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Bio 220 final

bio final exam

How do we know something is alive? Acquire & use Energy Have cells Pass on genetic information/respond to stimuli Sexual or asexual replication Evolution
Proximate immediate cause of an effect (how - mechanism)
causation neuro pathways, etc. environmental & physiological answers to the "How?" question
development sex specificity, learning, pubescent-onset, etc. answers to the "How?" question
Ultimate higher level reason for an effect (why – historical or functional)
Function how a behavior is used now - relation to fitness
Evolution how behavior was first needed/developed - phylogeny/ancestral traits
genetic diversity variation in genes enabling organisms to adapt & evolve to new environments
taxinomic diversity number, abundance, and distribution of species (taxa)
ecosystem diversity variety of habitats & communities of different species that interact in a complex web of interdependent relationships
darwin's 4 postulates individual orgs that make up a pop vary in the traits they possess some trait differences are heritable in each gen, born > survive. Only some live long enough to reproduce. organisms with desirable traits are more likely to survive/reproduce.
evolution change in allele frequencies in a population over time
allele gene variant
population contiguous group of breeding individuals
mechanisms of change – Selection (fitness advantage to some alleles) ex:peppered moth – Randomness (drift) ex:volcano – Movement (gene flow) ex:urbanisation – Mutation (direct change to genes) ex:polarbear
historical contributions by old white dudes Plato - species are fixed Aristotle - some animals are more equal than others Lamarck - giraffe neck Darwin & Wallace - evolution & nat selection Mendel - heritable variation
restatement of Darwin’s 4 postulates into 2 simple relationships • natural selection occurs when (1) heritable variation leads to (2) differential fitness outcomes
components of behavioral ecology -mating -aggression -shelter -foraging -dispersal -movement -environmental stressors
Spatial Scales in Ecology -individual-based ecology = behavioral ecology -population ecology – group of the same species -community ecology – interaction of different species -ecosystem ecology – predators, competitors, biome, etc
behavior the integration between -genotype influences phenotype which is influenced by con-specifics (individuals within the same species) -hetero-specifics (influence from other species) • predatory • competition -physical environment • hibernation
Tinbergen’s 4 questions -causation (mechanism) • proximate -development (ontogeny) • proximate -function (current role) • ultimate -evolution (phylogenetic effects) • ultimate
inclusive fitness • direct fitness – individual’s offspring • indirect fitness – helping relatives produce more offspring
Hamilton’s rule (Gains of kin selection x relatedness) – cost has to be = greater than 0
Hamilton's rule equation Br – C > 0 • B – benefit to recipient • C – cost to actor • r – coefficient of relatedness (probability that actor and recipient share alleles)
Methods for calculating relatedness Both/and rule (multiplicative) and Either/or rule (Additive)
Both/And rule o probability of two independent events occur together o ex: probability of rolling a 2 on two dice o 1/6 X 1/6 = 1/36
Either/or rule o probability of an event when there are several different ways for the outcome to occur  A from father and a from mother = 1/2 x ½ = ¼  A from mother and a from father = ½ x ½ = ¼  Aa or aA = (1/2 * 1/2) + (1/2 * ½) = 0.5
Bees and kin selection females are diploids (2 chromosomes) males are haploids (1 chromosome). Sisters are more related to each other than they are to their mother.
Null hypothesis o no effect of treatments, no difference between groups, any observed difference is due to natural variation and chance
Alternate hypothesis o the difference we observed is not best explained by chance, and there is a notable difference between our groups (at a particular level of probability)
variance • average deviation of the data from the population
What is a P value? the probability that the test statistic we calculated (F ratio) is explained by the null hypothesis
Population ecology study of members of the same species living in the same ecosystem at the same time, and how/why the number of individual population changes over time/place
Population density patterns -random – like seeds scattered by the wind (independent of others) -clumped – patchy, social groups, like fish -uniform – if there is competition for space, food, etc
Metapopulation population separated into clumps. We’re making this happen by reducing continuous natural areas.
types of survivorship • type one (high until old age – like humans) • type 2 (steady – same chance of dying in any year) • type 3 (low when young, then grow – like plants)
3 properties of populations size, distribution, density
survivorship • proportion of offspring that survive to a particular age
age-specific fecundity • average # of female offspring produced by females in a given age class • increases as females figure out what to eat and how to avoid predators
average births/year/female • ASF x survivorship • Adds up to # of female offspring/lifespan (net reproductive rate)
Population pyramids (shapes) Ro=1, every female replaces herself, rectangle. Ro>1, many young, die off as they get older, triangle. Ro<1, fewer young many middle age, inverted coffin.
