Thesis (Ph. D.)--Illinois State University, 1999. / Title from title page screen, viewed July 24, 2006. Dissertation Committee: David W. Borst (chair), Angelo P. Capparella, Sabine S. Loew, Edward L. Mockford, Carleton J. Phillips, Douglas W. Whitman. Includes bibliographical references (leaves 77-89) and abstract. Also available in print.

Thesis (M. Sc.)--University of Canterbury, 2009. / Typescript (photocopy). Includes bibliographical references (leaves 101-114). Also available via the World Wide Web.

Made available in DSpace on 2014-06-11T19:26:05Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-02-23Bitstream added on 2014-06-13T19:12:56Z : No. of bitstreams: 1 orrego_leo_me_botib.pdf: 1487561 bytes, checksum: 90a7f6e8635b374d9485785d05ccddfa (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Brachyplatystoma platynemum é uma espécie de bagre amplamente distribuída no eixo Amazonas/Solimões e muitos de seus tributários e, apesar de ser considerado de baixo valor comercial, o declive do estoque de outras espécies de grandes bagres de interesse comercial tem levado ao incremento na captura desta espécie. Por outro lado, o estado atual da estrutura e variabilidade genética das populações desta espécie são desconhecidos. Neste sentido foi realizada uma análise filogeográfica através do sequenciamento de dois genes do DNA mitocondrial (região controle e o gene citocromo b) e de marcadores nucleares microssatélites, com o objetivo de determinar se a espécie esta composta de um único estoque geneticamente homogêneo ou se existe algum tipo de segregação genética associada com o espaço e o tempo, que possa ser relacionada com o comportamento de homing. Foi analisado um total de 216 indivíduos para a região controle, 140 para o gene citocromo b e 169 para seis locus microssatélites, em sete localidades. Os resultados indicam altos níveis de diversidade haplotípica e evidenciam estrutura genética dos indivíduos desta espécie em duas populações: rio Madeira e demais pontos de coleta, no entanto, a estrutura observada não constitui suficiente evidencia para ser associada ao comportamento de homing. Estimativas do tempo de divergência baseadas no mtDNA indicam que as populações divergiram entre 1,0 a 1,5 Ma, tempo durante o qual a influencia das mudanças climáticas podem ter contribuído para a estrutura atual das populações de B. platynemum. Embora o padrão filogeográfico concorde com as predições da hipótese dos refúgios do Pleistoceno, a influência de eventos paleogeográficos e hidrológicos não pode ser descartada. Nossos resultados mostram a interação das mudanças... / Brachyplatystoma platynemum is a catfish species widely distributed in the Amazonas / Solimões basin, despite being considered of little commercial interest, the decline of fish stock of other species has contributed to the increase in the catch of this species. However, the current state of the structure and genetic variability of populations of this species are unknown. In this sense a phylogeographic analysis was performed through sequencing of two mitochondrial molecular markers (control region and cytochrome b gene) and nuclear microsatellites. In order to determine whether the species is composed of a single genetic unit, or if there is any genetic segregation associated with space and time, which may be related to homing behavior. It was analyzed a total of 216 individuals in the control region, 140 for the gene cytochrome b and 169 individuals for six microsatellite loci in seven locations in the Amazon/Solimões basin. The results show high levels of haplotype diversity and evidence genetic structure in two populations (Amazon river channel and the Madeira River). However, the observed structure is not indicated of homing behavior. Divergence time estimates based on mtDNA indicated that the populations diverged between 1.5 to 1.0 Ma, during this time the influence of climate change may have contributed to the current structure of populations of B. platynemum. Although the phylogeographic patterns is consistent with the hypothesis of Pleistocene refuges, the influence of paleogeographic and hydrological events as a result of geological process in the Plio-Pleistocene, are important in the diversification of populations. Our results show the interaction of climate change as a result of hydrological and geological processes in the Plio-Pleistocene in the diversification of fish populations in the Amazon region. Finally... (Complete abstract click electronic access below)

