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BIO EXAM NOTES.docx

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Department
Biology
Course
BIO1130
Professor
Jon Houseman
Semester
Fall

Description
ORGANIZING THE LIVING WORLD Adaptive Radiation - cluster of closely related species that are each adaptively specialized to a specific habitat or food source. - groups of organisms filling ecological niches Advanced Characters - a new version of a trait found in the most recent common ancester of a group. -more recently evolved -opposite of primitive characters - "derived" character Analogous - performing a smiliar function but has different evolutionary origins -eg. wings of a bird and a bat Apomorphy - trait that is shared by two or more taxa and their most recent ancestor - is a derived character within a group Artificial Taxonomy - a prominent or easily observed feature is taken as the mark of resemblance or dissemblance Autoapomorphy - derived trait that is unique to a given group - found in only one member of a clade --> not in any other groups or taxa Binomen - name of a species - genus + species - eg. Homo sapiens Camera Eye - ?? - Has pigmented cells that can detect light. They wrap around each other into cups and the cup closes with a pinhole. If you put a lense in there you can change the focus of what your looking at. - If we took the cladogram and put the camera eye as arising at the bottom near the common ancestor, it has to later disappear 5 times. Only two groups still have it (mollusk and vertebrates). - If we’re willing to accept that it’s an independent event (i.e. not monophyletic), you can say it arose twice (with the mollusk and vertebrates) and the cladogram would follow parsimony. Character convergence - similar to convergent evolution - homoplasy - simmilar adaptiations in distantly related organisms that occupy similar environments --> environment puts pressure on the organisms to take a specific shape Character Polarity - hypothesized sequence of evolutionary transition from character state to character state -denoted by 0, 1, 2, 0 = the ancestral character, 1 = derived, and 2 = secondary derived character -polarity is needed in order to successfully construct the cladogram -discerning polarity is a fundamental task in phylogeny; we need to be able to figure out which character came first in order to polarize it correctly Character Reversal - a character that reveses to a more ancestral state can cause a homoplasy -caused by environmental/genetic factors etc ex: snakes losing their legs Clade - A monophyletic group of organisms that share homologous features derived from a common ancestor -can be an extinct or extant species -a single branch on the ―tree of life‖ -clades are the essential units of cladistics Cladistics - method or grouping organisms that is based ond erived traits - infers phylogenetic relationships and evolutionary history of groups of organisms -invented by German entomologist Willi Henning -a ―branching tree‖; with the outgroup having the ancestral and common characters -critcisms: can be extremely subjective Cladogram - a dichotomous phylogenetic tree that branches repeatedly - end points of branches represent different species-generated by morphological characters, DNA/RNA sequencing and through computational phylogentics Classical Taxonomy - (natural or evolutionary taxonomy) - based off darwin's principle -was biased (e.g. embyologists wanted their field to be used as the method of classification but morphologists wnated morphology to be the basis) -followed by the unbiased phylogenitcs (cladistics). -after mechanical taxonomy Classification - an arrangement of organisms into hierarchical groups that reflect their relatedness -first classifications of the living world were based on morphologies ex: Linnaean system of classification Common Ancestor - ancestor from which two or more species have evolved -all living organisms have a common ancestor -common ancestor to all animals is the choanoflagellate; all plants is the green alga Convergent Evolution - see character convergence Dendrogram - tree diagram - shows taxonomic relationships - based on phenetic similarity Derived characters - see advanced characters Dichotomy - splitting of a whole into tow non-overlapping parts - repeated branching into tow equal parts -if dichotomy doesn’t work, the branch MUST be resolved -based on if a character is present or not: i.e. does it have a backbone? à split into vertebrates vs. invertebrates Divergent Evolution - homology - accumulation of differences between groups which can lead to the formation of new species - naturally selected changes in related species that once chared a characteristic in common Evolutionary Taxonomy - classifying organisms using a combination of phylogenetic relationships and overall similarity -SHOULD get the same branching pattern no matter, but the problem is: this method is biased -Darwinian classification -founded in the early 1940’s -produces a tree, vs a list -allows for groups to be excluded from their parent taxa, ex: dinosaurs are not included as birds, but gave rise to them Folk taxonomy - biological calssification - the way people make sense of and organize their natural surroundings - 'word of mouth' -embedded in cultural and social systems & serve various functions --> problems: since it stays within the culture, they can’t describe something they have never seen…so not universal Fungi - kingdom - any group of spore-forming organisms feeding on organic matter - can dissolve rock and create minerals and nutrients that are beneficial to plants - started the beginnings of soil systems Henning (Or Willi Henig, I believe) German biologist who is considered to be the founder of cladistics. as a taxonomist, he specialized in Dipterans (flies, mosquitoes). Hierachical - classification system where entities are arranged based on some hierarchical structure (the entities are represented as being above, below or the same level) -based on simple dichotomies -creates branching patterns Homologous - having the same evolutionary origin but not necessarily the same function - eg. bones of a human hand, bat wing and whale flipper --> have the same interal structure Homology - characteristics shared by a set of species because they inherited them from their common ancestor - similar Homoplasy - see convergent evolution KISS principle - Keep It Simple Stupid - concept that the simplest way is probably the best way (when building cladograms) -also known as ―Occam’s Razor‖ -IN GENERAL: it is the principle that can be applied to many disciplines that simplicity is a key goal in design and complexity should be avoided if possible Linnaeus - sorted all the names into a hierarchical system that was strictly mechanical (not biological) - Created by binomen-was the first to organize animals and plants by similar features-Swedish Naturalist, 18th Century Mechanical Taxonomy: taxonomy based on mechanical structures of organisms -based on types of linkages, provided by M. Muller (i.e. skeletal structures) -basically a morphological way of looking at taxonomy -ex: joints, knees, cranical mechanism of animals, linkage mechanisms of jaw protusions Monophyletic - group of organisms that includes a single ancestral species and all of its descendants -the aim in cladograms is to make monophyletic groups -can turn into polyphyletic or paraphyletic groups as more characters are added to the tree -the first step in making a cladogram is to include all species under study as being monophyletic Natural Taxonomy - things classified are arranged according to the totality of their morphological resemblances Node - point on a stem where one or more leaves(species) are attached--different types of nodes define different groups; ex: monophyletic, paraphyleic, polyphyletic-where branching occurs on cladograms Out Group - group of organisms not belonging tot he group whose evolutionary relationships are being investigated via a cladogram - Must score "0" on all traits, yet still be related to the organisms being examined - basically serve as a reference point -hypothesized to be rather closely related to the other groups, but less closely than any single one of the species to each other -conclusion: out group must have branched from the parent group before other two groups branched from each other Paraphyletic - a group of organisms that includes an ancestral species and some, but not all, of its descendants -paraphyletic groups can form from monophyletic groups as they branch out -while the group has a common ancestor, we are actually ignoring a subset of its descendants example: dinosaurs and birds; birds are dinosaurs i.e. they are descendents of an ancestor that spawned the dinosaurs but paleontologists refer to dinosaurs as dinosaurs, not birds Parsimony - KISS principle - in phylogenetic analysis using cladograms, the least number of changes is accepted as a biological principle since this is what likely occured in evolution Phenetic (Numeric) Taxonomy - grouping by numerical methods - aims to create a taxonomy using numeric algorithms (cluster analysis) - may not correlate with evolutionary relationships Phylogenetic Taxonomy - groups of organisms based on shared evolutionary heritage - eg. DNA and RNA sequencing tehcniques Phylogenetic tree - branching diagram depicting the evolutionary relationships of groups of organisms Phylogeny - evolutionary history of a group of organisms the evolutionary history of a group of organisms -often conflicting interpretations because there can be more than 1 branching pattern possible -ex: the construction of cladograms Plesiomorphy - sharring a character state with an ancestral clade - primitive-is at the base of the cladogram ; ex: ectothermy is a plesiomorph Polyphyletic - group of organisms that belong to different evolutionary lineages and do NOT share a recent common ancestor Polytomy - brance point on a tree that has more than two immediate descendants Primitive Characters - traits retained