Wednesday, December 7, 2011

Other questions that the class had trouble with, and their explanations

I wanted to go through a bunch of the final exam questions to broadly address topics I wanted you to understand. Below are questions that less than 50% of the class got correct. If you have any questions, comments or concerns, please post a comment.

7. The remarkably high frequency of sexual reproduction in most taxonomic groups is paradoxical given what facts?
a. In sexual populations, females contribute to population growth
b. In sexual populations, individuals contribute only half of their genetic material to their offspring
c. In asexual populations, recombination is more frequent
d. A and B are correct
e. All of the above

The correct answer is D, this is the two-fold cost of sex. However, I gave full credit for all answers but C and E. Unfortunately, I think it would have been clearer if I had put "In sexual populations, ONLY females contribute to population growth".

8.  You find a species of bird with a ridiculously long tail in males that is clearly maladaptive for the organism's niche. You can conclude conclusively that:
a. The tail is a honest indicator of the males genetic quality
b. The tail catches the attention of the females because of sensory bias
c. Females prefer the costly trait because it means that their sons will be sexy
d. All of the above
e. None of the above

The correct answer is E. The key word here is "conclusively". In fact, A, B and C all could be true, but none of them are conclusively true. All three are mechanisms for the evolution of secondary sexual ornaments that may be maladaptive from a viability perspective.

9. Which of the following can result in a decrease in mean fitness in the population?
a. Stabilizing selection
b. Disruptive selection
c. Frequency-dependent selection
d. Balancing selection
e. Adaptive evolution

The correct answer is C, as in the Hawk-Dove game. I sense that most of you chose B because it "sounds bad". Don't fall into that trap, rely on what you know. Disruptive selection increases mean fitness, it just means that the extremes of the population survive the best.

11. The figure above is taken from Hanifin et al. (2009) with regard to prey toxicity of Rough-skinned newts and garter snakes resistance to those newts. Which of the following can you conclude from this figure?
a. Garter snakes are so resistant to TTX that there are rarely any fitness consequences to consuming them.
b. TTX is so high in most newts that the coevolutionary arms race with garter snakes could not be an explanation.
c. The coevolutionary arms race between newts and garter snakes generally ends with garter snakes winning.
d. Stabilizing selection favors an optimum ratio between TTX toxicity and resistance to be about 50%
e. none of the above

The correct answer is C. Not much to say about this one other than it was covered in the worksheet you did in-class, and reading the paper. Answer D was popular, but is gibberish. Stabilizing selection cannot select for a ratio between two different species' phenotypes. Both would have fluctuating or directional selection being applied on them during coevolutionary arms races, not selection to stay the same.

21. A Darwinian demon cannot exist because of the existence of:
a. Semelparity
b. Trade-offs
c. Senescence
d. Unstable equilibria
e. B and D are correct

B is correct. I suspect many of you chose E because of test-taking beliefs rather than because you thought unstable equilibria limit Darwinian Demons. Fundamentally, answer D doesn't actually mean anything in this context.

25. This modeling approach is especially useful for studying frequency-dependent selection
a. Game theory
b. Optimality theory
c. Quantitative genetic theory
d. Neutral theory
e. None of the above

The correct answer is A. Seemingly, every question that involved frequency-dependent selection was a struggle. Suggestions on how I could have made this concept clearer would be appreciated.

41. Helacyton gartleri, or HeLa cells, is a species under all of the following species concepts EXCEPT:
a. Biological species concept
b. Morphological species concept
c. Evolutionary species concept
d. Phylogenetic species concept
e. None of the above

The correct answer was D. Many chose A. However, unless you believe a human will mate with HeLa cells and produce viable offspring, you are wrong. B is wrong because HeLa cells on a petri dish look morphologically different than Homo sapiens. C is wrong because A is wrong, these species are distinct evolutionary species and will never interbreed again. D is the only one in which HeLa cells fail to be a distinct species. While HeLa cells are monophyletic, naming them their own species would make humans paraphyletic.

42. Which of the following is an ultimate explanation for why organisms senesce and die?
a. Antagonistic pleiotropy
b. Shortening telomeres
c. Oxidative stress
d. The failure of cellular repair mechanisms
e. All of the above

Answers B, C and D are proximate explanations. Only A provides an evolutionary explanation for aging.

44. SAT analogy time! Humans : Sexual reproduction
a. Viruses : coinfection
b. Viruses : infection
c. Viruses : Mutation
d. Viruses : Red Queen
e. Viruses : Virulence

I was going for A, but I realized that B is also potentially a correct answer and have given full credit to that question. I was hoping to draw a parallel between both being processes that allow for genetic recombination, but both also are processes that replicate the species.

51. Life history traits (which are usually complex, polygenic traits with many inputs) are characterized by:
a. Low heritability, but high genetic variance.
b. Low genetic variance due to constant directional selection
c. High heritability and low genetic variance
d. High phenotypic variance and high genetic variance
e. Low phenotypic plasticity and high heritability

It turns out that both A and D are correct, and have been given full credit.  B is wrong because life history traits actually have abundant genetic variance. C is impossible given the equation for heritability. E is false on both counts.

57. In general, if genetic drift were the only force acting on populations (there was no natural selection), we would expect to observe:
a. More morphological diversity than we observe today
b. Less morphological diversity than we observe today
c. About the same amount of morphological diversity that we observe today
d. Genetic drift is not strong enough to result in evolutionary change.

A is the correct answer. Many chose B. One student commented on their exam that we have not covered this in class. However, we did cover the example of human cranial capacity, and showed that even this extreme case of rapid evolution was easily explained by genetic drift. In problem set III we showed that genetic drift would change human body size far more than it has. Stabilizing selection and stasis are the dominant patterns we observe in nature, genetic drift would result in far more variability and variance than we observe today.

62. Consider a population with two alleles at a locus and an effective population size of 100. Assuming neutrality, what is the probability that the population will become fixed for only one allele at that locus?
a. 0
b. 1/100
c. 1/200
d. 1
e. It's stochastic so we can't know

Only 11% of you got the right answer. The correct answer is D. This looks similar to a question on the last exam, but you need to read the questions carefully. I don't mean to be asking trick questions here, just testing your understanding. The question on the last exam was "what is the probability of a new mutation drifting to fixation?", which would be in this case, 1/200. However, this question asks "What is the probability that ANY allele drifts to fixation?", which is 1. It's like asking "What is the probability that you become president?" vs. "What is the probability that SOMEONE becomes president?".

