Browsing Richard Gilder Graduate School by Issue Date
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- ItemA phylogenomic perspective on annelid evolution with emphasis on the evolution of bloodfeeding in leeches (Clitellata, Hirudinida)(2012-07-30) Kvist, Sebastian.Annelida Lamarck, 1809 embodies over 17,000 species of segmented worms such as leeches, earthworms, lugworms, sandworms and clamworms. The phylum has traditionally been divided into two main orders: Sedentaria Lamarck, 1818 and Errantia Andouin & Milne Edwards, 1834, yet Sedentaria is seldom recovered as monophyletic and Errantia has only been recovered as monophyletic in one study. Recently, a large amino acid data set of expressed sequence tags (EST’s) was created for Annelida and its close allies. The phylogenetic analyses of this data set, based on Bayesian inference and Maximum Likelihood estimations, recovered both Errantia and Sedentaria as monophyletic groups. Herein, I assess whether or not this hypothesis is also recovered by a nucleotide representation of the amino acids, and if the result is general across optimality criteria. Whereas parsimony analyses of the largest molecular character data set compiled for Annelida fails to recover Sedentaria or Errantia as monophyletic entities, re-analysis of the original amino acid data set does recover Errantia as monophyletic but with low support. In conjunction with previous studies, the analyses presented here suggest that the phylogenetic hypotheses of relationships both within Annelida, and between the phylum and its constituent taxa are still unstable and that finding suitable data for resolving this is an important yet problematic issue. Although medicinal leeches have long been used as treatment for various ailments because of their potent anticoagulation factors, the debates regarding the evolution of bloodfeeding and the ancestral feeding preference of leeches are still contentious. Moreover, neither the full diversity of salivary components that inhibit coagulation, much less the evolutionary selection acting on them, has been thoroughly investigated in a comparative manner. To address these questions, the full genome of the non-bloodfeeding leech Helobdella robusta was screened for anticoagulation factors. In addition, EST libraries from salivary glands of two species of medicinal leeches, Hirudo verbana and Aliolimnatis fenestrata, were constructed. For H. robusta, a total of eight loci matching leech antiplatelet proteins and positioned as a tandem array, were recovered with significantly low e-values, suggesting that this leech possesses ancestrally-inherited anticoagulants. In the medicinal leeches, expression of salivary peptides greatly exceed expectations and also suggest the feasibility of identifying the important active sites of the proteins through selective pressure analyses. Although symbiotic associations between bacteria and leeches are well documented, several questions concerning the function of the bacterial symbionts and their phylogenetic positioning still remain. To address this and other issues, herein I characterize and annotate a large subset of the genome of Reichenowia parasitica, an phaproteo-bacterial endosymbiont of the freshwater leech Placobdella parasitica. Results suggest that R. parasitica possesses genes coding for proteins related to nitrogen fixation, iron/vitamin B translocation and plasmid survival, and that the bacterium interacts with its host in part by transmembrane signaling. The phylogenetic analyses support the nesting of R. parasitica within the plant-inhabiting Rhizobiaceae, as sister to a group containing Agrobacterium and Rhizobium species.
