The evolutionary ecology of lampreys (Petromyzontiformes)

Lampreys (Petromyzontiformes) are an ancient vertebrate group, comprising 40 currently recognised species that range throughout the Northern and Southern Hemispheres. Despite a conserved morphology, lampreys nevertheless express a diverse range of life history strategies. Unusually for vertebrates larval lampreys are filter-feeding organisms prior to undergoing an extensive anatomical reorganisation, and the adoption of either a parasitic or a non-parasitic adult life. Parasitic lampreys consume the flesh and blood of actinopterygian fishes, either in marine or freshwater environments, while non-parasitic lampreys do not feed following their metamorphosis from the larval form. Morphological and genetic similarities between pairs of parasitic and non-parasitic lampreys have led to taxonomic confusion regarding the specific status of many non-parasitic forms, and the suggestion that the loss of the trophic adult phenotype is the result of a single species capable of producing alternative life history strategies. In this thesis it is argued that at least some paired species of lampreys do not comprise two distinct evolutionary lineages; rather, that non-parasitic lampreys represent one extreme in a continuum of life history variation expressed by a parasitic species. Some lamprey species, such as the European river lamprey Lampetra fluviatilis, are morphologically variable, exhibiting divergent phenotypes in response to ecological pressures, such as alternative foraging environments. Loch Lomond, Scotland contains a population of L. fluviatilis that feeds exclusively in the lake and exhibits a reduced body size and an overall morphology distinct from the typical anadromous form. Its foraging strategy indicates that it may be capable of switching hosts in the face of declining numbers of a presumed favoured and formerly abundant host, suggesting a certain amount of plasticity in its trophic ecology that may have ensured its survival in this freshwater lake. This freshwater-resident form, as well as anadromous L. fluviatilis and the non-parasitic species L. planeri, were found to spawn in a single river system within the Loch Lomond basin, and this site is crucial for the continued presence of this life history variant in Loch Lomond. The appearance of sexually mature specimens of three discrete phenotypes in this river, each representing an alternative life history strategy that may, or may not, belong to a single species, provides a crucial opportunity to test the strength of assortative mating between lamprey species pairs. Within this system the strength of assortative mating was found to be weak, and points to the possibility that freshwater-resident L. fluviatilis are mitigating gene flow between large anadromous parasitic L. fluviatilis, and small, non-parasitic L. planeri. As well as weak behavioural isolation, inter-specific sneak male mating tactics were documented among these populations, and represents the first time this phenomenon has been observed between paired lamprey species. Such behaviour indicates a lack of species-specific cues acting between L. fluviatilis and L. planeri, and suggests that hybrid offspring could be common in some systems. Testing hybrid viability (survivorship) between Loch Lomond’s two L. fluviatilis life history strategies and the sympatric L. planeri revealed no post-zygotic barriers to gene flow, at least in the form of gamete incompatibility. Perhaps more convincingly though, when comparing traditional morphometrics and body shape variation, as well as mitochondrial DNA sequences, between L. fluviatilis expressing different foraging strategies with populations of L. planeri, no robust species specific differentiation was observed. In fact, species delimitation between L. fluviatilis and L. planeri appears to be related solely to overall body size, which is itself a function of life history strategy. However, life history strategy was not correlated with current species designation as relationships among mtDNA haplotypes indicate non-parasitic populations have evolved independently multiple times throughout the geographic range of L. fluviatilis in Europe. Therefore, L. planeri should not be considered as a distinct species, either morphologically or genetically. Instead, L. fluviatilis appears capable of expressing a range of life history strategies; from parasitic anadromous populations through to non-parasitic stream-resident populations. The overall research approach employed in this thesis, i.e., the combination of ecological, behavioural, taxonomic and molecular studies, could be used to robustly examine the evolutionary ecology of parasitic and non-parasitic lampreys elsewhere

TEST-RETEST RELIABILITY OF SELECTED ERGOMETER GRINDING PERFORMANCE MEASURES

Reliability of grinding performance on a custom-built ergometer was assessed using 18 highly trained America’s Cup sailors. Sixteen grinding conditions varied by load, deck heel (tilt), and grinding direction (forward or backward) were examined. Performance measures were peak power (W) and external work over five seconds (kJ). Statistics were difference in mean (Mdiff), standard error of measurement (SEM) and intra-class correlation coefficients (ICC). External work (SEM = 1.6-6.9%; ICC = 0.91-0.99) was more reliable than peak power (SEM = 1.3-9.6%; ICC = 0.84-0.99). Performance was more consistent when varied by load than by heel condition, and was most reliable in lighter load conditions. Within heel conditions, downhill-uphill tilt was more reliable than right-left tilt. Grinding direction did not appear to affect performance reliability

