430.Assignments

Biology 430/G Assignments

Final Exam (Due by 12:00 noon on Friday, May 9^th)

This is an open-book, take-home exam. Use your notes and/or any textbooks to answer the questions. DO NOT research primary journal articles or web resources related to the questions - your answers should be based only on material made available to you and the topics discussed in class. Limit your answers to 1-2 single-spaced pages for each subquestion; all exams must be word-processed or will not be accepted. Feel free to use diagrams, tables, or figures to illustrate your points, but be sure to explain them fully in the text of your answer. Avoid including information not directly relevant to the question; you will lose points for both failing to include pertinent information and for including extraneous information. All exams should be completed individually. Do not discuss your answers or efforts with others in the class - please ask me if you have questions about the meaning or intent of a question. Complete all questions.

1. The Galapagos flightless cormorant (Phalacrocorax harrisi) is a fantastic example of the creative power and contingency of the evolutionary process. The flightless cormorant exists in small demes on only two islands in the Westernmost Galapagos archipelago, Isla Fernandina and Isla Isabela; the species consists of 400-1500 individuals, making it among the rarest bird species on Earth. There are approximately 40 species of cormorants worldwide. Cormorants are coastal birds, diving from the surface to feed on fish and water snakes. They are strong underwater swimmers, sometimes hunting at depths of 45 m. After exiting the water, cormorants must dry their wings in the sun, as their feathers are not waterproof (which reduces their buoyancy, allowing them to dive deeper). Cormorants have a very high basal metabolic rate, even among birds as a whole, such that they cannot go more than 2-3 days without eating).

Flightless cormorants are unique in many ways. As it name implies, the species has very reduced wings that do not permit it to fly. They also have a unique feather structure that reduces buoyancy while providing better insulation, large body mass, and reduced pectoral muscle mass (making up about 1.2 % of their body mass, compared to 11 % in flighted cormorants). Nesting on the flat and gently sloping rocks at the edge of the water, individual birds do not ever move more than a few meters from their nest on land, and less than a kilometer in the water. Food is abundant in the very cold waters of the Humboldt current just offshore, except during El Nino years when waters warm and algal primary productivity decreases, which in turn decreases fish populations dramatically.. In addition, Isla Fernandina (at least) is very young island, less than 700,000 years old, and the only island in the Galapagos with no introduced species and no large land-based predators.

The evolutionary origin of the flightless cormorant is unclear. One hypothesis suggests that P. harrisi is derived from a clade (group) of North Pacific cormorant species, including P. pencillatus, P. perspicillatus, P. pelagicus, and P. urile. This group is common in marine habitats from the Bering Sea to California, and is relatively derived within the Family Phalacrocoracidae. Evidence for this An alternative hypothesis suggests that P. harrisi may be the only close relative to the red-footed shag, P. gaimardi, native to the Pacific coast of South America. P. gaimardi has been suggested to be a relatively basal (ancestral) lineage based on DNA sequence data; biogeographically, it makes sense to hypothesize that the Galapagos flightless cormorant is derived from a South American rather than North Pacific ancestor.

A seminal paper examined the phylogenetic relationships of cormorants, using a suite of 137 osteological characters. Some of the results of this study are in conflict with a more recent DNA sequence-based phylogenetic study, particularly in that the osteological study does not show P. gaimardi as a basal group (one branching off near the bottom of the tree); nevertheless, it is the only phylogeny that includes the flightless cormorant. The phylogenies developed from the osteological study are provided in the file cormorant.jpg; note that these figures fit together to form one large phylogeny, and are broken up just to make theme easier to read. Use these data to address the following questions:

a. Which hypothesis about the origin and phylogenetic relationships of the Galapagos flightless cormorant seem to be supported by the osteological data ? Why ? Make reference to specific aspects of the phylogenies to support your conclusion. (33 points)

b. Develop an adaptive scenario for the evolution of the flightless cormorant phenotype. Assume that its unique features are adaptive, and that the phenotype has been shaped by natural selection. Given that, what type(s) of fitness benefits might reduced wings, reduced muscle mass, modified feather architecture and large body size convey in the environment of the Galapagos ? Now consider what aspects of the Galapagos habitat make these adaptations possible; that is, why could they evolve on Galapagos and not elsewhere ? Making a logical argument is the key to getting a good score on this question. (33 points)

2. Bonobos (pygmy chimpanzees; Pan paniscus) reside in large communities composed of small subunits of individuals. Unlike common chimpanzees, the social interactions of individuals and subunits are quite non-aggressive. Sexual intercourse and other sexual behavior is used as a social signal in bonobos, serving as a greeting, favor to be traded, or a means of conflict resolution; they do not discriminate in the behavior by age or gender.

Bonobo societies consist of unrelated but socially-bonded females and those males associated with them. Females leave the group shortly after reaching sexual maturity, while males never leave their natal group. Females form social bonds that let groups of females dominate the society, even over the larger, stronger males. As such, females in general have a higher social standing than males. To a large extent, a male’s success in competition with other males derives from the support he receives from his mother.

