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Thesis (PhD) - Stellenbosch University, 2011. / ENGLISH ABSTRACT: The Albertine Rift is characterized by a heterogeneous landscape which may, at least in part, drive the exceptional biodiversity found across all taxonomic levels. Notwithstanding the biodiversity and beauty of the region, large areas are poorly understood because of political instability with the inaccessibility of most of the region as a contributing factor. The majority of studies in the Albertine Rift have focussed on charismatic mega fauna, with other taxa receiving less attention. One of the taxonomically and numerically more abundant small mammal genera is the genus Praomys, an African endemic with a wide distribution range spanning most of west, central and east Africa. Four species are typically recognized from the Albertine Rift namely P. degraaffi, P. jacksoni, P. misonnei and P. verschureni. In this study I used a combination of DNA sequence data (mitochondrial control region, mitochondrial cytochrome b and 7th intron of the nuclear ß-fibrinogen gene) as well as morphometric data (traditional and geometric) to investigate the systematics of the Praomys taxa occurring in the Albertine Rift. To allow meaningful DNA assessments and in an attempt to identify potential drivers of diversifications, other Praomys species were also included from public sequence data bases for comparisons. The main focus was on P. jacksoni (the numerically most abundant taxon; also, up to 2005, all Praomys in the Albertine Rift were mostly collected as “jacksoni”) and P. degraaffi (an Albertine Rift endemic). A surprising finding was the presence of P. mutoni; this represents a range extension for this species into the Albertine Rift. Distinct evolutionary lineages were found in both P. jacksoni (confirmed by sequence data as well as morphometrics) as well as P. degraaffi (based only on sequence data; insufficient samples precluded a full morphometric investigation). These lineages (in both P. jacksoni as well as P. degraaffi) appear to be separated along a north – south gradient; however, further investigations should confirm this. To further investigate the genetic patterns at local scales across the Albertine Rift, as well as introgression between species as revealed by sequence data, a species-specific microsatellite library was developed for P. jacksoni. Twelve polymorphic markers were identified of which nine also amplified in P. degraaffi. Introgression was confirmed between the two focal species with almost 20% of the individuals analysed being jacksoni-degraaffi hybrids. This is perhaps not so surprising given that there is considerable overlap in their ranges (between ~ 1500 m a.s.l. to 2450 m a.s.l.) as well as the relative ages of the species (the divergence time between these two species were estimated at 3.8 Mya). The presence of distinct lineages within each of these species was confirmed by microsatellite analyses (these lineages diverged approcimately at same time at ca. 3.4 Mya). As suggested by sequence and morphometric data, these lineages had a largely north – south distribution but with considerable overlap in the central Albertine Rift in the vicinity of Lake Kivu. The phylogeographic patterns obtained for both focal species were not consistent with the physical barriers such as the rivers, lakes or mountains, nor were they exclusively associated with Pleistocene phenomena such as the change of the course of the rivers or uplift; rather, the lineages predate the Pleistocene and fall firmly in the Pliocene (>3 Mya). Biogeographically, the north - south location of lineages with a centrally - located contact zone could be a result of parapatric speciation due to habitat fragmentation or past climate change, followed by secondary contact. Barcoding using genetic information provides a useful tool to identify unknown taxa, cryptic diversity or where different life stages are difficult to identify. From an invasion biology perspective, it allows for the rapid identification of problem taxa against a known data base. By adopting such a barcoding approach (senso lato), the presence of three invasive rodents was confirmed in the Democratic Republic of the Congo (DRC); these are Rattus rattus (black rat), R. norvegicus (Norway rat) and Mus musculus domesticus (house mouse). A comparison with global data available for these species revealed two possible introduction pathways namely via the shipping port at Kinshasa/Matadi (with strong links to Europe) and via the slave trade routes in the east (strong links to the Arab world and the east). Of these three taxa, only R. rattus is currently documented from the DRC although the others have received mention in the gray literature. These findings draw attention to the lack of any official policy regarding biosecurity in the DRC, and argue for the development of strict control measures to prevent further introductions. / AFRIKAANSE OPSOMMING: Die Albertine Rift word gekenmerk deur 'n heterogene landskap wat kan, ten minste gedeeltelik, die uitsonderlike biodiversiteit