<p>This dissertation explores philosophical problems in biology, particularly those relating to macroevolutionary theory. It is comprised of a series of three papers drawn from work that is currently at the publication, re-submission, and review stage of the journal refereeing process, respectively. The first two chapters concern the overarching contours of complex life, while the third zeroes in on the short and long-term prospects of human evolution.</p><p>The rhetorical journey begins with a thought experiment proposed by the late paleontologist Stephen Jay Gould. Gould hypothesized that replaying the "tape of life" would result in radically different evolutionary outcomes, both with respect to animal life in general and the human species in particular. Increasingly, however, biologists and philosophers are pointing to convergent evolution as evidence for replicability and predictability in macroevolution. Chapters 1 and 2 are dedicated to fleshing out the Gouldian view of life and its antithesis, clarifying core concepts of the debate (including contingency, convergence, constraint and causation), and interpreting the empirical data in light of these conceptual clarifications. Chapter 3 examines the evolutionary biological future of the human species, and the ways in which powerful new biotechnologies can shape it, for better and for worse. More detailed chapter summaries are provided below.</p><p>In Chapter 1, I critique a book-length excoriation of Gould's contingency theory written by the paleobiologist Simon Conway Morris, in which he amasses and marshals a good bulk of the homoplasy literature in the service of promoting a more robust, counter-factually stable account of macroevolution. I show that there are serious conceptual and empirical difficulties that arise in broadly appealing to the frequency of homoplasy as evidence for robustness in the history of life. Most important is Conway Morris's failure to distinguish between convergent (`externally' constrained) and parallel (`internally' constrained) evolution, and to consider the respective implications of these significantly different sources of homoplasy for a strong adaptationist view of life.</p><p>In so doing, I propose a new definition of parallel evolution, one intended to rebut the common charge that parallelism differs from convergence merely in degree and not in kind. I argue that although organisms sharing a homoplastic trait will also share varying degrees of homology (given common decent), it is the underlying developmental homology with respect to the generators directly causally responsible for the homoplastic event that defines parallel evolution and non-arbitrarily distinguishes it from convergence. I make use of the philosophical concept of `screening-off' in order to distinguish the proximate generators of a homoplastic trait from its more distal genetic causes (such as conserved master control genes).</p><p>In Chapter 2, I critically examine a recent assessment of the contingency debate by the philosopher John Beatty, in which he offers an interpretation of Gould's thesis and argues that it is undermined by iterative ecomorphological evolution. I develop and defend alternative concepts of contingency and convergence, and show how much of the evidence generally held to negate the contingency thesis not only fails to do so, but in fact militates in favor of the Gouldian view of life. My argument once again rests heavily on the distinction between parallelism and convergence, which I elaborate on and defend against a recent assault by developmental biologists, in part by recourse to philosophical work on the ontological prioritization of biological causes.</p><p>In Chapter 3, I explore the probable (and improbable) evolutionary biological consequences of intentional germ-line modification, particularly in relation to human beings. A common worry about genetic engineering is that it will reduce the pool of genetic diversity, creating a biological monoculture that could not only increase our susceptibility to disease, but even hasten the extinction of our species. Thus far, however, the evolutionary implications of human genetic modification have remained largely unexplored. In this Chapter, I consider whether the widespread use of genetic engineering technology is likely to narrow the present range of genetic variation, and if so, whether this would in fact lead to the evolutionary harms that some authors envision. By examining the nature of biological variation and its relation to population immunity and evolvability, I show that not only will genetic engineering have a negligible impact on human genetic diversity, but that it will be more likely to ensure rather than undermine the health and longevity of the human species. To this end, I analyze the relationship between genotypic and phenotypic variation, consider process asymmetries between micro and macroevolution, and investigate the relevance of evolvability to clade-level persistence and extinction.</p> / Dissertation