- ItemSystematics and morphological diversification of the Cordylidae (Squamata)(2013-09-05) Stanley, Edward L., 1982-The Cordylidae is a species poor but ecologically and morphologically diverse family of lizards endemic to sub-Saharan Africa. Although the majority of the cordylid species are strictly rupicolous (rock dwelling), the family also contains a diverse array of other specialist ecotypes. Due to this concentrated ecological and morphological variation, the family is an excellent system for studying macroevolutionary processes. Previous studies have hypothesized that the majority of diversity in the family evolved rapidly at the base of the viviparous subfamily (Cordylinae), possibly representing an adaptive radiation, but this has not been investigated empirically. The four central chapters of this thesis were designed to be synergistic, with each chapter providing information and helping develop hypotheses in the others. Chapter two places the phylogenetic relationships of the Cordylidae into a temporal framework using relaxed clock Bayesian analyses on an 11 gene, squamate-wide dataset with ten fossil calibrations. These analyses recover the viviparous cordylines as undergoing a period of rapid cladogenesis across the Oligocene-Miocene boundary, radiating into nine well-supported lineages, distributed around the edge of the great escarpment in South Africa. Chapters three and four focused on two different cordylid groups with complicated and unresolved taxomomic histories. By investigating species boundaries within the Smaug warreni species complex (chapter three) and Hemicordylus capensis (chapter four) I address whether the current taxonomy of the family accurately captures the actual species diversity of the family. A combination of phylogenetic, biogeographic and morphological analyses reveals new species within both groups. The fifth chapter attempts to test the hypothesis that the Cordylidae underwent an adaptive radiation following the evolution of viviparity. Morphological variation of the Cordylidae was represented through a combination of standardized ecomorphological measurements and novel, volumetric measurements of osteoderm distributions recovered using High-Resolution CT scanning. Ecological data for known cordylid localities was extracted from multiple commonly used climate layers. Morphological variation was correlated with microhabitat choice, but not with climatic variation. Existing analytical techniques and new methods reveal that the viviparous cordylids experienced an early burst of morphological diversification, while the oviparous subfamily, Platysaurinae, did not. These findings strongly support the hypothesis that the Cordylinae underwent a period of adaptive radiation during the Oligocene, possibly as a result of shifts in the climate and geological uplift of South Africa's Great Escarpment.
- ItemA time scale for scales : reconciling neontology and paleontology in Coccoidea (Hemiptera)(2013-09-20) Vea, Isabelle M.Scale insects (Hemiptera: Coccoidea), with 8,000 species, 33 Recent and 19 extinct families, are amongst the most destructive insects in agriculture. Perhaps 98% of the species feed on angiosperms. The superfamily is traditionally divided into the primitive archaeococcoids and the derived neococcoids, the latter with 90% of the species. The neococcoids were hypothesized to have diversified in response to the radiation of angiosperms ca. 100 Ma. Despite a sophisticated taxonomy based almost exclusively on the conspicuous neotenic adult females, there is a paucity of higher-level phylogenetic studies, and this compromises evolutionary understanding. Fossil scale insects are diverse in ambers around the world, 135 to 20 Ma, but are preserved mostly asthe highly dissimilar winged adult males, adding a challenge in understanding the relationships of fossil taxa. My dissertation is aimed at reconciling paleontology and neontology in Coccoidea and testing whether the neococcoids diversified as a result of the angiosperm radiations.My approach was to first assess whether fossil scale insects could be incorporated in a phylogenetic framework. To begin, I used the Ortheziidae (ensign scale insects), a morphologically well-defined family, where morphological features and fossil evidence suggests an early origin of the family in Coccoidea evolution. Based on 69 morphological characters of female ortheziids and using 39 exemplar Recent species, I provide the first analytical assessment of relationships among Recent and extinct genera of the family. Fossils included eight species, based on complete, well-preserved specimens in amber from 125-20 Ma (unlike other coccoid groups, ortheziids are fossilized mostly as females). Five new species and one new genus of fossil ensign scales are described from three amber deposits. Second, it was necessary to understand macropterous male morphology. However, because adult male Coccoidea do not feed and rarely live more than three or four days, they are seldom collected and their morphology has been little studied. In the Ortheziidae, for example, males of only four extant and three fossil species were known, in a family of over 200 species. Herein, the detailed male morphology of seven previously described species is provided, which, by knowing males of three additional genera, provides significantly better understanding of male morphological variation in Ortheziidae. The utility of laser confocal microscopy for the study of old, rare, uncleared collection slide preparations is shown to allow better visibility of macrostructures, but not for minute structures such as pores. A comprehensive study was made of macropterous males in four amber deposits: Eocene of the Baltic region and India (Cambay amber), mid-Cretaceous of Myanmar, and Early Cretaceous of Lebanon. Descriptions of 16 new species, 11 new genera, and three new families are provided, including very important records for six Recent families, such as the first fossil Margarodidae (Cambay amber) and another definitive Cretaceous neococcoid (in Burmese amber). These fossils are then discussed in a phylogenetic framework, obtained from analyzing 123 Recent and fossil taxa for 169 morphological characters. Finally, I assess whether fossil information can help resolve deep-node relationships in Coccoidea. Estimates of divergence times of the major lineages are made based on morphological and molecular data, and lineage ages are discussed with major biotic events in earth history. This study presents the first total-evidence (vs. nodecalibrated) approach to phylogenetic assessment for the Coccoidea, using 169 morphological characters and regions of the 18S, 28S and EF-1a genes. The taxon sampling includes 73 Recent and 43 fossil terminals covering 48 of the 54 recognized families in Coccoidea. Despite the large proportion of missing data and a very heterogeneous dataset, results indicate that most of the Recent families of Coccoidea were established by 100 Ma, revealing that the divergence of neoccoccoid families may have not affected by the angiosperm radiations. The origin of Coccoidea is estimated as Late Triassic, ca. 220 Ma.