    What went wrong?


    One of the questions on the final exam I was a little dismayed to see that only 36% of the class got correct.

    Here is the question:
    49. Humans probably evolved directly from which of the following:
    a. Chimpanzees
    b. Gorillas
    c. Tiktaalik
    d. An ancient unicellular eukaryote
    e. Darwinius masillae (an early primate fossil)

    Across the board, even among the top students in the class, folks chose A. Why? What was confusing about this question? Humans did not evolve directly from chimpanzees, chimpanzees are an existing species. We share a common ancestor with chimpanzees. We did however, necessarily evolve from an ancient unicellular eukaryote (i.e. an ancient unicellular eukaryote is everybody's great ^ 500,000,000 grandparent, no chimpanzee that has ever existed is any sort of grandparent of any human being). As you leave this class, make sure that you understand the common fallacies that are made about evolution. Make sure you directly confront your misconceptions. We did not evolve from any species that exists today!! A less important concept this question was trying to address was that almost all fossils we find are probably not direct ancestors, but side branches close to direct ancestors.

    Tuesday, November 29, 2011

    Charles Darwin

    "Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science."

    -Charles Darwin

    Charles Darwin is thought to be the father of evolution. His most famous book is the Origin of Species by Means of Natural Selection published in 1859 and his most well-known theory is the idea of natural selection or survival of the fittest (Nale, 2010). Shrewsbury, UK is the birthplace of this naturalist. He was born into an educated family, with a father that was a doctor, and was one of three children. His older brother studied literature and the arts (Darwin, 2008). However, Charles did not always intend to become the scientist that we know him as. He was originally a student studying medicine, but he was not cut out to follow in his father’s footsteps. He then transferred to Cambridge to become a minister. While at Cambridge, his interest in zoology and geography lead him to relationships with professors in both the biology and geology department. After a trip to Wales with the geology professor, he went to survey South America on the Beagle (Landry, 2011). This is when Darwin started to become the scientist that we know him to be.

    The idea of Natural Selection had been around from before Darwin was born, but it was Darwin’s use of real life observations and data that allowed this concept to become accepted (Landry, 2011). Darwin contributed to the scientific world with many of this other works, including The Descent of Man. Published in 1871, this novel compares lower and more basic species with the construction and behaviors of humans (Landry, 2011). Each chapter moves to a higher level of understanding, starting with similar body construction, and ending with sexual characteristics and behaviors (Darwin, 2008). One thing most people don’t know about is his contribution to the marine sciences. Darwin was first person to document the origin of corals. While sailing on the Beagle, he made many evolutionary discovers about organisms in general, but he also research small coral polyps with geologists aboard the ship (Rainbow, 2011). Darwin also showed a special interest in barnacle species. He studied their adaptive reproductive abilities and the differences between multiple barnacle species. These observations along with many others gave more evidence to his works, specifically The Origin of Species (Rainbow, 2011).

    Some of Darwin’s other works include Coral Reefs, Effects of Cross and Self Fertilization on the Vegetable Kingdom, Geological Observations on South America, The Autobiography of Charles Darwin, The different Forms of Flowers on Plants of the Same Species, The Expression of the Emotion in Man and Animals, The Formation of Vegetable Mould Through the Action of Worms, The Voyage of the Beagle, and Volcanic Islands (Darwin, 2008). While alive, he received the Royal Medal, the Wallaston Medal, and the Copley Medal (Landry, 2011). Charles Darwin passed away April 19th 1882. Even though Darwin had died, he continued to receive many awards for his work and four of his seven children became respected scientists (Darwin, 2008).

    "The fact of evolution is the backbone of biology, and biology is thus in the peculiar position of being a science founded on an improved theory, is it then a science or faith?"

    - Charles Darwin

    Works Cited

    2008. Charles Darwin Biography. Received at

    2008. Charles Darwin: The Descent of Man Overview. Received at

    Darwin, C. (2008). Charles Darwin Quotes. Received at

    Landry, P. (2011). Charles Darwin. Received at

    Nale, J. (2010). Biotic Competition and Progress in the Works of Charles Darwin. Southern Journal Of Philosophy, 4836-42. doi:10.1111/j.2041-6962.2010.00019.x

    Rainbow, P. S. (2011). Charles Darwin and marine biology. Marine Ecology, 32130-134. doi:10.1111/j.1439-0485.2010.00421.x

    Evolution in Schools: 2 Landmark Trials

    Note: I do not know why the background changes to white half way through my post. I've tried editing several times to correct the problem, but blogger continues to publish the wonky colors. If you highlight the text you will be able to read it. Anyone who can tell me how to fix this problem, please leave a comment on the post.


    The saga of evolution and education should not be news to anyone. Individuals and groups opposed to evolution being taught in schools raise the battle cry at the drop of a hat, and their persistence is bordering on sociopathiological. Some simply want evolution to be banned from the science curriculum, but others have decided to push for the inclusion of religion (dressed in the sheep’s clothing of “Intelligent Design”) in the science classrooms of public schools. I’d like to take some time to acquaint you with two landmark cases that made it to court trial.

    The first of these trials is the State [or Tennessee] v. John Scopes, also known as “The Monkey Trial.” William Jennings Bryan sought to banish the teaching of evolution in schools as part of his bid for presidency. At the time, teaching evolution in a public school was against the law in Tennessee, but John Scopes, a high school biology teacher, assigned readings on evolution because he believed that biology cannot be taught without evolution. He even got these readings from the state approved biology text, Hunter’s Civic Biology. Scopes, in league with George Rappalyea, agreed to stand for trial in defense of teaching evolution. The defense team was extensive, and included Herbert and Sue Hicks, John Neal, Clarence Darrow, Arthur Hays, and Dudley Malone. The prosecution team consisted of A.T. Stewart, Ben McKenzie, and William Bryan Jr. The goal of the trial was to overturn the law prohibiting the teaching of evolution in schools. The turnout for the trial was so impressive that it had to be held outdoors on the courthouse lawn. Scopes was found guilty and fined $100, which please the defense because it allowed them the opportunity to appeal to the state Supreme Court. Sadly, this case ends in a rather anti-climactic manner. The original court decision was reversed on a sentencing technicality, and then dismissed from further action. It is counted historically, as a win for the pro-evolution movement, however. This case took place in 1925. More information on this trial can be found here, and there are several books published on “The Monkey Trial.”

