Mesoamerica is considered a biodiversity hot spot with levels of endemism and species diversity likely underestimated. For mammals, the patterns of diversification of Mesoamerican taxa still are controversial. Reasons for this include the region's complex geologic history, and the relatively recent timing of such geological events. Previous studies, however, support the view that substantial migration between North (NA) and South America (SA) occurred prior or/and during the Great American Biotic Interchange (GABI) ~3.5 Ma. This was followed by repeated periods of isolation during Pleistocene climatic oscillations, which produced most of the diversification in the region. From a North American origin, the subfamily Sigmodontinae migrated to SA, where most of its present day diversity exists. The taxonomic history of this subfamily, and of Oryzomynii, its largest tribe, has been exceptionally complex. Recently, extensive studies have helped to clarify genealogical relationships among major clades, but have left the evolutionary histories of several groups unresolved. Such is the case for the genus Handleyomys that includes nine species; seven of which are endemic to Mesoamerica; and of its phylogenetic position among closely related genera Euryoryzomys, Hylaeamys, Oecomys, Nephelomys and Transandinomys. The results supported the monophyly of Handleyomys, and four clades with inter-generic levels of divergence within the genus, three of these clades restricted to Mesoamerica (the alfaroi, chapmani and melanotis species groups). Furthermore, the estimated time for the split of the Mesoamerican Handleyomys is on average, 2.0 Myr older than the proposed migrations to NA during the GABI. In addition, the position of Handleyomys as the sister clade to Euryoryzomys, Hylaeamys, Oecomys, Nephelomys and Transandinomys was well supported, as it was a biogeographic hypotheses that depicted a polyphyletic origin for these genera and Handleyomys 5.5-6.0 Ma. The integrative approach implemented in this dissertation allowed the development of more biologically realistic hypothesis than has previously been conducted in Mesoamerica, where half of the endemic mammals are listed under the IUCN Red list; and where mammals with small ranges, which are the most vulnerable to extinction, are found largely outside reserves. The continued decline of the ecosystems health in this region calls for a more precise account of its biodiversity for its proper conservation; and for rigorous biogeographic studies for its management, since the region also serves as a biological corridor for intercontinental connectivity.

Climate change, land use change and invasive species are transforming global biodiversity at multiple scales. Projections are for threats to biodiversity from these global changes to continue into the future, with varied and discernible distribution changes for many species. Concomitantly, these global changes will interact with each other to further exacerbate the problem, as exemplified in this study. In New Zealand, climate change is expected to affect landscapes, fragmented and disturbed by land use change, further increasing the potential invasibility of these landscapes for a suite of existing and emerging invasive species. This thesis is concerned with the combined effects of climate and land use changes on the spatial distribution of the sub-tropical invasive plant, Tradescantia fluminensis (Vell.). The contribution of this thesis is to undertake an integrated assessment of the distribution change for this species in New Zealand. On the basis that climatic variables affect species distribution at larger scales, while land use, habitat, disturbance and dispersal mechanisms affect distribution at smaller scales, two separate analyses were undertaken. At the national scale BioCLIM and the Ecological Niche Factor Analysis (ENFA) were implemented using the variables: minimum temperature (July-August), MTminJ-A, and annual water deficit (November-February). At the landscape scale, only ENFA was implemented, using the variables: MTminJ-A, ECOSAT riparian classes (habitat) and proximity to roads, urban areas and streams (disturbance and dispersal sources). Three scenarios of climate change (CCSR B1-Low, CSIRO9 A1B-Mid and HadCM A1FI-High) and two scenarios of land use change (SmartGrowth and Buildout) were developed to the year 2050, using the CLIMPACTS Open Framework Modelling System and Geographic