Species boundaries in bats: a philosophical, morphometric, environmental, and phylogenetic analysis of the genera Anoura, Carollia and Sturnira

Thesis (Ph.D.)--Boston UniversitySpecies are central to evolutionary biology, systematics and taxonomy. However, their precise definition and diagnosis is not straightforward. Species may be purely nominal constructs of the human mind or they may be real entities. Part of the difficulty of defining and diagnosing species lies in the continuous nature of variation from the level of the individual to the population, subspecies and species. It is here where systematics and taxonomy become challenging and exciting tools for understanding life on the planet. For bats, most of the efforts to describe and differentiate species have been qualitative. This may have worked in earlier times, during the first efforts to describe and name species. But, more recently, our perspectives have become sharper and the shortcomings of the qualitative approach have become obvious. This thesis is a collection of published essays, submitted studies, and ongoing research into the boundaries of bat species. In each chapter, I stress that species are not ideas or categories in the mind, but are real entities, based on testable hypotheses about the distribution of character states within multiorganismal entities. Therefore, these hypotheses and distributions of character states should optimally be analyzed through the prism of statistical inference. The dynamics of size and shape in the genus Anoura are discussed in the context of the space occupied by the different species within the genus, with novel insights into the interpretation of the distribution of these species in morphospace. For boundaries in the genus Carollia, I reassess current taxonomical knowledge, analyze morphological variation in relation to the environment, and the statistical uncertainty of species discrimination. In the species-rich genus Sturnira, I analyze a large morphological dataset for several species from Ecuador, describe a new species (S. peria) synonymize an old one (S. luisi), and provide a new perspective on phylogenetic relationships and species boundaries

The Size of Major Mammalian Sensory Organs as Measured from Cranial Characters, and Their Relation to the Biology and Evolution of Mammals