<p>Although evolution results from differential reproduction and survival at the level of the individual, most research in evolutionary genetics is concerned with comparisons made at the level of divergent populations or species. This is particularly true in work focused on the evolutionary genetics of natural populations. While this level of inquiry is extremely valuable, in order to develop a complete understanding of the evolutionary process we also need to understand how traits evolve within populations, on the level of differences between individuals, and in the context of natural ecological and environmental variation. A major difficulty confronting such work stems from the difficulty of assessing interindividual phenotypic variation and its sources within natural populations. This level of inquiry is, however, the main focus for many long-term field studies. Here, I take advantage of one such field study, centered on the wild baboon population of the Amboseli basin, Kenya, to investigate the possibilities for integrating functional, population, and evolutionary genetic approaches with behavioral, ecological, and environmental data. First, I describe patterns of hybridization and admixture in the Amboseli population, a potentially important component of population structure. Second, I combine field sampling, laboratory measurements of gene expression, and a computational approach to examine the possibility of using allele-specific gene expression as a tool to study functional regulatory variation in natural populations. Finally, I outline an example of how these and other methods can be used to understand the relationship between genetic variation and naturally occurring infection by a malaria-like parasite, Hepatocystis, also in the Amboseli baboons. The results of this work emphasize that developing genetic approaches for nonmodel genetic systems is becoming increasingly feasible, thus opening the door to pursuing such studies in behavioral and ecological model systems that provide a broader framework for genetic results. Integrating behavioral, ecological, and genetic perspectives will allow us to better appreciate the interplay between these different factors, and thus achieve a better understanding of the raw material upon which selection acts.</p> / Dissertation

<p>Scallops, a family of swimming bivalve mollusks, have dozens of eyes arrayed along the edges of their valves. Relatively little is known about the form and function of these unusual eyes. To learn more about them, we studied the visually influenced behavior of scallops, as well as the morphology and spectral sensitivity of their eyes. Of particular interest was whether or not the simple neural architecture of these animals constrains the number of visually-influenced behaviors they can perform. We were also interested to learn whether scallop eyes, despite providing relatively poor visual acuity, show optical refinements, such as corrections for spherical and chromatic aberration, that are known from the eyes of animals with better vision. In the following dissertation, Chapter 2 discusses the visually-influenced behaviors of scallops. It has been argued that bivalve mantle eyes only act as predator-detectors, but the behavioral trials described in this chapter suggest that vision may serve additional purposes in scallops. For example, it was found that visual cues relating to flow conditions may influence scallop feeding behavior. Chapter 3 presents a comparative study of scallop eye morphology. Here, it is found that eye morphology varies considerably between scallop species and that highly mobile scallops have better vision than less mobile or immobile species. Evidence is also presented that one of the two scallop retinas may perform tasks of similar importance to all species, such as predator detection, while the other retina may perform tasks more important to mobile species, such as those associated with the visual detection of preferred habitats. Chapter 4 investigates the spectral sensitivity of the two retinas in the mantle eyes of two scallop species. It is found that there is both inter- and intra-specific variation in scallop spectral sensitivity and that color perception in scallops may be influenced by both environmental light conditions and chromatic aberration caused by their lens. The research in this dissertation provides insight into how vision functions in animals that, like scallops, have a vast number of eyes, but a limited capacity for neural processing. Despite such limitations, it is evident that scallops display a wide range of visual behaviors and have eyes with highly-refined optics.</p> / Dissertation

I studied the in-water anthropogenic impacts on sea turtles, origins of sea turtles on foraging and developmental areas, their migration routes, and described regionally appropriate conservation needs. Sea turtles inhabiting Baja California waters originate on distant beaches in Japan, Hawaii, and southern Mexico. Results from genetic analyses, flipper tagging and satellite telemetry indicate loggerhead turtles (Caretta caretta) feeding along Baja California's coast are born in Japan and make a transpacific developmental migration of more than 20,000 km, encompassing the entire North Pacific Ocean and that East Pacific green turtles (Chelonia mydas) originate on and return to rookeries in Michoacan, and the Islas Revillagigedo, Mexico. Hawksbill turtles (Eretmochelys imbricata), once the target of a lucrative fishery for their shell, are now extremely scarce and only juveniles were encountered. The region's importance to the biology of sea turtles, regionally and Pacific-wide, warrants urgent conservation action. While protected legally, sea turtles are subject to furtive hunting and incidental catch. Coastal development, pollution, and boat collision are secondary threats. Annual consumption of sea turtles in the region is estimated at between 7,800 and 30,000 animals. Sea turtles are eaten regularly in most coastal communities and turtles are considered an irreplaceable traditional food. The decline of sea turtles in these waters has cost us both ecologically and culturally. Sea turtle recovery in Baja California, as all conservation activities, will be a matter of cultural and social evolution. For recovery to occur, strong, community-based incentives and educational programs are needed. In the near term, increased enforcement efforts, monitoring of mortality, and establishment of sea turtle sanctuaries are among the solutions. Without expansion to include community-specific initiatives such efforts may be futile. A long-term, multi-faceted sea turtle "conservation mosaic" program has been launched, consisting of community-based research on life history and population biology, an international education and public outreach campaign, regional sea turtle conservation areas, a monitoring and stranding network, and several policy initiatives that will permanently protect sea turtles and their habitat.