wat oor al die taksonomiese vlakke gevind word teweeg bring. Nieteenstaande die biodiversiteit en die skoonheid van die streek, is groot gebiede onbekend as gevolg van politieke onstabiliteit met die ontoeganklikheid van meeste van die streek as 'n bydraende faktor. Die meerderheid van studies in die Albertine Rift het gefokus op die charismatiese mega fauna, met ander taxa wat minder aandag ontvang. Een van die taksonomies en numeries meer volop klein soogdier genera is die genus Praomys, 'n Afrika endemiese groep met 'n wye verspreiding wat strek oor die grootste deel van van wes-, sentraal en oos-Afrika. Vier spesies word tipies erken van die Albertine Rift naamlik P. degraaffi, P. jacksoni, P. misonnei en P. verschureni. In hierdie studie het ek 'n kombinasie van DNA volgorde data (mitochondriale beheer streek, mitochondriale sitochroom b en 7de intron van die kern ß-fibrinogeen geen) sowel as morfometriese data (tradisioneel en meetkundig) gebruik om die sistematiek van die Praomys taxa te ondersoek. Om betekenisvolle DNA aanslae toe te laat en in 'n poging om potensiële aandrywers van diversiteit te identifiseer, is ander Praomys spesies van openbare volgorde data basisse vir vergelykings ingesluit. Die hooffokus is op P. jacksoni (die numeries volopste takson, ook, tot en met 2005 is alle Praomys in die Albertine Rift meestal as "jacksoni" versamel) en P. degraaffi ('n Albertine Rift endemiese spesie). 'n Verrassende bevinding was die teenwoordigheid van P. mutoni, dit verteenwoordig' n verspreidingsuitbreiding vir hierdie spesie in die Albertine Rift. Bepaalde evolusionêre ontwikkelingslyne was in beide P. jacksoni (bevestig deur die volgorde data sowel as morfometrie) sowel as P. degraaffi (wat slegs gebaseer is op die volgorde data, onvoldoende monsters verhinder 'n volledige morfometriese ondersoek). Hierdie lyne (in beide P. jacksoni sowel as P. degraaffi) word geskei langs 'n noord - suid gradiënt, maar verdere ondersoeke moet dit bevestig. Om die genetiese patrone op plaaslike skaal oor die Albertina Rift verder te ondersoek, sowel as introgressie tussen spesies soos geopenbaar deur die volgorde data, is 'n spesie-spesifieke mikrosatelliet biblioteek ontwikkel vir P. jacksoni. Twaalf polimorfiese merkers is geïdentifiseer waarvan nege ook amplifiseer in P. degraaffi. Introgressie is bevestig tussen die twee brandpunt spesies met byna 20% van die individue wat ontleed is as jacksoni-degraaffi basters. Dit is miskien nie so verbasend gegee dat daar aansienlike oorvleueling is in hul gebiede (tussen ~ 1500 m bo seespieel tot 2450 m bo seespieel), sowel as die relatiewe ouderdomme van die spesies (die divergensie tussen hierdie twee spesies is geskat op 3,8 Mya). Die teenwoordigheid van verskillende lyne in elk van hierdie spesies is bevestig deur mikrosatelliet ontleding (hierdie lyne het gedivergeer ongeveer 3,4 Mya). Soos voorgestel deur die DNA volgorde en morfometriese data, het hierdie lyne 'n grootliks noorde – suid verspreiding, maar met 'n aansienlike oorvleueling in die sentrale Albertine Rift in die omgewing van die Kivumeer. Die filogeografiese patrone wat vir beide die brandpunt spesies gevind is nie in ooreenstemming met die fisiese struikelblokke soos die riviere, mere of berge nie, en hou ook nie uitsluitlik verband met die Pleistoseen verskynsels soos die verandering van die loop van die riviere nie; die afstammelinge is eerder veel ouer as die Pleistoseen en val binne die Plioseen (> 3 Mya). Biogeografies, die noorde – suid plasing van die lyne met 'n sentraal geleë kontak sone kan die gevolg wees van parapatriese spesiasie te danke aan habitatfragmentasie as gevolg van verandering in die klimaat, gevolg deur 'n sekondêre kontak. Strepieskodering met behulp van genetiese inligting verskaf 'n nuttige instrument om onbekend taxa, kriptiese diversiteit of waar verskillende lewensfases moeilik is om te identifiseer, te identifiseer. Vanuit 'n indringerbiologie perspektief, maak hierdie benadering dit moontlik om vinnige identifikasies van die probleem taksa teen' n bekende data basis te bekom. Deur gebruik te maak van so 'n strepieskoderingsbenadering (senso lato), is die teenwoordigheid van drie indringende knaagdiere bevestig in die Demokratiese Republiek van die Kongo (DRK), naamlik Rattus rattus (swart rot), R. norvegicus (Noorweë rot) en Mus musculus domesticus (huis muis). 'n Vergelyking met die globale data wat beskikbaar is vir hierdie spesies het aan die lig gebring dat twee moontlike betree-roetes bestaan, naamlik via die skeepshawe by Kinshasa / Matadi (met sterk skakels na Europa), en via die slawehandel roetes in die ooste (sterk skakels na die Arabiese wêreld en die ooste) . Van hierdie drie taxa, is tans slegs R. rattus van die Demokratiese Republiek van die Kongo gedokumenteer, hoewel die ander melding ontvang in die grys literatuur. Hierdie bevindinge vestig die aandag op die gebrek aan enige amptelike beleid ten opsigte van biosekuriteit in die Demokratiese Republiek van die Kongo, en argumenteer vir die ontwikkeling van streng beheermaatreëls om verdere indringerspesies te voorkom.

