∙ Ex) how to test hypoth that chromosomal order is imp in pattern of gene expression?

 Compartmentalization- how if cell memb not coded for?

o Info containing biomols composed of single inorg compounds- from where?

∙ Fundamental principles of science: observation and repetition ∙ IDA(initial darwinian ancestor..before LUCA…primordial form o Organic life- genotype(ability to store/transmit info) and  phenotype(ability to express geno) o 3 traits essential for If you want to learn more check out understanding management 10th edition
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organic evol: ∙ Hereditary material capable of evolving- store/transmit info, can be  modified in resp to envir change ∙ Enzymatic activity- at min can make physical copy of hereditary  material ∙ compartmentalization(cell memb/bio chem rxs…allows geno/pheno to  be linked) o RNA world hypoth - dna enzyme(not P) ∙ Ribozymes(Catalytic rna)- has geno and pheno ∙ Evidence: ∙ Ribosome most conserved/universal component for info transfer ∙ Rna portion of ribosome has catalytic fx ∙ Ribonucleoside triphosphates(ATP/GTP)- basic biological E  currency ∙ Ribozymes can evolve by artificial sel BUT NOT NS BC NOT ALIVE…exp: ∙ Create mutant pool or ribozymes ∙ Incubate w dna for hour, add enzymes that would rep ribozyme  if it completed rx  Rx: ∙ Add complementary primer to sub ∙ Add reverse transcriptase to make cDNA copy of  ribozymes that had catalyzing rx w DNA sub ∙ Use additional primers, rev transcrip, and rna pol to make copies of successful ribozymes ∙ Some may have muts that improve  performance of ribozyme on dna sub  After 10 gens, rate of catalyzation inc 30x ∙ Exp: Trying to make self-rep'ing ribozyme: ∙ E' catalyzes ligation of A and B to make E ∙ E " " of A' and B' to make E' ∙ E' and E dissociate and restart cycle …evolved in exp from recombo ∙ Origin of 1st living thing… issues needing addressed: o Info containing biomols composed of single inorg compounds- from  where? o Chem rxs to construct larger mols must be favorable and have E  source o Building blocks must be able to polymerize o Larger biomols must be protected from harsh envir conds ∙ Oparian-haldane model- how cellular life could have evolved from simple  mols o Formation of bio building blocks o Polymers assemble that can store info(geno) o " express pheno that leads to dir of bio stxs o Issues:∙ How?  If early atmposphere was reducing(it wasn’t), methane  and ammonia would dom… so AA could form w lightning E  Meteorites- could have extraterrestrial AAs.. Could have  gotten here from that  Powner et all 2009- process that doesn’t work in seq could work if mix precursors together ∙ Ex) nuc production from sugar + base->nuc then  phosphor and activate to make nucs doesn’t work… but it  does if you combine the ingredients  Powner and southerland 2011: look for one pot recipe under  plausible conds ∙ Chains of AA and nucs have been made abiotically, but cant explain  how nuc acids and Ps arose  Chirality- living systems use only 1 of 2 sterioisomers of AAs and nucs  Activation- many building blocks need activated before can be  incorp'd into polymers  Instability- P and nuc acids break down easy in water… may not  last long enough for next steps to occur  ∙ "clay catalysis"- combining polynucs, activated nucs, and  clay mineral allows organic mols to attach easy and form  long nuc acid chains  Compartmentalization- how if cell memb not coded for? ∙ Ex: Spontaneous… Miller exp, but not right lipids that  formed ∙ Phylogeny approach- Carl Woese- seq'd DNA encoding 16s(small) rRNA  subunit ∙ Highly conserved, in all life, always has same job ∙ Major result 1: 3 domains of life ∙ Rooting: gene fams that arose thru ancient dups provided  molecular outgroup ∙ Major result 2: knowing shape of tree told more about characteristics of LUCA  ∙ gene trees are not consistent bc LGT (not mother to  daughter)had large influence on early genomes  NS couldn’t work at first bc LGT so common… NS started  as self rep replaced assembly by LGT and common ancestors  emerged  Ex) aphids have enzymes that produce carotenoids..  