Genetics Study Guide Test 3
Genetics Study Guide Test 3 BIL250
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Date Created: 02/23/15
EXAM 3 STUDY QUESTIONS 131 Compare vertebrate mtDNA plant mtDNA and plant chNA in terms of inheritance typical and exceptional genome size the types of genes they contain and structural elements such as position of tRNAs codingnoncoding regions presence or absence of introns types of genetic codes and transcriptionaltranslational control 1 mtDNA found in all aerobic eukaryotic cells make ATP mostly circular and supercoiled lack histone proteins high copy number there are multiple genomes per mitochondria and many mitochondria per cell easy to isolate and PCR humansvertebrates 16kb yeast 80kb and plants 100kb2Mb plants have lots of non coding mtDNA replication is semi conservative like normal DNA use DNA pol speci c to mitochondria non coding control region forms a displacement loop for replication mitochondria grow and divide mtDNA has genes for tRNA rRNA cytochrome oxidase NADH ATPase mitochondria39s genetic info also occurs in the nuclear DNA most required proteins coded by nuclear genes Transcription mRNAs from mtDNA are synthesized and translated in mitochondria gene products encoded by nuclear genes are transported from cytoplasm to mitochondria Vertebrate mtDNAs transcribed as single large RNA molecule polycistronic and cleaved to make mRNAs tRNAS and rRNas before they are processed no introns most mtDNA genes separated by tRNAs that signal transcription termination mtDNA is much larger in plantsyeast tRNAs dont separate genes large gaps btwn genes transcription signaled by non tRNA sequences intons occur transcription is monocistronic Translation mt mRNAs don39t have a 539 cap AUG is start codon only plants use universal genetic code wooble occurs in base pairing mt and chNA don39t follow mendelian inheritance since no meiosis genotypephenotype same as mom paternal leakage occurs at low levels heteroplasmy cpmtDNA organelles rarely occur 2 chNA chloroplast genome circular double stranded lacks structural proteins much larger than mtDNA 800600kb genome occurs in many copies and have lots of non coding DNA nuclear genome encodes some components and chNA codes rRNA tRN ORFs genes coded on both strands like mtDNA translation similar to prokaryotes initiation uses fmettRNA unique lfs EFs universal genetic code39 organelle genomes higher substitution rates than nuclear lack of proofreading diff DNA repair mechanisms more oxidative mutagens less selective pressure most cells have many mitochondria maternally inherited smaller effective pop size 132 What is the difference between maternal inheritance and maternal effect female gamete larger than male gamete female gives cytoplasm for developing embryo cytoplasm has factors that are released by nuclear genes of the female female cytoplasm contributes the mitochondria for all species and chloroplast for plants maternal effect phenotype of the offspring is controlled by nuclear factors found in cytoplasm of mother snail shells depend on mothers genotype you get nuclear DNA from the cytoplasm of mom sometimes paternal leakage occurs 0 proteinsmRNA deposited in oocyte before fertilization maternal inheritance phenotypes controlled by organelle genes mtDNA you get the DNA from organelle o Leberes neuropathy kearns syndrome myoclonic epilepsy C HAPTE R 14 141 Explain how Harriet Creighton39s and Barbara McClintock39s studies of corn in 1931 provided the rst convincing experimental evidence for Morgan39s hypothesis of recombination and chromosomal exchange 0 part of chromosome 8 attaches to 9 translocation detect if recombination happened by looking at chroms physical markers recombinant phenotypes correlated with cytological features seen stern saw recombination in drosophila translocation one chrom shorter phenotypes and cytologic features correlate 142 Describe the formation of the Holliday intermediate and explain how cleavage of this molecular structure can result in parental and recombinant allele combinations 0 single strands of each DNA break and anneal to the opposite chromosome forming intermediate as the ends pull apart branch point migrations occur making a 4 arm structure the intermediate is cut by endonucleases in one of 2 planes 0 one form makes the parental arrangement and the other makes recombinant allele combos 143 Use the twopoint recombination frequency data from question 156 at the back of your book to map the genes a b c d and e o if genes are linked the recombination rates are very low 144 Order tetrad experiments indicate that crossing over occurs at the 4chromatid stage prophase l of meiosis What is the alternative What features of the ordered tetrad experiments make them ideally informative in this respect lnterphase prior to meiosis during 2 chromatid stage before chroms are duplicated meiosis l prophase 4 chromatid stage crossing over occurs at chiasma breaking and rejoining of homologous