Formula for per capita growth rate where r = ln(Ro)/g • Ro = net reproductive rate • ln = natural log • g = generation time
Formula for population per generation (?) Ng = No e^rg • No is original population • r = per captia rate o if per cap birth > per cap death, r is positive • g = generation time
Formula for population size Nt = No e^rt • t is time • r is per capita growth rate • e is base of natural log • No is population size at time 0 • Nt is population size at the end of the year
Differences in per capita growth rate -low r • low pop size, high g time -medium r • med both -high r • high pop, low g time
Carrying capacity (K) upper limit of population dictated by available resources. influenced by availability of resources in the environment (food, shelter, breeding sites)
Formula for change in population size -delta N/delta t = rN (K-N/K) • deltaN/delta t = change in pop size from one year to another • rN = per capita growth rate • (K-N/K) = how close the current population is to carrying capacity
Differences in N -if N is really small, it almost follows the exponential growth curve • small N = proportion close to 1, growth rate high • large N = slower -if N is very close to K, it will slow down -when N=K it will be a flat line
Population density equation population size/range
Niche the range of resources that a species uses and the habitat it can tolerate
Fundamental Niche total possible (sum of all) niches
Realized Niche actual occupancy
Competitive exclusion competitive exclusion leading to narrower realized niches
Trophic flow influence on biodiversity top-down mechanisms: predators influence other species (top-down) • sharks and marine ecosystems -bottom-up mechanisms: producers influence other species (bottom-up) • grass in prairie
Island biogeography theory & biodiversity graph -immigration goes down, extinction goes up -number of species on island/fragment on x axis -rate of arrival of new species drops as species accumulate -equilibrium number is where the lines meet
What is biodiversity? -genetic – variation in genes enabling organisms to evolve and adapt to new conditions -taxonomic – the # types & distribution of species (taxa) in an ecosystem -ecosystem – the variety of habitats and communities of different species that interact
What does taxonomic diversity measure? • richness (#species/area) • evenness & diversity indices (relative abundances among species designations) • species composition (who the species are)
Why do I care about diversity? Ecosystem services/functions (nutrient cycling/storage, climate stability, protection from change), biological resources (food, meds, wood), social benefits (ecotourism, recreation, research).
Dilution effect competent hosts & incompetent hosts antigen reproduces (but doesn’t necessarily affect the reservoir host) -incomp hosts have an immune response against antigen (disease, etc) • diluting competent hosts via incompetent hosts
-unreplicated chromosome (chromatid) 1 squiggly
-replicated chromosome (held together by centromere) 2 squigglies (sister chromatids) each carries an allele.
-homologous chromosomes a pair of 2 squigglies held together by a centromere. 1 from each parent. Bivalent.
Mitosis mitosis explains basic cellular growth and repair, and cases of asexual reproduction -mechanism for growth and repair of cells -there is error in the process, but surprisingly very little
Meiosis forms gamedes in sexually reproducing organisms
Phenotype-based genetics -mendelian genetics -punnet square -basis of heritable change in populations over time
Stages of mitosis IPMATC. interphase prophase metaphase anaphase telophase cell division
Interphase • cells undergo metabolic activity to prepare for mitosis, including chromosome replication
prophase • chromatin in the nucleus begins to condense • centrioles begin moving to opposite ends of the cell • fibers extend from the centromeres
metaphase • spindle fibers align the chromosomes along the middle of the cell nucleus
anaphase • paired chromosomes separate and move to the opposite sides of the cell
telophase • chromatids arrive at opposite poles of cell, and new membranes form around the daughter nuclei
cell division • cell membrane (or wall) pinched in 2 daughter cells, each with one nucleus
meiosis -adds an extra step of reduction division • halves the amount of genetic material (diploid adult produces haploid gametes) -possibility of chromosomal crossover (exchange of genes between chromosomes) -basis of sexual reproduction
Meiosis 1 • parent cell is diploid and contains a homologous pair of replicated chromosomes • homologues separate
Meiosis 2 • sister chromatids separate • four daughter cells contain one chromosome each. In animals, these cells become gametes • daughter cells are haploid and contain just one homolog
mitosis vs meiosis • Mitosis 1 cell division, meiosis 2 • # chromosomes in daughter compared to parent cell mitosis same, meiosis ½ • Mitosis no crossover, meiosis 1 • Chromosomal similarity of daughter to parent cell is identical in mitosis, different combos of ma & pa
meoisis & sexual repro gamete egg and gamete sperm combine to form diploid offspring which contains homologous pair of chromosomes
Costs & benefits of sex • greater genetic diversity, which increases fitness • independent assortment promotes diversity • cross-over during meiosis further shuffles alleles • 2-fold costs of sexual reproduction • asexual reproduction produces half as many offspring
dominance expression of an allele at the expense of another. Dominant alleles often generate gene products that the recessive cannot and therefore will express itself whenever present
recessive an allele whose expression is suppressed by a dominant allele
homozygous when two alleles in an individual are the same
heterozygous when the 2 alleles in an individual are different.
DO TWO PUNNET SQUARES monohybrid & dihybrid
Mendel’s Conclusions -heredity is determined by transmitted genes -each parent has 2 representations of the genes – alleles • some are dominant, some are recessive -only one representation of the gene segregates into the gametes -gametes unite randomly
types of selection • modeling selection • measuring selection o fitness o heritability o change over time • types o directional o stabilizing o disruptive
genotype frequency equation -genotype frequency needs to = 1 -p^2 + 2pq + q^2 = 1 -allele frequency in a random mating situation will not change
Factors that cause deviation from H-W E? -selection • differential repro success • nonrandom mating -genetic drift • significant at small population sizes and over long time periods -new genetic variation • mutation • migration (gene flow)
evolution the change in allele frequencies in a population over time
Usefulness of HWE? H-W gives us a baseline for judging whether frequencies have changed. -demonstrates that populations are evolving and there is something to investigate -elucidate magnitude of evolutionary forces
natural selection -correlation between traits and variation in reproductive success -adaptive state – condition of trait that conveys a reproductive advantage
selection differs depending on reproductive system -asexual haploids are most common, because bacteria • only mutations lead to evolution -sexual diploid is second most common, us and plants • adaptations lead to evolution -asexual diploids can happen in lizards and fish
homozygosity increases, average fitness ...? decreases
How do you collect data for genotype frequencies? Take blood samples.