Thesis (PhD)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Fleas (Siphonaptera) are obligate ectoparasites of mammals and birds. Due to their economic importance as disease vectors, most contemporary studies on macroparasites now also consider the spatial variation of parasite communities and the underlying mechanisms involved in shaping current distribution patterns. Fleas differ in life history traits, such as the level of host specificity and microhabitat preferences, which can result in differential evolutionary responses to similar abiotic events. The main objectives of this study are to investigate: (1) the influence of vicariance and host association on the genetic structure of two generalist flea species, Listropsylla agrippinae, and Chiastopsylla rossi. The taxa differ in the time spent on the host (fur vs. nest) and the level of host specificity; (2) the taxonomy of Dinopsyllus ellobius to determine whether more than one species exist and if so to then elucidate the mechanisms of speciation; and (3) the influence of flea life history on species distribution model performance and see if the relative importance of predictor variables differ between species with different life histories. A total of 1423 small mammals were brushed to collect 2906 flea individuals originating from 31 geographically distinct localities throughout South Africa (SA). Phylogeographic structure of L. agrippinae and C. rossi were determined by making use of 315 mitochondrial COII (mtDNA) and 174 nuclear EF1-α (nDNA) sequences. The more host specific fur flea, L. agrippinae, displayed pronounced spatial phylogeographic structure, based on mtDNA, which was congruent with host vicariance in the region. In contrast, the more generalist nest flea, C. rossi, showed a higher level of inter-populational divergence, based on mtDNA and nDNA, and this may be attributed to comparatively higher restrictions to dispersal when compared to the more specific fur flea. In an attempt to resolve the taxonomy of D. ellobius, 151 mtDNA and 68 nDNA alleles were generated from individuals meeting the morphological description of D. ellobius. Two distinct D. ellobius lineages that corresponded to previously described species (D. ellobius and D. abaris) were recorded. The results indicate that the two species indeed differ morphologically and based on the distribution of the two species it was concluded that the diversification could be a result of climate driven vicariance and subsequent ecological segregation according to habitat use. Locality records from Segerman (1995) were digitized and used as background data in species distribution modelling. Sufficient information was obtained for 21 flea species. A total of 68 climatic and landscape feature predictor variables were obtained and through a process of elimination, 19 variables were ultimately used. Model performance was good to excellent on average and the contribution of climate and landscape feature variables differed between fleas with different life histories. Historical and contemporary climate has the most prominent effect on flea distribution at the regional scale, but the level of host association influences the phylogeographic pattern of fleas. This study provides the first evidence of congruent phylogeographic patterns between a generalist temporary parasite and its hosts. Our findings provide further support for the notion that more than one species exist within the D. ellobius complex and that speciation is a result of complex interactions. The study also provides novel data on the role of environmental variables in shaping the geographic distribution of flea species with different life histories. With the anticipated rise in flea-borne diseases worldwide, due to changes in vector distribution, the study further emphasize the need for studying the mechanisms involved in shaping flea distribution patterns. / AFRIKAANSE OPSOMMING: Vlooie (Siphonaptera) is verpligte ektoparasiete van soogdiere en voëls. As gevolg van hul ekonomiese belangrikheid as vektore van oordraagbare siektes, neem meeste kontemporêre studies oor makroparasiete nou die ruimtelike variasie (vikariansie) van parasiet gemeenskappe en die onderliggende meganismes betrokke by die vorming van die huidige verspreiding patrone in ag. Vlooie verskil in lewensgeskiedenis eienskappe, soos die graad van gasheer spesifisiteit en mikrohabitat voorkeur, wat kan lei tot differensiële evolusionêre patrone tot soortgelyke abiotiese gebeure. Die belangrikste doelwitte van hierdie studie is om ondersoek in te stel na: (1) die invloed van vikariansie en gasheer assosiasie op die genetiese struktuur van twee algemene vlooi spesies, Listropsylla agrippinae en Chiastopsylla rossi. Die taxa verskil in die hoeveelheid tyd wat gespandeer word op die gasheer (pels vs. nes) en die graad van gasheer spesifisiteit; (2) die taksonomie van Dinopsyllus ellobius om te bepaal of daar meer as een spesie bestaan, en indien wel, die meganismes van spesiasie voortbring; en (3) die invloed van vlooi lewensgeskiedenis op die prestasie van die spesies verspreidings model en kyk of die relatiewe belangrikheid van omgewingsvoorspellers verskil tussen spesies met verskillende lewensgeskiedenisse. 