from a common ancestory - opposite of derived Sister group - two groups resulting from the splitting of a single lineage - the groups are eachothers closest evolutionary relative Symplesiomorphy - primitive trait which is shared between two or more groups Synapomorphy -derives trait which is shared between two or more groups Systematics - branch of biology that studies the diversity of life and its evolutionary relationships Taxon - name designating a group of organisms included within a catergory in the Linnaean taxonomic hierarchy Taxonomy - the science of the classification or organisms into an ordered system that indicates natural relationships Weighted characters - characters are weighted by taxonomists according to their utility for different purposes, because a character can have little importance for an organism, but be very important to understand it’s relation to another species. MICROEVOLUTION AND SPECIATION Allele – one of two or more versions of a gene -different alleles can result in different observable phenotypic traits -each trait has 2 alleles -one allele/chromosome for diploid organisms -genetic variations in alleles can result in differences, also can be unnoticeable Allele frequencies: the abundance of one allele relative to others at the same gene locus in individuals of a population to describe genetic diversity -can be calculated by dividing the number of alleles for a certain trait/the total number of individuals in the population -usually expressed as proportion or a percentage -denoted as ―p‖ or q‖ Allopatric speciation: a reproductive isolating mechanism that results from geographical separation between two populations -a prezygotic mechanism - Populations evolve independently and diverge into different species -caused by glaciers, continental shifts, etc Allopolyploidy: having 2 or more complete sets of chromosomes from different parent species -only plants are capable of this, not animals -results in a fertile hybrid -can be created from previously sterile species (ex bread wheat) Autopolyploidy: having 2 or more complete sets of chromosomes from the same parent species -again only possible in plants through self fertilization -arise from a failure in the meiotic process -often resemble parents, except grow more slowly and flower later Behavioural Isolation: -a prezygotic isolation process -2 species do not mate because of differences in courtship behaviour -also known as ethological isolation -ex: songs of bullfrogs, fireflies example used in class (sequences of bursts of light vary for different speices of fireflies within males and females) Beneficial mutation: a mutation that proves to be beneficial for the individual; ex increases fitness -can help withstand diseases -ex: those who carry 1 allele of the sickle cell anemia disease are more resistant to malaria in areas of sub-saharan Africa Biological Species: the concept of a species based on the ability of populations to interbreed and produce fertile offspring -basically a reproductively isolated gene pool -no universal agreement to what it is -problems with the concept: how do you define a fossil species? how do you define populations that reproduce asexually? (ex archaea and bacteria) Bottleneck Effect: Type of genetic drift that occurs when an event, such as drought, or intensive selection pressure causes a population to significantly dwindle in size -the survivors reproduce, but there is limited genetic variability -Note: Bottle-neck different from Founder Effect. In Bottle-neck there is no movement of population whereas in Founder Effect there is. ex: elephant seals, tomatoe (taste) Chromosomal Inversion: a chromosome rearrangement in which a segment of a chromosome is reversed end to end -occurs when a single chromosome undergoes breakage with itself -occurs in the arm of the chromosome, does not involve the centromere -do not usually cause abnormalities as long as the re-arrangement is balanced with no extra genetic info --however increased production of abnormal chromatids result in heterozygous individuals à lowered fertility due to production of unbalanced gametes Chromosomal translocation: rearrangement of parts between nonhomologous chromosomes -ie: a piece of one chromosome breaks off and sticks to another chromosome -2 types: reciprocal & Robersonian -Reciprocal: 2 different chromosomes exchange places -Robertsonian: a whole chromosome attaches to another -Ex: results in Down Syndrome (Trisomy 21; the 21st chromosome has 3 chromosomes instead of 2) Crossing over: recombination in meiosis when chromatids exchange segments -IMPORTANCE: genetic variability -occurs during prophase I in a process known as synapsis -matching regions on matching chromosomes break and then reconnect to the other chromosome Deleterious mutation: a genetic mutation that proves to be harmful for the organism -cause errors in protein sequence making a partially functional of completely non-functional protein -when the protein plays a critical role in organism