Orientador: Claudio de Oliveira / Banca: Fernanda Simões de Almeida / Banca: Daniela Calcagnotto / Resumo: Brachyplatystoma platynemum é uma espécie de bagre amplamente distribuída no eixo Amazonas/Solimões e muitos de seus tributários e, apesar de ser considerado de baixo valor comercial, o declive do estoque de outras espécies de grandes bagres de interesse comercial tem levado ao incremento na captura desta espécie. Por outro lado, o estado atual da estrutura e variabilidade genética das populações desta espécie são desconhecidos. Neste sentido foi realizada uma análise filogeográfica através do sequenciamento de dois genes do DNA mitocondrial (região controle e o gene citocromo b) e de marcadores nucleares microssatélites, com o objetivo de determinar se a espécie esta composta de um único estoque geneticamente homogêneo ou se existe algum tipo de segregação genética associada com o espaço e o tempo, que possa ser relacionada com o comportamento de homing. Foi analisado um total de 216 indivíduos para a região controle, 140 para o gene citocromo b e 169 para seis locus microssatélites, em sete localidades. Os resultados indicam altos níveis de diversidade haplotípica e evidenciam estrutura genética dos indivíduos desta espécie em duas populações: rio Madeira e demais pontos de coleta, no entanto, a estrutura observada não constitui suficiente evidencia para ser associada ao comportamento de homing. Estimativas do tempo de divergência baseadas no mtDNA indicam que as populações divergiram entre 1,0 a 1,5 Ma, tempo durante o qual a influencia das mudanças climáticas podem ter contribuído para a estrutura atual das populações de B. platynemum. Embora o padrão filogeográfico concorde com as predições da hipótese dos refúgios do Pleistoceno, a influência de eventos paleogeográficos e hidrológicos não pode ser descartada. Nossos resultados mostram a interação das mudanças... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Brachyplatystoma platynemum is a catfish species widely distributed in the Amazonas / Solimões basin, despite being considered of little commercial interest, the decline of fish stock of other species has contributed to the increase in the catch of this species. However, the current state of the structure and genetic variability of populations of this species are unknown. In this sense a phylogeographic analysis was performed through sequencing of two mitochondrial molecular markers (control region and cytochrome b gene) and nuclear microsatellites. In order to determine whether the species is composed of a single genetic unit, or if there is any genetic segregation associated with space and time, which may be related to homing behavior. It was analyzed a total of 216 individuals in the control region, 140 for the gene cytochrome b and 169 individuals for six microsatellite loci in seven locations in the Amazon/Solimões basin. The results show high levels of haplotype diversity and evidence genetic structure in two populations (Amazon river channel and the Madeira River). However, the observed structure is not indicated of homing behavior. Divergence time estimates based on mtDNA indicated that the populations diverged between 1.5 to 1.0 Ma, during this time the influence of climate change may have contributed to the current structure of populations of B. platynemum. Although the phylogeographic patterns is consistent with the hypothesis of Pleistocene refuges, the influence of paleogeographic and hydrological events as a result of geological process in the Plio-Pleistocene, are important in the diversification of populations. Our results show the interaction of climate change as a result of hydrological and geological processes in the Plio-Pleistocene in the diversification of fish populations in the Amazon region. Finally... (Complete abstract click electronic access below) / Mestre