Ancestor probably got long time ago from LGT o Origins of 3 kingdoms: ∙ Universal gene exchange pool hypoth-rampant LGT.. then suites of  genes acting together formed which made genomes cohesive(less  modular and more swapable) to allow NS ∙ Ring of life hypoth- euk share metabolic genes w bac and genes  involved in info storage w archae Arch and bac genes in euks evolved in diff lineages  (fusion)  Chronocyte hypoth- euks are fusion btwn archean and  chronocyte(org that can phagocytose)… hypothetical ∙ Archean gave rise to nuc ∙ Pahgocytosis of bac gave rise to mito ∙ 3 viruses, 3 domains hypoth: Viruses that infect all 3 domains share  genes  Viruses have all kinds of nuc acids as genetic material(ssRNA,  dsRNA, ssDNA, dsDNA)  Ancestors of 3 domains may have diverged while RNA was  genetic material & converted to DNA by separate virus ∙ Explains why RNA related genes are shared across all  domains but DNA related genes are diff when compare bac  vs archae/euk ∙ May have switched from RNA to DNA to escape host  defenses(like RNAases) in resp to viral parasitism ∙ Species- smallest evolutionarily indep unit ∙ Evol indep- when forces of evolution operate on pops separately  ∙ Evol consists of changes in allele freqs across gens, species consist of  interbreeding pops that evolve indep of each other ∙ Essence of speciation is absence of gene flow btwn 2 pops that are in  contact w each other ∙ Good species concept should be: ∙ Mechanistic(imply process by which one species becomes 2) ∙ Testable ∙ Accurately reflect evol history ∙ 4 concepts: ∙ Morphospecies concept- defined on morphological sims  pros: applied for sexual/asexul, applicable widely to  macroorgs, useful for extant/extinct species  Cons: can be arbitrary, not helpful w microbes, species  can have similar morphology and have many other diffs ∙ Biological species concept(BSC)- based on reprod isolation- must be able to breed & produce viable offspring  Pros: reprod isolation is evol meaningful bc it confirms  lack of gene flow  Cons: can be diff to apply in practice, not useful for  extinct or asexual ∙ PSC(phylogenetic species concept)- ability to distinguish how  trees breakdown  Pros: good for macro/microorgs, useful for extant/extinct,  testable, can distinguish cryptic species  Cons: would cause large inc in # of named species  Species are smallest(highest lvl) monophyletic groups on  a tree  To be separate species pops must have diverged for  diagnostic traits to have evolved∙ ESC(ecological " ")- set of orgs sharing certain set of resources in envir  Diffs based on diffs in resource exploitations  Species- using/providing certain niche/resource  Pros: testable, widely applicable to macs/mics, can  distinguish cryptic species   Cons: cant study extinct, connection btwn definition and  evol history less strong  Ex) african elephant species #? ∙ ESC- use diff resources ∙ Morpho- forest vs savannah elephant diffs ∙ BSC- ambiguous, do not interbreed bc ranges don’t overlap ∙ 4 genes in 21 diff pops… forest and savannah elephants… asian  elephants are outgroup o Bac/achaea  Genetic exchange btwn taxa much more distant than euk  recombo assoc'd w meiosis  Gene flow can trigger speciation in microbes..  Unidirectional & involves only portion of genome  " " could trigger divergence in bac pops(opp in euks)  Traditional- % sim based on genome wide DNA-DNA  hybridization  Recent: gene content is link btwn geno and ecology of org o Speciation steps: Isolation, divergence, secondary contact o Isolation mechs  Allopatric- physical barrier cutting off pops ∙ Dispersal- separate to other areas  Hawaii… ex) fruit flies- many limited to one/few islands- >founder effect then local adaptation/divergence ∙ Predictions: ∙ Closely related indivs should be located on  adj islands ∙ Seq of branching should correspond to island formation ∙ Vicariance- land mass breaks into 2..can be slow or fast  Ex) squirrels geo isolated, now 2 pops  Ex) panama land bridge- shrimp species found on both  sides of it from bridge cutting them off…. Almost no  interbreeding when put together   Sympatric- w/out phys separation…Chromosomal polyploidization ∙ Other genetic forms-emergence of mutant that can use new  resource due to antagonistic pleoi allele  Antagonistic pleiotropy ex- aphid preference for clover vs  alfalfa  ∙ Become specialists on certain plants, could result in