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18 Oct 2018

Cladistic methods of phylogenetic inference are based on which of the following?

synapomorphies (shared derived characters) that are shared by taxa that descend from a common ancestor

similarities in characters between taxa that suggest common ancestry

clustering algorithms that group taxa based on their degree of similarity

uniquely derived characters show the most recently evolved taxa

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Casey DurganLv2

19 Oct 2018

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I'm having trouble simplifying this 6 question paper. Pleaserewrite this then post in comments. thanks! just 1-5 senstences perquestion please. please!

1.Among systems for study of macro evolutionary change (e.g.,major change in anatomy, moving from water to land or vice versa,acquisition of flight, etc.), the cetaceans have become the 'posterchild'. Explain why cetaceans are a better system in which to studyevolutionary transitions than each of the following vertebrategroups:

Cetaceans have primitive taxa thatrecords sequences of change at three critical phases:

-Initial aquatic specialization

-Evolution of filter feeding withbaleen

-Derivation of echolaction.

Divergence times in cetaceans areconducive to detection of positive selection and inactive loci.Evolutionary splits in cetacea are deep enough to provide adequatechange for statistically robust analyses of molecular evolution butare not so deep that substitution patterns are saturated andrecognition of pseudogenes is hindered.

They have an impressive fossilrecord.

Whole genomes for both cetaceans andterrestrial cetartiodactyles can illuminate transitions andcandidate loci associated with aquatic features and degenerativeevolution have been characterized by several research groups.

turtles: highly derived taxa but areancient clades and more difficult to study from a molecularperspective.

manatees: The extant diversity ofaquatic manatees is limited.

bats: have a poor fossil record.

pterosaurs (ancient winged reptiles):Lack genetic Data.

2. What is myoglobin?

A myoglobin is a small 153-amino acidprotein that is the primary carrier and storage center of oxygen inmuscle.

Explain why increased diving ability should be correlated withspecific types of replacement mutations of the gene encoding theprotein myoglobin.

Amino acid replacement that increasedcharge occurred overwhelmingly in lineages of extreme divers withsemiaquatic or aquatic lifestyles. The greatest increase in chargeoccurred independently in cetaceans, pinnipeds, and the bever, allof which share at least two convergent amino acid replacementswithin each lineage.

What specific kinds of amino acid replacements are favored bypositive selection when increased diving ability is favored?

High net surface charge enableselectrostatic repulsion that might reduce deleterious selfassociation of myoglobin molecules; protein folding stability couldhave a similar impact by limiting the percentage of misfoldedmolecules at high expression levels.

Explain how the maximum dive capability of an extinct whalespecies can be estimated.

By combining body mass with inferredconcentration of myoglobin based on net surface charge they wereable to estimate the maximum dive times of extinct cetaceans.

3. What is the general function of the protein prestin?

Is involved in conferringelectromotility to the outer hair cells of the cochlea, enablingsensitive to sound by driving the cochlear amplifier.

Explain why a phylogenetic treereconstructed using the characters of prestin amino acid sequencesshowed at first that the whales form a subgroup within thebats!

A phylogenetic analysis of prestinamino acid sequences supported a tree in which some odontocetecetaceans were nested within bats with high support, despitephylogenetic analsysts of nucleotides sequences favoring a moredistant relations.

This pattern was driven by convergentamino acid changes in that were shared between toothed whales andecholocating bats.

4. Relative to terrestrial mammals, what changes occurred togive deep diving cetaceans 'rod monochromacy'?

Rod monochromancy is unique amongmammals due to extreme adaptation to low light levels.

What is the advantage of rod monochromacy?

Allows you to see in low lightlevels.

Why does it make sense that rhodopsins of cetaceans are shiftedfrom red (low energy) to blue (high energy) sensitivity?

The mechanisms underlying the spectraltuning of two of these blue-shifted pigments have recently beenelucidated and depend on three amino acid substitutions(⁸³Asn, ²⁹²Ser, and ²⁹⁹Ser) indolphin rhodopsin, but only one amino acid substitution(³⁰⁸Ser) in the dolphin long-wavelength-sensitivepigment. The objective of this study was to investigate themolecular basis for changes in the spectral sensitivity of rodvisual pigments from seven distantly related marine mammals. Theresults show a relationship between blue-shifted rhodopsins([lambda]_max [less-than-or-equal] 490 nm), deep-divingforaging behavior, and the substitutions ⁸³Asn and²⁹²Ser. Species that forage primarily near the surfacein coastal habitats have a rhodopsin with a [lambda]_maxsimilar to that of terrestrial mammals (500 nm) and possess thesubstitutions ⁸³Asp and ²⁹²Ala, identical torhodopsins from terrestrial mammals.