chromatids orange bread mold experiments arrangement of ascospores indicate crossing over tetrad 4 haploid gametes produced by meiosis phenotype corresponds directly with genotype in haploid crossing over sometimes happens in mitosis somatic cells curt stern saw in drosophila 145 What is the process of gene conversion 0 DNA sequence info is transferred from one helix to another whose sequence gets altered non mendelian inheritance 0 can be caused by mismatch during recombination when mismatch is excised by exonucelease and replaced with DNA pol overwriting the previous base pairs so one helix is xed and one is messed up 31 0 conversion is a duplication vs crossing over both helixes get new DNA CHAPTER 15 151 Compare and contrast three different methods used for mapping genes in bacteria How do the types of data that result from these methods differ transfer of DNA is always unidirectional no complete diploid stage forms 1 conjugation transfer of genetic material btwn donor and recipient by direct contact a segment of the donor39s chrom recombines with the homologous recipient chrom recipient with new DNA are transconjugants F is a self replicating circular DNA plasmid has origin sequence that initiates DNA transfer has F pili genes Donor is F and gives to F recipient F plasmid gets nicked at origin and single strand transferred by rolling circle mechanism both cells are F double stranded after NO chromosomal DNA gets transferred by standard sex factor Hfr high frq recombination strains transfer chrom DNA with special F strains bacterial chrom and F factor crossover and make Hfr cell F nicked and Fchrom DNA transferred to recipient recombinants then made by crossing over recipient bacterial chromosome with the new transferred hfr spontaneously the F factor gets looped out of hfr chrom along with a gene and becomes F39 lac mapping genes by interrupted mating and see which genes are transferred rst 2 transformation transfer of extracellular DNA into cells making a phenotypic change in recipient DNA from donor is added to recipient they have diff phenolgenotypes and if recombination occurs a new recombinant phenotype occurs some bacteria like bacillus subtilis take up DNA naturally other need to be treated to take up DNA 0 ds donor DNA enters cell and one strand gets degraded forms triple strand and crosses over donor strand gets degraded after replication progeny have recombinant DNA recombination frq infer gene order if genes cotransform they are close together pq o 3 transduction bacteriophages transfer genes to bacteria generalized any gene specialized transfer speci c genes phages carry very small amnts of DNA phages can do lytic cycle progeny phages burst cell or lysogenic phage DNA integrates into host chrom and cell divides with new chrom until lytic cycle where host DNA breaks down and phage take over 0 map gene order if recombination rates are high then genes are far apart if genes cotransduced they are close infect bacteria with diff phages and count recombinant phage phenotypes by see growth on bacterial lawn CHAPTER 16 161 What is a polytene chromosome where do they occur and why are they important for study of chromosome mutations occur in insects usually ies they are chromatid bundles that result from repeated cycles of duplication wo cell division 0 used to study structural mutations as they can be seen under microscope 162 Distinguish between chromosome deletion duplication inversion and translocation deletion heat radiation viruses chemicals transposable elements or recombination errors cause section to be deleted there is a break with sticky ends that aren39t protected by telomeres 0 single allele deletion of homozygous wild type normal 0 deletion of heterozygote o deletion of centromere loss of chromosome o pseudodominance deletion of dominant allele of heterozygote results in phenotype of recessive allele duplication doubling of chromosome segments making un paired loops that are visible 0 tandem duplicates and adds ahead 0 reverse tandem duplicates and adds inverted o tandem terminal end duplicates inversion segment excised and inserted in opposite orientation usually don39t cause DNA loss but unequal crossing over happens with heterozygotes o pericentric includes centromere o paracentric no centromere translocation change in location of chrom segment no DNA lost or gained 0 intrachromosomal on the same chrom o interchromosomal btwn chroms reciprocal 2 way exchange non reciprocal 1 way exchange 163 How can unequal crossingover result in chromosome duplication one chromosome gives a piece to the other chromosome and it crosses over again with another chromosome which gives it a third copy of a segment now the chromosome has duplicated ex Bar and double bar phenotype in drosophila ones get a deletion and one gets a duplication 164 How might presenceabsence of chromosome inversions in uence speciation if there is inversion then the two zygotes cant produce a viable offspring