- ItemMorphological and molecular evolution of sea anemones as revealed by an emerging model organism, Aiptasia (Cnidaria, Actiniaria, Aiptasiidae)(2014-01-01) Grajales, Alejandro.;Sea anemones (Cnidaria: Actiniaria) of the family Aiptasiidae Carlgren, 1924 are conspicuous members of shallow-water environments and several species within the family are widely used as model systems for studies of cnidarian-dinoflagellate symbiosis and coral bleaching. Although previously published phylogenetic studies of sea anemones recovered the family Aiptasiidae as monophyletic, they only included partial sampling of its diversity. This study explores the diversity within this group of organisms in an integrative way, from the family to population levels. In this study, I explored the morphological and molecular diversity of the group using newly collected material covering the distribution of most of the described genera and species. The family Aiptasiidae was found to be a monophyletic lineage. Similarly, most of the genera within the family represent monophyletic lineages, with the exception of the genus Aiptasia, now divided into Aiptasia and Exaiptasia. Bellactis Dube, 1983 and Ragactis Andres, 1883 are now genera included within Aiptasiidae, in agreement with previous morphological studies and the morphological homogeneity observed here by the members of this family. In addition, I discovered new diagnostic morphological characters supporting the relationships among the major clades within the family. The molecular phylogenetic results provided evidence to diagnose two species within Exaiptasia: E. pallida -- a single widespread species -- and a new cryptic species, E. brasilensis sp. nov. -- restricted geographically to the southwestern Caribbean Sea and the southwestern Atlantic Ocean. Finally, although the algal diversity within the group showed no evidence of coevolution at the family level, an interesting pattern of adaptation and cladogenesis of the endosymbiotic algae (Symbiodinium spp.) was found within host species.
- ItemPaleobiology, paleoecology, and morphology of vertebrates : new approaches to old questions.(2014-02-11) Montanari, Shaena A.Physical, chemical, and osteo-histological signatures in fossils can be extremely informative about organismal life history and ecological characteristics, yet these signatures have not yet been exploited to their fullest potential. Tools such as microscopy and mass spectrometry have the potential to address issues and questions in vertebrate paleontology that have, until now, remained elusive. First, this dissertation begins with traditional methods of anatomy and systematics with the addition of improved sampling and visualization of a historic specimen, Macrerpeton huxleyi. The edopoid temnospondyl Macrerpeton huxleyi is redescribed on the basis of new peels of the holotype. Phylogenetic analysis recovers Macrerpeton as the sister taxon of Cochleosaurus within the edopoid clade Macrerpetidae (formerly Cochleosauridae). Histological signatures in fossil bone can be used to reconstruct information about extinct organisms, such as genome size. Nonetheless, intra-skeletal osteocyte lacunae size variation, which could cause error in genome size estimation, has remained unexplored. While there is variance in the sizes of these bone structures over the skeleton of modern tetrapods, this variation is not necessarily causing any issues with genome size estimate; instead, the actual methods of estimation create a wide range of potential values that these methods are not able to answer certain genetic questions at a fine scale.Examining the carbon and oxygen isotopes in tooth enamel represents a quantitative method for discerning the paleoenvironments and paleoecology of fossil fauna. The Chinchilla Local Fauna from southeastern Queensland is a diverse assemblage of terrestrial Pliocene vertebrates from the Chinchilla Sand Formation. Isotopic analysis results from Chinchilla show that there were distinct dietary niches within the large marsupial vertebrate community. This study suggests that southeastern Queensland hosted a mosaic of tropical forests, wetlands and grasslands during the Pliocene. A review of the uses of biogenic materials in eggshells for stable isotope analysis is also provided. Stable isotope analysis is also used to determine paleoenvironments and paleoecology of dinosaurs during the Late Cretaceous in Mongolia. This study, which is the first to utilize stable isotope geochemistry on Mesozoic fossil tooth enamel from central Asia, documents that the environment was arid, but more importantly that dinosaur remains, such as eggshells, can be used for this type of study. These objectives are united by a need to use quantitative measurements to more accurately reconstruct vertebrate traits throughout earth history.