5. What is the function of the protein ameloblastin?

Is an enamel matrix protein. Theprotein that encodes AMBN gene. Allows growth activity andstructure of the tooth enamel.

Characterize the specific nucleotide sequence and functionaldifferences in ameloblastin genes between baleen whales versusother mammals.

Baleen whale a toothed whale and moredistantly related mammals with single base pair frameshiftinsertion in the baleen whale AMBN pseudogene. Clear cut molecularsignature of a shared signature of shared aquatic ancestry forhippos and whales is currently lacking. Loci related to underwatercision, deep diving and lung surfactant do not show evidence ofmolecular adapation in the common ancestor of these taxa.

6. What are the two main general categories of convergentevolution described in cetaceans and other vertebrates?

Auditory genes. Bats and odontecetshave many similar capabilities with regards to high frequency soundperception.

Selection has driven the independentloss of both OPNI1SQ and OPN1LW in deep diving cetaceans tooptimize visual acuity at depth and at night.

Loss of functional TAS1R genes alsooccurred independently in Otariidae (sea lions) and many carnivorsmammals convergently lack the fuctional sugar taste perception geneTAS1R2

Based on these studies why is it important to use neutral ornearly neutral characters in phylogenetic analyses wheneverpossible?

Comparison amobg a broader taxonomicsample of geneoms can reveal learge suits of genes that haveundergone convergent recruitment and subsittuions among multipleclades of aquatic tetrapods.

orangebear508

What problems does horizontal gene transfer cause for evolutionary biologists?

It can make reconstruction of phylogenetic trees difficult because it can obscure phylogenetic relationships.

It can cause physiological problems in some organisms, making it hard to study them.

It can make breeding between different individuals of the same species difficult.

Because it is transfer of genes between the same species, it can make individuals look more similar than they actually are.

All of the above

Which statement best describes the maximum parsimony approach to the reconstruction of phylogenetic trees?

A pathway is constructed that requires the minimum number of changes to arrive at the modern species from a common ancestor.

The tree is based on relationships that show the maximum probability of obtaining a set of characteristics.

Relationships on the tree are based on overall similarity between species.

Branches on the tree are constructed from the predicted date of speciation, measured in millions of years.

The best phylogeny is selected by comparing models representing random mutation and adaptive radiation.

ambermouse112

1. What is the correct sequence of steps inthe scientific method?

I. Make observations and ask a question

II. Analyze the data

III. Develop a hypothesis

IV. Share the results with otherscientists

V. Design and perform an experiment to testthe hypothesis

a) I>II > III > IV > V

b) III > I > V > II > IV

c) V> IV > III > II > I

d) I> III > V >II > IV

e) V > II > I > III > IV

2. You have formulated a hypothesis: ï¿½Applescontain more vitamin C than oranges.ï¿½

To test your hypothesis you measure vitamin Clevels in 20 oranges and 20 apples from trees that were grown inthe same orchard under the same environmental conditions(temperature, rain, sunlight). This experiment was conducted twice.The control in the experiment is

a) type of soil, temperature, amount of rainand sunlight in the orchard

b) vitamin C levels

c) oranges

d) apples

e) a large sample size and repeatedexperiment

***Use the following information to answerquestions 3, 4, 5 & 6 below***:

A group of medical researchers investigatedthe effects of Drug X on lowering cholesterol levels in a group ofmen between the ages of 50 and 70 years old. The researchers didthe following experiment and obtained the indicatedresults: One group of 150 men took a tablet containingDrug X for 3 weeks ï¿½ 95 of these men decreased their cholesterollevels by at least 10% (three men from this group dropped out ofthe study). Another group of 150 men wasgiven a tablet with no added Drug X for 3 weeks ï¿½ 10 of these mendecreased their cholesterol levels by at least 10% (two men fromthis group dropped out of the study).