'n Totaal van 1423 klein soogdiere is geborsel om 2906 vlooi individue afkomstig van 31 geografies verskillende plekke in Suid-Afrika in te samel. Filogeografiese struktuur van L. agrippinae en C. rossi is bepaal deur gebruik te maak van 315 mitochondriale COII (mtDNA) en 174 kern EF1-α (nDNA) volgorde bepalings. Die meer gasheer spesifieke pels vlooi, L. agrippinae, het ruimtelike filogeografiese struktuur aangetoon, gebaseer op mtDNA, wat ooreenstem met gasheer vikariansie in die streek. In teenstelling hiermee het die minder gasheer spesifieke nes vlooi, C. rossi, 'n hoër vlak van inter-populasie divergensie getoon, gebaseer op mtDNA en nDNA, wat toegeskryf kan word aan relatief hoër beperkings op verspreiding teenoor die meer gasheer spesifieke pels vlooi. In 'n poging om die taksonomie van D. ellobius op te los is 151 mtDNA en 68 nDNA allele gegenereer uit individue wat voldoen aan die morfologiese beskrywing van D. ellobius. Twee afsonderlike D. ellobius afstammelinge wat ooreengestem het met voorheen beskryfde spesies (D. ellobius en D. abaris) is aangeteken. Die resultate dui daarop dat die twee spesies inderdaad morfologies verskil en gebaseer op die verspreiding van die twee spesies is daar tot die gevolgtrekking gekom dat die diversifikasie moontlik toegeskryf kan word aan klimaat gedryfde vikariansie en daaropvolgende ekologiese segregasie volgens habitat gebruik. Geografiese verspreidings rekords van Segerman (1995) was gedigitaliseerd en gebruik as agtergrond data in die spesie verspreidings modelle. 'n Totaal van 68 klimaat en landskap kenmerk voorspeller veranderlikes is verkry, en deur 'n proses van eliminasie, is 19 veranderlikes gebruik. Model prestasie was oor die algemeen goed tot uitstekend en die bydrae van klimaat en landskaps veranderlikes het verskil tussen vlooie met verskille in lewensgeskiedenis. Historiese en kontemporêre klimaat het die mees prominente effek op vlooi verspreiding by die plaaslike skaal, maar die vlak van die gasheer assosiasie beïnvloed die filogeografiese patroon van vlooie. Hierdie studie bied die eerste getuienis van ooreenstemmende filogeografiese patrone tussen 'n minder gasheer spesifieke, tydelike parasiet en sy gashere. Ons bevindinge bied verdere ondersteuning vir die idee dat meer as een spesie bestaan binne die D. ellobius kompleks en dat spesiasie 'n gevolg is van komplekse interaksies. Die studie bied ook nuwe data oor die bydrae van die omgewingsveranderlikes in die vorming van die geografiese verspreiding van vlooi spesies met verskillende lewensgeskiedenisse. Met die verwagte styging in vlooi-oordraagbare siektes wêreldwyd, as gevolg van veranderinge in vektor verspreiding, beklemtoon die studie verder die noodsaaklikheid vir die bestudering van die meganismes betrokke in die vorming van vlooi verspreiding patrone. / National Research Foundation (NRF)

Natural habitat in the eastern United States has diminished over the past century because of the effects of invasive species. Both plant and animal invaders can alter habitat structure and may decrease survival of native species. The degree to which an invasive species alters ecosystem function depends on the functional characteristics of affected species and the resulting cascading effects. The loss of important native species, such as foundation species, can potentially influence the structure and distribution of animal communities because of the foundation species' unique ecosystem roles. The foundation species concept is relatively new to the terrestrial ecology and the impact on animal communities resulting in the loss of terrestrial foundation species is generally unknown. Eastern hemlock (Tsuga Canadensis), a foundation species in the eastern United States, is declining in abundance due to the invasive sap-sucking insect, hemlock woolly adelgid (Adelges tsugae, Annand). The loss of hemlock may impact the distribution and microhabitat associations of dependent species such as small mammals. I hypothesized that the distribution, population