disruptive selection • bimodal distribution, peak on low end and peak in high end. 2 hills. • Anisogmy – opposite pressures for male and female • Speciation – geographical barrier stopping flow
directional selection • mean would shift toward the direction that the good trait is
stabilizing selection • after selection, it gets closer to the mean • ex would be clutch size
directionality of selection Stabilizing is an inverted parabola (bell curve). directional is positive linear. disruptive is parabola
Directionality of selection equation G^2 = sum (x-xbar)^2/N
sexual selection selection leading to differential mating success
Evolutionary forces selection. genetic drift.
selection • differential reproductive success • nonrandom mating (sexual selection)
genetic drift • more influential in small pops • random events that can be significant at small pop sizes over long periods due to random processes, there is a change in allele frequencies. Consequence of sampling error
new genetic variation • migration - immigration of new alleles or emigration of old ones • mutation – physical change in alleles
Mechanisms of genetic drift (Mendelian lottery, random events, dramatic reductions in pop size) • founder effects and bottlenecks • founder effect – change in allele frequency when an allele frequency when new population is established • genetic bottleneck
genetic bottleneck a sudden reduction in allele frequency
founder effect change in allele frequency when an allele frequency when new population is established. amish. you get fucked up. barrel-chestedness, hemophilia, muscular dystrophy
outcomes of drift -loss of genetic diversity • random fixation and loss of alleles -unpredictable (random) changes to traits that may or may not influence fitness
evolutionary force - migration movement of alleles from one population to another.
outcomes of gene flow -homogenization of populations -potential breakdown of local adaptation -potential introduction of new alleles to populations
point mutation change in a nucleotide sequence that results in a different protein
lateral gene transfer gene transfer from one species to another, or inclusion of DNA from the environment
inversion occurs when a single chromosome rearranged after breakage
outcomes of mutation -introduction of new alleles – primary mechanisms for the generation and genetic variation -probably the slowest evolutionary force
coevolution when 2 species interact with each other reciprocally so they influence each other over time Within species -genetic correlations and pleiotropy Among species -mutualistic
Genetic correlations -genes located close to each other on the same chromosome will tend to be correlated -not correlated if it’s on another chromosome
pleiotropy one gene has multiple phenotypic effects -selection on one phenotype can cause correlated responses in other phenotypes
Mutualistic coevolutionary interactions examples -mycrorrhizae form mutualistic relationships with plants -fungus gains carbon from plants -plants benefit from enhanced uptake of soil nutrients -reduced pathogen infections -also honey birds.
Red queen hypothesis parasite-host interactions -now, here, you see, it takes all the running you can do, to keep in the same place -coevolutionary arms race. Keep evolving defenses.
4 treatment groups in plant paper • natural (control) • self-pollination (does it happen? Keep insects away) • self-pollination by hand (researchers pollinated flowers with its own pollen) • cross-pollination by hand (researchers pollinated it with pollen from another plant)
fossils -trace of an extinct organisms (tells morphology, sometimes behavior) -important because they provide phenotypic record of history of life. Most species to have ever lived are now extinct
fossil formation -compression • external phenotype -casts/molds – buried then decomp • same -permineralization • external or internal phenotype, 3d shape, fine structures -intact remains • entire organism, possibly genetic info
Fossil limitations -taxonomic • hard shells, exoskeletons, burying (burrowing organisms), shallow marine -tissue bias • harder tissues (shells) -abundance bias • more fossils of more abundant organisms -habitat bias • fast sedimentation, anaerobic -temporal bias top
adaptive radiation (rapid diversification from a single ancestor to numerous lineages)
types of adaptive radiations • ecological opportunity: new niches • morphological advancement – flower increase pollination, feathers enabled ability to fly
Why cambrian explosion? • increased oxygen level (aerobic respiration) • evolution of predation exerted pressure for predator avoidance (shells, mobility): the red queen hypothesis • new niches led to more new niches
• Non-independence of traits in evolution, within-species, and among-species Within - genetic correlations & pleiotropy Among - mutualistic interactions, predator prey, host-parasite, & red queen hypothesis
Genetic correlations: mechanisms and evolutionary consequences Genes located close to each other on same chromosome will tend to be correlated. if they're far away from each other, they become uncoupled in crossover. Makes some traits appear together.
Pleiotropy: mechanisms and evolutionary consequences one gene has multiple phenotypic effects. Mechanisms? Consequences - also some stuff inevitably is always together. selection on one phenotype can cause correlated responses in other phenotypes
Red Queen hypothesis So much running just to stay in place. Coevolutionary arms race.
Evolutionary consequences of predator-prey relationships red queen. diversity is low with just prey & no evolution. diversity increases then drops back out with evolution & just prey. Diversity is highest with predator & evolution.