3. Which of the following is the besthypothesis for this experiment?

a) Will drug X lower cholesterol levels in menbetween the age of 50 and 70 years?

b) Drug X will lower cholesterol levels inmen.

c) Since high cholesterol levels significantlyincreases several health risks for men, drug X is most likelybeneficial.

d) Men between the age of 50 and 70 years willhave reduced cholesterol levels if they take drug X over a 3 weekperiod.

e) There is no significant difference incholesterol levels between men that take drug X and those thatdonï¿½t take it.

4. Which of the following was the controlgroup in this experiment?

a) the amount of Drug X contained in thetablet

b) the number of participants in each group atthe end of the experiment

c) the group of participants that receivedtablets containing Drug X

d) the group of participants that receivedtablets that did not contain Drug X

e) the number of participants in each group atthe beginning of the experiment

5. Which of the following is a dependentvariable in this experiment?

a) the amount of Drug X contained in thetablet

b) participants that received tabletscontaining Drug X

c) the average age of the participants

d) number of participants in each group at thebeginning of the experiment

e) cholesterol

6. Which of the following is an independentvariable in this experiment?

a) the amount of Drug X contained in thetablet

b) participants that received tabletscontaining Drug X

c) the average age of the participants

d) number of participants in each group at thebeginning of the experiment

e) cholesterol

7. A chemotherapy drug affects theenzyme DNA polymerase. In which part of the cell cycle does itinhibit cell division?

a) Metaphase

b) S phase

c) G1

d) Cytokinesis

e) Prophase

8. A researcher planted seeds from four typesof tomatoes (Roma, Cherry, Big Boy and Early Girl) in a greenhouseto determine which type of tomato produce the largest number oftomatoes per plant. The plants were grown for 70 days under thesame temperature and light conditions. The average results for 20plants of each type are shown below. Choose thedata set that demonstrates that Cherry tomatoes produce the largestnumber of tomatoes per plant.

a) Roma: 20 tomatoes, Cherry: 18 tomatoes, BigBoy: 30 tomatoes, Early Girl: 10 tomatoes

b) Roma: 1.8 lbs, Cherry: 2.8 lbs, Big Boy:2.7 lbs, Early Girl: 1.0 lbs

c) Roma: 3 cm, Cherry: 1 cm, Big Boy: 10 cm,Early Girl: 7 cm

d) Roma: 2 cm, Cherry: 10 cm, Big Boy: 7 cm,Early Girl: 6 cm

e) Roma: 23 tomatoes, Cherry: 28 tomatoes, BigBoy: 10 tomatoes, Early Girl: 27 tomatoes

9. The majority of climate scientists believethat the current change in climate is caused predominantly by________.

a) an enhancement of the greenhouse effect

b) a decreased reliance on fossil fuels forenergy

c) a thinning of the ozone layer

d) a melting of the polar icecaps

e) an increase in solar radiation

10. Based on the following phylogenetic tree,which of the following conclusions are *NOT*correct? Each letter represents a hypotheticalspecies.

a) A and E share a common ancestor

b) B is one of Aï¿½s ancestors

c) E and D are more closely related to eachother than to C

d) C is more closely related to E than toB

e) A and B are closely related

11. You are taking a cruise from California toHawaii. About halfway there the ship begins to sink. You are ableto board a lifeboat, but now you are floating in the ocean waitingto be rescued. After several days you are so thirsty that you bendover the side of the boat and drink lots of salty seawater. Whathappens to your body?

a) You throw up because sea salt is toxic tohumans.

b) You get thirstier because of osmosis.

c) Salt diffuses into your cells, waterfollows, your cells start to expand and you feel bloated.

d) Since sea water consist of 96.5% freshwater (and only 3.5% salt) you will feel much better.

e) You get dehydrated because water is unableto cross the semi-permeable membranes of your cells.

12. You are spraying your garden with apesticide and you accidentally swallow a smallamount. You read on the package that this pesticideinhibits ATP synthase. Should you be worried?

a) ATP synthase is part of the light dependentreaction in photosynthesis; this pesticide will therefore notaffect humans. So donï¿½t worry!

b) ATP synthase is an enzyme involved in thecitric acid cycle so all animals, humans included, will beaffected. Call the doctor.

c) ATP synthase found in the pesticide is avery toxic compound. Call the doctor.

d) ATP synthase is involved in bothphotosynthesis and cellular respiration. Call the doctor.

e) ATP synthase inhibitors will not affecthumans, but there might be other toxic ingredients in thepesticide, so it is best to call the doctor to be on the safeside.

