Midterm 3 PDF - Guest Lecture on Nectar Evolution

Guest Lecture #1 - Dr. Irene Liso toStudyin...

Guest Lecture #1 - Dr. Irene Liso toStudying the of Nectar and Nectarines Comparative Approaches Evolution Nectar of for microbial interactions : the nexus plant-animal interactions , an environment nectar contains the compound nesocodin , which makes nectar red attracts certain pollinators the structures/mechanisms of nectar producing organs are diverseacross angiosperm 1. How do diverse nectaries form ? Mechanisms differences underlying nector between two species many plants produce no nectar could be because it gets pollinated by wind/water /does not require animals could be because primary pollinator rewards changed /produces oils/scents/pollen instead could be because of shift a in mating system  Shifts in Mating System outcrossing when pollen from flower transfers to another of different individual : mating occurs one a selfing : mating occurs via self-pollination to produce seeds/fruits for itself 20 % of flowering plants are selfing Selfing Syndrome : a swite of traits associated w/ the transition from outcrossing > - selfing reductions in floral traits flower scent nectar floral size pollen pigmentation : , , , , traits are often phenotypically integrated , such that differences/selection on one trait affect each will indirectly other , causing them to evolve together could be broken into two distinct modules , where traits from the same module evolve together , and traits from different modules evolve independently Dr. Liao's Research Does reduced nectar production evolve independently from other floral traits in the selfing syndrome ? (independent : biochemical A physiological processes, non-independent : overall reduction in flower size) Methods : Ipoems study system Outcrosser : Ipoema cordatotriloba (CORD) selfer : Ipoema lacunosa (LAC) Methods : Approaches to identify modules by using recombinant inbred lines (RILs) * creation of RILs : 1. crossed CORD w/ LAC to generate FI. 2 selfed the F1 to create F2 mapping population 3. the F2 should now be a shuffled population of different genotypes/phenotypes * Dr. Liao selfed each F2 line 1. selfing the F2 results in a more homozygous F3 identify genomic regions of the of interest 2. used stastically to phenotypes  Methods : traits of RILs measuring phenotypic * nectar traits : volume , sugar concentration , nectary size & seed traits (control) : length , width , mass * because each line is genotypically similar and homozygous (inbred line) , can measure more than one indivival and control for environmental variations calculate genetic variance using variance-co-variance components used ddRADseq to find genotype ; use genotype + phenotype to identify quantitative trait loci (QTLs) General Results : * 3 distinct clusters rather than clusters * average genetic correlations are higher within clusters between * seeds , nectar , and flowers each form their own clusters Results : QTL plots * peaks = stastical significance between traits of interest and genetic difference & lots of differences/peaks result in there being less nectar in the selfer Does reduced nectar production evolve independently from other floral traits in the selfing syndrome ? * Yes, nectar traits form module ; therefore , a distinct , nectar traits evolve independently from other floral traits in selfing syndrome * Multiple loci contributes to the differences in nectar volume and concentration which includes 200 + genes sugar  Genetic Basis of Flowering Nectary Development Across Plants & Nectaries are found at the base of the plant in the "Core Eudicots" in cotton , petunia , soybean , a transcription factor called Crab's Claw is important for nectary development * Nectaries are found at the tips of the spurs in the "Non-Core Erdicots" in columbines , a transcription factor called Stylish is important for nectary development Dr. Liso's research focuses on Monocots and the Septal Nectaries * Many monocots have septal nectaries (others might have tepal nectaries or no nectaries at all visualize these nectaries , must transfer section the embedded to we plant , since the nectary is in the gynoecium * Septal nectaries likely evolved once in monocots , most likely from the split from "Acorales" What are some experimental approaches you could apply to identify genes responsible for monocot nectary development ? use in-situ hybridization for known candidates to see if specific homologues are expressed in some monocot nectaries (could also be used w/ reporter lines between two and without nectaries use genomic comparisons organisms with * one complication of working w/ monocots is that you cannot easily transform the species Methods RNA : single-cell sequencing scRNA-seq differs from bulk RNA because scRNA is individual fruit while bulk RNA is smoothie sequencing an to do scRNA-seq cells be isolated from have cell walls , must plant tissues because they form protoplasts /plant cells who cell walls) create single-cell libraries where each cell has a "barcode" of microfluidic beads that tells you which cell that gene is coming from * based on similarities in gene expression profiles/patterns , cells are grouped into clusters , where clusters = possible distinct cell populations  Methods RNA : single-cell sequencing * Lido examined Banana , Musa "Ice Cream" (Zingiberales nectary cells are located at the top half of the gynoecium there few to nectary cells the base half of the are no in gynoecium libraries of the top cell * by comparing the & bottom halves to identify clusters only in the top half putative nectary cell clusters Summary : Banana : some candidate cell clusters associated w/ the nectary with function : sucrose-phosphate synthase, metabolic genes associated sucrose synthase , B-fructofuranosidase transcription factors : copies of AG , AGL11/STK , YABBYZ Drawback of scRNA-seq is that don't know where cells are placed within the context of the issue you information use spatial transcriptomics to conserve spatial and identify which kinds of cells they are coming from lose of depth how much is being sequenced combine scRNA-seq spatial transcriptomics to results with get comprehensive -  Guest Lecture #2 - Dr. Siobhan Braybook Tracing Stephanocystis : Understanding Branching in Brown Algae Brown Algae are considered Stramenopiles (they are all marine , but vary vastly in size ( they are on a completely separate branch of eukaryotic life from redd green algae , so they are completely independently evolved from all other multicellular eukaryotes look like plants , have cell walls , undergo photosynthesis , but they are absolutely (shows of be different) NOT PLANTS conservation morphological mechanisms , but may Convergent Evolution of Radial Branching seaweeds look like plants seaweed & A Thaliana similar radial branching patterns between. shows the evolutionary importance of branching patterns * of branching patterns determine the 3D structure an organism order family V ~ Radial in the Fucales Sargassacese Branching , the order Fucales the , , is only brown algoe that exhibits radial branching patterns all of the growth occurs at the growing tips aka terminal/apical meristems these tips revered for ↑ cell-division undifferentiated stem cells are , branching patterning , very similar to plants , but independently derived/evolved characteristic growth at tips/meristems is common in brown algoe , but radial branching is not What variation in exists ? branching Sympodial Monopodial III 11. III.. dichotomous alternate distichous radial pseudomonopodial tip always tip splits w/ tip always one each tip splits w/the each one one tip always maintains dominance maintains dominance maintains dominance same dominance one being more dominant (alternating one at a time) (two emerge at the same time) (one at a time in different planes produces a flat a erial view produces a flat a erial view produces a flat derial view produces a flat derial view produces a radial derial view X What is a branch ? * Latin : limb ramus branch , bough , * true branches are indeterminate : keeps on producing new things (new branches) of flower fruit in some plants , true branches will terminate upon formation a or * brown will true branch alge not lose its indeterminate status as a & Mapping brunching patterns in extent Sargassacese (22 : 42-26 : 31 blanks REVIEW Building a stronger phylogeny for Sargassacede 5000 of brown species algae ~ only genomes know the of about 10 (mostly kelps) * using transcriptomics (does not require genome) de novo transcriptome assembly /existing Asian Sargassum data) & new data for & CA Stephanocystis Sargossums How is radial branching executed developmentally ? * in dichotomous (sympodial) branching , Woodworth 1888 hypothesized that branching stems from a singular apical cell (stem cell) in 1970 , Betty Moss saw the rise of a second apical cell , which must have split to form the next two dichotomous branches /apical cell periodically divides Oltmanns Apical cell division patterns give to and therefore 1880s Theory rise branching patterns : , organismal form * the - apical cell should divide more * with some period , a child cell will r > - from the sides w/larger surface area "retain" AC identity , giving rise to two Als that spread apart and form dichotomous 4- sided branches Apical cell How is radial branching executed developmentally ? * Radial false statements Monopodial Branching ( divisions V 3-sided rusne AC identity Apical cell * divisions to maintain children fates most eukaryotic systems require symmetrical , whereas assymmetrical division results retaining AC status while the other differentiates usually in one , * Radial branching # 1200 , but rather at 137 50. Jaka the Golden Angle in order for this to occur and deviate from the idealized 1200 , there would need to be some form of specification asymmetry in division patterns