- ItemMolecules, morphology and monophyly : resolving pleuronectiform phylogeny and investigating why it has been so difficult to do.(2014-09-23) Roje, Dawn M.Although adult flatfishes (order Pleuronectiformes) start out in life as bilaterally symmetrical larvae, they undergo a remarkable metamorphosis, where one eye of the symmetrical larva migrates to the opposite side of the cranium, resulting in highly asymmetrical juvenile and adult forms. Because all flatfishes exhibit this bizarre morphology and variation, both the degree of asymmetry and handedness (direction of eye migration) exists within the order, this group provides multiple tests of hypotheses regarding the evolution of bilateral asymmetry and underlying mechanisms. Unfortunately, undertaking such studies has been elusive because of three major issues confounding pleuronectiform phylogenetics: 1) relationships of the major groups within the order remain mostly unresolved, 2) the sister group of flatfishes is unknown, and 3) monophyly of the assemblage is weakly supported. To resolve these issues in pleuronectiform phylogenetics, my dissertation research has focused on: 1) evaluating the effects non-neutral markers on phylogeny estimation, principally rhodopsin1 (rho), 2) rigorously testing both flatfish monophyly and sistergroup hypotheses and 3) resolving relationships within the order, re-examining characters of adult morphology and comparing them to often overlooked larval characters in light of new phylogenetic hypotheses. In the first study, Chapter II, I use previously published sequence data from 78 iv acanthomorph (including flatfishes) taxa for rho, rnf213, irbp and mll, perform tests for neutrality, and compare neutral versus non-neutral markers for congruence using tree distance metrics and topology testing. I find that while the signal provided by rho may be discordant with the others, neutrality alone does not predict congruence and therefore should not be used as a justification to omit data. In the second study, Chapter III, I optimize new molecular markers and sequence them along with rho and rnf213 for 58 flatfishes and 90 putative outgroups to test monophyly, intraordinal relationships and sister-group hypotheses. Those sequences along with data from a previous study are analyzed to determine possible causes for gene tree incongruence or phylogenetic error. I discover that the new markers are variable, providing large amounts of data, while being conserved so that alignment is unambiguous. When combined with the others and analyzed simultaneously, these markers provide overwhelming support for a monophyletic Pleuronectiformes. Additionally, I demonstrate that abundant missing data is likely the cause of low resolution, validate the importance of investigating substitution saturation as a cause of error and discuss asymmetrical taxonomic distribution as a cause of low resolution at the base of Carangimorpha. Finally, in the third study (Chapter IV) I infer an ultrametric tree, recode a previously published matrix of characters of adult morphology, combine those with new larval characters and test whether life history is correlated with phylogenic signal. Further, I investigate the accuracy of ML ancestral character state estimation (ACE) to determine if these morphological characters provide additional support for hypotheses of relationships among major pleuronectiform groups. My results suggest that larval v characters should not be treated as a source of independent data, but do provide resolution and additional support for novel relationships within Pleuronectiformes, although they may be in violation of the condition of low rates on ML ACE. Lastly, I show that because larval characters are mostly pleisiomorphic for the order, and that larval morphology is similar to that of putative sister groups, these characters are a potential source of evidence needed to resolve the placement of this lineage within Acanthomorpha.
