Odonatopera exhibit a wide diversity of morphologies for an ancient group of winged insects. A morphological matrix of 463 characters is compiled for 347 extant and fossil representatives used in parsimony analyses, implemented in TNT, to document arrangements of taxonomic groups above the family level. Missing data and other challenges approaches implemented and interpretation of the results. We employ a novel approach to testing monophyly relative to quantities of missing data for each taxon. Phylogenetic reconstructions recover patterns of monophyly and trends based on missing data. We discuss the implications of our findings on missing data as well as limitations to systematics in general for Odonatoptera.

<p>The goal of my thesis is to understand the genetics of a complex behavioral trait, vocal learning, which serves as a critical substrate for human spoken language. With the available genomes of 23 mammals, I developed a novel approach based on molecular homoplasy to reveal Single Non-random Amino Acids Patterns (SNAAPs) that are associated with convergent traits, a task that proved intractable for standard approaches, e.g. dN/dS analyses. Of 73 genes I identified in mammalian vocal learners, ~25% function in neural connectivity, auditory or speech processing. Remarkably, these include a group of 6 genes from the ROBO1 axon guidance pathway. In birds, I found ROBO1 and its ligand SLIT1 show convergent differential expression in the motor output song nucleus of the three independent lineages of vocal learners but not in analogous brain areas of vocal non-learners, and ROBO1 is developmentally regulated during song learning critical periods in songbirds. In a different set of genes, I came across an unexpected discovery of the excess sharing of homoplastic substitutions in humans and domesticated species. I revealed biased nucleotide transitions (mostly favoring A/G mutation) for above amino acid substitutions and found that this rule was significantly relaxed during domestication for artificial selection. Overall, my thesis has resulted in a novel approach for studying convergent complex traits and provided critical insights into the evolution of vocal learning specifically, and complex traits generally.</p> / Dissertation

<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

The Canary Island pine, Pinus canariensis, is an endemic tree that forms one of the main forest ecosystems within the archipelago, and whose distribution has been reduced in the last five centuries by clear cutting for the extraction of timber and tar. It was in the XXth century that exploitation declined and reforestation programs were brought forward for the restoration of an ecosystem that harbours a number of endangered endemic species of plants and animals. In addition to reforestation efforts, an understanding of population genetic processes is also necessary for the successful conservation management of the Canarian pine forest, particularly in light of gathering evidence for local adaptation.<br /><br />In this thesis historical and contemporary gene flow within P. canariensis was studied with nuclear and chloroplast microsatellite markers. High immigration rates (0.68–0.75) were estimated as expected for an outcrossing windpollinated tree. Nevertheless, significant population differentiation (theta = 0.019, RST = 0.044) was detectable for sites separated by only a few kilometres. Within the context of reforestation programs the high levels of gene flow detected would appear to have a positive effect on reforested stands by facilitating the immigration of local alleles from natural stands into potentially genetically depauperate first generation gene pools of reforested stands.<br /><br />Historical population growth was revealed with chloroplast microsatellites for most populations of P. canariensis. Population expansions for the pine parasite weevil Brachyderes rugatus were also detected, broadly coinciding with the population expansions within the Canary Island pine forests. Given the estimated times of expansion, these population demographic increases would seem likely related to the process of colonisation of newly emerged islands or local patches after volcanic disturbance. Detection and dating of these expansions from chloroplast microsatellites was, to some degree, negatively affected by homoplasy (i.e. parallel and back mutations).<br /><br />Coalescent simulations of the evolution of chloroplast microsatellites were applied to study the effects of homoplasy in the statistical analysis of population structuring. Measures of genetic diversity based on number of haplotypes and genetic distances were differently affected. Genetic distances were underestimated but were proportional to the actual value. These effects help to explain the lower performance of statistical analyses for the detection and dating of population expansions. Further research on the effects of homoplasy in the analysis of population differentiation using chloroplast microsatellites is essential.