size, community composition, and microhabitat associations of small mammal species differ in response to canopy disturbance from the effects of logging and invasive species. In this dissertation, Chapter One provides an exploration of the past research conducted on 1) invasive species and how they affect habitat structure, 2) foundation species and how they affect ecosystem function, 3) small mammal habitat associations and population cycling, 4) occupancy modeling and its usefulness and limitations in the analysis of local occupancy, colonization rates, and extinction rates. Chapter Two presents a large-scale experiment on how the hemlock woolly adelgid impacts distribution and community assembly of small mammals. Chapter Three presents how forest disturbance, food resources, and habitat structure effects local colonization and extinction patterns of southern red-backed voles. Chapter Four presents how a paper published in 2005 brought the foundation species concept to terrestrial research and how the foundation species concept can be misleading in research.

Small mammals, namely those species larger than microfauna like rats and murids but smaller than medium, sheep-size fauna, are generally one of the less studied areas of zooarchaeology. While this may be partly influenced by modern cultural biases, it is more often because finding small, rabbit-sized, mammal remains in archaeological deposits presents a problem in accurately differentiating between those arising from natural, biological and anthropogenic agencies. This thesis tackles this subject using a synthesis of different methods, examining the exploitation and role of small, non-ungulate mammals in early Western European prehistory by combining existing ethnographic knowledge and archaeological research with actualistic experiments and bone assemblage analysis. It first presents a detailed summary of the various taphonomic effects on bone from natural, biological and human action, with particular reference to those of small mammals, using empirical evidence to describe the processes and likely resultant effects. Small mammal utilisation is then contextualised using archaeological and ethnographic evidence to examine past and present practices in Europe and other areas of the world. Different acquisition methods, such as hunting and trapping, are described, and using small mammals for dietary and non-dietary purposes is outlined, along with the rationale for such utilisation given their size. Also considered are other, more abstract ideological and symbolic roles they fulfilled within different cultures, whether physically using parts of the animal, or conceptually. To extend the existing methods available to zooarchaeologists, and improve identifying human exploitation of these species, the ‘chaîne opératoire’ of small game use is examined from an osteological perspective, starting with acquisition, through processing, cooking and consumption to discard, using a series of experiments and microscopic analysis to explore potential bone modification signatures and fracture patterns arising from such activities. Finally, it places these results into broader context by comparing the fracture patterns with bones from British and North American archaeological sites, to demonstrate that similar changes can be seen.

The extensive material of skeletal remains of mammals from a diet of barn owl in the eastern Mediterranean has been processed and evaluated with different techniques of chorological and morphometric analysis. At least 8400 individuals of 45 species of insectivores, rodents and bats were found in our total collection of samples, which represents a significant portion of fauna of the region. We have evaluated a chorological composition of the taphocoenoses and the interregional differences, manifested primarily by differences in the representation of satellite and accessory elements. We found a highly significant impoverishment of the isolated island taphocenoses (Cyprus, Karpathos, partly on Crete), where Cricetidae, Arvicolidae, C. leucodon etc. are missing. On the other hand the essential part of the dominance structure takes up the Rattus rattus, which acts here as an invasive species, significantly more successful than in the ragged continental contexts. The species diversity of the examined samples is positively correlated with the geographic latitude (taphocenoses of the northern regions are significantly richer) and negatively with the island effect and the degree of aridization. The morphometric analysis of the three most abundant species of Soricidae within the studied region showed...