Information Systems, GIS, techniques respectively. The baseline species distribution model was extrapolated in ENFA, using the 2050 scenarios. Changes to potential threat from this species to protected areas at the landscape level were assessed spatially at the landscape level. This approach and its results are novel for this species. At the national scale the results for the modelling show that climate change will increase the potential habitat suitability of Tradescantia under all combined scenarios of CCSR, CSIRO9 and HadCM for mean minimum temperature (July-August), MTminJ-A and Annual Water Deficit, AWD. At the case study landscape, in the Western Bay of Plenty and Tauranga also the modelling results showed that climate change and land use changes will increase the suitability for Tradescantia by 2050. The 'core' or highest suitability areas increase under all future scenarios. At the national level core suitability increased by about 13% for the CCSR:B1-Low and CSIRO9:A1B-Mid and 22% for HadCM:A1FI-High combined scenario on the North Island. On the South Island, core areas increased by a much lower margin - 1.4%, 2.3% and 2.9% for CCSR:B1-Low, CSIRO9:A1B-Mid and HadCM:A1FI-High combined scenarios respectively. At the landscape level core areas increased by 5%, 8% and 21% for the CCSR:B1-Low+SmartGrowth, Darlam:A1b-Mid+SmartGrwoth and HadCM:A1FI-High+Build-out combined scenarios, respectively. This is true also for the Protected areas within the case study landscape, and indicate that the increasing if Tradescantia is able to track both climate and land use change through its dispersal and migration within the landscape 9 primarily in the inland and upland direction), then is will pose a greater risk to native habitats than at present. Integrated assessments and the outputs they produce are essential to exploring anticipated changes (through scenario-building) and in understanding the change spatial context and magnitude of projected changes from the combined effects of climate and land use changes into the future and need to be integrated into biodiversity-biosecurity management at multiple scales.

Polyploidization is exceptionally cosmopolitan in plants. One common observation is that polyploids inhabit larger geographic distributions than their diploid progenitors. Differences in distribution between cytotypes are largely attributed to differences in mating system and ecological breadth among cytotypes. In Crataegus series Douglasianae, allopolyploids have larger ranges than their diploid progenitors. Range size increase is coupled with a shift to predominant asexuality in polyploids. This thesis explores 2 additional hypotheses that may contribute to differences in distribution among cytotypes: ecological breadth and dispersal ability. We find evidence that tetraploid C. douglasii occurs in a wider range of habits and has a greater dispersal ability than diploid C. suksdorfii. Overall, we suggest that differences in mating system, ecological breadth, and dispersal ability have contributed individually and collaboratively to differences in distribution among cytotypes of Crataegus series Douglasianae. Large ranges in polyploids may help maintain cytotype diversity by providing buffering capacity against demographic stochasticity.

Polyploidization is exceptionally cosmopolitan in plants. One common observation is that polyploids inhabit larger geographic distributions than their diploid progenitors. Differences in distribution between cytotypes are largely attributed to differences in mating system and ecological breadth among cytotypes. In Crataegus series Douglasianae, allopolyploids have larger ranges than their diploid progenitors. Range size increase is coupled with a shift to predominant asexuality in polyploids. This thesis explores 2 additional hypotheses that may contribute to differences in distribution among cytotypes: ecological breadth and dispersal ability. We find evidence that tetraploid C. douglasii occurs in a wider range of habits and has a greater dispersal ability than diploid C. suksdorfii. Overall, we suggest that differences in mating system, ecological breadth, and dispersal ability have contributed individually and collaboratively to differences in distribution among cytotypes of Crataegus series Douglasianae. Large ranges in polyploids may help maintain cytotype diversity by providing buffering capacity against demographic stochasticity.