Evolutionary consequences of parasite-host relationships like nematodes & bacteria. nematodes can reproduce asexually normally, because sexual is more costly. But they become sexual because asexual gets knocked out fast by parasites. diversity is higher with both than just host.
Evolutionary consequences of mutualisms like the fungus and the tree. if one species is dependent on another, and you remove the fungus, the dependent species will decline and independent will increase. use absence of one as a control.
• What is a fossil and how is it formed, in what habitats/conditions? trace of an extinct organism, found in places with rapid burial, anaerobic environments, places like peat bogs
• What information about ecology and evolution can you get from fossils? Phenotypic history of life, (morphology, sometimes behavior). compression & casts/molds give you external phenotype. intact remains gives genetic info. permineralization gives internal/external phenotype, 3D shape, fine structures.
What are the limitations of the fossil record? taxonomic (hard shells, exoskel, burrowing, shallow marine), tissue (no soft parts), abundance (less rare organisms), habitat (fast sedimentation/anaerobic), temporal (younger rocks have better samples)
How do you date fossils? Isotopic dating techniques, of either the sample or the surrounding rock
Adaptive radiations: definition, causes, consequences (rapid diversification from a single ancestor to numerous lineages) -two types • ecological opportunity: new niches • morphological advancement – flower increase pollination, feathers enabled ability to fly
The importance of the Cambrian Explosion to animal and human evolution • increased oxygen level (aerobic respiration) • evolution of predation exerted pressure for predator avoidance (shells, mobility): the red queen hypothesis • new niches led to more new niches
Learn the “top 10 moments in the history of life”, and be able to scale each of those to a 5m piece of rope 4.6 Ga, earth. 3.7 Ga, first life. 1.8 Ga, first eukaryotes (plants fish etc). 1.2 Ga, first sexual repro. 600 Ma, first animals. 540 Ma, cambrian explosion. 435 Ma, land plants. 395 Ma, land vertebrates. 65Ma, loss of dinos. 200,000 Ka us.
Speciation: understand and be able to explain each of the three steps involved 1. Isolation of populations 2. Divergence between populations 3. Reproductive isolation of populations
Allopatric speciation speciation by geographic isolation. something extrinsic to the organisms prevents two or more groups from mating with each other regularly.
Modern Extinction Measurement Extinction is recorded locally but interpreted globally. How? – Direct observations. measure species/ area for half the area then use graph to interpret – Interpretation of Species-Area Curves (allows you to compare habitat loss to # of species lost)
What are the causes of extinction? Humans causing it at 1000 x background rate (habitat degradation, climate change). Natural - astrological, disease, acid rain, invasive species, sea level change, global temp cycles
What are the consequences of extinction: ecology AND evolution? WHAT DOES THIS EVEN MEAN?
Details of the K-P mass extinction event: specific causes, evidence for those causes, specific consequences Meteorite - iridium, shocked qtz & microtektites. SO2 acid rain, dust clouds, fire/soot/smog lead to cooling. Earthquakes, volcanism, co2 lead to warming & ocean acidification. Killed 75% of marine, 50% of genera. mz reptiles & dinos, ammonites, rudists X
• Be able to see both speciation and extinction on “the graph” of how selection works. Speciation and extinction are “species level” indices of fitness. the fuck is THE GRAPH? All we were told is that smaller/less distributed populations are more likely to go extinct.
Species concepts: biological o Definition o Application o Pros and cons If you reproductively isolate 2 populations entirely, they will begin speciation. Ex: orioles & salmon Problem: they need to be geographically close to prove it, can't find evidence in fossil record, doesn't apply to asexuals or most plants.
Species concepts: phylogenetic o Definition o Application o Pros and cons monophyly descendants of a single common ancestor most important, species should be defined by smallest statistically significant monophyletic groups. Issues: not easy to define what constitutes "significant" & # of species would double. Ex: afrielephants
Species concepts: morphological o Definition o Application o Pros and cons A more subjective classification. Organisms are classified in the same species if they appear identical by morphological (anatomical) criteria. This is used when species do not reproduce sexually, some are known only from fossils.
Isolation of populations Physical - stopping migration, no gene flow. Most common in small pops isolated at species edge. Vicariance - splitting into 2 pops. either fast (volcano, forest fragmentation etc) or slow (glaciation, orogeny, etc) Genetic - changes in chromosomes
Divergence between populations Genetic drift. Selection - via adaptation to novel environments. (Ex. apple maggots & hawthorn flies).
Reproductive Isolation If populations have diverged enough, hybrid offspring will have reduced fitness, so more assortative mating will happen.(reinforcement). Like mules & ligers.