that occurs AFTER daughter AC X also predict that the "handedness" of cell division would match the "handedness" of the branching order (NOT TRUE STATEMENT) Results of modelling a lineage-based branching mechanism branching angle is highly variable between and within simulations retain the capacity to become if become apical cell children AC later , they triangular Alternative cell positionally patterned AC Hypothesis apical identity is after divisions : new that to predicts hypothetical morphogen patterning would give rise a new AC upon the destruction of the central apical cell Results : Cell Detection Apical in 3D specimens presence of apical * events without the cells we see branching something else must be going on Guest Lecture #3 - Dr. Zachary Morris  In-Class Lecture Plasticity #1 What is plasticity? plasticity refers to the property by which the same genotype produces distinct phenotypes depending on the environmental conditions under which development takes place * plasticity does not have to be advantageous different to environment * same genotype , phenotype , due during development differing ranges of plasticity minor + quantitative like height like color of could be things something that but there example : mouse lines are inbred to the point they exhibit the same genomes , etc. is still variation in mouse size , whisker length , could be due to nutrients mutant variation , different environments in , etc. receiving more , womb Example : butterflies born in the wet-season Bicyclus Ananya colorful have larger a more eyespots. Those born the dry-season tend to during be absent or muted in size and color.  Research KATY PRUDIC Butterfly by Bicyclus Ananya large eyespots ? 1. Why does have in the wet , but not dry season What is the selective advantage?. 2 What environmental factors could be driving eyespot size in Bicyclus Ananya? * inductive environment is the set of environmental stimuli that trigger a developmental response ↑ hypothetical example wet environmental like humidity temperature predator activity : season causes cues , , , which induces signals to butterfly larvae for phenotypic differences NOTE environmental results phenotype which is then selected for natural selection signal in : in , * inductive environment to summarize , causes a specific phenotype to develop is the set of stimuli that determine the fitness selective environment environmental consequences of phenotypes * hypothetical example : large eyespots 4 fitness due to high predator presence in wet season ; whereas small eyespots persist during dry seasons because predators may be less active or for better camouflage NOTE : environment determines which phenotypes confer a selective advantage to if * summarize , selective environment determines phenotype is advantageous and shapes evolutionary trajectory  Research Results from KATY PRUDIC ① ② ③ - ① males and females led to change In both , increasing environmental temperature no in the of dorsal However , in both males and females size eyespots. increasing environmental led to increased ventral diameter. temperature eyespot ② Under the 20 ° C condition , endysteroid levels remain low through eyespot development but rise drastically towards the end of the developmental period AFTER eyespot patterning. ③ Under the 27°C condition , edysteroid levels peak much earlier and then decrease , which to be concurrent with the timeline of appears eyespot patterning. * edysone [the messured edysteroid] is the major steroid hormone in insects which is essential for coordinating developmental transitions such as larval molting and metamorphosis Further Results : * Like temperature , increasing edysteroid concentrations has no effect on dorsal eyespot size ; however , it does contribute to significantly increased ventral eyespot size How does relate to evolution? plasticity * Plasticity is a heritable trait that can evolve through 3 modes : & Enabling mutation : a genetic alternation conferring environmental sensitivity to a phenotype that was not originally plastic ; allows expression of plasticity which can thereafter be shaped by selection introduces the for plasticity where it didn't basically , an enabling mutation capacity previously exist (before mutation , a phenotype was fixed , regardless of the environment. After the mutation , the phenotype can now respond flexibly to environmental cres) * Genetic Accommodation : process by which selection shapes the properties/magnitude of a plastic response accommodation basically , once plasticity exists , genetic is the process by which natural selection shapes the magnitude , direction , or properties of the plastic response /selection acts on the plastic response , favoring genetic variants that 4 fitness ( * Genetic Assimilation : genetic accomodation but there is a fixation of what were previously environmentally induced phenotypes it's basically , a type of genetic accommodation where the environmentally