The study intends to find easily recognizable indicator species for water quality in the constructed wetland of Flemingsbergsviken. The study is relevant since indicator species can be difficult to determine for common people. Easily recognizable indicator species could improve dialogue between the scientific community, administrative authorities and the general public. Such species could be used in education systems, associations or in information campaigns. Therefore, I have chosen to refer to these species as didactical species. Water quality was examined by measuring conductivity, pH and oxygen content in relation to distance from the wetland inlet. The results demonstrate a significant correlation between conductivity and distance. Species occupy different ecological niches and distribution patterns of species in the wetland can be expected to follow changes in abiotic factors, such as water quality. Potential indicator species were investigated by inventorying twelve species of plants and animals. The results show significant linear or curvilinear correlations between one or several water quality factors and the species reedmace, common reed, yellow iris, freshwater woodlouse, twisted ramshorn, damsel- and dragonfly larvae. By carrying out a questionnaire aimed at a group of adults and by talking to a group of children, conclusions could be made regarding indicator species that were easy to recognize and associate to. The results demonstrate that adults found common reed and reedmace most easy to recognize while children found the freshwater woodlouse most interesting. Thus, these indicator species for water quality can be included in the concept didactical species. / Studien syftar till att finna indikatorarter för vattenkvalitet i Flemingsbergsvikens våtmarksanläggning som är lätta att känna igen och associera till. Studien är relevant då indikatorarter kan vara svårbestämda för gemene man. Arter som är lättigenkännbara skulle kunna förbättra dialog mellan forskarsamhället, allmänheten och myndigheter och kan användas i utbildningssyfte inom skolor, föreningar eller i informationskampanjer. Jag har därför valt att kalla arterna för didaktiska arter. Vattenkvalitet undersöktes genom att mäta konduktivitet, pH och syrgashalt i förhållande till avstånd från inlopp. Resultaten visade att det finns ett signifikant samband mellan konduktivitet och avstånd. Eftersom arter upptar olika ekologiska nischer kan artutbredningsmönstret i våtmarken förväntas följa förändringar i abiotiska faktorer, såsom vattenkvalitet. Potentiella indikatorarter undersöktes genom att inventera tolv växt- och djurarter i anläggningen. Resultaten visar signifikanta linjära eller kurvlinjära samband med en eller flera utav vattenkvalitetsfaktorerna och arterna bredkaveldun, vass, gul svärdslilja, sötvattengråsugga, remskivsnäcka samt trollsländelarver. Genom en enkätundersökning för en grupp vuxna samt samtal med en grupp förskolebarn kunde det dras slutsatser om vilka av indikatorarterna för vattenkvalitet som var lättast att känna igen och associera till. Resultaten visar att de vuxna upplevde vass och bredkaveldun som lättast att känna igen medan barnen upplevde att sötvattengråsugga var mest intressant. Dessa indikatorarter för vattenkvalitet kan således inkluderas i begreppet didaktiska arter.

The spread of an agricultural lifestyle played a crucial role in the development of social complexity and in defining trajectories of human history. This dissertation presents the results of research into how agricultural strategies were modified during the spread of agriculture into Southwest China. By incorporating advances from the fields of plant biology and ecological niche modeling into archaeological research, this dissertation addresses how humans adapted their agricultural strategies or invented appropriate technologies to deal with the challenges presented by the myriad of ecological niches in southwest China. This dissertation uses ecological niche modeling to examine the options and constraints associated with practicing different types of agriculture in the specific ecological niches of southwest China. The predictions made by these models are then tested against archaeobotanical data from a series of sites from across the region. This approach allows one to understand how the spread of agriculture took place in its particular social and economic contexts. / Anthropology

Behavior determines how organisms interact with their environment, and has long been posited as a pacemaker for evolution. The classical view is that novel behaviors expose organisms to new selective pressures, in turn "driving" evolution. Behavior can also restrain evolutionary change. Some behaviors, such as thermoregulation, help organisms maintain a constant selective environment, thus "inhibiting" evolution. This thesis seeks to understand the role of behavior in influencing the evolutionary process. In the first part, I test the hypothesis that the same behavior can simultaneously impede and impel evolution in different traits. I focus on the lizard, Anolis cybotes, from the Caribbean island of Hispaniola. Through a replicated field experiment I show that behavioral flexibility allows these lizards to maintain a constant body temperature in markedly different thermal habitats. I determine that this similarity in body temperatures is associated with physiological stasis, as the preferred temperature and heat tolerance are nearly identical among populations. I demonstrate that the behavioral change allowing lizards to maintain a constant body temperature involves a perch switch. Finally, I demonstrate that this shift in structural habitat use from trees at low elevation to rocks at high elevation in turn impels morphological evolution in traits associated with rock use, and that these traits are likely genetically based. Thus, a perch switch to rocks at high elevation is simultaneously impeding physiological evolution, whilst impelling morphological evolution. In the second part of my study, I asked whether rates of evolution differ among physiological traits, and how thermoregulation influences these rates. I found that cold tolerance evolves significantly faster than heat tolerance in the cybotoid anoles, a clade of anoles that contains A. cybotes and its relatives. I demonstrate that thermal variation is considerably greater during the day than at night and, at high elevation, nighttime temperatures are so cold that they would incapacitate most lizards. In the absence of thermal refuges and behavioral buffering, lizards at high elevation have no choice but to adapt their physiology. Thus, the ability to thermoregulate during, but not at night, likely influences differences in rates of evolution between heat and cold tolerance.

