Please read the section 21chapter20, (Summary and conclusions), of this document / Thesis (DSc (Zoology))--University of Pretoria, 2008. / Zoology and Entomology / DSc / Unrestricted

Cricetidae, which includes a wide range of mice, rats, and voles, is the second-most diverse and abundant family of mammals. Distributed across the Americas and Eurasia, this rodent family has been extensively studied for its success and adaptability in the face of climate and habitat change, and its utility for ecological reconstruction and the biochronology. While cricetids are known from many fossil sites in western North America, few have been found and studied from the terrestrial sites in the east prior to the Pleistocene. The Gray Fossil Site (GFS) in eastern Tennessee is well-known for its diverse flora and fauna, particularly large mammals. Small mammals from the site have remained understudied, and although a few studies have mentioned cricetids, a comprehensive investigation is needed to describe the large number of cricetid specimens found at GFS. This project uses qualitative and quantitative methods to examine the morphology of fossil cricetids from GFS, focused on molars and jaw elements because of their abundance and the rich taxonomic and ecological information they provide. Materials have been studied using a stereomicroscope and photographed using a digital microscope camera. Occlusal morphology is described and compared to modern cricetids and published records from across North America. Specimens from GFS include at least 5 taxa, and the two most abundant taxa at the site are the woodrat Neotoma, which has high-crowned molars and still lives in the region today, and the deer mouse-like Postcopemys, which has low-crowned molars. While many GFS specimens can be categorized into these two genera, distinctive morphological variations seen in some individuals suggest the presence of new species. The array of cricetids present is distinct from those at contemporaneous sites and reinforces the spatial and temporal uniqueness of the Gray Fossil Site. Situated in the biodiversity hotspot in the Appalachian region today, GFS provided habitats for cricetid taxa with diverse body sizes and dietary preferences in the Pliocene.

Inner hair cells (IHCs) are the primary sensory receptors of the mammalian cochlea. I employed the whole-cell patch-clamp technique to study voltage responses and ionic currents of IHCs in mice bearing mutations in hair bundle proteins. These mutations, all associated with Usher syndrome, lead to structural and functional defects of the mechanosensory hair bundle. I observed developmental failure in the electrical properties of IHCs from these mutants: a continuation of neonatal spiking instead of the graded receptor potentials seen in control adult IHCs. Voltage-clamp recordings revealed the main cause as the absence of the adult fast potassium (IK,f) current. Outer hair cells (OHCs) are required to amplify the travelling wave to be detected by the IHCs. Optical and whole-cell patch clamp techniques in these same mutants were employed to investigate the development of adult OHCs. I observed a developmental failure in the electrical properties of these OHCs, seen by an absence of the potassium current IK,n. Electromotility and the associated non-linear capacitance were however observed, indicating that prestin is expressed in the mutants. Acid sensitive ion channels (ASICs) have recently been found to be present within the organ of Corti. Here I present data showing the presence of an acid sensitive ion current in both IHCs and OHCs. ASIC1b knockout mice show a response to changes in the extracellular pH suggesting that the current may be carried through a different channel subtype or that compensatory changes occur. The electrical properties of the IHCs develop to maturity in these mice, however the OHCs appear to remain functionally immature displaying a lack of expression of the IK,n current and electromotily. This lack of electromotile function suggests that ASIC1b may be required either for the function of prestins electromotility or for the targeting of prestin to the cell membrane.

This dissertation has two major sections. In Chapter II, complete mitochondrial (mt DNA) genome sequences were used to construct a hypothesis for affinities of most major lineages of rodents that arose quickly in the Eocene and were well established by the end of the Oligocene. Determining the relationships among extant members of such old lineages can be difficult. Two traditional schemes on subordinal classification of rodents have persisted for over a century, dividing rodents into either two or three suborders, with relationships among families or superfamilies remaining problematic. The mtDNA sequences for four new rodent taxa (Aplodontia, Cratogeomys, Erethizon, and Hystrix), along with previously published Euarchontoglires taxa, were analyzed under parsimony, likelihood, and Bayesian criteria. Likelihood and Bayesian analyses of the protein-coding genes converged on a single topology that weakly supported rodent monophyly and was significantly better than the parsimony trees. Analysis of the tRNAs failed to recover a monophyletic Rodentia and did not reach convergence on a stationary distribution after fifty million generations. Most relationships hypothesized in the likelihood topology have support from previous data. Mt tRNAs have been largely ignored with respect to molecular evolution or phylogenetic utility. In Chapter III, the mt tRNAs from 141 mammals were used to refine secondary structure models and examine their molecular evolution. Both H- and L-encoded tRNAs are AT-rich with different %G and GC-skew and a difference in skew between H- and L-strand stems. Proportion of W-C pairs is higher in the H-strand and GU/UG pairs are higher in the L-strand, suggesting increased mismatch compensation in L-strand tRNAs. Among rodents, the number of variable stem base-pairs was nearly 75% of that observed across all mammals combined. Compensatory base changes were present only at divergences of 4% or greater. Neither loop reduction nor an accumulation of deleterious mutations, both suggestive of mutational meltdown (Muller's ratchet), was observed. Mutations associated with human pathologies are correlated only with the coding strand, with H-strand tRNAs being linked to substantially more of these mutations.