    Fast forward to 2004, and we’re still fighting the same battle over evolution being taught in schools. This time the battle ground is in Dover, Pennsylvania and started when the school board passed a policy requiring science teachers to read the following disclaimer before teaching evolution:

    “The Pennsylvania Academic Standards require students to learn about Darwin's Theory of Evolution and eventually to take a standardized test of which evolution is a part.

    Because Darwin's Theory is a theory, it continues to be tested as new evidence is discovered. The Theory is not a fact. Gaps in the Theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations.

    Intelligent Design is an explanation of the origin of life that differs from Darwin's view. The reference book, Of Pandas and People, is available for students who might be interested in gaining an understanding of what Intelligent Design actually involves.

    With respect to any theory, students are encouraged to keep an open mind. The school leaves the discussion of the Origins of Life to individual students and their families. As a Standards-driven district, class instruction focuses upon preparing students to achieve proficiency on Standards-based assessments.”

    Science teachers and parents alike pushed back, with teachers sending in a formal response and refusing to read the statement, and parents filing case in court for the violation of the separation of church and state. An excerpt of the response from teachers:

    “Central to the teaching act and our ethical obligation is the solemn responsibility to teach the truth. Section 235.10 (2) guides our relationships with students and provides that "The professional educator may not Knowingly and intentionally misrepresent subject matter or curriculum."


    I believe that if I as the classroom teacher read the required statement, my students will inevitably (and understandably) believe that Intelligent Design is a valid scientific theory, perhaps on par with the theory of evolution. That is not true. To refer the students to "Of Pandas and People" as if it is a scientific resource breaches my ethical obligation to provide them with scientific knowledge that is supported by recognized scientific proof or theory.”

    The full text of the response can be read here.

    In contrast with the Stokes trial, which simply sought to ban evolution from being taught, the Dover trial (formally known as Kitzmiller v. Dover) was focused on the inclusion of “Intelligent Design” (ID) in the science classroom. Jerry Coyne, in his book Why Evolution is True (2009) mentions that the Dover trial was “billed as the ‘Scopes Trial of our century’,” and the trial is nicknamed “The Panda Trial” after the name of the ID book that was being offered up as the scientific counter to evolution, Of Pandas and People.

    This trial attracted as much attention as its predecessor, and the pro-evolution group was worried, since the judge for the trial, Judge John Jones III, was appointed by G.W. Bush and a conservative Republican. However, these fears proved to be unfounded as the following verdict was read:

    “It is our view that a reasonable, objective observer would, after reviewing both the voluminous record in this case, and our narrative, reach the inescapable conclusion that ID is an interesting theological argument, but that it is not science…In summary, the [school board’s] disclaimer singles out the theory of evolution for special treatment, misrepresents its status in the scientific community, causes students to doubt its validity without scientific justification, presents students with a religious alternative masquerading as a scientific theory, directs them to consult a creationist text [Of Pandas and People] as though it were a science resource, and instructs student to forego scientific inquiry in the public school classroom and instead seek out religious instruction elsewhere” (Coyne, 2009).

    The Panda Trial is an unambiguous win for the pro-evolution group, and its importance in school policy is ongoing as the battle for evolution education continues. More information on the Dover trial can be found here, and is based on the excellent NOVA documentary of the trial (in recreation) called Judgment Day: Intelligent Design on Trial.

    J B S Haldane: The Life of a Scientific Beast

    “I have no doubt that in reality the future will be vastly more surprising than anything I can imagine. Now my own suspicion is that the Universe is not only queerer than we suppose, but queerer than we can suppose.”

    -Possible Worlds and Other Papers

    John Burdon Sanders Haldane is well known for many achievements. Of his numerous achievements, his contribution to the founding of population genetics is most recognized, but to limit Haldane’s brilliance to so small a subject does him great injustice. Even attempting to summarize his life into words is somewhat of a fruitless act. From the time he was born in 1892 until his death in 1964, he dedicated his life and body to science.
    "My body has been used for both purposes during my lifetime and after my death, whether I continue to exist or not, I shall have no further use for it, and desire that it shall be used by others. Its refrigeration, if this is possible, should be a first charge on my estate."

    Haldane was born into a family of aristocrats and scientists. He inherited a knack for scientific self-experimenting from his father, John Scott Haldane, a Scottish physiologist known for his extensive research on the dangers of natural gases to the human body. During his early education, Haldane excelled at mathematics, and after graduating from Eton, received a mathematics scholarship to New College at Oxford. After being wounded during the First World War, Haldane was taken to India to recover, a place to which he would return in 1957.
    At Oxford, in order to relax from mathematical studies, Haldane attended E S Goodrich’s course in Zoology which led to his eventual study of genetics. In addition to his studies of genetics, Haldane took up the study of the classics and writing, allowing him to become one of the, still, few skilled scientific writers. A few of Haldane’s most well known publications include Daedalus (1924), Enzymes (1930­), Animal Biology (1929), The Causes of Evolution (1932), On Being the Right Size (1926), and perhaps the most influential of all his publications, A Mathematical Theory of Natural and Artificial Selection (1924). Haldane’s skill in writing stayed in him until his death. Even in India, his pupils noted that he was not only an extremely good writer, but spent a good part of the day writing letters and answering mail. “He believed that a written communication gave the writer time to think carefully before expressing his thoughts and was then less likely to be influenced by emotions. Also he felt that a statement in writing eliminated possible disputes in what had been said or not said….he was known to use certain abbreviations involving numbers and letters, for example, best wishes 2 U” (Dronamraju).