functioning, it can be crucial à i.e. a medical condition can result -ex: genetic disorders -are often repaired by the ―double checking system of DNA‖ Diploid: an organism that contains 2 sets of chromosomes -grow through cell division (mitosis) and reproduce by meiosis (production of gametes) -ex: animals Directional selection: type of selection in which individuals at one extreme of the phenotypic expression have a higher fitness -the frequency of the phenotype becomes higher & is eventually fixed -occurs most often naturally under environmental changes. -ex: breeding for the most desirable trait; i.e. the smallest possible Chihuahua Disruptive selection: type of selection in which extreme phenotypes have higher fitness than intermediate phenotypes -results in speciation -driving force behind sympatric speciation -ex: different species of birds with very long and very small beaks Dominant allele: an allele that expresses its phenotypic effect even when heterozygous with a recessive allele -important for masking recessive phenotypes & preserving recessive alleles in a population -ex: if the pea plant is dominant for green seeds and recessive for yellow seeds, and the individual is heterozygous then the green seed phenotype will show Ecological isolation: a prezygotic isolation mechanism -species that live in the same geographic region occupy different habitats -thus making it difficult for them to mate with one another -ex: a marsh species vs. a woodland species Ecological species: the species concept where a group of organisms is adapted to a particular set of resources (niche) in the environment -the ecological & evolutionary processes that control how resources are divided up produce these clusters -good for ecological foodwebs -PROBLEM: the observations are just as subjective as the morphospecies concept Female choice: -the females having control over whether reproduction occurs based on their choices of the males -due to the fact that females produce the eggs, and want the best possible sperm to fertilize her eggs -results in elaborate courtship and extravagant visual appearance on the part of the males in order to attract females Fitness: the ability to survive and reproduce à stronger fitness means that you are more likely to survive and reproduce and vice versa for a weaker fitness -alleles with higher fitness become more common; produces natural selection -manifested through the phenotype ; affected by developmental environment as well as by genes Fixation: the state in which where only one allele remains of a particular gene -the probability of fixation is higher in small populations due to genetic drift -in fixation, if one allele is fixed, the other coordinating allele is lost -otherwise known as the domination of a particular allele -IMPORTANCE: it’s BAD – we’ve lost genetic variation Founder Effect: a phenomenon in which a colonizing population has only a fraction of the genetic variety of the parent population -a reduced gene pool (loss of genetic variation) -often caused by migrating populations, island populations etc. -ex: Quebecois in the Saguenay region à increased change of muscular dystrophy in this region because of the founder effect Frame Shift Mutation: a mutation that causes the reading frame of the mRNA to be altered, usually by one codon, which can mess up everything -produces a different, non-functional amino acid sequence in the polypeptide -caused by insertions or deletions of nucleotides -the earlier the frame shift, the more mutated the protein Gametic Isolation: prezygotic reproductive isolating mechanism -is the incompability of the sperm of one species and the egg of another species to join together -ex: giant clams/ sponges/organisms that release their egg and sperm into the water column recognize only each other and don’t end up combining with other species Gene Duplication: a segment of one chromosome is broken off and inserted into its homologue (resulting in duplication of the gene on the homologue) -the opposite of the deletion -identical genes can undergo changes and diverge into 2 different genes -occurs during unequal recombination (crossing over) that occurs between misaligned homologous chromosomes during meiosis Gene flow: the transfer of genes from one population to another through the migration of individuals, thus introducing new genes -can solve the problems of the founder effect, bottleneck effect, genetic drift etc -can also result in loss of genetic variety of the gene flow is out of the population instead of into the population -mobility affects the rate of gene flow Gene pool: the sum of all alleles at all gene loci in all individuals in a population -large gene pool = large genetic diversity, small gene pool = small genetic diversity & lower biological fitness/selection -total gene pool is important for calculating the allele frequency (*remember allele frequency is a percentage) Genetic Drift: random fluctuations in allele frequencies as a result of random change in a finite population -usually happens in smaller populations -basically a sampling error – if the population is large, the effect of chance = low -ex: 50/50 heads/tails coin tossing done 25 times vs. 5000 times Genetic Equilibrium: the time at which allele frequencies and genotype frequencies do not change from one generation to another -defined by the Hardy Weinberg Equilibrium equation -only happens if all of these conditions are met: 1) Random Mating, 2) No Natural Selection 3) No Genetic Drift (A very large population) 4) No Mutation 5) No Gene Flow Genotype frequencies: percentage of individuals in a populations that contain a particular genotype (ex: AA, Aa, aa) -Denoted by p^2, q^2, or 2pq -represented as a proportion of the total number of inidividuals Habitat Isolation: species that live in different habitats -a prezygotic isolation mechanism -basically the same thing as an ecological isolation. Haploid: -contain 1 set of chromosomes -may be gametes in diploids (egg and sperm) or an organism that already exists in a haploid state (fungi) -biologically referred to as ―n‖ Hardy-Weinberg Principle: the ―rule of thumb‖ that states when a population of diploid organisms achieves genetic equilibrium *see genetic equilibrium for the conditions under which this is true IMPORTANCE: It is important to know when things are NOT changing in order to determine if things are changing! Heterozygote Advantage: when heterozygotes have a higher relative fitness than homozygotes -due to dominating allele masking the possible harmful effects of the recessive allele -results in heterozygotes surviving more than homozygotes in the case of diseases -also known as balancing selection ex: sickle cell anemia heterozygotes in sub-saharan Africa have higher resistance to malaria Heterozygous: the state of possessing 2 alleles of a gene – can be dominant + recessive ex: Aa -if dominant + recessive, only the dominant trait will show in the phenotype -ex: a pea plant containing alleles for both yellow and green seeds, if green is dominant; they will have green seeds, but since they still contain the allele for the yellow seed it is possible for it to pass it onto the next generation Homozygous: the state of possessing 2 alleles of the same gene – ex: both alleles are recessive, or both alleles are dominant -ie identical allies for a single trait -ex: the green seeded pea plant has alleles that both code for green seeds, the yellow seeded pea plant has alleles that both code for yellow seeds -2 different homozygous individuals can breed to form heterozygotes Hybrid breakdown: -a post zygotic isolation mechanism -hybrids are capable of reproduction, but the offspring have reduced fertility or reduced viability (fitness) -the hybrids eventually die out from the population -this ensures speciation b/c the species in the long run do not mix successfully Hybrid sterility: post zygotic isolation mechanism -the offspring hybrid is sterile -meaning that it cannot produce progeny so the line of hybrids also dies out -ensures speciation ex: mules are sterile (cross between a horse and a donkey) Hybrid viability: whether or not the hybrid organism will be able to come to term -the zygote may form, but may end up being destroyed -if the hybrid is inviable, this ensures speciation because the hybrid will never exist -or the hybrid will survive, but not to a reproductive age -this is because the developmental programs of the parent organisms are incompatible Ex: goats and sheep can fertilize each other but their ova will never come to term Hybrid zone: geographical area where the hybrid offspring of 2 divergent populations are common -can occur if 2 populations undergo allopatric speciation and then regain contact after isolation -generally very narrow zones -some persist for hundreds or thousands of years Hybridization: when 2 species interbreed and produce fertile offspring -can be the interbreeding between 2 homozygous individuals that creates a heterozygote -ex: more hardy and disease resistant crops can be formed from hybridization -leads to speciation Inbreeding: a form of non random mating -genetically related individuals mate with each other -reduces heterozygosity -increases homozygosity -therefore increases the chances of offspring inheriting deleterious traits Male competition: competition between males for dominance over the females - in order to pass on their genes to the next generation -can be in 3 forms: 1) sperm competition 2) male-male combat 3) infanticide 1) sperm competition à promiscuous mating, ex: dragonfly males attaching onto females, dumping out male sperm and replacing with their own 2) male-male combat: elephant seals & dominance over a harem of females 3) infanticide – a new alpha male kills old alpha male offspring to ensure only his genes will be passed on Mechanical isolation: pre-zygotic reproductive isolation mechanism -differences between reproductive organs make it physically impossible for the sperm and egg o
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