Thesis (Ph. D.)--Case Western Reserve University, 2009. / [School of Medicine] Department of Biology. Includes bibliographical references.

Spermophilus lateralis, the golden-mantled ground squirrel, while euthermic exhibits a strong hypoxic ventilatory response, but a relatively blunted hypercapnic ventilatory response similar to other semi-fossorial mammals. Under resting conditions, carotid body chemoreceptors provide a tonic excitatory input to the frequency component of ventilation. Carotid body denervation (CBX) results in a 40% decrease in minute ventilation (V). The overall ventilatory response to hypoxia is unaffected by CBX, although the ventilatory threshold is significantly shifted to lower levels of inspired O₂. CBX also has little effect on the overall response to hypercapnia. Thus, in S. lateralis, it appears that changes in the partial pressure of O₂ (P0₂) In the blood act centrally, rather than peripherally, to play a predominate role in ventilatory control. Chronic exposure to hypoxia and hypercapnia (CHH, 17% O₂ and 4% CO₂) does not result in overall ventilatory acclimation, with minute ventilation being similar to control squirrels acutely exposed to hypoxic and hypercapnic conditions. In spite of this, CHH exposure does result in adjustments to respiration; frequency is decreased and tidal volume is elevated compared to control squirrels acutely exposed to CHH conditions. Overall V sensitivities to both hypoxia and hypercapnia are not significantly altered by CHH exposure. It appears that acclimation to chronic hypoxic and hypercapnic conditions in S. lateralis may increase alveolar minute ventilation relative to total minute ventilation and thus minimize the changes in arterial PO₂ and Pco₂ during hypoxic and hypercapnic exposure. During entrance into hibernation, as metabolic rate and body temperature decline, concomitant decreases in ventilation occur. Two patterns of respiration occur during deep hibernation; a burst breathing pattern characterized by long non-ventilatory periods (Tnvp) separated by bursts of several breaths and a single breath pattern characterized by single breaths separated by a relatively short Tnvp. In S. lateralis during hibernation at body temperatures between 6° and 10°C, a burst breathing pattern prevails. At slightly lower body temperatures, less than 4°C, a single breath breathing pattern prevails. Both burst breathing and single breath breathing squirrels have similar overall levels of resting minute ventilation. Burst breathing squirrels exhibit a significant respiratory response to hypoxia (3% O₂) and when the decreases in metabolic rate during hibernation are taken into account (air convection requirement) their hypoxic sensitivity is similar to that in awake S. lateralis. In contrast, single breath breathing squirrels do not respond to hypoxia at any level tested (down to 3% O₂). Both burst breathing and single breath breathing squirrels show large ventilatory repsonses to hypercapnia. In the burst breathing state hypercapnic sensitivity is significantly higher compared to the single breath breathing state, due to an augmented frequency response during burst breathing. In both groups of hibernating squirrels ventilation is increased during hypercapnia solely by decreases in the nonventilatory period. When ventilation is standardized for the decreases in metabolic rate during hibernation both burst breathing and single breath breathing S. laterlis exhibit a much higher hypercapnic sensitivity than that seen in awake S. lateralis. Carotid body denervation has little effect on ventilatory pattern generation or ventilatory sensitivities to hypoxia and hypercapnia in hibernating squirrels. It appears that during hibernation in S. lateralis, ventilation is controlled primarily by changes in the partial pressure of CO₂ (Pc0₂) in tne blood acting centrally to stimulate ventilation. The burst breathing pattern is produced centrally, as are the respiratory responses to hypoxia and hypercapnia. Thus, central mechanisms involved with ventilatory control are extremely important in both the euthermic state and the hibernating state, but the chemical stimuli regulating ventilation appear to be fundamentally different in euthermic and hibernating S. lateralis. / Science, Faculty of / Zoology, Department of / Graduate