The basic functional principles of the major sensory systems of mammals (e.g., vision, hearing and olfaction) are fairly well understood. Within certain limits, increasing the size of the structures that collect the adequate physical signals and transduce them into neural responses is a priori expected to improve sensory performance, and the relative size of a sensory organ might provide a simple measure of the relative importance of the corresponding sense. If investments into complex sensory organs can be expressed by simple anatomical measures, this would facilitate large-scale comparative studies of the ecology and evolutionary history of the sensory modalities in different groups. Although sensory organs mainly consist of soft tissues, they are embedded in bony structures and some include functional bony components. Thus it is possible to define potentially relevant osteological dimensions that can be measured from both extant and extinct (fossil) species, and this is the point of departure of the present thesis. The original measurements focus on two senses, olfaction and vision. In the first study, the area of the cribriform plate of the ethmoid bone is defined, measured, and validated as a useful hard-tissue anatomical proxy for the sensitivity of olfaction in various mammalian groups. It is shown that cribriform plate area (representing olfactory organ size) grows proportionally to skull area (representing animal size), with no sign of levelling off in the highest range. There are only a few taxa that have smaller olfactory organs than expected : these include monkeys and apes on the one hand, and the aquatic dugong on the other. The semi-aquatic pinnipeds, by contrast, have cribriform plate areas comparable in size to those of similar-sized terrestrial carnivores. In the second study, the analysis of orbit size as a proxy for eye size, which has previously been used for primates by several authors, is applied to a comprehensive mammalian data base of 355 species representing most major orders, largely based on new original measurements. It was first shown that the eyes of the groups included are effectively spherical and that the relation between eye and orbit size is regular enough for the orbit to be informative of eye size and thus visual sensitivity/acuity. The earlier primate studies have found that (small) nocturnally active species have relatively larger orbit diameters than diurnally active species of similar size. While this was confirmed for primates, no general diurnal/nocturnal difference in orbit size at the same skull size was found in non-primate mammals. The allometric growth of orbit size with increasing skull size was steeper for nocturnal than diurnal mammals, but the significance of this is unclear, as the former sample was dominated by smaller species compared with the latter sample. In cathemeral species (i.e., species active during both night and day), the allometric relation of orbit size to skull size was more similar to that of nocturnal than of diurnal species. Taken together, the results suggest that relative orbit diameter is not a useful indicator of the diel activity pattern of non-primate mammals, and cannot be used to infer the pattern of fossil species. In the third study, the question of the trade-off relations between three major senses, vision, hearing, and olfaction, was investigated. The proxy measure used for the auditory organ was the size of the middle ear bones as reported by Nummela et al. (1995). The residual size of each organ in each species was calculated as its deviation from the global mammalian regression line relating the respective organ proxy size to body size. The residuals were plotted into a three-dimensional sensory space , where the coordinate axes represent vision, hearing, and smell. This provides a graphic representation of correlations between organ sizes, both positive and negative. The results suggested that good vision and hearing are often positively correlated in mammals; thus, it seems that investments in eyes and ears are likely to co-operate rather than compete. By contrast, it appeared that a keen sense of smell rarely occurs together with equally keen vision and/or hearing.I denna avhandling visar jag hur man genom skallmätningar kan undersöka nu levande däggdjurs sinnesorgan och deras relativa betydelse för livsföringen hos diverse olika arter. För att kunna kvantitativt undersöka de olika sinnesorganen har jag mätt utvalda anatomiska delar av däggdjurs skallar. De sinnesorgan som jag i första hand har undersökt är doft- och synsinnet. Som mått på doftsinnet har jag använt det så kallade silbenets yta i förhållande till själva skallens yta, och som mått på synsinnet har jag använt ögonhålans diameter i förhållande till skallens längd. För att kunna använda dessa respektive skelettstrukturer som mått på sinnesorganens skärpa är det först nödvändigt att påvisa att dessa strukturers storlek verkligen hänger funktionellt sett direkt ihop med de relevanta mjukvävnadsstrukturerna. Jag påvisar i min avhandling att silbenets yta korrelerar direkt med doftepitelets yta (som i sin tur funktionellt hänger ihop med doftskärpan), och att ögonhålans diameter korrelerar direkt med själva ögats storlek (som i sin tur funktionellt hänger ihop med synskärpa och -känslighet). Med andra ord, genom att mäta silbenets eller ögonhålans storlek i förhållande till skallens storlek hos ett givet däggdjur kan man säga hur pass väl utvecklade dessa respektive sinnen är hos den. Mina resultat visar att silbenets yta inte varierar med kroppsstorlek: små däggdjur har relativt sett lika stora silbensytor som stora däggdjur. De mest avvikande däggdjuren beträffande silbenets yta/doftsinnets storlek är dels de mest strikt vattenlevande arterna, dels aporna och människan; dessa däggdjur har relativt sett betydligt mindre silbensytor (och i vissa fall till och med funktionellt fullständigt förkrympta sådana) än övriga däggdjur, vilket tyder på att de har ett relativt svagt utvecklat doftsinne. Beträffande ögonhålans relativa storlek hos däggdjur har jag jämfört denna mellan dags- och nattaktiva arter; dylika undersökningar har tidigare utförts på primater, men inte i någon större skala på övriga däggdjur. Mina mätningsresultat visar att till skillnad från primater, bland vilka nattaktiva arter har relativt sett tydligt större ögonhålor än dagaktiva arter, uppvisar övriga däggdjur inga tydliga skillnader mellan dag- och nattaktiva arter. Detta betyder att ögonhålans storlek inte kan användas för att rekonstruera levnadssättet hos utdöda, fossila icke-primater. Slutligen har jag också undersökt hur och på vilket sett doft-, syn- och hörselsinnet samarbetar med eller ersätter varandra (som mått på hörselsinnet använder jag hörselbenens relativa storlek). Resultaten tyder på att god syn och god hörsel ofta hänger ihop hos däggdjur, medan däremot en art som har ett stort doftorgan sällan har särskilt stora ögon eller stora hörselben. Med andra ord, det tycks råda en viss "arbetsfördelning" mellan dessa tre sinnen

ANALYSIS OF THE ROLE OF TWO AUTOPHAGY PATHWAY RELATED GENES, BECN1 AND TSC1, IN MURINE MAMMARY GLAND DEVELOPMENT AND DIFFERENTIATION