Submitted by Cláudia Bueno (claudiamoura18@gmail.com) on 2015-10-20T17:21:43Z No. of bitstreams: 2 Dissertação - Túlio Max de Oliveira Guimarães - 2014.pdf: 2190502 bytes, checksum: 95a9c8660ff6a8f4fee3c71a61784e47 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2015-10-21T10:06:29Z (GMT) No. of bitstreams: 2 Dissertação - Túlio Max de Oliveira Guimarães - 2014.pdf: 2190502 bytes, checksum: 95a9c8660ff6a8f4fee3c71a61784e47 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2015-10-21T10:06:29Z (GMT). No. of bitstreams: 2 Dissertação - Túlio Max de Oliveira Guimarães - 2014.pdf: 2190502 bytes, checksum: 95a9c8660ff6a8f4fee3c71a61784e47 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-04-23 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Understand how species are spatially distributed has been exhaustively discussed in ecology over the last decades. Recently, frameworks based on Ecological Niche Models (ENM) have emerged to avoid problems related to the lack of species geographical information, once it identify which environmental suitable conditions of geographic space enable the persistence of species. Recently this approach has become a significant component in Systematic Conservation Planning, helping managers to select better areas to create reserves. Several factors limit the fundamental niche of species and poor geographical information about species distribution may lead to be an underestimation of suitable conditions that one specie occur,, revealing an non-equilibrium with climate. Thus, using good fossil records to construct ecological niche models can be a better way to evaluate and improve ENM predictions and it allows us to estimate other suitable conditions not seen before. Thereby, our aim was to investigate if ENMs built for Mauritia flexuosa, and Tapirus terrestris improve with the addition of fossil information. So, different ENMs were built using, first, current records and, second, using different proportions of fossil data. The results showed that species closer to equilibrium with climate (M. flexuosa) had an improvement in model’s performance with the addition of fossil records, while species with higher non-equilibrium (T. terrestris) decreased the model’s performance. / Entender como as espécies estão espacialmente distribuídas pelo planeta tem sido um assunto exaustivamente discutido em ecologia ao longo das últimas décadas. Recentemente, abordagens baseadas nos Modelos de Nicho Ecológico têm surgido com o intuito de eliminar problemas relacionados à lacuna de informação geográfica sobre as espécies, uma vez que identifica locais no espaço geográfico que apresenta as condições ambientais favoráveis à persistência das mesmas. Vários fatores limitam o nicho fundamental das espécies e informações geográficas enviesadas acerca de sua distribuição podem levar a uma subestimativa das condições adequadas à ocorrência, revelando um desequilíbrio com o clima. Deste modo, a utilização de registros fósseis na construção dos Modelos de Nicho Ecológico pode ser uma maneira de melhorar as predições dos modelos, já que adiciona novas informações ambientais que não haviam sido encontradas atualmente. Deste modo, nosso objetivo foi investigar se os Modelos de Nicho Ecológico construídos para Mauritia flexuosa e Tapirus terrestris apresentaram melhora no poder preditivo pela adição de informação fóssil. Para isso, foram construídos diferentes modelos utilizando dados atuais apenas e modelos utilizando tanto informação atual quanto informação fóssil, em diferentes porcentagens. Através de uma Análise de Variância Fatorial, medimos se a adição de informação fóssil apresentava melhora significativa no poder preditivo dos modelos. Nossos resultados mostram que quando há pouca variação na informação ambiental adicionada (M. flexuosa), os modelos apresentam uma melhora significativa no poder preditivo, ao passo que para aqueles dados com maior variação (T. terrestris) o efeito é inverso. Isso se deve pela variação dos erros de omissão e comissão gerados durante o processo de modelagem.