Cranial and external measurements in 422 museum specimens of the common vole, Microtus arvalis, from Switzerland were examined to determine whether they varied with altitude in accordance with either (1) Bergmann's Rule, or (2) subspeciation. Correlation coefficients between altitude and size were calculated on 32 dimensions, each of which had been divided into sex segregated age groups. In not one of the 108 tests was correlation significant. The lack of adherence to Bergmann's Rule was investigated by (1) reviewing the basic concepts of the Rule, as applied to homeotherms; (2) identifying the major abiotic and biotic selection pressures that might affect growth in Microtus arvalis, including climate and competition with sympatric congenerics; and (3) indicating deficiencies in data derived from museum specimens which might have influenced the computations. There were several references in the literature to the occurrence of two subspecies of Microtus arvalis in Switzerland - the nominate subspecies M. a. arvalis (Pallas, 1779) and a montane subspecies called either M. a. incertus (Selys-Longchamps, 1841) or M. a. rufescentefuscus (Schinz, 1845). The lack of evidence in this study for the existence of two phenotypically and distributionally distinct subspecies was considered by (1) examining the general appropriateness of discussing variation in Microtus arvalis in terms of subspeciation; and (2) reviewing the literature on the diagnostic characters and distribution attributed to the montane morph. Two major conclusions were drawn. The first was that Bergmann's Rule should not be considered a "rule" until firm definitions are established on at least two of its founding precepts - the groups of animals to which it applies and the taxonomic level at which it applies - and until it is found to apply to a majority of the cases for which it is intended. The second conclusion was that for species like Microtus arvalis, in which growth is highly variable and distribution is by and large continuous, the usefulness of formal recognition of in-fraspecific populations is questionable until an overview of the geographic variability of the species as a whole is well documented. / Science, Faculty of / Zoology, Department of / Graduate

O cultivo florestal do eucalipto foi introduzido no Brasil no início do século XX com o intuito de suprir de matéria prima as fornalhas e ferrovias em construção na época. A produção é destinada para os mais diversos propósitos e está ainda em ascensão, de tal forma que a área plantada ocupa atualmente mais de quatro milhões de hectares no país. Seu avanço, porém, traz consigo preocupações sobre os efeitos de seu cultivo sobre a fauna nativa, pois, embora possua perfil florestal, é ainda uma monocultura. A área do presente estudo localizase no município de Angatuba, Estado de São Paulo, na Bacia do Alto Paranapanema. O presente estudo abrangeu plantios com idades de um ano e quatro meses a quatro anos e dá continuidade ao estudo desenvolvido no início do plantio (0 a 2 anos e 11 meses) na mesma área por Martin et al. (2012), seguindo a mesma metodologia. A coleta dos pequenos mamíferos foi realizada por meio de armadilhas de interceptação e queda (pitfall) distribuídas em grade em trinta unidades amostrais numa paisagem silvicultural, formada remanescentes florestais nativos, capoeira e eucaliptal a partir da metodologia amostral utilizada pelo Programa de Pesquisa em biodiversidade (PPBio), do Ministério da Ciência e Tecnologia (MCT). Foram capturadas 11 espécies pertencentes às ordens Rodentia e Didelphimorphia comumente encontradas em ambientes alterados e paisagens agrícolas. Não houve diferença significativa entre os ambientes testados em termos de riqueza de espécies e abundância de indivíduos. Dessa forma, os eucaliptais atuaram como habitat para as espécies e não apenas como matriz permeável. Por esta razão, seu manejo, incluindo práticas culturais (e.g., adubação e controle de plantas \"daninhas\") deverá levar em conta seu uso pela fauna silvestre e não apenas sua rentabilidade. Pesquisas futuras nessa área devem ser por isso, priorizadas a fim de garantir a missão multifuncional da paisagem silvicultural. / Eucalyptus plantation was introduced in Brazil on early twentieth century and it aimed to supply with feedstock the furnaces and railroads under construction at the time. The production had various purposes and is still rising; therefore, currently eucalyptus plantation occupies more than four million hectares in Brazil. Its progress, however, highlights some concerns about the effects of cultivation on the native fauna because eucalyptus plantation is a monoculture although it has forestry profile. The present study area is located in the municipality of Angatuba, State of Sao Paulo, in the Upper Paranapanema Basin. This study sampled plantations aged between one year and four months and four years and continued the study developed on early planting (0-2 years and eleven months) by Martin et al. (2012) in the same area therefore the present study followed the same methodology. The capture of small mammals was conducted using pitfall traps distributed in a grid with thirty sample units in a silvicultural landscape formed by native forest remnants, \"capoeira\" and eucalyptus plantation. This method is based on the sampling methodology developed by Biodiversity Research Program (PPBio) and Ministry of Science and Technology (MCT). We captured 11 species from the orders Rodentia and Didelphimorphia commonly found in disturbed habitats and agricultural landscapes. There was no significant difference between the tested environments in terms of species richness and abundance of individuals. Thus, the eucalyptus plantation acted as habitat to those species and not just as permeable matrix. For this reason, eucalyptus plantation management, including cultural practices (e.g., fertilization and weed control) should take into account its use by wildlife and not just its profitability. Future research in this area should therefore prioritize to ensure the multifunctional mission of silviculture landscapes.