The mammary gland is a dynamic organ that undergoes the majority of its development in the postnatal period in four stages; mature virgin, pregnancy, lactation, and involution. Every stage relies on tightly regulated cellular proliferation, programmed cell death, and tissue remodeling mechanisms. Misregulation of autophagy, an intracellular catabolic process to maintain energy stores, has long been associated with mammary tumorigenesis and other pathologies. We hypothesize that appropriate regulation and execution of autophagy are necessary for proper development of the mammary ductal tree and maintenance of the secretory epithelia during late pregnancy and lactation. To test this hypothesis we examined the role of two genes during development of the mammary gland. Beclin1 (Becn1) is an essential autophagy gene. Since the Becn1 knockout model is embryonic lethal, we have generated a Becn1 conditional knockout (cKO). We used two discrete mammary gland-specific Cre transgenic lines to interrogate the role of BECN1 during development. We report that MMTV-CreD; Becn1fl/fl mice have a hyper-branching phenotype and WAP-Cre; Becn1fl/- mice are unable to sustain a lactation phase. Becn1 mutants exhibit abnormal glandular morphology during pregnancy and after parturition. Moreover, when autophagy is chemically inhibited in vitro, mammary epithelial cells have an increased mean number of lipid droplets per cell. MTOR inhibits autophagy upstream of BECN1; we looked higher in the regulatory pathway for regulatory candidates. It has been well characterized that Tuberous sclerosis complex 1 (TSC1), in a heterodimer with its primary binding partner TSC2, inhibits MTOR signaling via inhibition of RHEB. Using the Tsc1 floxed model we generated a mammary gland specific Tsc1 cKO and found that these mice phenocopy the Becn1 cKO mice, including a gross lactation failure. Tsc1 cKO glands have altered morphology, retained lipid droplets in secretory epithelia, and an overall increase in MTOR signaling. We show that TSC1 and BECN1 are interacting partners, and that the interaction is nutrient responsive. These results suggest that Becn1 and Tsc1 are necessary for proper mammary gland development and differentiation. Furthermore, we have demonstrated a novel murine protein-protein interaction and an important link between regulation of MTOR pathway and regulation of autophagy in a developmental context

Why do whales exist? cancer resistance in cetaceans

Cancer is the inevitable fate for all multicellular organisms should they live long enough. However, if all mammalian cells have approximately equivalent probabilities of cancer-associated gene mutation then, all else being equal, the number of cells susceptible to transformation should scale with body size and longevity, implying larger, longer-lived mammals such as whales should be disproportionately more prone to cancer than smaller mammals, such as mice, simply due to cell number alone. Empirical evidence to date does not support this prediction, and the discrepancy between theory and observation is known as Peto’s paradox. The mere existence of whales and other large mammals demands the evolution of a suite of cancer suppressive mechanisms in order to resolve the paradox; the establishment and understanding of which being the focus of this research. First, cancer incidence rates across the animal kingdom are collected and assessed, quantitatively revealing the veracity of Peto’s paradox and the relationship between incidence risk and scaling basal metabolic rate. Next, computational models are developed to test the hypothesis that intrinsic metabolic scaling may itself be sufficient to explain Peto’s paradox. Results reveal that though incorporating scaling life-history traits into the narrative helps, they alone aren’t sufficient to explain cancer suppression in large mammals. Instead, genetic control is established as playing a crucial role. Finally, comparative analysis of the available cetacean genomes and transcriptomes uncovers several gene duplication events in key cancer-associated pathways, alongside lineage-specific and size-dependent selection in gene families associated with cancer resistance. This work demonstrates though there exists no singular explanation for Peto’s paradox, the disparate mechanisms that underlie the trajectory towards cancer resistance in independent lineages are all variations on a theme - the understanding of which may elucidate insight towards the development of future targets for human cancer therapies

Integrating genomics with the fossil record to explore the evolutionary history of Echinoidea