chromosomal inversions suppress recombination and make inviable gametes since genes are missing when populations mate their offspring may survive but the subsequent offspring have gametes that are not viable isolating mechanism that can cause speciation due to partial sterility 165 Explain how nondisjunction might lead to alternate forms of aneuploidy such as X0 XXX XXY XXXY XXYY and XYY nullisomic one homologous chrom pair lost monosomic single chromosome lost doubly monosomic two chromosomes are lost trisomic one extra chromosome tetrasomic one extra homologous pair double tetrasomic two extra homologous pairs sex chromosome aneuploidy occurs most often during meiosis I when homologous chroms fail to separate into tow cells or II when chromosomes fail to separate into 4 cells 166 If a trisomy21 carrier and normal parent mate and produce offspring what percent of the zygotes are expected to be inviable What percent of viable offspring have trisomy21 What fraction are carriers for trisomy21 What fraction are normal 0 if you39re a carrier one gene is normal and one has an extra 14 o 3 offpsring are inviable 2 are normal one is normal and one is carrier and 1 has trisomy 21 167 What is the difference between aneuploidy and monoploidy Distinguish between haploid diploid monoploid and triploid aneuploidy variation in number of indiv chroms monoploidy one of each chromosome and no homologous pairs meant to have 2 but u only have one diploid each chromosome has a homologous pair haploid a cell with a single copy of each chrom polyploidy more than the normal number of homologous pairs 0 triploid three homologous pairs in each seedless fruits CHAPTER 17 171 Describe the organization and control of the lac operon of E coli 4 Genes that work together are organized into operons Adjacent genes are transcribed together onto a polycistronic mRNA lac Z YA to make polygenic mRNA 5 operon has a promoter repressor operator controlling site coding sequences and terminator 6 inducible genes get turned on by adding a substance the inducer is a regulatory substance that is a type of effector molecule that helps control gene expression ecoi continuously expresses glucose metabolism genes but not lactose lactose is a disaccharide glucose galactose that stimulates expression of 3 proteins a Bgalactosidase IacZ breaks down to glucose and galactose converts lactose to allolcatose inducer for regulating lac operon expression of these enzymes 1000 fold increase b Lacrose permease lacY transports lactose across membrane into cell c Transacetylase lac A transfers acetyl group from acetyl coA to Bgalactosidase RNA pol initiates transcription at promoter and a polycistronic mRNA is synthesized in order ZYA lac operator is a regulatory sequence upstream doesn39t make a product affects production of downstream molecules lacl gene has its own promoter and terminator and encodes the repressor when there is no lactose the repressor binds to operator RNA pol cant bind to promoter and transcription inhibited Lacl makes repressor protein lac operon is under negative control since lacl blocks pol if inducer is absent normally off 0 also under positive control when lactose is sole carbon source CAP binds cAMP activates and binds to a CAP recognition site upstream of the promoter CAP facilitates binding of RNA polymerase and transcription QM 172 Describe the organization and control of the Trp operon of E coli 2 9 genes for AA synthesis are repressed if AA are present in medium when they are absent genes turned on for synthesis 10two mechanisms of regulation 1 repressoroperator interaction if tryptophan is present it binds to trpR which binds to trop operator and prevents transcription repression reduces transcription 2 termination of initiated transcripts attenuation translating short incomplete polypeptide trp genes expressed when lacking tryptopan attenuation regulates transcription levels 221 Explain the basis of quantitative traits and how they differ from discrete traits discrete traits have a few distinct phenotypes and can be descried in qualitative terms continuous traits display a wide range of phenotypes and must be described in quantitative terms quantitative traits traits with continuous distribution of phenotypes height eight personality quantitative traits arise from multiple loci pleiotropy one gene has many effects epistasis variable expressivity penetrance and environment quantitative trait loci QTLs there is a range of phenotypes since many loci contribute QTL is a speci c genomic segment correlated with continuous phenotypic trait variation VP V5 1quot V5quot VGXE Phenotypic variance Genetic effect enviro effect 2covariance milk cow how genotype and environment interact CHAPTER 18 181 Eukaryotic gene expression is regulated at six levels What are these levels and how do they operate Give some examples to illustrate your answers 1 Transcription promoters determine whereif transcription begins activated by TFs