Sympatric speciation speciation when groups occupy the same location when 2 conditions are met • strong selection for divergence • mate choice correlated with factor that is promoting divergence • behavioral isolation o birdsong o bonobos & chimps
Paleontological extinction measurement -global in extent, broad range of organisms -rapid effect relative to expected lifespan of taxa • end-Ordovician • late-Devonian • end Permian o most intense • end-Triassic • Cretaceous-Tertiary (K-P) o Most dramatic - acidification, meteorite
Stages of mitosis IPMATC. interphase prophase metaphase anaphase telophase cell division
Interphase • cells undergo metabolic activity to prepare for mitosis, including chromosome replication
prophase • chromatin in the nucleus begins to condense • centrioles begin moving to opposite ends of the cell • fibers extend from the centromeres
metaphase • spindle fibers align the chromosomes along the middle of the cell nucleus
anaphase • paired chromosomes separate and move to the opposite sides of the cell
telophase • chromatids arrive at opposite poles of cell, and new membranes form around the daughter nuclei
cell division • cell membrane (or wall) pinched in 2 daughter cells, each with one nucleus
phylogeny hypothesis of how taxa are evolutionarily related to each other
Systematics Looks at evolution of taxa (phylogeny) and taxonomy (naming of species)
Node shared common ancestor
Sister taxa 2 taxa that share a common ancestor
Lungfish can estivate (live in ponds and then bury when it dries up)
Monocots one cotyledon (eg grasses, orchids, palms, lilies) o like a grass, just straight
Dicots two cotyledon (eg beans, roses, dasies, oaks, maples) o like a branchy maple leaf
Cotyledon a nutrient storage thing for embryos
are monocots and dicots evolutionary groups? • An angiosperm has a seed that’s buried in some sort of tissue • In gymnosperms the seed is naked & no flowers
How to collect data to create a phylogeny Collect data (morph or genetic). Data must be homologous. Data must vary (have different character states, like have it or not)
Homology vs analogy -homology – similar due to shared ancestry -analogy – similarity not due to shared ancestry, due to coevolutionary processes
synapomorphy a shared derived trait (that is homologous) • character states vary from outgroup, and vary across the tree but also have shared ancestry
homoplasy shared traits and character states, but not through shared ancestry • convergent evolution • reversals in character states (loss of characters and states) o short and long interspersed nucleotide elements can overcome this
parsimony the smallest number of states changes needed to generate tree
character states like # of legs, do you have hair or not, etc
Polytomy breaks it into 3+
Character any characteristic to be studied
Ancestral trait same as in the ancestor
Derived trait similar to ancestral, but changed up a bit via mutation, selection, etc.
Ancestral vs derived If you’re comparing current mammals to ancient mammal-like reptiles, fur and lactation are derived, but if we’re comparing whales and humans those characters are ancestral.
Homology similarity in organisms due to a shared ancestor
Monophyletic group includes ancestor and all the descendants of that ancestor
Synapomorphy shared, derived trait is found in 2 or more taxa that is present in most recent common ancestor but missing in more ancient ancestors
Homoplasy trait that is shared due to reasons other than ancestry. So like flamingos and pigs are both pink but it’s not because they shared a common ancestor that was also pink.
Polyphyletic group an unnatural group that does not include the most recent common ancestor
Paraphyletic group a group that includes an ancestor and some of its descendants but not all
Convergent evolution when evolution arrives at the same conclusion for what’s best. Like even though a shark and a dolphin haven’t shared a common ancestor in a long time, they both ended up in a similar shape because that’s what works best for their environment.
Distinguishing between homoplasy and homology • Homology – genes occur in similar sequence. Like same order, same chromosome • Homology - homeobox base pair sequence • Homology – found in interverning lineages
Steps to supporting a claim about phylogeny • Phylogeny based on morphological traits • Phylogeny based on dna sequence data • Transmutable diseases…? SINES?
WOT is an ANIMAL? -multicellular • no cell walls -heterotrophs – obtain carbon from other organisms -embryos show gastrula stage • blastula to gastrula • its complex looking -collagen – a fiberlike protein (in tendons, collagen) -motile
WOW SUCH DIVERSITY HOW EXPLAIN? • Selection pressure (predation, environmental) • Niches → niches • Cellular (mutation, etc)
What's in your developmental tool kit, kid? tissue layers, bilateral symmetry, central nervous system, coelom
Tissue, glorious tissue. diploblasts vs triploblasts • both have ectoderm – skin & nervous system • both have endoderm – lining of digestive tract • both have digestive cavity • only triploblast has mesoderm – circulatory system, muscle, organs, bones o only diploblast has non-living....jelly layer
Radial vs bilateral symmetry • bilateral is rotifer down to chordates o bilateral has 1 plane of symmetry like humans & crabs o has anterior & posterior end o also dorsal & ventral side • radial is that everything is arranged around a central point o like a jellyfish
Advantages to bilateral symmetry? Distinct head and tail • Helps move in directed ways through the environment  Find prey  Seek shelter • specialization of sensation organs at front end for guidance • specialization of structures on sides  movement  sensing the environment
How about that central nervous system, doe? • radial symmetry o senses all around o diffusive nervous net • bilateral symmetry o directional sensation o clustered nervous system o focus on sensation in head (cephalization) o bilateral organisms don’t have nerve net
coelom – tube within a tube o Acoelomates - flatworms • no cavity outside digestive tract o Pseudocoelomates - nonsegmented worms • body cavity doesn’t completely surround the internal organs o Coelomates - segmented worms • body cavity completely surrounds internal organs
Why do we like a coelom? o hydrostatic skeleton Contraction of muscles against H2O pressure in cavity = movement in a direction o protection of organs. Fluid filled cavity cushions against hard blows and body twists o expansion of organs (digestive tract, enhancing function)
What's a hydrostatic skeleton like...or something? squeezing a water balloon?