A fauna de pequenos mamíferos e de carrapatos da Reserva Florestal do Morro Grande, Cotia, SP, foi investigada assim como microrganismos associados a eles. Coletas foram realizadas bimestralmente, e resultaram na captura de 158 pequenos mamíferos silvestres e cães, distribuídos em 126 roedores de 10 espécies, 26 marsupiais de 3 espécies, um tapiti, além de 6 cães domésticos inspecionados. Destes hospedeiros foram recolhidos 327 carrapatos de 9 espécies de 4 gêneros, e larvas de Amblyomma sp. Novos registros de hospedeiros foram acrescentados para as espécies I. aragaoi, I. loricatus, I. schulzei e de espécie morfologicamente semelhante a I. fuscipes. Simultaneamente, fizemos a pesquisa de exemplares em vida livre na vegetação por arraste e busca visual. Um total de 597 exemplares foram recolhidos e identificados, representando 9 espécies de 3 gêneros, além de larvas do gênero Amblyomma. Na sorologia por RIFI, com exceção dos cães domésticos que foram todos negativos, a soro reatividade apresentada para pequenos mamíferos silvestres sugere a circulação de cepas de Rickettsia naquela região. Dos 102 animais testados, 39 foram soro positivos e em 6 amostras nós sugerimos provável antígeno homólogo para R. bellii (3), R. rickettsii (2) e R. rhipicephali (1). Encontramos na quase totalidade dos espécimes adultos de I. aragaoi uma Rickettsia próxima à cepa endosiombionte de I. scapularis, e em uma fêmea de A. sculptum, sequências parciais do gene ompA foram similares a R. parkeri isoladas de A. triste no Brasil e na Argentina. Sequências geradas a partir de um fragmento do gene 18S rRNA de Hepatozoon sp. foram obtidas de amostras dos carrapatos I.c.f. fuscipes e I. schulzei, coletados sobre o roedor A. montensis. Outro hemoprotozoário encontrado foi um genótipo de Babesia sp. proveniente de pools de larvas e de ninfas de A. incisum, coletados em vida livre. Na investigação da presença de bactérias do gênero Coxiella, 14 amostras de diferentes espécies do gênero Amblyomma (A. aureolatum, A. brasiliense, A. incisum, A. naponense e A. sculptum) foram positivas, e as análises de homologia utilizando o marcador molecular 16S rDNA foram compatíveis com Coxiella endosimbiontes de carrapatos. / The fauna of small mammals and ticks of the reserved forest of Morro Grande (RFMG) was assessed and investigated, as well as associated infectious microorganisms. Sample collections were performed bimonthly, and resulted in 158 wild small mammals and dogs inspected, distributed in 126 rodents of 10 different species, 26 marsupials of 3 different species, a Tapiti, and also 6 domestic dogs. 327 ticks were collected from the mentioned hosts; these ticks were representatives of 9 species of 4 different genera, and Amblyomma sp. larvae. New hosts records were appended for 4 species of the genus Ixodes; I. aragaoi, I. loricatus, I. schulzei and a I. fuscipes simile species. Simultaneously, free roaming ticks were collected from the vegetation by dragging a flannel through the forest and visual search. A total of 597 ticks were collected and identified belonging to 9 species of 3 genera, as well as Amblyomma genus larvae. Serology arrays using RIFI technique were performed, and with exception of the domestic dogs that all were negative, the serum reactivity showed in the wild small mammals demonstrated the circulation of Rickettsia strains in the studied region. 39 animals of the 102 tested were positive and 6 samples had strong evidences of being homologous antigens for R. bellii (3), R. rickettsii (2), and R. rhipicephali (1). Molecular research of microorganisms in ticks showed that almost all the adult individuals of I. aragaoi were positive for a Rickettsia similar to an endosymbiont strain of I. scapularis, and in a female of A. sculptum partial sequences the gene of ompA were similar to R. parkeri isolated from A. triste in Brasil and Argentina. Sequences obtained from a fragment of the gene 18S rRNA of Hepatozoon sp. amplified from samples of the tick species I.c.f. fuscipes and I. schulzei, collected from a rodent A. montensis. Another Hemo-protozoon found was a genotype of Babesia sp. from pools of A. incisum larvae and nymphs, collected in the vegetation. For the bacteria of the genus Coxiella, 14 samples of different species of the genus Amblyomma (A. aureolatum, A. brasiliense, A. incisum, A. naponense and A. sculptum) were positive, and the similarity analyses using the 16S rDNA molecular marker were compatible with Coxiella endosymbiont of ticks.