induced phenotype becomes fixed in the population , no longer requiring the environmental trigger to induce expression (natural selection favors a particular plastic response , causing genetic changes that make the phenotype appear regardless of the presence/absence of the environmental trigger. Plasticity is "lost" because the phenotype becomes permanent.) CASE STUDY On TOBALCO HORNWORMS * Tomato exhibit due to environmental temperatures hornworms plasticity less than 28° black pigment when green pigment when more than 280C * Tobacco hornworms are always green & Heat-shocking (dramatically increasing the temperature over a short period of time) the tobacco hornworm black mutant resulted in a plastic response in pigment. collected those that were the most black (considered to be monophenic and non-plastic) and those that were the most green (considered to be polyphenic and plastic) into new population RESULTS from NEW POPULATION (monophenic vs. polyphenic) ACROSS GENERATIONS & through breeding they , were able to increase and decrease the for the plasticity over generations green polyphenica black monophenic groups respectively * B corroborates this that the Fig. , showing line is green polyphenic very plastic , while the black line exhibits NO PLASTICITY monophenic RESULTS from LIGATION EXPERIMENT (monophenic vs. polyphenic Question : which is true? & * Abdominal ligation enables anterior access to both the corpora allata (secretes juvenile hormonel and the prothoracic gland (secretes ecdysone ( allata which secretes the juvenile * Neck ligation results in the exclusion of the corpora , hormone (TH) neck resulted color change in either line ligation in no response - abdominal ligation resulted in the green color change in the anterior (head-side) of the larvae , while the posterior region remained black * this indicates that the color change (from black to green) due to heat shock is a result of (secretion juvenile hormone from allata of signaling the corpora Dopa decarboxylase (DDC) is an enzyme that converts dops > - dopamine in the melanin synthesis pathway , bling mutation therefore , more DDC = darker phenotypes geneticcomodation geneti assimitation  In-Class Lecture Plasticity #2 evolution ? How does plasticity impact adaptive buying time hypothesis environmental * when colonizing habitat facing perturbation : a new or , a "plastic population" can first adjust to the new conditions by expressing distinct plastic phenotypes and thereby persist enough time for new mutations to happen and fuel adaptive evolution basically plasticity , allows a population to survive in a new or changing environment long enough for beneficial mutations to arise and drive adaptive evolution (enables persistence during challenging conditions , thereby facilitating long-term genetic adaptation * first hypothesis laka plasticity led evolution PLE) plasticity initiate and : plasticity can - of accelerate the rate phenotypic change in that plastic adaptive phenotypes can emerge earlier and faster than phenotypic changes due to genetic mutation, basically , plasticity actively initiates and accelerates adaptive evolution by exposing individuals to new phenotypes that selection can act upon (plasticity can precede genetic evolution , jumpstarting adaptation by providing useful traits early in the evolution process * flexible stem hypothesis same idea : "plasticity first"as hypothesis , but focuses explicitly on plasticity in ancestral species/populations facilitating phylogenetic diversification ancestral facilitates basically plasticity , in an species evolutionary divergence in descendant species "stem" from which diverse traits evolve by acting as a (plasticity in a common ancestor sets the stage for evolutionary diversification , contributing to the branching of the evolutionary tree) CASE STUDY ON SIDE-BLOTCHED LIZARDS N * side-blotched lizards their color to adapt to their environment can adjust Hypothesis : these lizards were ancestrally plastic (not an enabling mutation) and they acquired them to of the mutations in melanin-related genes that enabled change the magnitude response (genetic accommodation this could be part of the "buying time" hypothesis and "plasticity-led evolution" How does plasticity-led evolution work? * Two critical predictions of PLE : ancestral I *. Pre-existing plasticity was expressed in lineage * 2. Pre-existing plasticity was refined by selection into a novel adaptive phenotype in a derived lineage  JTUDY CASE : PLE in SPADEFOOT TOADS (Genus Spea) 1) A change in environment triggers a change in phenotype via phenotypic plasticity Spacefoot toads lay eggs (which hatch into tadpoles) in ephemeral ponds small amount of the ponds are highly ephemeral during drought years , giving tadpoles a time to mature How did this obstacle? they overcome * they normally develop as omnivorous tadpoles , but if they eat larger prey, they develop into a carniverous tadpole (same