RADseq and mate choice assays reveal unidirectional gene flow among three lamprey ecotypes despite weak assortative mating: Insights into the formation and stability of multiple ecotypes in sympatry

Adaptive divergence with gene flow often results in complex patterns of variation within taxa exhibiting substantial ecological differences among populations. One example where this may have occurred is the parallel evolution of freshwater‐resident nonparasitic lampreys from anadromous‐parasitic ancestors. Previous studies have focused on transitions between these two phenotypic extremes, but here, we considered more complex evolutionary scenarios where an intermediate freshwater form that remains parasitic is found sympatrically with the other two ecotypes. Using population genomic analysis (restriction‐associated DNA sequencing), we found that a freshwater‐parasitic ecotype was highly distinct from an anadromous‐parasitic form (Qlake‐P = 96.8%, Fst = 0.154), but that a freshwater‐nonparasitic form was almost completely admixed in Loch Lomond, Scotland. Demographic reconstructions indicated that both freshwater populations likely derived from a common freshwater ancestor. However, while the nonparasitic ecotype has experienced high levels of introgression from the anadromous‐parasitic ecotype (Qanad‐P = 37.7%), there is no evidence of introgression into the freshwater‐parasitic ecotype. Paradoxically, mate choice experiments predicted high potential for gene flow: Males from all ecotypes were stimulated to spawn with freshwater‐parasitic females, which released gametes in response to all ecotypes. Differentially fixed single nucleotide polymorphisms identified genes associated with growth and development, which could possibly influence the timing of metamorphosis, resulting in significant ecological differences between forms. This suggests that multiple lamprey ecotypes can persist in sympatry following shifts in adaptive peaks, due to environmental change during their repeated colonization of post‐glacial regions, followed by periods of extensive gene flow among such diverging populations

Predicting Crystal Structures with Data Mining of Quantum Calculations

Predicting and characterizing the crystal structure of materials is a key problem in materials research and development. It is typically addressed with highly accurate quantum mechanical computations on a small set of candidate structures, or with empirical rules that have been extracted from a large amount of experimental information, but have limited predictive power. In this letter, we transfer the concept of heuristic rule extraction to a large library of ab-initio calculated information, and demonstrate that this can be developed into a tool for crystal structure prediction.Comment: 4 pages, 3 pic

John Rawls between two enlightenments

John Rawls shares the Enlightenment's commitment to finding moral and political principles which can be reflectively endorsed by all individuals autonomously. He usually presents reflective autonomy in Kantian, rationalist terms: autonomy is identified with the exercise of reason, and principles of justice must be constructed which are acceptable to all on the basis of reason alone. Yet David Hume, Adam Smith and many other Enlightenment thinkers rejected such rationalism, searching instead for principles which can be endorsed by all on the basis of all the faculties of the human psyche, emotion and imagination included. The influence of these sentimentalists on Rawls is clearest in his descriptive moral psychology, but I argue that it is also present in Rawls's understanding of the sources of normativity. Although this debt is obscured by Rawls's explicit "Kantianism," his theory would be strengthened by a greater understanding of its debts to the sentimentalist Enlightenment

Space-based research in fundamental physics and quantum technologies

Space-based experiments today can uniquely address important questions related to the fundamental laws of Nature. In particular, high-accuracy physics experiments in space can test relativistic gravity and probe the physics beyond the Standard Model; they can perform direct detection of gravitational waves and are naturally suited for precision investigations in cosmology and astroparticle physics. In addition, atomic physics has recently shown substantial progress in the development of optical clocks and atom interferometers. If placed in space, these instruments could turn into powerful high-resolution quantum sensors greatly benefiting fundamental physics. We discuss the current status of space-based research in fundamental physics, its discovery potential, and its importance for modern science. We offer a set of recommendations to be considered by the upcoming National Academy of Sciences' Decadal Survey in Astronomy and Astrophysics. In our opinion, the Decadal Survey should include space-based research in fundamental physics as one of its focus areas. We recommend establishing an Astronomy and Astrophysics Advisory Committee's interagency ``Fundamental Physics Task Force'' to assess the status of both ground- and space-based efforts in the field, to identify the most important objectives, and to suggest the best ways to organize the work of several federal agencies involved. We also recommend establishing a new NASA-led interagency program in fundamental physics that will consolidate new technologies, prepare key instruments for future space missions, and build a strong scientific and engineering community. Our goal is to expand NASA's science objectives in space by including ``laboratory research in fundamental physics'' as an element in agency's ongoing space research efforts.Comment: a white paper, revtex, 27 pages, updated bibliograph