As várzeas do Alto Tietê e do Alto Paraíba do Sul, na Mata Atlântica do sudeste brasileiro, têm sido severamente exploradas e ocupadas por cidades, agricultura, e mineração nos últimos 500 anos. Endêmico destas áreas, o bicudinho-do-brejo-paulista (Formicivora paludicola) passou muito tempo desconhecido para a ciência, até sua descoberta em 2005, quando sua situação de ameaça parecia preocupante. Esta ave (Thamnophilidae) foi descoberta à beira da extinção, e nada se sabe sobre sua distribuição, história natural, estrutura populacional e seleção de habitat, o que gera perspectivas de conservação pessimistas e desacreditadas. Este trabalho traz uma investigação da distribuição da espécie e das áreas mais adequadas à sua sobrevivência usando modelos ecológicos de nicho, amostragens de campo e modelos de ocupação. Nossos resultados mostram que a espécie deve ser considerada Criticamente Ameaçada de acordo com os critérios da IUCN. A ocupação humana na região resultou em uma perda de mais de 300 km2 de habitat adequado à ocorrência de F. paludicola, que agora apresenta uma área de ocupação severamente fragmentada de 1,42 km2. Além disso, esta espécie apresenta capacidade de dispersão limitada, alta especificidade de habitat e disponibilidade de habitat restrita. Também apontamos que brejos com menor densidade de taboa (Typha dominguensis) apresentam maiores probabilidades de ocorrência de F. paludicola, e que essas áreas devem ser priorizadas em futuros esforços de conservação. Usando estimativas geradas por Kernel, nós ainda mostramos que a espécie apresenta pequena área de vida de apenas 0,55 ha, e ocorre em altas densidades nas áreas ocupadas remanescentes, apresentando tamanho populacional entre 383 e 985 indivíduos maduros. Por fim, usando \"Torus shift\", nós demonstramos que a espécie exótica invasora, lírio-do-brejo (Hedychium coronarium) é evitada por F. paludicola, e que a invasão biológica representa mais uma ameaça às populações existentes. A conservação desta espécie reside na criação de uma rede de unidades de conservação conectadas, com áreas naturais e restauradas. Por causa de sua estrutura populacional marcada pela alta densidade, a espécie pode prosperar em áreas alagadas adequadas protegidas da ocupação humana, contaminação dos corpos d\'água e plantas exóticas invasoras. Estes esforços poderiam ajudar não só esta ave extremamente ameaçada, mas também restaurar uma parte das áreas alagadas da Mata Atlântica no estado de São Paulo / Wetlands in Upper Tietê and Upper Paraíba do Sul basins, in southeastern Atlantic Forest, Brazil, have been severely transformed by urbanization, agriculture and mining in the last 500 years. Endemic to these areas, the São Paulo Marsh Antwren (Formicivora paludicola) persisted through this period unknown to science until its discovery in 2005, when its threatened situation became worrying. This bird (Thamnophilidae) was discovered on the verge of extinction, and virtually nothing is known about its natural history, population structure and habitat selection, which made conservation perspectives pessimist and discredited. We investigated both the species distribution and the distribution of its suitable areas using ecological niche modeling, fieldwork surveys and occupancy models. Our results show that the species should be considered \"Critically Endangered\" according to IUCN criteria. Human occupation has resulted in a loss of more than 300 km2 of suitable habitat, so that it now occupies a total and severely fragmented area of only 1.42 km2. Additionally, F. paludicola has limited dispersal ability, narrow habitat specificity, and restricted habitat availability. Furthermore, we showed that marshes with lower cattail (Typha dominguensis) densities have higher probabilities of being occupied. Thus, these areas should be prioritized in future conservation efforts. Using Kernel home range estimations, we show that the species has a small home range of about 0.55 ha, and occurs in high densities in those areas where it is still present, with a total