Echinoidea constitutes one of five major clades of living echinoderms, marine animals uniquely characterized by a pentaradial symmetry. Approximately 1,000 living and 10,000 extinct species have been described, including many commonly known as sea urchins, heart urchins and sand dollars. Today, echinoids are ubiquitous in benthic marine environments, where they strongly affect the functioning of biodiverse communities such as coral reefs and kelp forests. Given the quality of their fossil record, their remarkable morphological complexity and our thorough understanding of their development, echinoids provide unparalleled opportunities to explore evolutionary questions in deep-time, providing access to the developmental and morphological underpinnings of evolutionary innovation. These questions cannot be addressed without first resolving the phylogenetic relationships among living and extinct lineages. The goal of this dissertation is to advance our understanding of echinoid relationships and evolutionary history, as well as to explore more broadly the integration of phylogenomic, morphological and paleontological data in phylogenetic reconstruction and macroevolutionary inference.In Chapter 1, I report the results of the first phylogenomic analysis of echinoids based on the sequencing of 17 novel echinoid transcriptomes. Phylogenetic analyses of this data resolve the position of several clades—including the sand dollars—in disagreement with traditional morphological hypotheses. I demonstrate the presence of a strong phylogenetic signal for these novel resolutions, and explore scenarios to reconcile these findings with morphological evidence. In Chapter 7, I extend this approach with a more thorough taxon sampling, resulting in a robust topology with a near-complete sampling of major echinoid lineages. This effort reveals that apatopygids, a clade of three species with previously unclear affinities, represent the only living descendants of a once diverse Mesozoic clade. I also perform a thorough time calibration analysis, quantifying the relative effects of choosing among alternative models of molecular evolution, gene samples and clock priors. I introduce the concept of a chronospace and use it to reveal that only the last among the aforementioned choices affects significantly our understanding of echinoid diversification. Molecular clocks unambiguously support late Permian and late Cretaceous origins for crown group echinoids and sand dollars, respectively, implying long ghost ranges for both. Fossils have been shown to improve the accuracy of phylogenetic comparative methods, warranting their inclusion alongside extant terminals when exploring evolutionary processes across deep timescales. However, their impact on topological inference remains controversial. I explore this topic in Chapter 3 with the use of simulations, which show that morphological phylogenies are more accurate when fossil taxa are incorporated. I also show that tip-dated Bayesian inference, which takes stratigraphic information from fossils into account, outperforms uncalibrated methods. This approach is complemented in Chapter 2 with the analysis of empirical datasets, confirming that incorporating fossils reshapes phylogenies in a manner that is entirely distinct from increased sampling of extant taxa, a result largely attributable to the occurrence of distinctive character combinations among fossils. Even though phylogenomic and paleontological data are complementary resources for unraveling the relationships and divergence times of lineages, few studies have attempted to fully integrate them. Chapter 4 revisits the phylogeny of crown group Echinoidea using a total-evidence dating approach combining phylogenomic, morphological and stratigraphic information. To this end, I develop a method (genesortR) for subsampling molecular datasets that selects loci with high phylogenetic signal and low systematic biases. The results demonstrate that combining different data sources increases topological accuracy and helps resolve phylogenetic conflicts. Notably, I present a new hypothesis for the origin and early morphological evolution of the sand dollars and close allies. In Chapter 6, I compare the behavior of genesortR against alternative subsampling strategies across a sample of phylogenomic matrices. I find this method to systematically outperform random loci selection, unlike commonly-used approaches that target specific evolutionary rates or minimize sources of systematic error. I conclude that these methods should not be used indiscriminately, and that multivariate methods of phylogenomic subsampling should be favored. Finally, in Chapter 5, I explore the macroevolutionary dynamics of echinoid body size across 270 million years using data for more than 5,000 specimens in a phylogenetically explicit context. I also develop a method (extendedSurface) for parameterizing adaptive landscapes that overcomes issues with existing approaches and finds better fitting models. While echinoid body size has been largely constrained to evolve within a single adaptive peak, the disparity of the clade was generated by regime shifts driving the repeated evolution of miniaturized and gigantic forms. Most innovations occurred during the latter half of the Mesozoic, and were followed by a drastic slowdown in the aftermath of the Cretaceous-Paleogene mass extinction