<p> The Brownsberg Nature Park (BNP) in Suriname is home to eight monkey species: <i>Saguinus midas, Saimiri sciureus, Cebus apella, Alouatta seniculus. Pithecia pithecia, Cebus olivaceus, Chiropotes satanas (sagulatus), </i>and <i>Ateles paniscus.</i> Several studies have undertaken the task to better study the feeding and behavioral ecology of these species within the park. However, studies on the black spider monkey (<i>Ateles paniscus</i>) have been absent. As part of my thesis, I decided to conduct a baseline feeding and behavioral ecology study of this species during the period May 2008 &ndash; July 2008. In addition, I developed a field method for determining mercury levels (in parts per million = ppm) in fecal and urine samples of wild monkeys. Since the park is under enormous pressure from illegal gold mining activities, I decided to collect baseline data on potential exposure of wild monkeys to mercury in the environment. I also collected samples from monkeys at the zoo in Paramaribo and monkeys born in captivity at Hiram College in Ohio. I collected data on the frequency of feeding, resting, and traveling by black spider monkey subgroups every 10 minutes during all day follows. Feeding ecology data consisted of identifying fruits eaten by these subgroups. For the mercury analysis I used the OSUMEX LTD. home testing kit. Results from the behavioral data show the following frequencies of activities for the entire study period: 32% feeding, 43% resting, and 25% traveling. The feeding data further justifies spider monkeys as ripe fruit frugivores: 76% of food items consisted of ripe fruit, while 22% consisted of leaves, and 2% was comprised of flowers. The mercury testing results from the Brownsberg and zoo populations ranged between 0.025 ppm to 0.1 ppm (toxic level = 0.8 ppm). The Hiram College monkeys all displayed levels at 0.000 ppm. The results from the mercury analyses indicate that 1) wild monkeys in the vicinity of gold mining activities may not be under the same threat as humans, with regards to mercury exposure through food, and 2) that wild monkeys are still relative exposed to mercury in the environment whether it be natural or anthropogenic.</p>

Although food quality is thought to play an important role in the survival of marine copepods, the extent of natural variability in food quality remains poorly characterized. Here I characterize the different scales at which food quality varies in copepods of the Strait of Georgia, British Columbia, Canada. Significant interannual variability occurs in the diet of Neocalanus plumchrus in the Strait of Georgia. Between 2001-06 the fatty acid profiles of N. plumchrus switched from omnivorous, oceanic signatures to herbivorous, diatom-dominated signatures. An index of food quality (DHA/EPA) is strongly correlated to the abundance of diapausing N. plumchrus, suggesting that the relative proportion of essential fatty acids provided by dinoflagellates and diatoms are related to the survival of this species. Combined fatty acid and stable isotope analysis indicated that the spring calanoid copepods of the Strait of Georgia occupy three trophic positions: Eucalanus bungii is herbivorous, Calanus marshallae and N. plumchrus are omnivorous, while Euchaeta elongata is carnivorous. Oceanic conspecifics of Strait of Georgia copepods experience a more omnivorous diet, as indicated by the presence of higher proportions of flagellate and carnivory markers, and lower proportions of diatom-based markers in their fatty acids. Despite spatial differences in the quality of their diets, the relative trophic positions of these copepods are constant as indicated by their stable isotope signatures. There is a correlation between the trophic information provided by stable isotopes and fatty acids. However, stable isotopes are not sensitive enough to capture the range of dietary variability observed in fatty acids, and fatty acids do not always provide reliable markers of carnivory and trophic position. Over the span of a season, copepods can utilize a wide range of dietary items including diatoms, flagellates, bacteria, detritus and microzooplankton. Copepods can switch from herbivory to carnivory in response to declining chlorophyll concentrations after the spring bloom, and are occasionally able to utilize detrital and bacterial sources. I conclude that the quality of copepod diets in the SoG varies on interannual, interspecific and seasonal scales. The implications of these findings are discussed in relation to ecosystem models of the area, and to copepod physiology.