Essa dissertação de mestrado objetivou avaliar a importância dos corredores ripários para a fauna em uma paisagem fragmentada de Mata Atlântica. Em quatro sistemas compostos por fragmento - corredor fragmento avaliamos tanto a assembléia de pequenos mamíferos (capitulo 2) como a qualidade do habitat através da estrutura da vegetação e da disponibilidade de recurso alimentar para a fauna (capitulo 3). No capitulo 2 comparamos a assembléia de pequenos mamíferos entre áreas abertas do entorno, corredores ripários, bordas e interiores de fragmentos. Verificou-se uma forte segregação na distribuição das espécies entre áreas abertas da matriz e os habitats florestados. Todas as espécies endêmicas só foram capturadas nos habitats florestais, enquanto que a matriz de áreas abertas abrigou uma assembléia de pequenos mamíferos composta exclusivamente por espécies não endêmicas ao bioma Mata Atlântica e apenas duas espécies não-endêmicas ocuparam todos os habitats. Observou-se ainda, que as flutuações temporais na abundância das espécies não diferiram entre habitats, ou seja, as diferenças que encontramos na distribuição das espécies não dependeram da sessão de captura. Além disso, a riqueza e abundância das espécies endêmicas foram maiores nos ambientes florestais em comparação a matriz aberta, enquanto que a abundância das espécies não-endêmicas foi maior na matriz comparada aos interiores de fragmentos. As duas espécies endêmicas mais abundantes na área de estudo ocorreram apenas nos habitats florestais, e a abundância das duas foi menor nas bordas do que nos interiores e, em um caso, também do que nos corredores. Por outro lado, a abundância de uma das três espécies não-endêmicas mais comuns foi maior nas bordas do que nos interiores. Assim concluímos os corredores ripários funcionam como elemento conector para a fauna endêmica de pequenos mamíferos da Mata Atlântica, amenizando os efeitos deletérios da fragmentação. No capitulo 3, ao avaliar a qualidade do habitat entre os corredores ripários, e bordas e interiores de fragmentos secundários, observamos que a oferta de recursos alimentares (artrópodes e frutos) para a fauna, assim como a estrutura da vegetação, em termos da estratificação da densidade da folhagem, não variou entre os diferentes tipos de habitat florestal. Nesse sentido, nossos resultados sugerem que, ao contrário do observado em florestas tropicais primárias, em florestas tropicais secundárias não há um efeito de borda claro sobre a qualidade do habitat em termos de estrutura da vegetação ou disponibilidade de alimento para a fauna nem mesmo em estruturas lineares como os corredores. Os resultados apresentados nos dois capítulos evidenciam a importância da manutenção dos corredores ripários para a conservação, em paisagens fragmentadas de Mata Atlântica, da fauna de um dos grupos mais diversificados de mamíferos. / This master thesis aimed to evaluate the importance of riparian corridors for the fauna in an Atlantic Forest fragmented landscape. In four systems composed by fragment corridor fragment, we evaluate both the small mammal assemblage (chapter 2) and the habitat quality measured through the vegetation structure and food resources availability for the fauna (chapter 3). In chapter 2 we compared small mammal assemblages among open areas of the surrounding matrix, riparian corridors, edges and interiors of forest fragments. We verified a strong segregation in species distribution between the open matrix and the forested habitats. Endemic species were captured only in forested habitats, while the open areas of the matrix harbored a small mammals assemblage composed exclusively by species non-endemic to the Atlantic Forest biome, and only two non-endemic species occupied all habitat types. We also observed that temporal fluctuations in species abundance did not differ among habitats, that is, observed differences in species distribution were not dependent on capture session. Moreover, richness and abundance of endemic species were higher in forested habitats than in the open areas of matrix, while the abundance of nonendemic species was higher in the matrix than in the interior of forest fragments. The two most abundant endemic species occurred only in forested habitats and their abundance was lower at edges compared to forest interiors and, for one of them, also compared to riparian corridors. On the other hand, the abundance of one of the three most common non-endemic species was higher at edges than in interiors. We conclude that riparian corridors function as a connector element for the endemic small mammals of the Atlantic Forest, minimizing the deleterious effects of habitat fragmentation. In chapter 3, through the evaluation of habitat quality in riparian corridors, edges and interiors of second-growth fragments, we observed that food resource availability (arthropods and fruits) for the fauna, as well as the vegetation structure, measured as foliage vertical stratification, did not differ among the three forested habitats. Thus, our results suggest that, contrary to the observed in primary tropical forests, there is no clear edge effects on vegetation structure or on food resources availability for the fauna in secondary forest fragments even in linear habitats such as corridors. The results reported in these two chapters highlight the importance of the maintenance of riparian corridors for the conservation, in fragmented landscapes of the Atlantic Forest, of one of the most diverse group of mammals.