species , same genotype , different phenotypes * carniverous forms are able to metamorphose up to 10 days faster than omnivores carnivorous form has advantage in drought conditions where ponds dry up quicker - carnivorous forms have larger mouthparts jaw , muscles , guts 1st requirement of PLE : pre-existing plasticity in an ancestral lineage JTUDY CASE : PLE in SPADEFOOT TOADS (Genus Spea) continued plasticity evolves at the base of the Spea lineage , where the Scaphiopus does not exhibit phenotypic plasticity * diet influences plasticity * if spea toads are fed shrimp , there are differential levels of mitotic activity , which thereby causes more cell division and a larger animal to generate the carniverous morphs * if spea toads are fed detritus (a small animal) they will form omniverous morphs , * if scaphiopus toads are fed shrimp only or detritus only they only , form omniverous morphs * the plasticity confers a selective advantage to the Spea lineage , and the expectation is that the plasticity will be maintained when the environment is variable (sometimes wet , sometimes dry if the ponds were not ephemeral , it might be more advantageous to have that omniverous morph , allowing thetoads to spend more time developing to reach a larger adult size, so it has more potential to generate more offspring (higher fecundity down the line * although carniverous toads are more likely to survive drought seasons in ephemeral ponds , their lacking size will reduce their potential to generate more offspring 2nd requirement of PLE refined Pre-existing plasticity by selection into novel adaptive phenotype : was a JTUDY CASE : PLE in SPADEFOOT TOADS (Genus Spea) continued bombitrons loss of (genetic assimilation) to hyper-carnivore exclusively & spea exhibit a plasticity produce a compared to spea multiplicate carnivores (due to plasticity , can express both morphs) , the spea bombitions exhibit significantly more extreme carnivorous morphology (has super etc. ) large mouthparts , jow muscles , & PLE and been able this you wouldn't have to is because this population makes hyper-carnivores produce a hyper-carnivorous morph who having a step where a carniverors morph previously emerged the result of this is plasticity  Tn-Class Lecture Teratogenesis * 2 % -5 % of human infants are born with observable anatomical variant which is , also known as a congenital anomaly can be structural (physical variant) or functional (cognitive or physiological variant) * Teratogen (in greek, environmental agents that non-inheritable congenital variants : cause teratogen translates to "monster-former" than 90, 000 artificial used in the and only have been more chemicals are U S.. ~10 % for effects screened teratogenic doctors discovered that contracted * in the 1940s , pregnant women that rubella during 1st trimester had 1 in6 chance of birth to infant with eye cataracts , heart their a giving an malformations , and/or deafness US rubella epidemic caused 10 , 000 fetal deaths and 20 000 , births with congenital variations * Gene Tierney : famous actress out of in 1943 , a female soldier with rubella snuck quarantine to meet Gene during a WWIl USO appearance and gave Gene rubells. Gene then gave birth prematurely to a daughter who weighed 3 pounds , was deaf , blind , and mentally disabled  Wilson's 6 Principles of Teratology (1959) Types of Teratogens Summary of Wilson's 6 Principles CASE STUDY : Fetal Alcohol Syndrome * terms of frequency of effect and its in cost to society , the most devastating human teratogen is ethanol brains of children with FAS smaller defects in can also be dramatically and show neuron migration children might also have intellectual deficits and behavioral variations & and alcohol-induced variants alcohol and severity types of depends on dosage developmental stage at the time of prenstal exposure (Wilson's 22d and 6th principle) e # Critical Periods of Development (2nd principle) 1st * most critical areas during trimester weeks 1-13) and embryonic phase (weeks 1-8) but brain development can be impacted throughout any point during pregnancy level of no such thing as universally safe alcohol/teratogen exposure during pregnancy ANIMAL-BASED CASE STUDY : Fetal Alcohol Syndrome (3rd Principle) Wilson's 3rd Principle : teratogenic agents act in specific ways * ethanol induces through many cell migration of cranial neural crest cells terstogenic effects mediums , including * usually migrate from dorsal of region neural tube to the bones of the generate the face * ethanol treated cranial neural crest cells migrate significantly less than controls I cell death * shortly after (12 urs) exposure neural crest cells are highly sensitive (other cells a t * instead of migrating/dividing , ethanol neural crest cells prematurely differentiate into facial bones * under variable levels of alcohol treatment , they transplanted a stained cranial neural crest cell and studied migration * Shh is critical for