Fish are not abundant at hydrothermal vents due to the toxicity of venting fluids. Those that are present usually roam the periphery of the vent field or visit occasionally to feed on the abundance of life supported by chemosynthesis. In the past decade, dense aggregations of a newly described flatfish, Symphurus n.sp, have been observed in association with hydrothermal vents in the western Pacific hydrothermal vent biogeographic province. In this thesis I provide evidence that Symphurus n.sp is a vent obligate and consider the ramifications that this association with hydrothermal vents may have for its distribution, population characteristics, behaviour and diet. Symphurus n.sp has a widespread but disjunct distribution throughout the western Pacific hydrothermal vent biogeographic province. Symphurus n.sp appears to be restricted to hydrothermally active, shallow, sulphur rich seamounts. Symphurus n.sp occurs on unconsolidated volcanoclastic ash and solid sulphur crusts and in close association with molten elemental sulphur. The obvious affinity that this species has for native sulphur is unusual and remains unexplained. Unlike most vent-associated fish, Symphurus n.sp occurs in close contact with point source venting and its distribution extends to the periphery of vent fields but not beyond. The density of flatfish on these seamounts surpasses density estimates of flatfish nursery grounds on the continental shelf. On Daikoku Seamount (Mariana Volcanic Arc), mean flatfish abundances were 100 and 66 individuals m-2 in 2005 and 2006 respectively. The prey items that support such high densities of flatfish vary over spatial scales. Differing prey, in turn, results in differing foraging modes. On Nikko Seamount (Mariana Volcanic Arc), Symphurus n.sp is a “sit and wait” predator that feeds exclusively on a vent endemic shrimp, Opaepele loihi. On other seamounts, Symphurus n.sp is an opportunistic forager that preys mostly on polychaetes and small crustaceans. By counting annuli on otoliths I constructed growth curves and determined that growth rates differ between seamounts. This difference in growth rates is likely due to differences in their diet and foraging strategies. Symphurus n.sp may be allocating more energy to growth when less energy is required to forage. Furthermore, size distributions also differ between populations, likely due to variability in growth rates as well as differences in strong recruitment years.