    Having a strong knowledge of mathematics allowed Haldane to become a leading contributor to the study of population genetics. He was a major contributor to the Modern Evolutionary Synthesis. In A Mathematical Theory of Natural and Artificial Selection, Haldane analyzed the processes of natural selection from a mathematical point of view. During his occupation at University College, London from 1937 to 1957, Haldane was able to devise methods to calculate human mutation rates, prepare linkage maps for human chromosomes, better understand different modes of inheritance, measure the degree or intensity of natural selection operating in human populations, study the effects of close inbreeding, and even developed a better understanding of nature and nurture and the genetic basis of psychological and other behavioral characteristics.

    Although much of Haldane’s work was theoretical, he was as much of a keen experimenter has his father. Early on in his scientific career, Haldane subjected his body to many rigorous and dangerous scientific experiments. He stated “An experimental animal is not capable of describing the physiological reactions of pain, smell and so on….and make no serious attempt to cooperate with the scientists” (Dronamraju). In one experiment to test the theory that carbon dioxide in the human blood enabled the regulation of breathing under different conditions, he ingested large quantities of bicarbonate of soda to raise the alkalinity in h is blood stream and drank ammonium chloride to raise the acidity. In another he tested the effects of carbon monoxide poisoning in mines, a subject his father rigorously studied.

    Haldane left University College, London in 1957 and moved to India where he stayed until his death in 1964. In the 1950’s, Haldane grew dissatisfied with his life in England, finding the political situation intolerable. Although many colleagues in England considered his move scientific suicide, Haldane quickly embraced the new customs. He became an Indian citizen and grew interested in Hinduism. To his pupils in India, Haldane’s life in India was a sort of second life to the one he had in England. In 1962, Haldane moved to Bhubaneswar, India to carry out his last projects before succumbing to cancer in 1964.

    Clark, Ronald. J. B. S.: The Life and Work of J.B.S. Haldane. 1st. Oxford University Press, 1984. Print.

    Dronamraju, Krishna. Haldane: The life and work of JBS Haldane with special reference to India. 1st. Aberdeen: Aberdeen Univeristy Press, 1985. Print.

    Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck: A Man with Too Many Names

    By: Lauren Wolf

    On August 1, 1744 Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck was born in a small village in the north of France called Bazentin (University of). He was born into a noble but un-wealthy family with a background rich in military service and was the youngest of eleven children. When Lamarck was eleven he enrolled in the Jesuit seminary at Amiens as his father expected his youngest son to become a priest (Bookrags). In 1760, after the death of his father, Lamarck purchased a horse and rode off to join the French Army who was campaigning in Germany at the time (Clifford). At the age of 17, while fighting in the Seven Years War, Lamarck distinguished himself and as acknowledgment of his actions on the battlefield was rewarded with a commission for bravery (Macroevolution). His given name, Jean-Baptiste Pierre Antoine de Monet was changed because of this and he became the Chevalier de Lamarck and was know as Jean-Baptiste Lamarck from then on (Macroevolution). After the war ended Lamarck continued to serve in the military until 1768 when he left because of an injury (Bookrags). After the military Lamarck worked as a bank clerk in Paris, during which time he began study medicine and botany.

    In 1778 he published a three volume book on French plant life which was known as Flore Française, in which he used a dichotomous key to identify each plant (Macroevolution). The book was highly praised. Afterwards he acquired a position at the Jardin des Plantes. In 1793 the Jardin des Plantes was converted to the Musée National d'Histoire Naturelle (Bookrag). The newly converted museum was run by twelve professors in different fields and Lamarck was appointed to the professor of zoology (Bookrag). He was also in charge of organizing the collection of animals and fossils without backbones, which he called invertebrates (Bookrag).
    In 1809 Lamarck published Philosophie zoologique, including his theory of transmutation about which he wrote "Nature, in producing in succession every species of animal, and beginning with the least perfect or simplest to end her work with the most perfect, has gradually complicated their structure” (University of). Lamarck did not believe in extinction. He thought that the disappearance of species was due to their evolution into new species and that continued progression of this process meant that “less perfect” organisms vanished (University of). Although Lamarck had to claim that organisms such as protists that were simple were under continuous generation (University of).

    In 1815 he published his first volume of Histoire Naturelle des Animaux sans Vertèbres and in 1822 he published his second volume (University of). This work included his evolutionary theory founded on four laws. The first law was the idea that organic matter had a natural inclination to increase in complexity and defended the notion that evolution advanced to create plants and animals that became more complicated over time (Hannaby). The second law described the influence of the environment and the continual needs of animals to use new movements resulting in the development of new organs (Hannaby). The third law sums up the principle of use and disuse. This says that reoccurring actions or lack of actions caused modifications to the size and strength of an animal’s body (Hannaby). The fourth law talked about Lamarck’s theory of acquired characteristics or “Lamarckism,” stating that characteristics acquired by animals in their life span could be passed on to future generations and that inheritance was essential to account for the continuing accumulation of traits over time (Hannaby).

    For most of his life, Lamarck and his theories were ignored by the scientific community. George Cuvier valued Lamarck’s work with invertebrates but discredited his theories of evolution as they opposed his own. Though Lamarck was married three times and had a total of eight children, most of his life was a constant battle with poverty (Scoville). To make matters worse, Lamarck lost his eyesight at age 65 but continued his work with the aid of his daughter (Bookrags). Lamarck died on December 18, 1829 and because his family was so poor, his books and works were auctioned in order to pay for his funeral in which he only received a rented grave that he was removed from five years later (Clifford). The location of his remains is unknown to this day. While many of Lamarck’s theories were proved incorrect, he is one of the first scientists to publish the concept of adaption and to acknowledge the idea that adaption occurred in order to help species better survive in their given environment.

    Works Cited:

    Clifford, David. "Lamarck (1744 - 1829)." The Victorian Web: An Overview. 14 Sept. 2004. Web. 28 Nov. 2011.

    "Jean-Baptiste Lamarck – Biography." Web. 27 Nov. 2011.

    "Jean-Baptiste Lamarck Biography |" | Study Guides, Lesson Plans, Book Summaries and More. Web. 27 Nov. 2011.

    "Jean-Baptiste Lamarck Biography – French Naturalist «" Web. 26 Nov. 2011.