A central concept in Evolutionary theory is the character trait. It provides a context in which to explore differences and similarities among taxa, both extant and extinct. It is expanded in scope in Evolutionary Developmental theory to functional units with a biological role, "evolutionarily stable configurations." The talo-crural joint is such a configuration, a highly canalized structural unit in primates forming the interface between organism, and foot and substrate. It is a microcosm in which to examine the relationship of shape with environment and function and the interplay of genetics, ontogeny, and use. Geometric Morphometric analysis of landmark data was employed in studying the articular surfaces of the talus in a diverse sample of adult specimens in nine catarrhine taxa. The influence of four factors on talar shape was examined: superfamily, a proxy for phylogeny; size and mass, a proxy for physical attributes; and substrate preference, a proxy for behavior. All significantly affected shape, and substrate preference was unrelated to the others. Appositional articular morphology, the shape of the subchondral bone surfaces of the talo-crural joints in an expanded sample of 12 taxa, showed a significant effect of the four proxies on the tibial and talar components, and substrate preference was weakly related to the other proxies in each. Singular Warp analysis of the cross-covariance matrices of the joints demonstrated sorting of taxa by substrate use and signals of convergent and divergent evolution among hominoids and cercopithecoids in joint shape. The ontogeny of the appositional articular shape was examined using adult and subadult specimens grouped by molar eruption. Singular Warp analysis demonstrated a genetic signal in the subadults, strongest in the slowly maturing African hominoids, and an epigenetic signal across taxa to substrate use in the adults. The talo-crural joint, a highly canalized, modular, and integrated "evolutionarily stable configuration," provides a model for the study of the evolution of shape. The epigenetic signal observed is consistent with plasticity or developmental plasticity in response to the interaction of the joint complex with the environment due to a behavioral effect, substrate use. This dissertation included previously unpublished, co-authored material.

No description available.

These studies compare neurotransmitter localization and the behavioral functions of homologous neurons in nudibranch molluscs to determine the types of changes that might underlie the evolution of species-specific behaviors. Serotonin (5-HT) immunohistochemistry in eleven nudibranch species indicated that certain groups of 5 HT-immunoreactive neurons, such as the Cerebral Serotonergic Posterior (CeSP) cluster, are present in all species. However, the locations and numbers of many other 5 HT-immunoreactive neurons were variable. Thus, particular parts of the serotonergic system have changed during the evolution of nudibranchs. To test whether the functions of homologous neurons are phylogenetically variable, comparisons were made in species with divergent behaviors. In Tritonia diomedea, which crawls and also swims via dorsal-ventral body flexions, the CeSP cluster includes the Dorsal Swim Interneurons (DSIs). It was previously shown that the DSIs are members of the swim central pattern generator (CPG); they are rhythmically active during swimming and, along with their neurotransmitter 5-HT, are necessary and sufficient for swimming. It was also known that the DSIs excite efferent neurons used in crawling. DSI homologues, the CeSP-A neurons, were identified in six species that do not exhibit dorsal-ventral swimming. Many physiological characteristics, including excitation of putative crawling neurons were conserved, but the CeSP A neurons were not rhythmically active in any of the six species. In the lateral flexion swimmer, Melibe leonina, the CeSP-A neurons and 5-HT, were sufficient, but not necessary, for swimming. Thus, homologous neurons, and their neurotransmitter, have functionally diverged in species with different behaviors. Homologous neurons in species with similar behaviors also exhibited functional divergence. Like Melibe, Dendronotus iris is a lateral flexion swimmer. Swim interneuron 1 (Si1) is in the Melibe swim CPG. However, its putative homologue in Dendronotus, the Cerebral Posterior ipsilateral Pedal (CPiP) neuron, was not rhythmically active during swim-like motor patterns, but could initiate such a motor pattern. Together, these studies suggest that neurons have changed their functional relationships to neural circuits during the evolution of species-specific behaviors and have functionally diverged even in species that exhibit similar behaviors.