What's in ya GENETIC tool kit? hox genes – group of similar genetic codes. that's it.
Hox genes p1 • group of related genes that control body plan of an embryo along the anterior posterior axis • they specify identity of body segments • are homologous • more hox genes, more diverse animals • just bilateral animals
Hox genes p2 small variation in location and timing of expression of hox genes gives tremendous variation in body plans • add segmentation and this allows for very specialized functions along the anterior-posterior body axis
Diversification of life habits -features promoting functional diversity • sensory organs o light sound touch smell taste electromagnetic fields • types of feeders o suspension fluid • movement limbs o lobe like, jointed, tube feet, tentacles • reproduction (in sharks, KNOW)
Shark babymaking o viviparous • nourish embryos internally/birth live young • umbilical o oviparous • deposit fertilized eggs, embryos nourished by yolk o oviviparious • retain eggs internally/birth live young • no umbilical • intrauterine cannibalism
Why we like plants part 1 -fuels & energy • fossil fuels (coal) • wood burning • artificial photosynthesis to create energy -food • duh • 12,000 ya domestication -secondary compounds • pharmaceuticals • rubber, solvents, oils, glue, dyes, waxes, insecticides, fragrance,
Why we like plants part 2 taste -quality of life • gardening #1 hobby in US • importance of wild places to mental health -oxygen production • byproduct of photosynthesis -carbon sink -holds soils & slows runoff -primary producers
know main synapomorphies of SHITTY PLANT TREE OG red algae vs green algae: chloroplasts Green algae vs nonvascular plants: ability to live on land Nonvascular plants vs seedless plants: vascular tissue Seedless plants vs gymno/angiosperms: seeds Gymno vs. angio: seeds protected within ovary
origin of chloroplasts • came from cyanobacteria? o Very similar internal membrane structure (physical) o If you put it in a phylogenetic tree, it makes sense o Microscope data supports (molecular)
ability to live on land • aquatic, then evolved for land • cuticle – waxy stuff that limits water loss • stomata – Closed at night because obviously not photosynthesis. Guard cells will open when they’re full of water, close when they’re dry. gas exchange & water management
vascular tissue • simple water conducting cells (cellulose), vascular tissue (rigidity), tracheids (conductivity between cell walls), vessel elements (allowed water to go up) • water & nutrient transportation (against atmospheric pressure)
lignin like a plant skeleton. Polymer of sugars & alcohols. Allowed plants to get higher. When they got gaps, the water could go up
Seed types • angiosperms o have seeds inside ovary (deciduous) • gymnosperms o have seeds not in ovary • dicots are paraphyletic. Don’t really fit into unicots • magnolias are neither monocots or eudicots, but are definitely angiosperms
nutrient transport in plants most sugar stored in roots. phloem transport sugars from leaves to roots. Water is transported in the xylem. Then transport & intake of nutrients in roots. Enhanced through carbohydrates. Sugars can jump to plants in the surrounding area
Key features of angiosperm -flowers • stamen - pollen • ovaries - eggs -pollination -double fertilization -fruits (ripened ovary)
SHITTY ANGIOSPERM CHART with the stamen and the ovary and the fruit and the sporophyte
Ecology & Physiology of Angiosperms part 1 alteration of generations -angiosperms compromise about 80% of all current land -seeds protected -sporophyte is mature diploid -gametophyte is a haploid -meiosis in anther • microspore is haploid • pollen grain is 3 total cells
Ecology & Physiology of Angiosperms part 2 -meiosis in carpel • carpel is ovary with megasporangium • haploid ovary that undergoes mitosis -double fertilization • creates diploid zygote • then somehow triple fertilization and it’s an endosperm • fruit, dispersal, adult plant
Pollinators -insects like purple & yellow -hummingbirds like red -some flowers pretend to be female insect -seed dispersal • Velcro • Sticker plants • Floaty types • Coconuts • Ants eating the outside • Drilling into the soil
What is a protist? paraphyletic • no trait that is unique to protists • key features have often evolved more than once • Multicellular • Presence of endosymbiosis • Cell wall outside or inside of the plasma membrane • Motile: cilia, flagella, amoeboid motion • Sexual & asexual
Why should we study protists? Medical - chagas disease (kissing bug) & malaria (mosquito) Ecological - primary producers in oceans, marine C cycle
Marine carbon cycle o protists incorporate carbon into hard structures o carbon-full structures (foraminifera shells) accumulate on ocean floor o huge carbon sink carbon cycle speeds up if marine ecosystem fertilized with iron
Chagas disease • Zoonotic disease – reservoir hosts wood rat, dogs, cats, and opossums • Beetle is vector – parasite multiplies, enters system through open wounds.