Current patterns of faunal diversity, geographic distribution, phylogenetic relationships and biogeography constitute a tool for understanding the evolutionary history of taxa. The boundaries of these taxa and their phylogenetic relationships reveal speciation events and therefore allow us to raise general hypotheses about the diversification of a particular group. Into the Oryzomyini, one of the most diverse tribe of Sigmodontinae subfamily, we can found the genus Hylaeamys. Currently seven species were described to that genus: H. acritus, H. seuanezi, H. megacephalus, H. oniscus, H. perenensis, H. tatei and H. yunganus. These species are distributed throughout the tropical and subtropical evergreen cis-andinean forests, from sea level to an altitude of 1500 meters, from Venezuela and Guyana, through the Amazon and the Atlantic Forest, to the north of Paraguay. The distribution of taxa within the genus were confusing and phylogenetic relationships among these species have been little explored, as well as the positioning of the genus within the clade B of Oryzomyini tribe and consequently his sister group. So my proposal was to reassess the species currently described through morphometric and molecular data to better explore the diversity within the genus, and the relations within the genus Hylaeamys and clade where it is inserted. My results showed a greater diversity than the currently described. Morphometric analysis could be helpful in the delimitation of taxa, however did not translate all the phylogenetic diversity found within the genus, witch may present cryptic species. The genus is monophiletic and a new species of Hylaeamys related to H. yunganus populations, from eastern South America was recognized. The results, also highlighted a geographical structure present within H. megacephalus, so, samples from north of the Rio Amazonas showed to be genetically distinct to those samples in southern of Rio Amazon. But this pattern was not observed in morphometric analysis. The species of the Atlantic Forest were closer to the western amazonian species. Hylaeamys showed as a sister group of a clade containing Cis and Trans Andean genera: Oecomys, Euryoryzomys and Transandinomys, indicating that the dispersion for trans-Andean areas occurred after the diversification of the Forest clade in South America. / Padrões faunísticos atuais de diversidade, distribuição geográfica, relações filogenéticas e biogeográficas constituem uma ferramenta para a compreensão da história evolutiva dos táxons. As delimitações destes táxons e suas respectivas relações filogenéticas nos revelam eventos de especiação e consequentemente nos permitem levantar hipóteses gerais de diversificação de um determinado grupo. O gênero Hylaeamys está inserido na tribo Oryzomyini, a mais diversa da subfamília Sigmodontinae. Possui atualmente sete espécies descritas: H. acritus, H. laticeps, H. megacephalus, H. oniscus, H. perenensis, H. tatei, e H. yunganus. Estas espécies se distribuem pelas florestas tropicais e subtropicais sempre verdes cisandinas, do nível do mar até uma altitude de 1500 metros, desde a Venezuela e as Guianas, passando pela Amazônia e pela Floresta Atlântica, até o norte do Paraguai. A distribuição dos táxons dentro do gênero eram confusas e as relações filogenéticas entre estas espécies, também, foram pouco exploradas, assim como o posicionamento do gênero dentro do clado B da tribo Oryzomyini e consequentemente seu grupo irmão. Portanto, minha proposta foi reavaliar as espécies atualmente descritas abordando de forma integrativa os dados morfométricos e moleculares para melhor explorar a diversidade dentro do gênero, assim como as relações de parentesco dentro do gênero Hylaeamys e do clado onde este se encontra inserido. Como resultado, obtive uma diversidade maior do que a descrita atualmente. Análises morfométricas puderam auxiliar na delimitação dos taxa, porem não traduziu toda a diversidade filogenética encontrada dentro do gênero, podendo o gênero apresentar espécies cripticas. O gênero se mostrou monofilético e uma nova espécie de Hylaeamys, relacionada às populações de H. yunganus do leste da América do Sul foi reconhecida, assim como, ficou evidente a estruturação geográfica presente dentro da espécie H. megacephalus, onde as amostras ao norte do Rio Amazonas se mostraram geneticamente distintas das amostras ao sol do Rio Amazonas. Porém nas análises morfométricas não foi observado esse padrão. As espécies da Floresta Atlântica se mostraram filogeneticamente mais próximas das espécies do oeste Amazônico. Hylaeamys se mostrou groupo irmão de um clado contendo gêneros Cis e Trans- Andinos, sendo eles, Oecomys, Euryoryzomys e Transandinomys, indicando que a dispersão para áreas trans-andinas se deu após a diversificação do gênero na América do Sul.