L'un des objectifs centraux de la biologie est de comprendre comment l'ADN, la séquence primaire, donne lieu à des traits observables. À cette fin, nous examinons ici des méthodes pour identifier les composants génétiques qui influencent les traits microbiens. Par « identifier », nous entendons l'élucidation à la fois l'état allélique et de la position physique de chaque variante causale d'un phénotype d'intérêt à la résolution des nucléotides de paires de bases. Nous nous sommes concentrés sur les études d'association génomique (genome-wide association studies; GWAS) en tant qu'approche générale d’étudier l'architecture génétique des traits. L'objectif global de cette thèse était d'examiner de manière critique les méthodologies GWAS et de les considérer en pratique dans des populations microbiennes fortement clonales et non- clonales (i.e. avec recombinaison fréquent). Le domaine de la GWAS microbienne est relativement nouveau par rapport aux quinze dernières années de la GWAS humaine, et en tant que tel, nous avons commencé par un examen de l'état de la GWAS microbienne. Nous avons posé deux questions principales : 1) Les méthodes GWAS humaines fonctionnent-elles facilement et sans modification pour les populations microbiennes ? 2) Et sinon, quels sont les problèmes méthodologiques centraux et les modifications nécessaires pour la GWAS microbienne? À partir de ces résultats, nous avons ensuite détaillé le déséquilibre de liaison (linkage disequilibrium; LD) comme principal obstacle dans la GWAS microbien, et nous avons présenté une nouvelle méthode, POUTINE, pour relever ce défi en exploitant les mutations homoplasiques pour briser implicitement la structure LD. Le reste de la thèse présente à la fois les méthodes traditionnelles GWAS (comptage des allèles) et POUTINE (comptage d’homoplasies) appliquées à une population hautement recombinogène de génomes de vibrions marins. Malgré une taille d'échantillon modeste, nous donnons un premier aperçu de l'architecture génétique de la résistance aux bactériophages dans une population naturelle, tout en montrant que les récepteurs des bactériophages jouent un rôle primordial. Ce résultat est en pleine cohérence avec des expériences en laboratoire de coévolution phage-bactérie. Il est important de noter que cette architecture met en évidence à quel point la sélection positive peut sculpter certains traits microbiens différemment de nombreux traits complexes humains, qui sont généralement soumis à une faible sélection purificatrice. Plus précisément, nous avons identifié des mutations à effet important à haute fréquence qui sont rarement observées dans les phénotypes complexes humains où de nombreuses mutations à faible effet contribuent à l'héritabilité. La thèse se termine par des perspectives sur les voies à suivre pour la GWAS microbienne. / One of the central goals of biology is to understand how DNA, the primary sequence, gives rise to observable traits. To this aim, we herein examine methods to identify the genetic components that influence microbial traits. By "identify" we mean the elucidation of both the allelic state and physical position of each causal variant of a phenotype of interest down to the base-pair nucleotide resolution. Our focus has been on genome-wide association studies (GWAS) as a general approach to dissecting the genetic architecture of traits. The overarching aim of this thesis was to critically examine GWAS methodologies and to consider them in practice in both strongly clonal and highly recombining microbial populations. The field of microbial GWAS is relatively new compared to the over fifteen years of human GWAS, and as such, we began this work with an examination of the state of microbial GWAS. We asked and attempted to answer two main questions: 1) Do human GWAS methods readily work without modification for microbial populations? 2) And if not, what are the central methodological problems and changes that are required for a successful microbial GWAS? Building from these findings, we then detailed linkage disequilibrium (LD) as the primary obstacle in microbial GWAS, and we presented a new method, POUTINE, to address this challenge by harnessing homoplasic mutations to implicitly break LD structure. The remainder of the thesis showcases both traditional GWAS methods (allele counting) and POUTINE applied to a highly recombining population of marine vibrio genomes. Despite a small sample size, we provide a first glimpse into the genetic architecture of bacteriophage resistance in a natural population and show that bacteriophage receptors play a primary role consistent with experimental populations of phage-bacteria coevolution. Importantly, this architecture highlights how strong positive selection can sculpt some microbial traits differently than many human complex traits, which are generally under weak purifying selection. Specifically, we identified common frequency, large-effect mutations that are rarely observed in human complex phenotypes where many low-effect mutations are thought to contribute to the bulk of heritability. The thesis concludes with perspectives on ways forward for microbial GWAS.