speciation bc no contact since eat other plants  Temporal- timing..when come out (early vs late  flowering)o Divergence mechs- NS is main driver ∙ Drivers of diversification- reprod isolation, differential sel  pressure in hetero envir ∙ Adaptations to diff habitats..ex) monkey flower  Exp: Perennial or annual based on envir… 2  ecotypes  Coast- perennials  Inland- annual  Breed pops in other conds.. ∙ Crossing of rx norms.. Diff effect in fitness btwn 2  sites for any given variable ∙ Shows how sel acting on envir conds can cause  same species to have diff life history traits so could lead to  speciation eventually   Sex sel- changes in mate choice ∙ Ex) blue surface and red deep water cyclids in lake  victoria  Most light near surface blue, most at bottom red… males  develop location specific coloration(female choice.. sensory  drive) ∙ Assortative mating(nonrandom)- ex of indir sel  hypoth… variation in traits, certain preferred by females->reprod  isolation  Ex) crickets- males singing at faster pulse had females  that preferred faster pulse singing  ..sex sel can drive rep isolation ∙ Secondary contact o Ex) pops kept apart by pond, which is now gone.. recolonize that area ∙ Depends on fitness of species & hybrids relative to parents and  either species ∙ Possible outcomes:  Sel against hybrids bc have low fitness ∙ Differentiation in parental pops continues and can  result in full speciation ∙ Reinforcement:  Prezygotic reprod isolation: ∙ behavioral(mating/flowering time diff) ∙ Saw flies living off diff tree  types ∙ Mechanical/stx ∙ Gametic  Postzygotic " ": ∙ Hybrid inviability/sterility/breakdown  " favors hybrids in novel habitat ∙ Ex) mountainside gradient- hybrid could be favored at intermediate height where not competing w parental  species  Hybrid/parental fitness equal- diff of parental pops dec  and can reintegrate into single pop thru gene flow Hybrid fitness > parental- third species could form ∙ Ecological controls on species richness- dep on current conds/envir size o New habitat- adaptive radiation->many species form quick ∙ As # empty niches dec, # new species also dec ∙ Ex) lizard species, speciation tapers off over time ∙ Fossil types; o Trace- like footprints o Casts & molds- preserve info about external and internal stxs o Permineralized- dissolved minerals precipitate in cells. Preserves  tissues o Unaltered remains- info rich, but rare o Limitations on fossil record: ∙ Geographic bias- towards lowlands/marine habitats ∙ Variability among tissue types(and orgs) in how the readily  fossilize(hard v soft) ∙ Abundance- rare species may not be preserved in the fossil  record and diff envirs offer better preservation ∙ Variability in accessibility of fossils- under rainforest vs in  exposed outcroppings ∙ Variability in popularity- skulls over other body parts, dinos over  fish ∙ Docs change at a resolution of thousands of yrs ∙ Leads to taxonomix bias..phyla that disproportionately rep in  fossil record  o Edicaran biota- macroscopic life- 565mya o Burgess shale fauna- btwn precambian and cambrian- bilaterally symm animals o Cambrian explosion- larger, hard exoskel, complex body/body  parts(limbs) ∙ Protostome & dueterostome evol & diversification ∙ Explosion in morpho diversity..long fuse ∙ Causes: ∙ Major groups existed but as larva-like animals ∙ Complex intxs among biotic/abiotic changes ∙ Genome patterning  Major sea lvl rise->continental flooding->regolith(soil)  erosion  Inc'd habitable volume of oceans, access to new envir,  and changed in nutrient availability  Inc in calcium availability->  biomineralization(shells/bones) ∙ Origin: predatory and defensive stx evol ∙ Burrowing evol: results in changes in oxygenation  of envir  Inc in phosphate "->shallow waters more nutrient rich  Food web complexity inc- caused by many facs, including  morpho and behavioral innovations o Dino to bird transition ∙ Feathers probably first for thermoreg then exaptation for flight∙ Birds descendants of theropods-bipedal carnivorous dinos  o Extinctions: ∙ Mass- global, broad org range, rapid when compared to lifespan  of involved taxa("big 5") ∙ Permian-triassic- largest- 96% species death- large volcanic  activity, low O lvls, runaway greenhouse conds ∙ Ordovician-silurian ∙ Late devonian ∙ Triassic-jurassic ∙ Cretaceous-paleogene- high impact extinction  ∙ Mechs: short term catastrophic envir change ∙ Following impact:  Large influx of sulfur dioxide and water vapor into  atmosphere-inc acid rain  Sulfur dioxide along w dust particles in atm scatter solar  radiation->global cooling  Tsunami 4km high- sandstone deposit in texas is evidence …resulted in long term ecol destabilization and decline of many  groups over 500k yrs ∙ 6th mass extinction: habitat destruction… 100-1000x rate of  background extinctions  60% species in next 100 yrs o Background- most extinctions..cause 95% of extinctions  w/in org group, likelihood of extinction constant and indep of  length of taxa existence  Extinction rates constant w in clades, but variable btwn clades  Rates: decline in origination and extinction rates of marine orgs… overall slower turnover bc  Higher fitness  Dec E flow from sun  Bias in fossil record  Groups w high turnover replaced by groups w low ∙ Gradualism and stasis- anagenesis(evol w in lineages) vs cladogenesis(evol of new clades) o Gradualism- species change constantly in resp to NS (speciation  gradual) o Stasis- species remains unchanged in fossil record for millions of yrs --  from incompleteness o Phyletic gradualism- morpho changes gradual and not assoc w  speciation o Punctuated eq-morpho changes at speciation w periods of stasis btwn ∙ Stasis in fossil record is real under this theory ∙ Evaluating stasis- might not see strong correlation btwn  speciation and morpho change(bc morpho change is speciation)  To test PE: ∙ Clade of which phylogeny is known, so researchers  can ID which species are ancestral and which descendent ∙ Ancestral species that overlap w new descendent  species in the fossil record w/out overlap diff to det if new  morphospecies is product of speciation event or evol in ancestral form w out speciation happening  Some groups have overwhelming evidence for PE and  stasis ∙ Ex) analysis of cheilostomes from carribean- est  phylogeny of 19 species and scaled tree so the branch pts  and tip line up of first and last appearance on fossil record ∙ Ex) PE evident in cell size for Ecoli- caused by NS as rare beneficial muts go thru pop  Sel can cause PE dynamics ∙ How does stasis occur o Morpho stasis does not imply genetic stasis ∙ Ex)Horseshoe and hermit crabs both undergone sig genetic  change, but more morpho change in hermit o Habitat tracking- species resp to changes in envir by altering their  distributions(not by changing phenos) o Stabilizing sel occurs around optimal pheno ∙ Gradual Speciation and PE both occur  ∙ Macroevol- large scale evol and evol processes operating above species  lvl(species are focal pt of sel similar to indiv in pop)) o NS acts on variation in indivs w in species, then analogous process  should act on variation among species o Clade specific variation seen in fossil record ∙ Ex) Bivalves diversify slower than mammals, persist for 3-5my  and mammals only 1-2my o Relationship btwn geo range and extinction rate, taxa w narrower geo  ranges have greater prob of extinction(during background periods) ∙ Diff in rates also assoc w dispersal behavior   Ex)planktonic larva carried on currents and disperse over  long distances) inc range may dec background extinction ∙ Not beneficial during mass extinction ∙ Alternation of macroevol regimes ∙ Biotic replacement- If species survives mass extinction may be able to thrive  and diversity on new playing field  ∙ Adaptive radiations- when single or small group of ancestral species rapidly  diversify into large # of species o Ecological Triggers: both involve expansion into empty niches ∙ Dispersal and colonization ∙ Extinction of competitors  o Morpho triggers- allow species to invade and exploit new habitats and  resources ∙ developmental bio and evol bio worked together after discovery of dna o Modern synth originally ignored develop bio ∙ Evol develop bio(EDB)- understand mechs by which develop evolved ∙ Homeotic gene expression(HOX)- specifically expressed in body regions they  control o Drosophilia have 8 HOX genes o Sparked cowork by evol and develop bio o Expressed in specific domains along the anterior-posterior axiso Best known