- ItemPhylogenetic studies of apoid wasps (Hymenoptera, Apoidea) with insights into the evolution of complex behaviors.(2014-09-30) Payne, Ansel.The wasp superfamily Apoidea -- a group composed of more than 20,000 species of solitary, cleptoparasitic, and social bees, as well as a paraphyletic grade of more than 9,600 species of predatory and cleptoparasitic wasps -- has played an outsized role in the history of behavioral research. Favorite subjects of field naturalists and ethologists for more than two hundred years, these insects have evolved a tremendous diversity of behavioral strategies, each one an equally successful variation on a shared ancestral groundplan. Understanding the course of these evolutionary derivations and innovations is an important part of understanding insect behavior in toto, and one that requires a phylogenetically informed, comparative approach. As a contribution to ongoing efforts in apoid phylogenetic systematics -- and by extension to the study of behavioral evolution within the group -- the current work presents four phylogenetic studies of apoid taxa, with an additional fifth study examining the placement of Apoidea within Hymenoptera as a whole. Each provides some insight into the evolution of a complex behavioral syndrome, namely the development of predatory behavior from within a parasitoid wasp clade (Chapter II), the origins of cleptoparasitism in apid bees (Chapter III), trends in prey choice among philanthine wasps (Chapters IV and V), and innovations in nesting behavior within thread-waisted wasps (Chapter VI). In the first of these studies, I use a combination of direct optimization phylogeny reconstruction and clade sensitivity analysis to re-examine a previously published total evidence dataset based on 111 taxa from across Hymenoptera. This new analysis simultaneously reveals and formalizes deep topological instabilities within this important insect order, and shows how such instability can complicate back-of-the-envelope reconstructions of behavioral evolution (e.g., the origins of aculeate predatory behavior from within a paraphyletic "Parasitica"). In the second, I demonstrate once again the importance of combining multiple classes of phylogenetically informative characters through a simultaneous reanalysis of the bee family Apidae. By merging previously published datasets based on molecular, behavioral, and adult and larval morphological characters (and by providing new adult and larval character codings for taxa previously represented by molecular data alone), I add qualified support to a recently published, nucleotide-derived hypothesis concerning the origins of cleptoparasitism. This hypothesis -- that the trait evolved fewer times than previously supposed, with the nomadine and "melectine" lineages sharing a common cleptoparasitic ancestor -- is corroborated under a variety of different transformation cost parameters and appears relatively robust to the addition of morphological and behavioral data. The next two studies present the results of the most taxonomically comprehensive phylogenetic analyses of the digger wasp subfamily Philanthinae (Apoidea: Crabronidae) to date. While Chapter IV represents the first molecular analysis of the group to include species level terminals from all eight genera and all four tribes, Chapter V expands that work to include 66 newly coded morphological and behavioral characters. Although basal relationships among the four tribes remain either ambiguous or poorly supported, monophyly of the hyperdiverse, cosmopolitan genus Cerceris is strongly suggested for the first time -- a finding that challenges previous notions concerning the evolution of prey choice within the "beetlewolf" tribe Cercerini. Finally, the last study briefly examines relationships among the so-called "thread-waisted wasps" of the family Sphecidae sensu stricto as a prelude to a larger study of nest evolution within the group. While maximum parsimony analysis of 16 nest-related behavioral characters produces a largely unresolved topology, cladistic analysis of a three-gene dataset reveals new cases of paraphyly at both the tribal and generic levels. I briefly discuss the implications of this latter topology for our understanding of nest evolution within the group.