No Brasil e em alguns países da América Latina, a incidência de raiva transmitida por animais domésticos tem diminuído enquanto tem aumentado em animais silvestres. Durante os últimos anos, no Brasil, a raiva tem sido diagnosticada em morcegos hematófagos ou não, primatas não-humanos, cachorros-do-mato, quatis, guaxinins, capivaras, cervos, gambás e outras espécies silvestres. O presente estudo foi realizado em parceria com biólogos, pesquisadores na área de monitoramento de fauna silvestre, e o objetivo foi pesquisar a presença do vírus rábico em mamíferos silvestres de vida livre, provenientes de uma reserva natural particular, localizado no município de Ribeirão Grande, São Paulo, região que já foi alvo de raiva nos últimos anos. Durante o período de 2002 a 2004, 104 amostras de cérebro de animais capturados foram enviadas para diagnóstico no Laboratório de Raiva da UNESP de Araçatuba, SP, acondicionadas em pipetas plásticas do tipo Pasteur individuais. Os animais pertenciam a três ordens, Chiroptera (47,1%), Rodentia (46,2%) e Marsupialia (6,7%), sendo de diferentes idades e sexos. As amostras foram submetidas ao teste de imunofluorescência direta e inoculação intracerebral em camundongos e todas apresentaram resultado negativo para a raiva. Segundo dados da Coordenação do Programa de Controle da Raiva do Estado de São Paulo a raiva é endêmica na região estudada e a porcentagem de positividade em morcegos nos últimos dez anos é de 1,8%. Embora dos diagnósticos tenham sido negativos neste estudo, não é possível afirmar que o vírus rábico não circula naquela propriedade / In Brazil and some Latin American countries, the incidence of rabies transmitted by domestic animals has decreased while it has been increasing in wild animals. During the last few years rabies has been diagnosed in hematophagous or nonhematophagous bats, nonhuman primates, crab-eating foxes, coatis, raccoons, capybaras, deers, skunks and some other species. The present study was carried out with biologists, researchers in wild fauna monitoring and the objective was to search the presence of the rabies virus in wildlife mammals from a private natural reserve, in Ribeirão Grande city, SP, region that was target of rabies in the last few years. During 2002 to 2004, 104 brain samples of captured animals were sent for diagnosis to UNESP Rabies Laboratory from Araçatuba, SP, conditioned in individuals Pasteur plastic pipettes. The animals belonged to three different orders, Chiroptera (47,1%), Rodentia (46,2%) and Marsupialia (6,7%), and to different ages and sex. The samples were submitted to direct fluorescent antibody test and mouse inoculation test and all samples resulted negative for rabies. According to data of the Rabies Control Program Coordination from São Paulo State, rabies is endemic in the studied region and the percentage of positive cases in bats during the last 10 years was 1,8%. Although all diagnosis were negative in this study, it is not possible to affirm that the rabies virus do not circulate in that property