Metric Selection and Metric Learning for Matching Tasks

A quarter of a century after the world-wide web was born, we have grown accustomed to having easy access to a wealth of data sets and open-source software. The value of these resources is restricted if they are not properly integrated and maintained. A lot of this work boils down to matching; finding existing records about entities and enriching them with information from a new data source. In the realm of code this means integrating new code snippets into a code base while avoiding duplication. In this thesis, we address two different such matching problems. First, we leverage the diverse and mature set of string similarity measures in an iterative semisupervised learning approach to string matching. It is designed to query a user to make a sequence of decisions on specific cases of string matching. We show that we can find almost optimal solutions after only a small amount of such input. The low labelling complexity of our algorithm is due to addressing the cold start problem that is inherent to Active Learning; by ranking queries by variance before the arrival of enough supervision information, and by a self-regulating mechanism that counteracts initial biases. Second, we address the matching of code fragments for deduplication. Programming code is not only a tool, but also a resource that itself demands maintenance. Code duplication is a frequent problem arising especially from modern development practice. There are many reasons to detect and address code duplicates, for example to keep a clean and maintainable codebase. In such more complex data structures, string similarity measures are inadequate. In their stead, we study a modern supervised Metric Learning approach to model code similarity with Neural Networks. We find that in such a model representing the elementary tokens with a pretrained word embedding is the most important ingredient. Our results show both qualitatively (by visualization) that relatedness is modelled well by the embeddings and quantitatively (by ablation) that the encoded information is useful for the downstream matching task. As a non-technical contribution, we unify the common challenges arising in supervised learning approaches to Record Matching, Code Clone Detection and generic Metric Learning tasks. We give a novel account to string similarity measures from a psychological standpoint and point out and document one longstanding naming conflict in string similarity measures. Finally, we point out the overlap of latest research in Code Clone Detection with the field of Natural Language Processing

Symmetry in Human Evolution, from Biology to Behaviours

Our knowledge of human evolution has made particular progress recently, due to the discovery of new fossils, the use of new methods and multidisciplinary approaches. Moreover, studies on the departure from symmetry, including variations in fluctuating or directional asymmetries, have contributed to the expansion of this knowledge. This Special Issue brings together articles that deal with symmetry and human evolution. The notion of symmetry is addressed, including whether to reconstruct deformed fossil specimens, study biological variations within hominins or compare them with extant primates, address the shape of the brain or seek possible relationships between biological and behavioural data

Annual Report of the Board of Regents of the Smithsonian Institution, showing the operations, expenditures, and condition of the Institution to July, 1897.

Annual Report of the Smithsonian Institution. 14 Apr. HD 575 (pts. 1-3), 55-2, v78-79 (pts. 1 and 2), 1228p. [3706-3708] Research related to the American Indian

T.S. Eliot : a bibliography of T.S. Eliot criticism, 1987-2013.

This bibliography of scholarship related to the writer T.S. Eliot is arranged chronologically by year and alphabetically within each year. This bibliography contains 1624 entries. Select entries have been annotated. Where available, annotations have been taken from the research database and are enclosed in brackets ([ ]). Annotations that have been taken from the works themselves are enclosed by asterisks. Annotations written by the author of this thesis have no special characters to distinguish them from other annotations. An annotated bibliography of Eliot criticism is essential to keep up with the recent resurgence in Eliot studies. The last bibliography published regarding Eliot's works was Sebastian Knowles and Scott A. Leonard's T.S. Eliot: Man and Poet, Volume 2: An Annotated Bibliography of a Decade of T.S. Eliot Criticism, 1977-1986. This new bibliography creates a central location for Eliot research for the years of 1987-2013

What is the Avatar? Fiction and Embodiment in Avatar-Based Singleplayer Computer Games: Revised and Commented Edition

What are the characteristic features of avatar-based singleplayer videogames, from Super Mario Bros. to Grand Theft Auto? The author examines this question with a particular focus on issues of fictionality and realism, and their relation to cinema and Virtual Reality. Through close-up analysis and philosophical discussion, the author argues that avatar-based gaming is a distinctive and dominant form of virtual self-embodiment in digital culture. This book is a revised edition of Rune Klevjer's pioneering work from 2007, featuring a new introduction by the author and afterword by Stephan Günzel, Jörg Sternagel, and Dieter Mersch