- ItemAnts (Hymenoptera, Formicidae) through space, time, and sociality : a history from amber.(2015-06) Barden, Phillip.With over 13,000 ecologically diverse species exhibiting worldwide ubiquity in vegetated terrestrial ecosystems, ants are one of nature's greatest success stories. Colonies range from a few dozen tiny workers housed inside of an acorn to millions of nomadic army ants known to consume even vertebrates. The ant fossil record is very rich, comprising thousands of amber and impression specimens spanning a hundred million years, the vast majority of which is Cenozoic. Until very recently, early ant history has been obfuscated by a lack of well-preserved fossils from the Cretaceous. Here, utilizing CT-scanning methodology and traditional methods, diverse species of ~99 million-year-old Cretaceous ants are described from Burmese amber, which together comprise over one-third of all known Cretaceous ants. Among them are trap-jaw predators with scythelike mandibles not known in any living or extinct ants, as well as enigmatic feeders with hair-coated mouthparts, and several species with morphology analogous to that found in modern ants while retaining plesiomorphic features. These and other unusual Cretaceous taxa are contextualized for the first time, with results that challenge traditional viewpoints regarding the diversity, phylogenetic placement, and sociality of the earliest ants known. In the age of molecular phylogenetics the role of fossils can be unclear. Most frequently, fossils are included in analyses solely as calibration points for divergence date estimates, a practice that relies on assumed taxonomy and excludes biogeographic information. To explore alternative roles for fossils in molecular-based biogeographic, phylogenetic, and temporal reconstruction, combined analysis methodology is explored -- first, with respect to a small genus, and then finally applied to a large sampling of all ant subfamilies. The genus Leptomyrmex is endemic to eastern Australia, New Caledonia and New Guinea. Over 25 years ago, a putative fossil Leptomyrmex was described from Dominican amber dated to the Miocene. In the absence of compelling evidence other than taxonomic discussions in literature, researchers have typically excluded the Dominican fossil from phylogenetic and biogeographic reconstruction. To test the placement of the fossil, published molecular sequences for modern Leptomyrmex and related groups were merged with a novel morphological matrix. Through combined analysis the fossil was recovered among modern Australasian Leptomyrmex, indicating that the current distribution is a reflection of a great contraction and more complex biogeographic history. This same methodology is applied to a much larger dataset including members of all modern ant subfamilies in a preliminary total-evidence analysis of ants.
- ItemDiversification of malaria and pinworm parasites in Caribbean Anolis lizards.(2015-07-07) Falk, Bryan G.
- ItemMolecular and morphometric phylogenetics of Dryinidae and Bethylidae (Hymenoptera, Chrysidoidea)(2015-09) Tribull, C. M.Aculeata (Hymenoptera) is largely known for its bees, ants, and social wasps, from which most people would immediately recognize honey bees and paper wasps. However, sister to the clade of Apoidea and Vespoidea is the much smaller, and infinitely more enigmatic Chrysidoidea, which contains seven extant families that are relatively understudied. Unlike the other superfamilies, Chrysidoidea is exclusively parasitic -- although this behavior ranges from ectoparasitoidism to endoparasitoidism to cleptoparasitism (targeting solitary wasps and bees), as seen in Chrysididae (the cuckoo wasps). Dryinidae, which contains about 1700 species worldwide in 16 subfamilies, are parasitoids of Auchenorrhyncha (leafhoppers, planthoppers, and their allies) and are known to attack major rice and fruit crop pests. In Chapters II and III, the relationships within the family were investigated at the subfamily level. In Chapter II, a phylogeny reconstructed from 18S, 28S, Cytochrome Oxidase I (COI) and Cytochrome b (CytB) resulted in the resurrection of Thaumatodryinus to Thaumatodryininae to preserve the monophyly of Dryininae. Chapter III examined the utility of landmark analysis in parsimony using the methods implemented by Catalano et al. (2010) and subsequent publications. The trees constructed from the landmark analyses were incongruent with the combined molecular and morphological phylogeny, but landmark analyses could be utilized effectively to reconstruct species-level phylogenies for Dryinus and Gonatopus, both of which were found as nonmonophyletic in Chapters II and III. Chapters IV and V focused on Epyris, the largest genus within the subfamily Epyrinae, and Bethylidae as a whole. Epyris has long been suspected of being a taxonomic wastebasket, but the molecular phylogeny reconstructed from 16S, 18S, 28S, COI, and CytB is the first phylogeny to sample the worldwide breadth of its species diversity. Epyris was shown to be nonmonophyletic, although the type specimen, Epyris niger Westwood, was recovered in a clade with a distinct synapomorphy of large, nearly touching, scutellar pits. In Chapter V, five new species from Epyris sensu stricto were described from Western Australia and Queensland, and a key was provided to the known female Epyris of Australia.