The fables of pity: Rousseau, Mandeville and the animal-fable

Copyright @ 2012 Edinburgh University PressPrompted by Derrida’s work on the animal-fable in eighteenth-century debates about political power, this article examines the role played by the fiction of the animal in thinking of pity as either a natural virtue (in Rousseau’s Second Discourse) or as a natural passion (in Mandeville’s The Fable of the Bees). The war of fables between Rousseau and Mandeville – and their hostile reception by Samuel Johnson and Adam Smith – reinforce that the animal-fable illustrates not so much the proper of man as the possibilities and limitations of a moral philosophy that is unable to address the political realities of the state

Mice and Men: Their Promoter Properties

Using the two largest collections of Mus musculus and Homo sapiens transcription start sites (TSSs) determined based on CAGE tags, ditags, full-length cDNAs, and other transcript data, we describe the compositional landscape surrounding TSSs with the aim of gaining better insight into the properties of mammalian promoters. We classified TSSs into four types based on compositional properties of regions immediately surrounding them. These properties highlighted distinctive features in the extended core promoters that helped us delineate boundaries of the transcription initiation domain space for both species. The TSS types were analyzed for associations with initiating dinucleotides, CpG islands, TATA boxes, and an extensive collection of statistically significant cis-elements in mouse and human. We found that different TSS types show preferences for different sets of initiating dinucleotides and cis-elements. Through Gene Ontology and eVOC categories and tissue expression libraries we linked TSS characteristics to expression. Moreover, we show a link of TSS characteristics to very specific genomic organization in an example of immune-response-related genes (GO:0006955). Our results shed light on the global properties of the two transcriptomes not revealed before and therefore provide the framework for better understanding of the transcriptional mechanisms in the two species, as well as a framework for development of new and more efficient promoter- and gene-finding tools

A review of the dodo and its ecosystem: insights from a vertebrate concentration Lagerstätte in Mauritius

The dodo Raphus cucullatus Linnaeus,1758, an extinct and flightless, giant pigeon endemic to Mauritius, has fascinated people since its discovery, yet has remained surprisingly poorly known. Until the mid-19th century, almost all that was known about the dodo was based on illustrations and written accounts by 17th century mariners, often of questionable accuracy. Furthermore, only a few fragmentary remains of dodos collected prior to the bird's extinction exist. Our understanding of the dodo's anatomy was substantially enhanced by the discovery in 1865 of subfossil bones in a marsh called the Mare aux Songes, situated in southeastern Mauritius. However, no contextual information was recorded during early excavation efforts, and the majority of excavated material comprised larger dodo bones, almost all of which were unassociated. Here we present a modern interdisciplinary analysis of the Mare aux Songes, a 4200-year-old multitaxic vertebrate concentration Lagerstätte. Our analysis of the deposits at this site provides the first detailed overview of the ecosystem inhabited by the dodo. The interplay of climatic and geological conditions led to the exceptional preservation of the animal and associated plant remains at the Mare aux Songes and provides a window into the past ecosystem of Mauritius. This interdisciplinary research approach provides an ecological framework for the dodo, complementing insights on its anatomy derived from the only associated dodo skeletons known, both of which were collected by Etienne Thirioux and are the primary subject of this memoir.Additional co-authors: Anneke H. Van Heteren, Vikash Rupear, Gorah Beebeejaun, Alan Grihault, J. (Hans) Van Der Plicht, Marijke Besselink, Juliën K. Lubeek, Max Jansen, Hege Hollund, Beth Shapiro, Matthew Collins, Mike Buckley, Ranjith M. Jayasena, Nicolas Porch, Rene Floore, Frans Bunnik, Andrew Biedlingmaier, Jennifer Leavitt, Gregory Monfette, Anna Kimelblatt, Adrienne Randall, Pieter Floore & Leon P. A. M. Claessen

Macrophage Activation and Differentiation Signals Regulate Schlafen-4 Gene Expression: Evidence for Schlafen-4 as a Modulator of Myelopoiesis

Background: The ten mouse and six human members of the Schlafen (Slfn) gene family all contain an AAA domain. Little is known of their function, but previous studies suggest roles in immune cell development. In this report, we assessed Slfn regulation and function in macrophages, which are key cellular regulators of innate immunity