O morcego Desmodus rotundus é uma das três espécies de morcegos hematófagos existentes. Possui ampla distribuição, ocorrendo do sul do México até Argentina e Chile. Além de seu hábito alimentar incomum, esta espécie possui particular interesse por ser transmissor da raiva bovina. Apesar dos métodos de controle da população, estudos estimaram em até 33 milhões de dólares ao ano os prejuízos causados por esta espécie a pecuária no Brasil. Ao mesmo tempo, segundo dados oficiais, cerca de 200.000 indivíduos da espécie podem ter sido mortos no Estado de São Paulo no ano de 2000 através dos métodos de controle populacional. Além deste controle não surtir o efeito desejado (o número de casos de raiva não diminuiu no período), não se conhece qual o efeito desta matança nas populações naturais do morcego. Apesar de sua ampla distribuição e reconhecida variação morfológica, nenhum estudo foi realizado para procurar entender como a variabilidade genética desta espécie está distribuída geograficamente. Este estudo se propôs a estudar a filogeografia do morcego vampiro comum analisando um marcador mitocondrial, dois marcadores nucleares e morfometria de crânio. O marcador mitocondrial identificou cinco clados monofiléticos sem haplótipos compartilhados nem zonas de contato, cada um representando uma região geográfica diferente. São eles: Mata Atlântica sul (MAS), Mata Atlântica norte (MAN), Amazônia e Cerrado (AMC), América Central (AC) e Pantanal (PAN), sendo que os clados da Mata Atlântica formam um clado monofilético a Leste, se contrapondo aos demais clados a Oeste. Os índices de divergência entre estes clados são comparáveis a distâncias descritas para espécies congenéricas. Os tempos de divergência estimados entre os clados através de métodos coalescentes e não-coalescentes apontam para uma divergência pleistocênica, além de testes de neutralidade apoiarem a idéia de fragmentação por refúgios. O padrão biogeográfico descrito para D. rotundus possui um paralelo em uma série de outros organismos. Os marcadores nucleares por sua vez mostraram baixa variabilidade, e extenso compartilhamento de haplótipos entre as localidades pertencentes a distintos clados mitocondriais, num padrão que contrasta com os resultados descritos anteriormente. Simulações coalescentes foram realizadas com os parâmetros calculados para o gene nuclear RAG2 e mostraram compatibilidade entre os dados observados e vicariância pleistocênica para um marcador nuclear com o Ne calculados para D. rotundus. Os dados de morfometria de crânio mostraram que existe pouca diferenciação ao longo de toda a distribuição da espécie. Dados de Fst, funções discriminantes e variáveis canônicas mostram uma grande afinidade entre indivíduos dos clados AC e AMC, que juntos formam a distribuição de uma antiga subespécie atribuída a este táxon, Desmodus rotundus murinus. As análises de distância de Mahalanobis também são concordantes com os resultados obtido para o marcador mitondrial. Por fim, uma análise realizada com o software treescan mostra existir uma correlação estatisticamente significativa entre a árvore de DNA mitocondrial e os dados multivariados de crânio. Assim, por fim propõe-se que se reconheçam duas linhagens hoje atribuídas a D. rotundus como espécies distintas: uma a Leste (Mata Atlântica) e uma a Oeste. Uma amostragem mais cuidadosa do interior do Brasil e do restante da América do Sul deve determinar corretamente a área de ocorrência de cada espécie. / The bat Desmodus rotundus is one of the three extant vampire bat species. It has a broad distribution, occurring from southern México until Argentina and Chile. Besides its unique feeding habit, this species is of particular interest for being the main vector of cattle rabies. Even with population control methods, studies have estimated in 33 million dollars per year the damage caused by this bat to cattle farming in Brazil. At the same time 200.000 specimens might have been killed in São Paulo state in the year 2000 using the population control methods. Besides the fact that this control did not diminish the number of rabies cases, the impact of this killing in the bats\' natural populations is unknown. Although this species has a broad distribution and recognized morphological variation, no effort was made thus far to understand how this species\' genetic variability is distributed geographically. This work is aimed at studying the common vapire bats\' phylogeographic pattern using a mitochondrial marker, two nuclear markers and skull morphometrics. The mitochondrial marker identified five monophiletic clades without shared haplotypes or contact zones. Each clade represents a distinct geographic region: South Atlantic Forest (SAF), North Atlantic Forest (NAF), Amazon and Cerrado (AMC), Central America (CA) and Pantanal (PAN). The Atlantic Forest clades form an Eastern monophiletic clade opposing the other clade that lies westwards. The nucleotide divergence between these clades is similar to the one described to congeneric species. The divergence times estimated by coalescent and non-coalescent methods point to a Pleistocene vicariant event. The neutrality tests also point to refugia allopatric fragmentation. The biogegraphic pattern described for D. rotundus has a parallel in many other organisms. The nuclear markers showed low variability and sharing of haplotypes among all localities, contrasting with the previous results. Coalescent simulations were carried with populational parameters estimated for the nuclear gene RAG2 and showed compatibility between the observed data and Pleistocene vicariance effect on a neutral nuclear marker. Skull morphometrics showed low differentiation throughout the bats\' distribution. Data on Fst, discriminant functions and canonic variables shows affinity between CA and AMC clades. These two clades together form the distribution of a subspecies previously described to this taxon, Desmodus rotundus murinus. The Mahalanobis distance analyses are also congruent with the results obtained withn the nuclear marker. The analysis done with the software treescan shows a statistic significant correlation between the mtDNA tree and the skull multivariate data. On the basis of the results presented, it is proposed that two lineages currently atributed to D. rotundus are to be recognized as different species: one to the east (Atlantic Forest) and one to the west. A detailed sampling of the Brazilian and South American country will determine the exact range of each species.