can be or regulated enhancers upstream or downstream may form loops bind regulatory proteins that activaterepress can be or histones methylated histone bind to promoters and inhibit transcription acetylation enhances transcription hormone regulation short term hormones act as inducers in one cell and cause response in another cell steroid hormones pass thru membrane and bind to receptors that bind to DNA and regulate expression polypeptide hormones bind at surface and activate second messengers to regulate transcription i hormone response elements HRE regulated by steroid hormones when steroid present it displaces chaperone protein binds receptor and binds HRE transcription begins short term galactose genes in yeast in absence of galactose GAL genes are not transcribed processing regulates mRNA production from precursor RNAs alternative polyadenylation where poylA tail is added human CALC gene alternative splicing which exons get spliced sex determination in drosophila A transport eukaryote mRNA transport is regulated some never leave nucleus get degrade mRNA translation control in stored mRNA translation is inhibited unfertilized eggs are translated after fertilization stored mRNA have short polyA tails so they don39t translate readily some are deadenylated tail chopped before storage mRNA degradation control tRNA and rRNA very stable AU rich elements secondary ure deadenylation 539 de capping and internal cleavage of mRNA affect mRNA half protein degradation post translational control proteins can be short or long lived ubiquitin is a co factor that binds to proteins and identi es them for degradation by proteolytic enzymes AA at the N terminus determins ubiquitin binding a b c d e 2 RNA a b 3 mRN some 4 5 struct life 6 Pro ka ryotes polyci Euka ryotes only regulate by transcription gene expression regulated by an operon collection of coding sites adjacent to stronic coding sequence 6 options for gene expression regulation more complex don39t have operons but have protein coding sequences adjacent to controlling sites transcription and translation is uncoupled short term regulation genes turned onoff in response to environment or long term genes for development and differentiation CHAPTER 19 191 How do maternal effect genes segmentation genes and homeotic genes regulate development and differentiation of Drosophila Development process of regulated growth resulting from interaction of the genome with cytoplasmenvironment Programmed sequence of cellular events that are usually irreversible Differentiation formation of cells tissues and organs thru gene reg embryonic development before fertilization there are gradients in eggs polar cytoplasm at posterior end maternal effect zygote forms and two parental nuclei fuse making diploid nucleus that divides 9 times blastoderm forms development depends on anteriorposterior gradients in the egg mRNAs and proteins placed in egg by mom maternal effect and formation of parasegmentsembryonic segments that give rise to adult segments maternal effect genes expressed by mom during egg production control polarity of egg and embryo bicoid gene regulates formation of anterior structures transcribed during egg production and expressed after fertilization nanos gene regulates abdomen formation torso gene active at the poles of egg transcription and translation during egg production segmentation genes divide embryo into regions that correspond to adult segmentation patterns 0 gap genes subdivide embryo along anterior posterior axis into broad regions mutations delete segments 0 pair rule genes divide embryo into regions each with a pair of parasegments mutations cause deletions of every other segment 0 segment polarity genes determine regions that become segments of larvae and adults mutations replace segments with mirror images 3 homeotic genes specify the body part to develop at each segment after segmentation pattern is determined 0 adult body parts develop from undifferentiated larval tissues called imaginal discs homeotic mutants develop a diff body part at a disc than normal legs coming out the mouth homeoboxes gene groups of similar sequences regulate development and produce DNA binding proteins that bind upstream hox genes homoeotic gene complexes also specify body in plants and vertebrates CHAPTER 20 201 Contrast sporadic and hereditary retinoblastoma How does the existence of these two forms of cancer support Alfred Knudson39s 1971 quottwohit mutation modelquot 0 Two types of cancer sporadic more frequent no hereditary cause and familial less frequent hereditary Retinoblasma t two hit model and show both forms OMlM180200 o sporadic 60 of cases only in one eye 0 hereditary 40 of cases both eyes consistent pedigrees occur earlier in age 0 Alfred Knudon39s model two mutations are required for retinoblasma development disease appears dominant in pedigree but it is recessive chromosome 13 mutation occurs in a gene that encodes a growth inhibitory factor 0 