes that they would have never tested. resequencing easier if high quality reference genome. 

33-66 mutations common to cancer cells. gleevic makes tumour disappear but it comes back, large tumour, lots of genetic variation, some cells resistant to medicine so can grow back use combination of medicines. genomes mean you can find new antibiotics. on average siblings share around 0.5 of their parents genome. marker assisted selection - cross elite with donor - then F1 with elite. select backcross that resembles recurrent parent and cross with RP. repeat till left with elite with donor trait. marker assisted backcross- use background markers to select plants that have most RP markers and smallest % of donor genome. can genotype seeds.