    "Jean-Baptiste Lamarck." University of California Berkeley, 2006. Web. 26 Nov. 2011.

    Scoville, Heather. "Jean Baptiste Lamarck." Evolution - Natural Selection, History of Life on Earth, Darwinism, Lesson Plans and More! Web. 26 Nov. 2011. .

    *note: because most of the references begin with “Jean-Baptiste Lamarck…” I used the website or sponsor as internal references.

    Monday, November 28, 2011

    Ear Morphology of Butterflyfishes: evolution for specialization of generalization?

    The article I chose to summarize discusses the evolution of complex ear morphology of fish who possess an otophysic connection between the inner ear and swim bladder used for communication . The article particularly tries to determine if the complex ear morphology also evolved in fish who used communication with the swimbladder but did not have an otophysic connection, specifically the Butterflyfish.

    The coral reefs serve as a very noisy habitat, with sounds produced by many biotic and abiotic factors (Webb et al. 2010). This vast amount of background noise might make it hard for a fish to communicate acoustically with its swimbladder if the other fish cannot pick up on its vibrations. Fortunately, many fish have adapted to these conditions with specialized hearing mechanisms. The common specialization is an otophysic connection to the swim bladder (a connection of the swimbladder to inner ear) and large dense otoliths within their inner ear (Webb et al. 2010). This allows for lower thresholds for hearing and the ability to hear a broader frequency range (Coombs & Popper, 1979). The butterflyfishes are also known to communicate acoustically but are not known to possess the otophysic connection or specialized inner ear structure commonly associated with hearing specialists. J.F. Webb, J.L. Herman, C.F. Woods, and D.R. Ketten conducted an experiment which attempts to reveal whether Chaetodon
    (butterflyfishes) species are likely to have enhanced auditory capabilities like fish with an otophysic connection.

    It is typical that the presence of an otophysic connection is correlated with both enhanced hearing and modified ear morphology (Popper, 1977). The otophysic connection is an anterodorsal diverticula, or `horns’, of the swimbladder that approach or come in direct contact with the region of the skull containing the inner ear (Webb et al. 2006). Basically, the swimbladder amplifies the sound like a drum and is able to transfer these vibrations to the inner ear. The inner ear is composed of 3 dense calcium carbonate structures known as otoliths. The solid structure vibrates in response to sound pressure waves. Otoliths sit on sensory hairs (sensory macula) that have a connection to nerve cells which then can relay the detection of sound to the brain (Webb et al. 2006). To have specialized hearing associated with an otophysic connection it would be important for the otoliths, which respond well to sound, to be specialized and/or modified as well. The correlation between modified ear morphology, the presence of an otophysic connection, and advanced hearing capabilities among taxa can suggest that knowledge of the morphology of the ear and swimbladder can be used to predict whether a fish has enhanced auditory capabilities (Webb et al. 2010).

    Butterflyfishes do not fit into that predictive ideal quite as easily as most fish. The butterflyfish (family Chaetodontidae) have a laterophysic connection (LC), which interact with the swimbladder horns differently and appear to have a connection to the lateral line canals. This method is believed to enhance sound detection using a combination of acoustic inputs to both the lateral line and inner ear (Webb et al. 2010).

    The question that Webb et al (2010) proposes is if butterflyfish may also have a modified ear structure like the otophysic hearing specialists. Popper (1977) examined the otoliths of the millet butterflyfish (Chaetodon miliaris) and reported that it has an unmodified ear similar to other percomorph fishes that lack an otophysic connection. But, this particular species' behavior is not similar to other butterflyfish behaviors, who are monogomous, pair-forming coral-eaters. Instead, C. miliaris eats plankton and spawn in groups. Webb et al. (2010) discusses that this difference is likely to influence the ways in which C. miliaris uses sound. He discusses that it is also possible that variation in ear morphology and hearing capabilities exists among Chaetodon species with different LC variants ( vs. indirect LC, long wide swimbladder horns vs. long thin horns vs. short horns). If this hypothesis is true, then C. miliari may not be representative of the genus. This discrepancy warranted further study of the ear among Chaetodon species to see if there is a possibility that butterflyfishes may have a more complex ear structure then the morphology described by Popper (1977).

    The study was performed by J.F. Webb, J.L. Herman, C.F. Woods, and D.R. Ketten compared the ear morphology of three representative Chaetodon species and one species of Forcipigier (which lacks swimbladder horns). Scanning electron microscopes and computed tomographic imaging was used to analyze ear morphology and spatial relationship of the ear and swimbladder. The fish were collected in the waters around Oahu, Hawaii, dissected and then imaged. The sizes and shapes were then recorded for further analysis (Webb et al. 2010).

    The morphology of the three otolithic organs (sacculus, lagena and utriculus) and the hair cell orientation patterns in their sensory maculae were found to be similar among the three Chaetodon and one Forcipiger species examined (Webb et al. 2010). These aspects of ear morphology are similar to those reported by Popper (1977) for C. miliaris, despite the fact that its feeding and reproductive habits are different from that of the majority of Chaetodon species. Thus, it is expected that ear morphology is indeed the same among all members of the genus and perhaps among all members of the Chaetodontidae (Webb et al. 2010).

    Three-dimensional reconstructions of the swimbladder and otoliths (Fig. 1) illustrate the relationships of the swimbladder horns to the ears. The minimum distance from the swimbladder or horns to the inner ear appeared to be smaller for Chaetodon than for Forcipiger (Webb et al. 2010). The distance is similar to that of an otophysic connection but figure 1 shows that the simple anterior swimbladder horns in Chaetodon spp. (Fig. 1(a),(b)) sit dorsal and lateral to the otoliths, unlike the swimbladder horns in Myripristis (which has a well developed otophysic connection) that wrap around and come into contact with the otic capsule (Fig. 1(d),(e)), which characterize the otophysic connection in this genus (Webb et al. 2010). The swimbladder horns of Chaetodon spp. (which define the laterophysic connection) do not have an intimate association with the otic capsule as in fishes with an otophysic connection. Rather, the swimbladder horns only approach the ears (within 1–2 mm), but in doing so, may enhance pressure sensitivity (Webb et al. 2010).