population size between 383 and 985 mature birds. Furthermore, using a novel tool for animal habitat selection studies, the Torus Shift, we showed that the alien invasive ginger lily (Hedychium coronarium) is avoided by the species, and that this invasion represents a serious threat to the remaining populations. The successful conservation of F. plaudicola rests on the creation of a series of interconnected protected areas, with natural and restored wetlands. Given the high density of their population structure, this species could thrive in a relatively small area of suitable wetlands protected from human occupation, water contamination and invasive plants. Such efforts would also greatly contribute to the general conservation and restoration of Atlantic Forest wetlands

Estudos filogeográficos almejam compreender a distribuição da diversidade genética de uma espécie. E ainda, estudos de organismos co-distribuídos permitem inferir os processos atuantes na história da região de sua ocorrência. Dentro desse contexto o presente trabalho se propôs a estudar a filogeografia de duas espécies de passeriformes endêmicos da Mata Atlântica, Chiroxiphia caudata e Hemitrccus diops, visando auxiliar na compreensão da evolução da biota neste bioma. Foram utilizados indivíduos amostrados ao longo da distribuição das espécies: 112 de C. caudata e 82 de H. diops. Foram obtidas sequências parciais do gene mitocondrial ND2 (932 pb e 910 pb, respectivamente para C. caudata e H. diops), de um íntron do gene G3PDH (303 pb e 323 pb, respectivamente), e de íntrons do gene ODC (517 pb) para H. diops. Não foi encontrada estrutura filogeográfica em C. caudata, que apresentou sinal de expansão recente. A ausência de estrutura pode ser decorrência do longo tempo de geração da espécie. Modelos de distribuição da espécie durante o último máximo glacial apresentaram dois cenários divergentes, um com distribuição predominantemente ao norte e outro com distribuição similar ou maior que a atual. Em contraste, foi encontrada uma baixa, mas clara estrutura filogeográfica em H. diops. Os sinais de alteração demográfica, entretanto, são menos claros, havendo tanto sinal de expansão quanto de estabilidade populacional ao longo dos ciclos glaciais. A diversidade de padrões filogeográficos encontrada na presente Dissertação é congruente com achados sobre a distribuição da diversidade genética de outros organismos da Mata Atlântica, e ultimamente, refletem a complexidade do bioma como um todo / Phylogeographic studies aim to analyze the distribution of the genetic diversity of a given species. In addition, studies of co-distributed organisms enable to infer historic processes acting on the region where they occur. In this context the present work intended to study the phylogeography of two Atlantic Forest endemic birds, Chiroxiphia caudata and Hemitriccus diops to help to understand how this biome evolved. 112 individuals of C. caudata and 82 of H. diops were sampled throughout their distributions. We obtained partial sequences of the mitochondrial gene ND2 (932 bp and 910 bp, respectively, for C. caudata and H. diops), of an intron of the G3PDH gene (303 bp and 323 bp, respectively), and introns from the ODC gene (517 bp) of H. diops. No signal of phylogeographic structure was found for C. caudata,, which exhibits signal of recent demographic expansion. The absence of population structure may be a consequence of the species long generation time. Models of distribution during the last glacial maximum exhibited two discordant scenarios: one with its main distribution in the north and another with a similar or larger distribution than the current one. In contrast, we found a shallow, but clear phylogeographic structure for H. diops. The demographic history, however, was not clear, with signal of both demographic expansion and stability during the glacial cycles. The different phylogeographic patterns found here are congruent with the diversity of patterns observed in other Atlantic Forest organisms, reflecting the complex history of the biome