13. In the following chemical reaction, whatis carbon dioxide (CO2)?

12 H20 + 6CO2 -> 1glucose molecule + 6 O2

a) substrate

b) product

c) enzyme

d) activation factor

e) independent variable

14. Which of the following is NOT a feature ofDNA?

a) Adenine (A) forms a base pair with thymine(T)

b) Complimentary strands are anti-parallel,running in opposite directions

c) Complimentary strands are held together byhydrogen bonds between phosphate groups

d) Nucleotides within a single strand areconnected by covalent bonds

e) All of the above are features of DNA

15. A man who carries a harmful sex-linkedgene on his X chromosome, will pass the gene on to

a) All of his daughters

b) Half of his daughters

c) All of his sons

d) Half of his sons

e) All of his children

16. A double-stranded DNA molecule that has22% guanine will have

a) 28% thymine

b) 22% cytosine

c) 44% adenine

d) 26% uracil

e) Both A and B are correct

17. Which of the following variations could besubject to natural selection?

a) A dog with short legs due to malnutritionis able to crawl into holes better than his litter mates

b) A tree is not infested by a ground-dwellingbeetle when the homeowner cuts the lower branches

c) A hyena is born with a spotted fur patternthat allows it to hide in the grass better than his littermates

d) A pigeon learns than when its keeper comesnear it will be fed

e) All of these variations may be acted on bynatural selection

18. The ability of fireflies and angler fishto produce light is an example of convergent evolution. What canyou conclude about these two animals based on this information?

a) They share a recent common ancestor

b) They are both adapted to environments lowin light

c) The ability to produce light is an ancienttrait

d) They are found in the same location

e) All of the above

19. You observe the following outside yourwindow: A grasshopper is munching away on a leaf when ahawk swoops down and eats the grasshopper. What is the grasshopperin this situation?

a) secondary consumer

b) prey

c) herbivore

d) predator

e) both b, c and d

20. Which of the following statements is *NOT*true?

a) The cells resulting from meiosis arediploid and the cells resulting from mitosis are haploid.

b) Meiosis and meiosis both starts with onecell, but meiosis ends with four and mitosis withtwo.

c) Mitosis produces new cells for growth andrepair, meiosis produces gametes.

d) Mitosis goes through cytokinesis once,meiosis goes through cytokinesis twice.

e) Cross over happens in meiosis, but not inmitosis.

21. Neon, Ne, has an atomic number of 10 andan atomic mass of approximately 20. How many neutronsdoes neon have?

a) 5

b) 20

c) 10

d) 30

e) 15

22. An ionic bond is one in which

a) Outer shell electrons are sharedby two atoms in order to fill the electron shells of both atoms

b) Outer shell electrons of oneatom are transferred to the inner electron shell of anotheratom

c) Electrons are removed from oneatom and transferred to another atom so that the two atoms becomeequally charged

d) Electrons are removed from theouter shell of one atom and transferred to the outer shell ofanother atom in order to completely fill the outer shells of eachatom

e) Electrons are removed from theouter shell of each atom in order to give each atom a neutralnumber of electrons

23. Which characteristic of water results theconstant body temperature of mammals?

a) cohesion

b) density at differenttemperatures

c) polarity

d) heat absorption

e) solvency

24. Which of the following is thestrongest base?

a) black coffee

b) bakingsoda

c) stomachacid

d) water

e) ammonia

25. An ideal antibiotic damages only bacterialcells but not human cells. Which of the followingcellular structures would be a good target for antibiotics?

a) plasmamembrane

b) cytoskeleton

c) cell wall

d) nucleus

e) nucleolus

26. An erythrocyte is place in a beaker of seawater. The cell shrivels andshrinks. Why?

a) Sea water is hypertonic to the fluid insidethe cells.