sporadic child starts with two wild type alleles and both mutate to make disease probability of both mutations in same cell is low only one tumor forms one eye 0 hereditary child starts with heterozygous alleles only one mutation needed to make disease mutations resulting in loss of heterozygosity are more probable and multiple tumors occur both eyes 202 Describe the steps in the life cycle of a transducing retrovirus and explain how a retrovirus acquires an oncogene Protooncogenes are highly conserved among animal species What generalization can you make about the function of protooncogenes proto oncogenes have normal gene products and stimulate normal cell development they function to control cell growth across many species they are similar oncogenes arise from mutant proto oncogenes abnormally active at wrong times and stimulate unregulated cell proliferation some tumor viruses that infect cells have oncogenes 0 RNA tumor viruses have viral oncogenes that transform cells into cancerous state 0 DNA tumor viruses don39t have oncogenes but induce cancer by activity of viral gene products on the cell herpes retrovirus single stranded RNA virus that replicates via DNA intermediate RNA is converted to cDNA by reverse transcriptase DNA integrates into host chrom and is transcribed retroviruses have 2 copies of RNA genome protein viral core and glycolipid envelope transducing retroviruses have oncogenes altered forms of GF or GIF genes can cause cancer when integrated into host chrom all RNA tumor viruses are retroviruses but not all retroviruses are transducing cancerous life cycle 1 ssRNA genome is released from virus and reverse transcribed to dsDNA proviral DNA r transcriptase lacks exonucelease activity so lots of mutations 2 LTRs long terminal repeat sequences on each end of genome have transcription regulatory signals for viral genes and are ligated to produce circular dsDNA 3 proviral DNA and host chrom DNA cross over and joined by recombination 4 host RNA pol transcribes proviral DNA and produces viral mRNAs required for virus life cycle 0 Steps to create retrovirus oncogenes 1 retrovirus integrates into host chrom near cellular proto oncogene by recombination 2 deletion fuses retrovirus transcription signal sequences with proto oncogene sequences usually parts of the viral DNA sequences are deleted making defective oncogene 3 viral progeny carry cellular gene under in uence of viral promoters 4 most transducing viral oncogenes are defective and cant replicate independently 5 if mRNA is packed into virus particle along with a normal virus genome co infection r transcriptase produces a new defective oncogene by switching templates during cDNA synthesis template switching and lack of proofreading during DNA replication result in rapid evolution of oncogenic retroviruses CHAPTER 21 211 How do mutation selection genetic drift migration and nonrandom mating generally in uence genetic diversity mutation heritable changes in DNA that are source of variation mutation rate is low per genegeneration is 10394 to 10398 increases variation a neutral mutation do not affect reproductive tness act slowly b irreversible uADa c reversible v a A selection directly proportional to effect population size genetic drift random change in allele frq due to chance decreases variation in small populations chance factors can make large changes in allele frq make divergences thru bottlenecks founder events and isolation d causes allele frq to change over time and causes a reduction in genetic variation over time cause pops to diverge also explains how diff species accumulate differences on a regular basis forming neutral theory of molecular evolution non random mating inbreeding decreases variation and sometimes tness decreases effective population size migration brings genes to a new gene pool gene ow it introduces new alleles into the pop and when allele frq btwn migrant and recipient pop differ then gene ow changes frq in recipient makes diff pops more similar and usually reduces divergence migration increases pop size and reduces effects of genetic drift can be a stronger force than mutation 212 What is the equation for HardyWeinberg equilibrium What does it predict p2 2pq q2 1 AAAaaa1 if the conditions are met the pop is in genetic equilibrium e the frq of alleles will not change from one generation to the next f Alleles will remain in this proportion in every generation that follows if all conditions continue to be met explains what happens to allele and genotype frq as alleles are passed from generation to the next in the absence of evolutionary forces if the frq of alleles do not change over time then the frq remain in these proportions after one generation of random mating therefore the pop is in hardy Weinberg equilibrium and we can predict genotype frq from allele frq Zygotes form by random combinations of alleles in proportion to the abundance of the alleles in the population max heterozygosity pq 5 213 