class of homeotic selector genes that control patterning of  specific body stxs o Mutations cause transformations of one type of segment into another o Common AA stretch btwn 2 comlexes, showing evol relationship ∙ Homeodomain intx w dna as TF ∙ Homeoboxes- conserved in broad range of species ∙ Conserved both at seq lvl and have similar develop fx in variety of distantly  related orgs ∙ Orthologus- similar thru common ancestry… from gene duplications ∙ w/in species ∙ Ex)hox genes ∙ Paralogous- belong to same species ∙ Common characteristics of homeotic genes ∙ Org'd into multi-gene families ∙ All have dna binding motif ∙ Spatial collinearity- link btwn genome position and tissue where theyre  expressed ∙ Timing and extent of fene expression varies along anterior posterior axis(3' turned on earlier) ∙ Ex) how to test hypoth that chromosomal order is imp in pattern  of gene expression? 1 Manipulate genomes of model orgs -splicing… chromosomal inversion, see if spot on larvae change in same  way …Even when genes rearranged, still get same expression.. Doesn’t  depend on chromosomal order 1 Look for natural exps- find orgs that show variation in gene org a Canonical spatial expression pattern- spatial order of gene expression  mostly conserved Ordered clustering has been lost many times ∙ Particular gene has enhancers(regulatory modularity) enables evol changes  in develop of specific tissues ∙ Changes in ref regions(enhancers) rather than in coding AA seq can  significantly influence/drive phenotypic adaptations ∙ Ubx- role in epidermal cell hairs on legs of T3 segment map in drosophilia o 2 species don’t differ in AA seq..so… o Look at genes in hybrids btwn 2 species ∙ Diffs due to gene expression/regulation ∙ Half genes displayed diffs in cis-reg regions while other half had  changes in both cis and trans reg regions ∙ Role of develop processes w respect to homology and homoplasy o Homology- similar stx due to common ancestry o Homoplasy- similar traits not due to common ancestry o Development- process by which geno in coordination w envir produces  pheno o Ex)parallel evol of develop physiology in mangroves ∙ Plants must handle salt and seeds have to root fast or remain  bouyant  Hormone ABA gives salt tol when in high lvls  Low lvls ABA leads to vivipary(convoys buoyance)-Parallel evol- Indep evolved in mangroves share similar develop  pathway physiology underlying their convergent evol  Adds complexity to homoplasy  Ex) attachment stxs in distant chordate group ∙ Some neural input for nonhomo stxs w similar develop  pathway ∙ Develop constraints/bias  Notion of develop bias challenges modern synth which said that  variation has no directionality and that all directional evol is due  to sel  Darwin said variation is always present and unbiased- true? ∙ Ex) artificial sel on butterfly  Test for eyespot color and size to see if they could  respond to sel in all directions (10 gens) ∙ Were able to alter anterior and posterior eyespot  size how they wanted to  When repeated w diff butterfly, unable to get anticipated  resp ∙ Could select all gold or all black, but not certain  color for certain eyespot  Attributable to developmental timing of when developed  during lifespan ..sel will proceed more readily in one dir or the other So some develop pathways can more easily produce  something than others ∙ Ex) mimicry in heliconius butterfly  Look similar to each other.. Both toxic, comimic each other, have strong relatedness  Variation in OPTIX gene(TF) accts for coloration ∙ Parallel evol? Optix alleles arose indep ∙ Common color pattern alleles from common ancestor?