    Figure 1. Three-dimensional reconstruction of computed tomographic imaging slices demonstrating the relationship of otoliths (red) to the volume of air within the swimbladder. Reprinted from Webb et al. 2010

    The anatomical data that Webb et al (2010) presents, which suggest that Chaetodon and Forcipiger have unremarkable hearing capabilities (with regard to threshold and frequency range), are supported by preliminary physiological studies on the hearing capabilities of chaetodontids (Smith et al. 2006). Juvenile spotfin butterflyfish Chaetodon ocellatus (a Caribbean species with the same swimbladder horn and LC morphology as C. miliaris and C. multicinctus) have a relatively narrow audiogram with best frequency at 100–200 Hz (Smith et al. 2006), which is not unusual for teleosts lacking an otophysic connection. The best sensitivity for adult C. multicinctus, C. auriga and F. flavissimus is 200–600 Hz (Webb et al. 2010). This is a bit higher than that reported for C. ocellatus juveniles and a broader range that is typical for a laterophysic connection. Webb et al. (2010) suggest that this difference may be accounted for by some combination of methodological differences, species differences and ontogenetic effects.

    The evidence supports that butterflyfish do not have modified inner ears, but referring to them as hearing generalists may not be correct. Fishes with otophysic connections have been considered to be ‘hearing specialists'. In contrast, fishes that lack an otophysic connection (and those that lack a swimbladder entirely) tend to have unremarkable auditory capabilities and have been considered to be ‘hearing generalists' (Poper & Fay 2010). Popper and Fay, (2010) however, have recently proposed that this dichotomous description be abandoned and suggest that variation in the auditory capabilities of fishes lie along a wide spectrum. Popper and Fay relate to the instance of the butterflyfish who use sound communication, have a laterophysic connection, and no specialized ear morphology as an example of why the dichotomous description of hearing is outdated.

    Webb et al. (2010) findings concluded that the origin and diversification of the laterophysic connection in Chaetodon occurred in the absence of modifications in ear morphology and evidence for the enhancements of auditory capabilities like those in species with otophysic connections. Nevertheless, the fact that these fishes produce sound demonstrates that acoustic communication is important. The dependence on auditory communication probably favored the evolution of pairing behavior, a strategy that would increase the efficiency of communication in noisy coral reef environments (Webb et al. 2010). Such behavior is likely to exploit sensitivity to both particle displacement (hearing with the ears, given the short distances between animals) and pressure reception (via the swimbladder horns which amplifies sound to ears). Whatever the mechanism or mechanisms of acoustic detection in these fishes, the question of how fishes respond to increasing levels of sound on naturally noisy coral reefs is raised. There is possibility of affecting the social and reproductive behaviors of these important coral reef fish.

    Literature Cited

    Coombs, S. and A.N. Popper. 1979. Hearing differences among Hawaiian squirrelfishes(family Holocentridae) related to differences in the peripheral auditory anatomy.Journal of Comparative Physiology 132:203–207

    Popper, A. N. 1977. A scanning electron microscopic study of the sacculus and lagena inthe ears of fifteen species of teleost fishes. Journal of Morphology 153:497–418

    Popper, A. N. and R.R. Fay. 2010. Rethinking sound detection by fishes. Hearing Research doi: 10.1016/j.heares.2009.12.023 (in press).

    Smith, W. L., Webb, J. F. and S.D. Blum. 2003. The evolution of the laterophysic connection with a revised phylogeny and taxonomy of butterflyfishes. Cladistics 19: 287306.

    Webb, J.F., Herman, J.L., Woods, C.f. and D.R. Ketten. 2010. The ears of butterflyfish (Chaetodontidae): 'hearing generalists' on noisy coral reefs? Journal of Fish Biology 77: 1406-1423

    Webb, J. F., Smith, W. L. and D. R. Ketten. 2006. The laterophysic connection and swimbladder in butterflyfishes in the genus Chaetodon (Perciformes: Chaetodontidae). Journal of Morphology 267:1338–1355.

    The Life and Times of Statistician and Geneticist Extraordinaire, R.A. Fisher

    Ronald Aylmer Fisher

    “The fascination of Fisher for me is that my research is mainly in evolutionary biology, which involves a certain amount of genetics from time to time, and I teach and have done some research in statistics. So I look to Fisher as a founding father in all three of the disciplines that we are celebrating.”
    –Alan Grafen

    Ronald Aylmer Fisher was born on February 17, 1890 in East Finchley, London to George Fisher, who was a fine arts auctioneer, and Katie Heath. Fisher was the youngest of seven, and according to relatives, was a precocious child while also showing surprisingly advanced arithmetic skills at as young as the age of three. When Fisher was fourteen, his mother passed away, and in that same year, he also received a scholarship in mathematics to the school, Harrow. From a young age, Fisher’s eyesight was quite poor and because of this, he usually listened in class without ever taking any notes, and solved problems mentally, which proved to be useful later on in his life.

    In 1909, Fisher received a scholarship to Cambridge, concentrating mainly on mathematics, theoretical physics, and astronomy. In 1911, the formation of Cambridge University Eugenics Society was formed under Fisher’s persistence, and he often spoke on Charles Darwin’s theory of evolution and natural selection as he looked up to Darwin. Much of Fisher’s statistical interest stemmed from this group, and he also grew to have a great interest in evolutionary theory, specifically with genetics. In April of 1912, Fisher published his first paper, which showed what would later come to be known as the method of maximum likelihood. He graduated in 1912 with distinction, but his tutor, however, believed differently of him, saying, "...if he had stuck to the ropes he would have made a first class mathematician, but he would not."

    Fisher was awarded the Wollaston scholarship, which allowed him to stay at Cambridge for a year longer and he continued his studies on Theory of Errors by George Airy. This newfound interest led him to examine statistical problems. After finishing at Cambridge, Fisher briefly worked at a farm in Canada, but soon returned to London and became a statistician in the Mercantile and General Investment Company for a few years (1913-1915). Then he was a high school mathematics and science teacher for a handful of years. Teaching was his way of serving the country because he was rejected from the army due to his poor eyesight. It turned out that as a teacher, he was mediocre at best, but was definitely recognized as an exceptional thinker who usually had difficulties explaining his complex ideas to other people. His statistical work at the time drew attention from Karl Pearson who was a well-known statistician of the era. Pearson published Fisher’s article on general sampling distribution and without telling Fisher, included a critique of Fisher’s paper. This led to a heated confrontation between the two, and it turned out that Fisher was actually correct in his claims, but as Pearson was popular in the day, Fisher’s papers were withdrawn from the Royal Society due to the conflict between Pearson and Fisher.