What assumptions are made for HardyWeinberg equilibrium Are these assumptions realistic If not what is the consequence for t to HW proportions Population is in nitely large smaller pops have greater chance of genetic drift chance deviations from expected ratios that cause allele frq to change unrealistic since no population is in nite but very large pops behave similarly random mating mating btwn genotypes is proportional to the frq of the genotypes in the pop applies to any locus for which mating occurs randomly under study even if mating is non random for other loci few organisms mate randomly for all traits but this works bc diff loci assort independently due to recombination no mutation gene pool must be closed to additionsubtraction of new alleles mutation always adds to variation but can be accommodated with in nite allele modeling no migration can addsubtract variation with immigration or emigration no natural selection selection can subtract alleles or increase frq of allele APPLY ONLY TO THE LOCUS WE ARE STUDYING EVOLUTIONARY PROCESSES MAY BE ACTING ON OTHER TRAITS AND IT WILL STILL BE IN EQUILIBRIUM 214 How might assortative mating sex ratio inbreeding variable fecundity and age structure in uence the effects of genetic drift Why are these factors important for maintenance of genetic variation mating when you prefer one phenotype to another causes genetic drift inbreeding reduces variation 0 age structure the longer you live the more likely you are to reproduce fecundity reproduction rate 215 What is Wright s Fst How is it useful Wrights xation index for variation in natural pops identi es genetic differentiation and comparison of overall effect of population substructure measures reduction in heterozygosity expected with non random mating at any level of population hierarchy relative to another 0 when your favored to be heterozygote that means that both alleles have to present the same amnt in the pop 0 0 means there is no differentiation 1 means pops are xed for diff alleles Fst Htotal HsubpopHtotal 216 How do genetic drift and mutation balance What is the expected relationship between effective population size and heterozygosity if mutation is constant in nite alleles model each mutation that occurs in a gene is assumed to generate a novel allele assumes that random genetic drift occurs by sampling so there is a steady state 0 of alleles changes slightly each generation but tends not to stray too far from equil value inverse relationship btwn heterozygosity of the locus frq of heterozygotes in the pop and pop sizemutation rate at which pop loses heterozygosity from drift is inverse to its size 0 number of new mutations is directly proportional to population size 217 How are tness W and the selection coef cient 5 related Darwinian tness w is relative reproductive stability of a genotype 0 selection coef cient s1W 0 218 lf WAA and Waa lt 10 and WAa 10 what can you conclude The heterozygote has the highest tness and selects against the homozygous alleles 219 Describe the balance between selection and mutation What can you conclude about the frequency of lethal alleles and about the balance from the equation q xus when an allele becomes rare changes in frq due to natural selection are small when 51 and the lethal allele are selected against only mutation affects frq lethal alleles get reintroduced mutation occurs at the same time and makes new rare alleles balance makes evolution 2110 What is Haldane39s rule 0 if you are two different species your child will be sterile Haldane39s rule sterility and inviability occurs more often in the heterogametic sex eg because deleterious alleles are exposed on the Y chromosome Hybrid breakdown inviability occurs some generations later CHAPTER 23 231 Explain the concept of homology What types of homology exist for DNA sequence homology similar traits bc of similar ancestor refers to the structure behavior or other character of two taxa that is derived from the same or equivalent feature of a common ancestor positional homology vs character homology sequence alignment use algorithms to maximize number of possible matching nucleotides or AA and minimize the number of indels gaps don39t know if insertion or deletion divergence over generations makes sequences different JukesCantor model of nucleotide substitution assume that each nucleotide is likely to change into another nucleotide multiple substitutions at a single site can lead to underestimation of the number of substitutions that had occur Pat 14 34e394 t or rate of substitution Pprobabiity that it will still be a C at time t substitutionssite K34n143p pfraction of nucleotides that a simple count reveals to be different rate of nucleotide substitution btwn sequences since they last share a common ancestor Rate r K2T homologous proteins proteins in diff species that share a common ancestor 232 How are generation time and metabolic rates correlated with rates of substitution substitution rates