Neural control of reproduction in vertebrates and invertebrates has generated considerable interest due to the presence of common neuropeptides. Gonadotropin-releasing hormone (GnRH), a neuropeptide, is the final integrator of neural regulation governing reproduction in vertebrates by controlling the release of gonadotropins. Little is known about GnRH before the origin of vertebrates or about the biological significance of multiple GnRH forms in a single species. To understand the role of GnRH in invertebrates, I selected a tunicate, Ciona intestinalis, the sister group to vertebrates and amphioxus, Branchiostoina floridae, a group more basal than tunicates. Neural control of reproduction in these chordates was compared with that in the zebrafish, Danio rerio. From the zebrafish, I isolated four GnRH receptor cDNAs that each map to a distinct chromosome and are expressed in a variety of tissues. Each receptor was functional, as shown by its response to physiological doses of native GnRH peptides. Also, two receptors showed selectivity between GnRH1 and GnRH2. Protein localization of each zebrafish GnRH receptor with specific antisera showed that all four receptors are present in the pituitary. However, the most striking localization revealed the presence of GnRH networks in a major motor control centre and fibre tract system in the hindbrain and spinal cord. Both structures are major components in the control of motor movements, such as swimming. Phylogenetic and synteny analysis segregates the four zebrafish GnRH receptors into two distinct phylogenetic groups that are separate gene lineages conserved throughout vertebrate evolution. In Ciona intestinalis, we found two GnRH genes that each encode three GnRH decapeptides in tandem, for six unique GnRH forms from this species. These genes are expressed throughout development. With an immunocytochemical approach, at least one peptide was found in the dorsal strand nerve plexus adjacent to the gonads in adults. Injection near the gonads of gravid Ciona quickly induced spawning, suggesting a novel action for control of reproduction by GnRH. My further studies identified four novel GnRH receptors encoded within the genome of this protochordate, and showed that three receptors responded to Ciona GnRHs by stimulating intracellular accumulation of cAMP. In contrast, only one receptor activated inositol phosphate turnover in response to one of the Ciona GnRHs. My final study involved identifying the GnRH signalling components in amphioxus. I found four novel GnRH receptors, with three displaying sensitivity to the highly conserved vertebrate GnRH2 and one of these showing selectivity for GnRH1. My pharmacological testing showed that the capacity to respond to GnRH1 and GnRH2 is evolutionarily conserved between amphioxus and vertebrates, and that key motifs found to be important in GnRH binding, signalling and activation are present in the amphioxus receptors. Phylogenetic analysis showed that two receptors cluster with the recently identified octopus GnRHR-like sequence; the other two receptors group at the base of the vertebrate GnRHR clade and may represent the proto-vertebrate condition, after which gene duplication and sequence divergence resulted in the four contemporary vertebrate GnRHRs. This work reveals novel and important features of the GnRH signalling axis throughout chordate evolution.

Much of Natural Science involves the study of patterns in nature and the documentation of how these patterns reflect and affect evolution. It is in this spirit that I have analyzed three distinct life history traits of austral South American forest passerines' to investigate whether their evolutionary patterns can be linked to evolutionary processes. This thesis reports six years of data on ten avian species from regular mist netting on Navarino Island, Chile. I found that the majority of species adhere to the same ecogeographical rules that govern the life history strategies of high latitude Northern Hemisphere birds. Eight of the species (Nancy says to list species but UVIC says abstract can only be a few words) have ancestors that originated in the tropics. The other two species have ancestors that originated in the Northern Hemisphere and expanded into the tropics where they evolved tropical life history strategies. The results of this study confirm the importance of the environment on avian speciation in newly accessible niches.

Salmon aquaculture is a controversial industry in British Columbia (BC). First Nations in BC have expressed concerns about possible contamination of traditionally harvested foods by waste from salmon farms. Trace elements are released from farms via waste feed and feces, as well as leaching from netpens and antifouling paints. In addition to elemental analysis, farm waste can also be traced using stable isotopes of nitrogen and carbon. Due to the use in salmon feed of protein and oil derived from pelagic marine fish, farm waste is typically enriched in heavier isotopes of nitrogen and carbon when compared to marine particulate organic matter. in partnership with First Nations from Ahousaht, BC, I investigated these effects by determining the concentrations of three metals and one metalloid in salmon feed, sediment and Manila clams Venerupis philippinarum from six sites in Clayoquot Sound, on the west coast of Vancouver Island, BC. Samples were collected from three sites near salmon farms and three reference sites in four different months spanning the traditional clam harvesting season. The results suggested that salmon feed continues to be a source of trace elements in the marine environment; however, salmon farms did not appear to be elevating concentrations in nearby clam tissue and sediment. Different environmental conditions between sites may have exerted a greater influence on elemental concentrations than farm-derived elements. Contrary to findings in earlier studies, the nitrogen signature of salmon feed was not enriched relative to marine particulate organic matter and was not a useful tracer of farm waste. This may have resulted from the reformulation of salmon feed to include greater quantities of protein and oil from terrestrial rather than marine sources. Due to the importance of Manila clams in First Nations' diets, the high density of salmon farms in the study area, the likelihood of ongoing feed reformulation, and the propensity for contaminants to accumulate over time, ongoing monitoring of sediment and bivalves in the area would be advisable.