    “He was the greatest statistician in the world, a geneticist of such prescience that the genius of his conclusions is still unfolding itself today.”
    -E.B. Ford

    In 1917, Fisher married Ruth Eileen Guinness, and they had eight children together, but eventually separated. Fisher published many noteworthy papers, including establishing a way of doing sample measurement in statistics using mathematics. He also wrote a few papers on eugenics because of his concern coming from the upper class as he had the belief that “less talented” lower class families produced offspring at a faster rate than the “more talented” upper class families. In 1918, he wrote a paper on Gregor Mendel’s theory of inherited characteristics, which would lead to his work on the statistical analysis of variance later on. Fisher decided to stop teaching in 1919 after being offered a position by Sir John Russell as a statistician at the Rothamsted Experimental Station (as shown in the photo below), which was the oldest agricultural research institute in the UK. In his time there, Fisher made numerous contributions to the statistical approach of experiments including the design, as well as genetics.

    Fisher put together the analysis of variance, which is an important component still used in statistical analysis today. He also promoted sub-experiments in which several factors of an experiment are varied at one time instead of just one factor. With his skills as a newfound researcher and statistician, Fisher published Statistical Methods for Research Workers in 1925, which basically summarized the design and analysis of experiments during his time in Rothamsted. Apparently though, it is extremely difficult to read and understand that his colleague, M.G. Kendall, said, "Somebody once said that no student should attempt to read it unless he had read it before".

    As a statistician, he perfected many statistical tests, and he built on his earlier work of the maximum likelihood estimate, but his time in Rothamsted led him down an unlikely path. Due to his interest in genetics and the nature of his job, he began to breed various types of animals like mice, snails and poultry. He became so engrossed in this that he began to do this at home too! In doing this, he applied his findings and theories about gene dominance to Mendel’s work on inheritance. With these findings, he published The Genetical Theory of Natural Selection in 1930, which has been called the deepest book on evolution since Darwin!

    In his book, The Genetical Theory of Natural Selection, Fisher showed that selection always favors the dominance of beneficial genes. He connects Mendel’s mathematical results being matched to Charles Darwin’s natural selection. Fisher’s main contribution to evolution included a combination of all three necessary disciplines: genetics, evolutionary biology, and statistics. Perhaps what Fisher views to be his biggest contribution to evolutionary biology is the fundamental theorem. What exactly is the fundamental theorem? Due to the complexity in which Fisher illustrates it, most biologists can’t understand it in Fisher’s writing. Sewall Wright never even understood the fundamental theorem, and funny enough, Fisher did not find adaptive landscapes useful at all... Most population textbooks ignore the fundamental theorem or completely misunderstand it. In modern terms, according to A. W. Edward (1994), the fundamental theorem is “The rate of increase in the mean fitness of any organism at any time ascribable to natural selection acting through changes in gene frequencies is exactly equal to its genetic variance in fitness at that time.” Fisher along with Sewall Wright, and J.B.S. Haldane (all three shown in the photo below) were really the pioneers that provided the mathematical basis for evolutionary theory.

    In 1933, Fisher left Rothamsted and became the Galton Chair of Eugenics, while continuing to publish papers on statistical science. Fisher became a Balfour Professor of Genetics at Cambridge University in 1943, and served as president of the Royal Society for a few years. He received many accolades including the Royal Medal of the Society in 1938, Darwin Medal of the Society in 1948, Copley Medal of the Royal Society in 1955, and more. He left Cambridge in 1959 to Adelaide, Australia, and even then continued to be a statistical researcher until he passed away in 1962.

    “There seems little I can say by way of summary of so great a scientist and so great a friend except perhaps this: he was supremely an individualist, and if ever there was a man whose life was guided wholly by the truth, as he perceived it, it was Sir Ronald Fisher.”
    -E.B. Ford

    Literature Cited:
    1. Crow, J. F., and W. F. Dove. "Perspectives: Anecdotal, Historical and Critical Commentaries on Genetics." Genetics Society of America (2005).

    2. Fienberg, S. E., and D. V. Hinkley. R.A. Fisher, An Appreciation. New York: Springer Verlag, 1980.

    3. "Fisher Biography." MacTutor History of Mathematics. School of Mathematics and Statistics.

    4. Grafen, A. "Fisher the Evolutionary Biologist." Journal of the Royal Statistical Society: Series D (The Statistician) 52.3 (2003): 319-17.

    5. "Sir Ronald Aylmer Fisher." University of Minnesota Morris. http://www5555.morris. ~sungurea/introstat/history/w98/RAFisher.html.

    6. Skipper, R. A. "The Persistence of the R.A. Fisher-Sewall Wright." Biology and Philosophy 17 (2002): 341-42.

    Promiscuity and the Rate of Molecular Evolution at Primate Immunity Genes

    The article I chose to summarize and analyze focuses on the correlation between pathogen-interacting genes and promiscuity in primates entitled “Promiscuity and the Rate of Molecular Evolution at Primate Immunity Genes” (4). The idea for this study was largely generated by a previous study, which found a positive correlation between basal leukocyte counts and mating systems in primates (2). This conclusion prompted the formation of this study’s hypothesis; that perhaps promiscuity could correlate with the evolution of primate immune systems. The scientists heading this project used maximum likelihood to determine protein evolution rates of terminal branches of primates and concluded that immunity genes do evolve faster in more promiscuous primate species, but only those which interact very closely with pathogens.

    Many documented relationships between immunity and reproduction exist. One such example describes immune gene expression in Drosophila (female immune gene expression undergoes significant chances post-mating) (1). Another example is present in Zuk’s work, which suggests that sexual selection may be partially dependent on the interference between a particular male’s ejaculate and the female’s immune function (5). Other studies detail the nature of STDs, finding that they differ in their character when compared to most infectious diseases. These differences include the focal point at which the disease is effective. STDs most often target fitness with respect to reproductive ability, not in mortality. This suggests that perhaps STDs impose selective pressures on their host that differ from other breeds of infectious disease (2).