relate to generation time metabolic rate correlates with body size and generation time rodents are small with high metabolic rate have short generation and higher substitution compared to apes 233 What is the difference between mutation and substitution mutation changes in nucleotide sequences that occur bc of mistakes in DNA replication or repair substitution mutations that have passed thru the lter of selection on at least some level synonymous substitution are re ective of mutation rate nonsynomous substitution are NOT sequences with the most functional importance to an organism like protein binding sites in a promoter or nucleotides that result in AA substitution evolve at the slowest rate and have least substitution 234 Which of the following are expected to have the lowest and highest rates of substitution intron exon 539promoter 339 anking region pseudogene pseudogene noncoding sequences that no longer produce functional gene products bc they have accumulated inactivating mutations they don39t get eliminated in natural selection since they have no harmful effects on tness 0 highest overall rates of sub occur in nonfunctional pseudogenes and other non coding are like microsatellites subsitutions in 339 anking region often have no effect and are tolerated by natural selection 339 regions gt introns gt exons 539 regions lt 339 regions 539 important for promoters and other regulatory elements Leader and trailer regions lt 539 regions leadertrailer not transcribedtranslated but important for mRNA processing and translation 0 lowest nonsynonymous coding sequence leader sequence trailer 539 anking 339 anking synonymous coding sequence pseudogenes highest 235 What is the difference between a taxon and a category taxon monophyletic group of organisms recognizable by a set of shared characters distinct from other such groups 0 category hierarchal level to which taxa are assigned in a classi cation kingdom phylum 236 Contrast monophyly and polyphyly monophly descent from a common ancestor every true taxon is monophyletic polyphyly descent from more than one ancestral lineage 237 Distinguish between homology and homoplasy homology shared similarity derived from common ancestry homoplasy similarity derived from convergence parallelism or reversal 238 What is the difference between convergence and parallelism convergence Independent acquisition of a similar character by two or more taxa whose common ancestor lacked that character generally refers to more distantly related lineages Ancestral lineages possessed different character states parallelism Independent acquisition of the same or similar characters by more closely related lineages ie similar to convergence Ancestral lineages possessed the same character state reversal Reappearance of an ancestral character as the result of the loss of a derived character 239 Why does searching for the quotbestquot phylogenetic tree present a potential problem when more than ten taxa are involved 0 you can make a tree with the shortest genetic distances shortest parsimonious tree that minimizes steps to evolved shared character Bayesian method uses statistical methods 2310 Which of the following are useful types of characters for the cladist synapomorphy symplesiomorphy autapomorphy Why are the some of these types of characters not useful synapomorphy shared derived homologous characters inferred to have been present in the nearest common ancestor of 2 or more taxa but not in earlier ancestors outside this group informative symplesiomorphy shared ancestral homologous characters inferred to have been present in the nearest common ancestor of two or more taxa and in earlier ancestors outside this group non informative autapomorphy unique derived character present in only one of 2 sister groups non informative 2311 Gene trees and species trees do not always match Why might this occur gene trees tree based on divergence observed within a single homologous gene may represent history of a gene but not necessarily that of the species in which it is found species trees come from analysis of multiple genes One or more perhaps many trees may best describe the data Equally parsimoniouslikely trees may not be consistent character support can be assed in different ways eg bootstrap resampling to determine con dence levels attached to branching patterns sequence polymorphisms often predate speciation events it is possible that trees made from a single gene do not always re ect the relationships btwn species Gene trees and species trees a gene tree does not necessarily re ect the species tree Common ancestor or two gene lineages can predate species split ancestral polymorphism Trees derived from different genes or linkage groups may con ict andor show very different patterns hybridization and gene ow btwn species can mess up the species tree recombination complicates phylogenetic inference by erasing info and attening tree
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