Estudos morfológicos constataram que a espécie Tropidurus torquatus apresenta dois morfotipos geograficamente distintos ao longo da área ocupada pela espécie. Um com preferência por ambientes saxícolas, situado mais para o interior do continente e, outro, mais costeiro, ocupando predominantemente os solos arenosos de dunas e restingas. Estes morfotipos possuem características morfológicas externas distintas associadas a estes ambientes. Porém, estas diferenças morfológicas observadas não foram determinantes para um estudo mais conclusivo dos padrões de diferenciação e da história zoogeográfica da espécie em questão. Dentro deste contexto teórico, este trabalho abordou a história das populações de T. torquatus com o uso de dados moleculares mostrando como a variabilidade genética da espécie esta distribuída geograficamente. Esta espécie se mostrou muito mais diversa do que se imaginava inicialmente. Quatro diferentes linhagens foram recuperadas na maioria das análises e apresentam relação com a geografia. Os resultados mostraram que esta espécie está se expandido e que possivelmente pode ocorrer uma diferenciação intraespecífica. Também mostrou que pode estar ocorrendo fluxo gênico não só dentro desta espécie, mas como entre as outras espécies do gênero, porém somente uma filogenia mais robusta poderá elucidar a relação entre elas / Morphological studies have showed that Tropidurus torquatus presents two geographically distinct morphotypes along the area occupied by the species. The first morphotype is saxicolous and exhibits a preference for rocky environments located farther inland, and the other morphotype is located in more coastal areas, occupying predominantly sandy soils of dunes and sandbanks. These morphotypes have distinct external morphological traits associated with the environments they occupy. However, these differences were not observed morphological determinants for a more conclusive study of the differentiation patterns of differentiation and zoogeographical history of the species. Within this theoretical context, this work addressed the history of T. torquatus populations using molecular data, in order to understand the geographical distribution of genetic variability. Results showed that this species is far more diverse than initially hypothesized. Four different lineages were recovered in most analyzes, each one related to its intrinsic distributional pattern. Besides, this study shows that this species is expanding its distribution area and for this reason a differentiation among populations is likely to occur, potentially with formation of new species. Also results show that gene flow may be occurring not only within the species, but also between other Tropidurus species. Nonetheless, only a more robust phylogeny may elucidate the relationship between these species

Abstract Analyses of mitochondrial control region sequences were used to infer phylogeny of Anser species, phylogeography of the lesser white-fronted goose, and genetic background of a captive stock. The genetic distances among the Anser species ranged from 0.9 to 5.5% in the complete control region sequences and supported the view of close relatedness of these species. Among the four most closely related species, the bean, pink-footed, white-fronted and lesser white-fronted goose, the branching order is uncertain. The short internal branches and low support for the branching order suggest that the species have diverged recently within short time-intervals. The mtDNA tree obtained is incongruent with the traditional view of the species relationships, but the reasons for this remain to be clarified. Two diverged mitochondrial lineages were found in the lesser white-fronted goose and a refugial origin was proposed. Basal haplotypes are geographically widespread and indicate a recent common ancestry for populations. The derived haplotypes are confined to singular breeding populations and suggest restrictions to the present female gene flow. A shift in the frequency of the mtDNA lineages approximately coincides with a migratory divide in the Taimyr Peninsula. Low mtDNA diversity and significant difference in the haplotype frequencies observed in Fennoscandian subpopulation suggested that it should be considered as a management unit. The fossil record was examined to gain additional information about the colonisation history of the species, but was found to be of limited use. The captive lesser white-fronted goose stock used for reintroduction/restocking was shown to be incompatible with the Fennoscandian wild population. Some captive individuals carried the mtDNA of the white-fronted goose suggesting a hybrid origin. Hybridisation has probably occurred during captive propagation, but to clarify further the extent of introgression, nuclear markers should be applied. The structure and evolution of the control region were studied by comparing complete avian sequences. Saturation was found to occur at pairwise divergences of 10% as shown for third codon positions of the mitochondrial genes previously. In pairwise comparisons of the control region and cytochrome b sequences, the rate of divergence varied among the lineages. Two conserved sequence blocks showed considerable sequence conservation when compared to mammalian sequences.