    These previous articles helped the scientists who conducted this study form their questions. The authors of “Promiscuity and the Rate of Molecular Evolution at Primate Immunity Genes” (Gabriela Wlasiuk and Michael W. Nachman) decided to expand on this topic, with an increased focus on, specifically, the study question of Nunn (3). The authors decided that if basal leukocyte count actually correlates with disease risk, then by natural selection, other factors of the immune system may also be affected. The authors formed their predictions based on these findings and with respect to primates, as the studies with supportive evidence were performed with primates, and primates exhibit a wide variety of mating systems and, thus, promiscuity. Along with promiscuity, the effect of group size, density, habitat and diet on the rate of molecular evolution of immunity genes was recorded.

    This study collected previously published data on 15 immune defense genes in primates and sought to find a relationship between particularly promiscuous species and positive selection in these genes. One factor that was not initially accounted for, but later realized, was the difference in pathogen-important genes and non-pathogen important genes. The sociological variables investigated (diet, density, group size, and habitat) resulted in information already recorded in separate studies, showing that these factors influence the incidence of disease in different ways. The influence of diet on disease is relative to the area in which food is found. Food in trees will be less likely to carry disease than food found on the ground because fecal matter (found on the ground) is often disease ridden. Also, primates who consume foliage have been found to be at a higher risk for disease than those who consume hardier foods. This is because foliage eating animals must consume a higher volume of food to reach the same level of nutrition as those who eat fruit or meat; with a larger amount eaten comes an increased chance of infection.

    Overall, the authors chose to use group size and mating system as core variables in this study. They denoted large group sizes as LG and small group sizes as SG. They categorized mating system as either unimale (UM) or multimale (MM). With the rearrangement of phylogenetic trees (with respect to protein similarities; using parsimony, maximum likelihood, and distance) and dN/dS ratios, the study took off. The authors used dN/dS ratios as the dependent variable, and all other sociological factors as independent variables. They performed a single analysis of each independent variable separately with respect to the dependent variable, but for future analyses only used group size and female promiscuity as independent variables. Variance in dN/dS ratios across species of MM vs. UM mating systems were compared using z-tests and t-tests, means and variances were compared in LG vs. SG, and multiple regression models were created. Additionally, proportions of branches with >1 dN/dS (positive selection) were compared between UM and MM, LG and SG.

    These analyses yielded fascinating results! It was found that when pathogen interacting immunity genes were separated from non-pathogen interacting immunity genes, significant data existed. Group size also showed a significant difference in dN/dS ratios, suggesting that group size and female promiscuity may influence the rate of evolution of immunity genes. However, what I find most interesting is that mating system was only found to be a significant factor in pathogen important genes, not in those genes which do not interact with pathogens. Since a dN/dS ratio greater than one is the definition of positive selection, the occurrence of that value was compared across MM vs UM and LG vs SG. When this occurrence was summed across groups, a significant difference was found between the number of MM groups that had dN/dS greater than one and UM groups that had dN/dS greater than one. Statistically speaking, MM groups had a significantly higher amount. The incidence of dN/dS ratios that were greater than one were also compared across SG vs. LG and no statistical difference was found between the two sets. This data promotes the argument that sexual promiscuity among primates may results in positive selection in immunity genes!

    The argument found in the discussion that I personally offer most support to is that which takes STDs into account. One possible explanation for this data speaks to the evolutionary arms race proposal. This idea states that, since individuals are more promiscuous, fast-evolving pathogen-interacting immune genes are selected for, rather than slow-evolving pathogen-interacting immune genes. Individuals in this scenario who have slow-evolving immune genes would theoretically end up with STDs, which directly affects one’s ability to reproduce, thus that individual would be removed from the gene pool. This selection for fast-evolving genes would eventually result in a correlation between fast-evolving immunity genes and high levels of promiscuity. This idea also transmits to the finding in smaller groups, that there is a significant correlation between pathogen-important immunity genes and promiscuity. This finding was limited to SG, but LG were found to have a significant increase in the dN/dS ratio with an increase in promiscuity across all immunity genes, not pathogen-important immunity genes specifically. The fact that in SG, pathogen-important immunity genes experienced a significant increase in dN/dS with increased promiscuity shows that the pathogen evolution and the pathogen-interacting immunity genes must also compete with each other in a co-evolutionary arms race. If immunity genes, which are specific to pathogen protection, did not evolve as quickly as the pathogens themselves, eventually the species would fail. By natural selection acting on slow evolving immunity genes, pathogens and pathogen-specific immune genes may grow to evolve in very similar speed.

    Published scientific literature varies widely in reliability, soundness, and thoroughness of background research. I find that this article was very interesting and well conducted. I do not find any gaps in knowledge, and was able to apply what I have learned in BI 445 to understand difficult concepts. The way the study was carried out makes sense and seems water-tight, with different methods of statistical analysis employed in order to catch errors in computation or the incidence of false significance. The topic is of personal interest, and the relationship between pathogen specific immunity genes and promiscuity in females is a correlation I would have never thought of, but is logical. The article was well written and valid, I do not have issue with its research tactics and find the results of interest and inherently logical.

    Literature Cited

    1. Lawniczak MKN and Begun DJ. A genome-wide analysis of courting and mating responses in Drosophila meanogaster females. Genome 2004;47:900-910.

    2. Lockhart AB, Thrall PH, Antonovics J. Sexually transmitted diseases in animals: ecological and evolutionary implications. Biological reviews of the Cambridge Philosophical Society 1996;71:415-471.

    3. Nunn CL. A comparative study of leukocyte counts and disease risk in primates. Evolution 2002a;56:177-190.

    4. Wlasuik G and Nachman M. Promiscuity and the rate of molecular evolution at primate immunity genes. Evolution 2010;64(8): 2204-2220.

    5. Zuk M, Stoehr AM. Immune defense and host life history. American Naturalist 2002;160:s9-s22.