Chapter One: Raven's 1985 phylogenetic analysis of the Mygalomorphae placed a number of previously unrelated genera into the rastelloid family Cyrtaucheniidae. Although Goloboff's 1993 reanalysis of mygalomorph relationships retained the familial composition of the Rastelloidina it di not support cyrtaucheniid monophyly. This study resolves the issue of cyrtaucheniid monophyly within the context of the Rastelloidina. Using 71 morphological characters scored for 29 mygalomorph taxa we find that the Cyrtaucheniidae is polyphyletic and propose the following families in its place: Cyrtaucheniidae, Kiamidae (new family), Aporoptychidae (new rank), Ancylotrypidae (new family) and Euctenizidae (new rank). We also propose two new euctenizid genera, Apachella and Sinepedica, revise the taxonomy of the euctenizids of the Southwestern United States, and present a key for these six genera. In addition to the morphologically based phylogeny we test and refine the euctenizid intergeneric phylogeny using molecular data (mitochondrial 16S rRNA and COI genes and 28S rRNA nuclear genes). The results of the combined morphological and molecular analysis are used to construct a composite rastelloid phylogeny that is used to investigate biogeographical relationships, burrow entrance evolution, and homoplasy. Chapter Two: This systematic study of the predominately Californian trapdoor spider genus Aptostichus Simon, 1890 describes 28 species, 25 of which are newly described: A. atomus, A. improbulus, A. insulanus, A. icenoglei, A. ebriosus, A. muiri, A. cahuillus, A. luiseni, A. serranos, A. calientus, A. chemehuevi, A. shoshonei, A. pauitei, A. tipai, A. cochesensis, A. indegina, A. gertschi, A. kristenae, A. fornax, A. spinaserratus, A. brevifolius, A. brevispinus, A. agracilapandus, A. tenuis, and A. gracilapandus. Aptostichus stanfordianus Smith, 1908 is considered to be a junior synonym of A. atomarius Simon 1890. Using 72 quantitative and qualitative morphological characters we propose a preliminary phylogeny for this group. Based on the results of this phylogenetic analysis, we recognize the Atomarius, Simus, Hesperus and Pandus species groups. Additionally, our phylogenetic analysis indicates that adaptations favoring the invasion of the very arid desert habitats of southern California have evolved multiple times in the Aptostichus clade. The existence of both desert and non - desert species in three of the four species groups makes this genus an ideal candidate for the study of the evolutionary ecology of desert arthropods. Chapter Three: Aptostichus simus is a trapdoor spider that is endemic to the coastal dunes of southern California and is recognized as a single species on morphological grounds. Mitochondrial DNA 16S rRNA sequences demonstrate that populations from San Diego County, Los Angeles County, Santa Rosa Island, and Monterey County are extremely divergent (6 - 12%). These results are comparable to, or higher than recent reports of species - level differences in other invertebrate taxa. A molecular clock hypothesis shows that these four populations have been separated for 2 - 6 million years. A statistical cluster analysis of morphological features demonstrates that this genetic divergence is not reflected in anatomical features that might signify ecological differentiation among these lineages. The species status of these divergent populations of A. simus depends upon the species concept utilized. The time - limited genealogical perspective that is employed separates A. simus into two genetically distinct species. This study suggests that a species concept based on morphological distinctiveness in spider groups with limited dispersal capabilities probably underestimate taxonomic diversity. / Ph. D.

Microsatellites are repetitive DNA characterized by tandem repeats of short motifs (2 – 5 bp). High mutation rates make them ideal for population level studies. Microsatellite allele genesis is generally attributed to strand slippage, and it is assumed that alleles are caused only by changes in repeat number. Most analyses are limited to alleles (electromorphs) scored by mobility only, and models of evolution rarely account for homoplasy in allele length. Additionally, insertion/deletion events (indels) in the flanking region or interruptions in the repeat can obfuscate the accuracy of genotyping. Many investigators use microsatellites, designed for a focal species, to screen for genetic variation in non-focal species. Comparative studies have shown different mutation rates of microsatellites in different species, and even individuals. Recent studies have used reciprocal comparisons to assess the level of polymorphism of microsatellites between pairs of taxa. In this study, I investigated the evolution of microsatellites within a phylogenetic context, using comparisons within the rodent family Bathyergidae. Bathyergidae represents a monophyletic group endemic to sub-Saharan Africa and relationships are well supported by morphological and molecular data. Using mitochondrial and nuclear DNA, a robust phylogeny was generated for the Bathyergidae. From my results, I proposed the new genus, Coetomys. I designed species-specific genotyping and microsatellite flanking sequence (MFS) primers for each genus. Sequencing of the MFS provided direct evidence of the evolutionary dynamics of the repeat motifs and their flanking sequence, including rampant electromorphic homoplasy, null alleles, and indels. This adds to the growing body of evidence regarding problems with genotype scores from fragment analysis. A number of the loci isolated were linked with repetitive elements (LTRs and SINEs), characterized as robust phylogenetic characters. Results suggest that cryptic variation in microsatellite loci are not trivial and should be assessed in all studies. The phylogenetic utility of the nucleotide variation of the MFS was compared to the well-resolved relationships of this family based on the 12S/TTR phylogeny. Variation observed in MFS generated robust phylogenies, congruent with results from 12S/TTR. Finally, a number of the indels within the MFS provided a suite of suitable phylogenetic characters.