Abstract Genetic diversity in three taiga specialists – the Siberian tit (Parus cinctus), the Siberian jay (Perisoreus infaustus) and the Siberian flying squirrel (Pteromys volans) – was assessed by comparing DNA sequence variation across the mitochondrial control region and allele frequencies of microsatellites from samples collected from Fennoscandia and Siberia. Population sizes of these species have declined in association with fragmentation and loss of suitable forest habitat due to modern forestry practices in Fennoscandia. The red squirrel (Sciurus vulgaris) served as a reference for the flying squirrel. Genetic differentiation among species studied ranged from a panmictic population in the Siberian tit to that of the strong differentiation of populations (θST = 53%) in the flying squirrel in Finland. MtDNA and microsatellite data, together with assignment studies, showed the Siberian jay population to be significantly genetically structured and supported the existence of a metapopulation like structuring in Fennoscandia. Division of genetic variation among flying squirrel populations along the ancient shoreline of the Littorina Lymnea Sea stage of the Baltic Sea (7000 BP) and two geographically associated branches in the minimum spanning network supported a two-way colonisation history for the species. The Finnish inland appears to have been colonised from the east in association with the arrival of Norway spruce. At the same time, Coastal Finland was colonised from the south-east through the Karelian Isthmus. Gene flow of the species appeared female biased and restricted. Species exhibiting more restrictive dispersal characteristics and habitat requirements possessed stronger population genetic structure than those with opposite characteristics. Growth or contractions in population size leave characteristic signatures in mtDNA that can be studied by comparing different sequence diversity estimates among populations. I applied this method to the species studied. Significant differences in nucleotide diversities indicated restrictions in gene flow among populations in all species studied. Half of the Siberian jay populations gave a signal of population size bottleneck. All the species studied showed differences in their population genetic structures across their entire distribution ranges consistent with the multirefugia model, most likely to be attributable to differences in their ecological characteristics and Pleistocene histories.

The Indian Ocean represents one of the oldest exchange networks connecting South-East-Asia with India, the Arabian peninsula, as far as Africa in the West. Since the beginning of the Common Era, extensive trade between geographically distant and culturally diverse people enabled the transmission of not only new technologies, exotic goods and food items, but also diverse plant and animal species. Although archaeological remains, particularly from the 1st millennium AD, reflect an intensification of maritime connectivity across the Indian Ocean, the exact routes of travel and trade across this vast area in early times are still subject to discussion. This thesis presents different projects that aim to assess the potential of using commensal animals, such as the house mouse Mus musculus, the black rat Rattus rattus, and the Asian house gecko Hemidactylus frenatus, as proxies to infer pathways of human travel and trade. Commensal species are usually small animals, that live in close association with humans and opportunistically exploit their habitat and food sources. Utilisation of these new resources has led to a close relationship between humans and certain species, and thus favoured their global distribution due to translocations through humans. Therefore, genetic analyses from modern and museum samples of the species in question have been employed, and embedded in a phylogeographic approach. This integrative methodology connects genealogy and geography, with the aim to reconstruct evolutionary, demographic, and biogeographic processes that led to the contemporary distribution of genetic lineages of the commensal species and subsequently mirrors travel routes of the humans who carried them. The incorporation of ancient DNA analysis provides a powerful method, not only enabling the detection of source populations, but direct monitoring of their genetic change through time. Given that people have moved them around for a long time, undirected distribution pattern of populations were expected for each species. However, the results demonstrate that several unique and geographically restricted lineages have been identified, reflecting past human-mediated translocation throughout the Indian and Pacific Ocean from the 1st millennium AD onwards.

The amphibian fauna of Mesoamerica is one the most diverse, yet the most endangered in the area, perfectly exemplifying why the region is one of the world biodiversity hotspots. I carried out analyses from three interrelated perspectives: Conservation Genetics, species delimitation and Comparative Phylogeography of two genera of the family Hylidae in most of Mesoamerica: Agalychnis and Dendropsophus. First I performed a species delimitation analysis for the genus Agalychnis, with the specific aim of testing for cryptic diversity within the species A. callidryas, which exhibits wide morphological variation and the uncertainty of whether or not it represents more than one species has not been solved. Secondly, I did a conservation analysis of the genus Agalychnis adopting a comparative approach between endangered and non-endangered species and integrating ecological modelling and genetic information, with the aim of gathering key information for a better management and conservation planning at a regional scale of this genus in particular and Hylid frogs in general. This analysis resulted in the suggestion of short-term alternatives for conservation of critically endangered species and the management of non-endangered species at regional scale. Finally, I applied a comparative phylogeographic analysis between the two genera Agalychnis and Dendropsophus with the general objective of identifying factors and processes underlying species origin and dispersal within Mesoamerica. I proposed hypotheses for the colonization and dispersal of species of these two genera within Mesoamerica, on the basis of genetic data, geographical information, and ecological niche modelling. As part of data gathering for the latter analysis a new country record leading to the considerable extension of the geographical distribution of D. phlebodes is reported.