Submitted by Silvana Teresinha Dornelles Studzinski (sstudzinski) on 2015-06-25T15:58:23Z No. of bitstreams: 1 PauloH.D.Machado.pdf: 795005 bytes, checksum: 03018293cef47592c176e954e9ce2228 (MD5) / Made available in DSpace on 2015-06-25T15:58:23Z (GMT). No. of bitstreams: 1 PauloH.D.Machado.pdf: 795005 bytes, checksum: 03018293cef47592c176e954e9ce2228 (MD5) Previous issue date: 2012 / Nenhuma / Uma das hipóteses para explicar a diversidade da fauna associada a florestas tropicais é a variedade de recursos abióticos e alimentares, os quais podem ser influenciados pelas variações da heterogeneidade das paisagens locais. A ação destes aspectos físicos sobre os componentes ecológicos das comunidades são de extrema importância para pequenos mamíferos. Os aspectos ecológicos sensíveis à variações da paisagem podem responder pelas diferenças nas distribuições geográficas apresentadas por pequenos mamíferos, além de influenciar na composição das comunidades, principalmente em decorrência dos efeitos da fragmentação e do isolamento de habitat. O presente estudo objetivou a investigação da abundância e da variação sazonal de pequenos mamíferos não voadores do Parque Estadual de Itapuã (PEI), Viamão, RS (30°20’45,09”S; 51°01’33,27”W), avaliando a relação entre heterogeneidade da paisagem, oferta de recursos alimentares e abundância nas populações de três espécies de roedores Sigmodontíneos (Oligoryzomys nigripes, Akodon montensis e Sooretamys angouya) que apresentam uma distribuição geográfica no Brasil relativamente ampla e sujeita a influências da paisagem. O esforço amostral total foi de 2.520 armadilhas/noite, em que foram capturados 167 indivíduos das três espécies. A espécie de maior abundância foi A. montensis (N = 117), e a menos abundante S. angouya (N = 19). Houve diferença significativa para a abundância das espécies entre as diferentes áreas de estudo, e entre as estações do ano (H = 10,874; g.l. = 4; P = 0,028). A oferta de recursos variou significativamente entre as estações do ano, mas não entre as áreas. Características do micro-habitat diferiram estatisticamente entre as áreas, e colaboraram para a formação dos agrupamentos na PCA. De maneira geral, apontou-se que as composição das áreas estudas parece ter maior relevância sobre os aspectos ligados a potencialidade de uso e ocupação de hábitats pelas três espécies, tendo suas variações de abundância justificadas pelos aspectos intrínsecos das formações vegetais, associado às mudanças climáticas sazonais. / The variety of abiotic resources and food stands as one hypothesis trying to explain the diversity of fauna associated with tropical forests, which can be influenced by variations in the landscapes’ heterogeneity. The action of those physical aspects on ecological communities is extremely important for small mammals. The ecological aspects of the landscape that is susceptible to variations may explain the differences in geographic distributions presented by small mammals, besides influencing the composition of the communities, mainly due to effects of fragmentation and habitat isolation. This study aimed to investigate the abundance and spatial variation of non-flying small mammals of Parque Estadual de Itapuã (PEI), Viamão, RS (30°20'45,09 "S, 51°01'33, 27" W) evaluating the relationship between landscape heterogeneity, resource availability and abundance in populations of three species of rodents from the Sigmodontinae subfamily (Oligoryzomys nigripes, Akodon montensis and Sooretamys angouya) that showed an extensive geographic distribution in Brazil and susceptibility to influences from the landscape. The total sampling effort was 2,520 traps/night, in which 167 individuals from three species were captured. The most abundant species was A. montensis (N = 117), and the less abundant was S. angouya (N = 19). There was a significant difference regarding species abundance between areas and between seasons (H = 10.874, df = 4, P = 0.028). The availability of resources varied significantly among seasons but not between areas. Aspects of micro-habitat differed among the areas, thus contributing to the formation of clusters in the PCA. So, we consider the composition of the areas studied apparently has the greatest relevance upon aspects related to the potential use and habitat occupation by those three species, and their abundance variations are justified by intrinsic aspects from the vegetation, associated with seasonal climatic changes.