Key features of protsits -there are a ton, very diverse -nuclear envelope (root of eukaryotes) -mitochondria – endosymbiosis -supercell -amoeboid form -plant chloroplasts
Formation of nuclear envelope • infolding of plasma membrane o elaborated by mutation and selection • formation of nuclear envelope: separates transcription from translation o new mechanisms of gene regulation • formation of endoplasmic reticulum: Translation of RNA to protein
2 mitochondria hypotheses • H1 – ancient amoeba-like eukaryote engulfed in a bacterium: resulted in failed • H2 – endosymbiosis between prokaryotes: archaeal host and a bacterium o Leads to mutualistic interactions o Additional membrane
Formation of chloroplasts • photosynthetic protist is engulfed, nucleus from photosynthetic protist is lost, organelle has 4 membranes
Red algae • human health o red algae produce mannose-binding lectins (protein) to fight off viral infections o mannose-binding lectins break down glycoprotein cell wall of viruses o mannose-binding lectins given to mice result in immunity to ebola
Foramaniferans • morphology o calcium carbonate shells • bio-indicators of pollution o species richness, morphology, shell chemistry, metabolic activity • important stratigraphic marker o allows interpretation of paleo-ecology and time periods
Dinoflagellates • causes toxic algal blooms (red tide) • detrimental to animals • results in hypoxia • toxins into human food chain through filtering organisms, such as oysters & clams
Bacteria and Archaea (Prokaryote) Diversity Bacteria was common ancestor of all life, proks are paraphyletic, proks have most biomass
Bacteria & Archaea similarities • no membrane around DNA o single circular chromosome • no energy-producing organelles • very few cell compartments • no sexual reproduction, yet huge diversity
Bact vs Arch vs Euk p 1 DNA closed by nuclear envelope? • Bact no • Arch no • Euk yes Circular chromosome present • Bact yes • Arch yes • Euk no Organelles enclosed by membranes? • Bact No • Arch no • Euk yes
Bact vs Arch vs Euk p 2 Rotating flagella? • Bact yes • Arch yes • Euk no (flagella and cilia) Multicellular species • Bact no • Arch no • Euk yes
Value in knowing about Bacts & Arcs? -oldest bacterium 3.5 Ga -oldest euk 1.75 Ga -what to find a new species? Look at bacteria & archaea -total number of bacteria and archaea 5x10^30 • if all lined up side by side, they’re longer than the milky way
Extremophiles (Bacts & Arcs) -10,000m depth -temp > 120 C (boiling of water or greater) -pH<1 -water saturated with salt -water temp of 0 C (freezing)
Medical (Bacts & Arcs) -archaea causes periodontitis (receeding gumline) -most bacteria are not pathogenic (disease causing). Most are decomposers & energy creators -what makes a bacterium pathogenic? • Heritable • Have larger genome with genes coding for protein toxin
Antibiotics • naturally produced by fungi and soil dwelling bacteria • extensive use in medicine & animal feed led to resistant strains • biofilm of bacteria growing in polysaccharide matrix reduces effects of antibiotics
Bioremediation -use of bacteria and archaea to clean up polluted sites • break-down compounds toxic to eukaryotes • examples: oil spills, arsenic -methods • enhance growth of bacteria already there • seed contaminated areas with specific bacteria
Morphological diversity (Bacts & Arcs) -tree of life • based on ribosomal RNA. Matrix made of ribosomes. -variation • size o 0.3 to 100 um • shape o round, squiggly, rod • motility
Horizontal gene transfer -in general, bacterial genomes smaller bc they lack non-coding DNA -lack sexual repro & cell fusion but have lots of diversity o Conjugation • Pilus connection o Transformation • As a bacteria dies, it releases DNA. It’s taken up by a live bacteria
Morphological diversity (Bacts & Arcs) part 2, cell walls -cell wall structure • gram-positive have pepdoglycan o use penicillin • gram-negative o arythromiacin
Metabolic diversity (Bacts & Arcs) -aerobic water -anaerobic water -anaerobic sediment -proks have lots of metabolic diversity, while euks have more multicellular diversity
Metabolic diversity remix: Where do you get your energy? -photoauto • E - sun & C - CO2 (cyano, plants and algae) -chemoauto • E - chem reactions & C - CO2 (unique to proks) -photohetero • E - sun & C - enviro (heliobacteria) -chemoheterotrophs • E & C from enviro (many proks & fungi, and animals)
Conclusions about proks & euks -some biologists suggest phylogenetic tree of proks should be viewed as a series of diverting branches that reconnect as new organisms because of lateral gene transfer -astrobiology studies extremophile possibilities on other planets
Research part 1 -drawing conclusions from your findings -understand importance of your discoveries -read literature & talk to colleagues -make 1 or 2 clear points from your findings
Research part 2 -tell a coherent story (apparent in abstract) -communicate at a conference (internal or external poster talk) -write a publication for a scientific journal -target mass & social media – blogs, videos, facebook, twitter -talk to a journalist
types of scientific lit 1st literature – peer reviewed (at least 2 reviewers) scientific journal 2nd lit – books gray – publications from the federal government
who do research? -Shows you can identify a problem & solve it. -Builds analytic and quantitative skills. -Learn how to manage time. -Work in team & independently. -communicate effectively -be self-motivated
Conservation -gov, NGO, private sector are hiring -research state/federal, universities, NGOs, private corps, seasonal field jobs -environmental consulting
humans are pieces of shit part 1 - economic development -human pop is increasing dramatically -impact on environment related to standard of living
• bioaccumulation & biomagnification DDT, Hg (heavy metals), persistant organics, fracking & mtn top removal
light pollution o causes earlier breeding season in birds, and much earlier before sunrise o mismatches breeding with food availability
Sound pollution o amplitude (sound intensity, volume) higher in water than air o the period (pitch) and amplitude are effected, and specific sounds are the main communication o we fuck up whale communication with sea vessels. Also hurt their ears. Birds increase amp
martha case • My evolutionary projects currently focus on how insects, particularly pollinators, impose selection pressures on plants and contribute to plant population divergence and speciation.
rowan lockwood • The overall goal of my research is to understand how extinction and environmental change influence the evolution and ecology of fossil marine invertebrates.