b) Sea water is isotonic to the fluid insidethe cells

c) The fluid inside the cells is hypertonic tothe sea water

d) Sea water is hypertonic to the fluidoutside the cells

e) Sea water is hypotonic to the fluid insidethe cells

27. Most of the ATP of aerobic respiration isproduced in the

a)chloroplast

b)mitochondria

c)ribosome

d) plasmamembrane

e)cytoplasm

28. Which of the following does notnegatively affect the rate of an enzyme reaction?

a) Reduction in temperature

b) Reduction in the amount of a competitiveinhibitor

c) Reduction in the amount of substrate

d) Reduction in the amount of enzyme

e) Reduction in the pH of the solution

29. If a germ cell has 30chromosomes, how many chromosomes will be found in the gametes?

a) 60

b) 30

c) 10

d) 15

e) 20

30. In what stage are the sisterc33.hromatids lined up at the center of the spindle?

a) Interphase

b) Telophase

c) Prophase

d) Metaphase

e) Anaphase

31. Which of the following could betrue for a child with Downï¿½s Syndrome?

a) Non-disjunction occurred during theproduction of the egg

b) The sperm could have had two copies ofchromosome 21

c) One gamete had two copies of chromosome 21and the other had one copy

d) None of a) through c) could betrue

e) All of a) through c) could be true

32. Which of the following statements is notconsistent with Darwinï¿½s theory of evolution?

a) Fossils indicate the structures of extinctorganisms

b) The Earth is approximately 100,000 yearsold

c) Organisms on earth have survived or dieddepending upon the environment in which they were born.

d) All living species are related to commonancestors

e) Individuals do not evolve

33. A trait that influences the mating ofindividuals having that trait is called

a) Genetic drift

b) Gene flow

c) Artificial selection

d) Natural selection

e) Sexual selection

34. The formation of new biological lineagesis called

a) Mutation

b) Natural selection

c) Speciation

d) Genetic drift

e) Sexual selection

35. Which of the following organisms iscapable of both using carbon dioxide to produce starch and usingoxygen to produce ATP?

a) dog

b) human

c) earthworm

d) houseplant

e) none of the above

36. Which density-dependent factor controlsthe size of a population?

a) wind velocity

b) light intensity

c) nutrient supply

d) rainfall

e) all of the above

37. According to Darwin, natural selectionoccurs when the environmental conditions cause specific ___________found in populations to become ______________.

a) selections, exponential growth

b) variations, adaptations

c) weakest members, strongest members

d) non-competitors, competitors

e) similarities, differences

38. Which of the following statements is trueabout a bond formed between two carbon atoms?

a) the bond requires the sharing ofprotons

b) the bond requires the sharing ofelectrons

c) the bond requires the sharing ofneutrons

d) the bond contains ADP

e) the bond cannot be broken

39. Which of the following is abiotic?

a) Roots

b) Bacteria

c) Seawater

d) Slime mold

e) Algae

40. Which density-dependent factor controlsthe size of a population?

a) wind velocity

b) light intensity

c) nutrient supply

d) rainfall

e) all of the above

***********************************************************************************************************

MATCHING SECTION #1 ï¿½ 1 point each

**Do not enter your answers here.** Type inthe letter you select from the Definition/Association column as thebest answer on the Answer Sheet for the number represented belowfor the Term or Concept.

Term or Concept

1. Water molecule

2. Carbon

3. Homeostasis

4. Ionic Bonding

5. Covalent Bonding

6. Carbohydrate

7. Enzyme

8. Acid

9. Base

10. Lipid

Definition/Association

A. energy source

B. two atoms sharing electrons

C. electron donated/received

D. hydrophobic

E. element found in all living organisms

F. catalyst

G. OH-> H+

H. polar

I. characteristic of all living organisms

J. H+ > OH-

MATCHING SECTION #2 ï¿½ 1 point each

**Do not enter your answers here.** Type inthe letter you select from the Definition/Association column as thebest answer on the Answer Sheet for the number represented belowfor the Term or Concept.

Term or Concept

1. Ribosome

2. Mitochondria

3. Nucleus

4. Golgi apparatus

5. Smooth Endoplasmatic Reticulum

6. Membrane

7. Cell Wall

8. Lysosome

9. Chloroplast

10. Cilia

Definition or Association

A. packaging and transport

B. digestion

C. genetic material storage

D. protein assembly

E. structural support

F. lipid production

G. glucose breakdown

H. movement

I. oxygen production

J. contain transport proteins andreceptors

sangriaotter215

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