-  would have similar/same alleles  Analysis, along w wing patterns, point to parallel evol  … some aspects of pheno variation can more easily resp to variation ∙ Pleiotrophy and develop tradeoff o Ex) smaller males use alternative mating strat to get around horned  beetle… can dig holes in way larger males cant ∙ Tradeoffs:  Teste size vs horns  Neg co-relation btwn antenna size and horn size (front of  head) ∙ Large horn or large antenna   Neg " " btwn eye size and horn size (back of head)  " " " btwn horn size and wings(from back) o Ex) sticklebacks ∙ Pleiotropy- single gene affecting multiple traits.. Constrains gene specialization ∙ Marine armored, freshwater not ∙ Loss of armor active resp to growth advantage∙ Sel depends on envir ∙ Modern synth as gradualist paradigm o Pleiotropy was major driver of gradualist paradigm, as muts w large  effects should be deleterious o Fishers model of adaptation- center is fitness optimum, beneficial move closer to it, deleterious move further away ∙ Many small changes  ∙ Gradualism vs saltational change: hopeful monsters o Small changes in gene reg can have large fitness effects o Certain mechs can result in discontinuous evol steps  ∙ Ex) sticklebacks- invitro fert to make hybrids-> QTL mapping o 1 gene responsible for 66% variation in spine length ∙ PitX1  If knocked out in mice, caused many diff abnormalities ∙ 500bp deletion that enhanced PitX1 in tissues where would be  beneficial  ∙ Indep deletions in reg region of PitX1 gene almost always have  reduced spines ∙ HGT can lead to evol jumps- all or none… can lead to  discontinuous evol ∙ Single alleles can have major life-history effects o Ex) honeybee queens.. When dies, haplodiploidy prevents colony being re-queened ∙ Cape honeybee may be able to lay female eggs-->  pseudoqueens-> chaos and colony collapse  Genetic basis- orthologous to gemeni(TF) gene in  drosophila (9 bp change)-> verified by RNAi study ∙ 5% of wing problem.. Gradual change doesn’t work o Original fx: thermoreg.. Gradual change ok o When large enough, could help flight ∙ Exaptation's o Ex) major stx P's in lens cells are crystallins ∙ Long lived cells w no nuc or organelles… Transparent and stable  contents o Anatomical stxs that are examples of homoplasy often use similar reg  genes during their development ∙ Deep homology or homoplasy? o Ex)Similar reg mechs btwn vert and invert is evidence of common  ancestor w rudimentary heart ∙ Homologous ∙ Or original fx of reg genes was involved in rhythmic  contractions-> evolved to have more elaborate fxs ∙ Ex) Key homeobox TF in invert heart cell  NK4 genes(heart cell specification) and VEGFR(vascular  GF)  Expression broadly assoc w contractile tissue.. Could have been utilized in indep evol of complex stx ∙ History is contingent… linked.. Likely to get diff outcomes∙ Experimental evol(EE)- alt research framework that allows researchers to  study evol processes in real time and test evol theories o Ideal org- large pop, short gen size, small genome ∙ Factors to control in exp o Replication o Starting conds o Reducing effect of exp error o Making sure exp design matches hypoth o Ex) start w single ancestor, see freq at which something occurs Diversity of orgs is product of 3 evol forces: o Chance- mut and genetic drift govern stochastic appearance and subseq  loss/fix of new traits o Adaptation- NS.. Sole driver of pheno diff o History- constrain/promote certain outcomes from genetic/develop  integration of ancestral pheno o Changes in cell size not correl w fitness  Historical constraints can be overpowered by NS in traits under sel o Chances and history combined bc no replication.. Inc in fitness from  adaptationo Sig role of history and chance… previous evol influenced fitness in this  evol o Conclusions- all 3 evol facs influence pheno evol o Can be disentangled and quantified o Pops often show parallel evol o History may be able to be obscured over time after deep sel/adaptation o exp 2 o Trait found, was it long delayed rare single mut or was the evol of this  trait contingent on previous evol/muts? o Ecoli can only ferment citrate under anoxic conds.. Most profound  adaptation ∙ Was added at start to see if they could ever evolve to it o If had been dep on historical contingency, would expect later pops  would be able to re-evovle citrate pheno o Cit- remained stable in pop… used glucose better o Follow up study: gene dup of cit operon evolved to allow citrate use (cit+) o 3 steps: potentiation, actualization, refinement ∙ Random muts, gene dup o If replay pop… something doesn’t really repeat easy o Resistance to antibiotics- if make 5 pt muts in TEM allele… can inc ab  resistance of strain by 100k 6t7mfold o Can occur in any order, 120 orders possible.. How many viable for sel? ∙ Epistasis(allele effct dep on genetic background)… only 18 paths possible, only 10 likely  ∙