Dan Cristol • My current focus is on mercury contamination in the headwaters of the Shenandoah River in central Virginia. mercury overlapping fluvial & terrestrial systems
francis paper experiment design • control plots: no gas pumps • experimental: yes gas • analyzed nesting success
solutions to gas pollution -no oil & gas exploration during migration -reduce boat activities in calving areas -reduce noise footprint on summer feeding grounds
biological pollution (invasive species & characteristics) • high rate of growth • large # and geographic range in native habitat (generalist vs specialist) • genetic isolation in new range (effective population size) o capability of hybridization • novel defensive & offensive traits to resist new predators
vulnerable pops to invasion • disturbed habitat • vacant niches • lack of mutualism • low species richness
why adopt an ecological framework? -evolution/ecology offers a framework to more fully understand all applications of biology -opens up new forms of medical research that could benefit society -may lead to some immediate improvements in medical practice (ex: dilution effect, flu)
Cholera • caused by bacterium • spread by food or water, enters the body & rapidly reproduces • if it multiplies too fast, the host can die before it’s transmitted • if we make transmission more difficult, we will select for less virulent strains of bacteria
Swine 09 • both human mobility & virus evolution predict H1N1 strain • china & southeast asia are source populations, USA spreads it because of our mobility • allows us to make better management/health due
6 explanations to why we get sick: • mismatch with modern environment • pathogens coevolve with host • constraints on what selection will do • tradeoffs on how selection is manifested • selection maximizes repro, not health • fever & pain are useful defenses, which cause suffering
Carbon cycle know that shit
Low certainty climate data o amount of SLR o precipitation o extreme weather events
higher certainty climate data o rising temp • increase predicted by 23 models o ocean acidification • measured data
ocean acidifcation • cool dense water can absorb more CO2, decreases pH • pH for 2100 has marine calcium exoskeleton organisms extinct • ocean currently alk, will be neutral by 2100 •CO2 increases H ions, decreases Carbonate ions, inhibits binding of aragonite & calcite
immediate regional changes -areas that already receive a lot of rain are going to get more -dry areas get drier -extreme weather events may increase (flooding, etc)
species that will not be able to shift geographical ranges at speed of climate change • most plants (can’t move) • small mammals (can’t hibernate in cold weather) • freshwater mussels (not dispersed)
marine climate response • lower O2 • accelerated acidification • increased ocean temps
kelp climate response • northern fish decreasing, southern fish increasing • species will turn over as long as there is a pathway
bird climate response • would expect all bird species to go north • some species moved because of temp & precip • some just temp • some not at all • it’s difficult to predict how species will respond • how far away they can migrate is the environmental envelope
climate change and evolution -moving bioclimatic envelope -community composition & biodiversity are interesting in leading and rear edges
Climate & evolution blob p1 -leading edge is generalists & dispersers, decreased diversity • founder populations, founder effect -middle is high diversity & differentiation, most diversity • increased gene flow, decreased genetic differentiation of sub-pops
Climate & evolution blob p2 -trailing edge has lots of extinctions (disruptive selection @ trailing edge) • reduced gene flow & reduced migration -stabilized relicts possibly increased resilience • evolution of endemics
-propagules are frozen ….something embedded in sediment. Genetic something. -like reconstructing plant communities based on pollen -you can reconstruct a population & use it to predict
climate change and evolution -moving bioclimatic envelope -community composition & biodiversity are interesting in leading and rear edges
Climate & evolution blob p1 -leading edge is generalists & dispersers, decreased diversity • founder populations, founder effect -middle is high diversity & differentiation, most diversity • increased gene flow, decreased genetic differentiation of sub-pops
Climate & evolution blob p2 -trailing edge has lots of extinctions (disruptive selection @ trailing edge) • reduced gene flow & reduced migration -stabilized relicts possibly increased resilience • evolution of endemics
Reconstruction of evolutionary processes based on dormant propagules -propagules are frozen ….something embedded in sediment. Genetic something. -like reconstructing plant communities based on pollen -you can reconstruct a population & use it to predict
humans ruin stuff via? • oil & gas • science exploration • security • shipping • fishing • tourism • who owns/regulates the sea?
climate solutions reduce current green house emissions, decrease societal inequality, proactive approach to ameliorate ecological impacts
reduce current green house emissions -reduce current green house emissions • reduce traveling • use solar/wind energy • eat locally • reforest & implement sustainable forestry
decrease societal inequality -decrease societal inequality • avoid food scarcity • provide financial incentives to relocate pople to avoid risk from catastrophic floods/droughts & displacement due to SLR
proactive approach to ameliorate ecological impacts -proactive approach to ameliorate ecological impacts • establish additional protected areas to allow dispersal of organisms • human-aided dispersal of organisms? • Establish no-take zones in marine organisms
Created by: haleyBUGoxox