In many species, there arises a conflict between parents and offspring once offspring become self-sufficient; at this point, it becomes more evolutionarily profitable for a female to invest in the next brood than it is in continuing to care for the now-sufficient current offspring. However, this situation does not appear to hold in bonobos. The mother-son relationship in particular is the closest bond that ever develops between males and females. Bonobo males often stay with their mothers long after becoming adults, and occasionally beg food from them.

a. How can you account for this deviation from standard predictions about the relative value of current vs. future offspring to a female ? Assuming this pattern is adaptive in bonobos, why would females allow adult offspring to continue to draw resources from them that might otherwise be dedicated to her subsequent or even future offspring ? How can this apparently altruistic be beneficial to her reproductive fitness ? Employ concepts of individual selection, group selection kin selection, and/or reciprocal altruism as appropriate to frame your answer; DO NOT feel like you need to include all of these ideas in your answer, only the one that seems best at explaining the social patterns observed. As in 1b, making a logical argument if the key to getting a good score on this question. (33 points)

Midterm Exam (Due by 3:00 pm Wednesday, April 2nd)

1. Polar bears are distributed throughout the circumpolar Arctic. Polar bears are solitary and roam over large areas of the ice in search of ringed seals and other prey. Unlike brown bears, polar bears do not hibernate (with the exception of pregnant females). Polar bears prefer to travel on sea ice with open water leads (water channels) near coastlines. Individual home ranges vary between 50,000 and 350,000 square kilometers, and bears are capable of traveling 30 km or more per day. Often unappreciated is the fact that polar bears are prodigious swimmers; individuals have been spotted 60 miles from the nearest shore, and have been tracked swimming continuously for 100 km. This swimming ability is particularly beneficial during spring, when the sea ice is beginning to break up and there is the potential for bears to become trapped on chunks of ice that break free from the pack ice.

Their tremendous dispersal capabilities over land and sea might lead to the hypothesis that polar bears populations are genetically homogeneous over large areas. However, radio telemetry and other tracking studies suggest that polar bears are relatively philopatric, or faithful to certain areas. This would suggest an alternative hypothesis, that there may exist multiple, genetically distinct subpopulations of polar bears throughout the Arctic region. A recent paper employed 8 VNTR loci to examine this question of population structure for four breeding areas in the southeastern Canadian Arctic (SB = Southern Beaufort Sea, NB = Northern Beaufort Sea, WH = Western Hudson Bay). A map of sampling locations and summary of the data collected is available here. Use these data to address the following questions:

a. Assuming populations are each in hardy-Weinberg equilibrium, is there any evidence to suggest the existence of significant population genetic structure Among these four regions ? Carry out and present representative calculations to support your interpretation. (25 points)

b. What types of patterns can you see in the data (or through resulting calculations) regarding the distribution of genetic variation within or among these four populations ? Consider things such as the relative level of genetic variation within populations, the tendency for isolation-by-distance or other patterns of gene flow that may be evident among populations. What do these patterns suggest about the biology and/or conservation management of polar bears ? (25 points)

2. Sika deer (Cervus nippon) are a species of small deer native to Asia, throughout southeastern Siberia, China, Korea, Vietnam, the Japanese Islands, and Taiwan. A number of subspecies (regionally-distinct forms) have been identified on morphological grounds, but there is no strong genetic support for these designations. As such, we could provisionally consider deer from different regions to be part of one species.As with white-tailed deer in the US, sika deer populations decreased in size and distributional range after the mid 1800s; currently , sika deer are distributed in a fragmented manner, with populations of deer separated from one another by unsuitable habitat. It is of interest to examine the potential genetic consequences of hanting-induced reductions in population size and/or the effects of habitat fragmentation on the genetic diversity and structure within and among sika deer populations.

A recent publication used nine microsatellite loci to examine the extent and patterns of genetic variation within and among 14 populations of sika deer throughout the Japanese archipelago (set of islands), as well as in 4 populations introduced from Japan to the United Kingdom (nor relevant to this question). In particular, 265 deer were sampled, from 4 different locations on the island of Hokkaido in the north, 4 locations on the large island of Honshu, 2 locations from the island of Kyushu in the south, as well as single locations on each of 3 small islands close to Honshu. A summary of the data and results is available here. Use these data to address the following questions (do not worry about the UK samples):

a. Is there any evidence that the levels of genetic variation within any of the populations have been relatively more impacted than others by genetic drift ? If so, what are the general patterns evident in the data, and what do they suggest about the possible causes of genetic drift that might have been at work ? That is, are the patterns of drift consistent with human-induced demographic bottlenecks (caused by hunting or habitat loss), or are they more consistent with basic geographical or ecological conditions that may have been long-standing ? Justify your conclusions logically, and support your interpretations by making reference to specific numerical values in the data presented. (25 points).

b. What are the overall patterns of population structure among these Japanese populations of sika deer. Does it appear that there populations are relatively genetically similar, or is there evidence of significant differences in allele frequency among certain locations ? What are the broad-scale patterns in this structure; that is, how is the structuring you identify distributed geographically ? Consider north to south gradients, intra- and inter-island comparisons, and the potential effects of habitat fragmentation as determining factors. Again, make reference to specific numerical values from the data provided to support your interpretations. (25 points)