• Refine Query
  • Source
  • Publication year
  • to
  • Language
  • 23
  • 11
  • 4
  • 3
  • 2
  • Tagged with
  • 46
  • 15
  • 11
  • 10
  • 10
  • 10
  • 7
  • 7
  • 6
  • 6
  • 6
  • 6
  • 6
  • 5
  • 5
  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
1

Understanding the importance of taxonomic sampling for large-scale phylogenetic analyses by simulating evolutionary processes under complex models

Heath, Tracy Ann. January 1900 (has links)
Thesis (Ph. D.)--University of Texas at Austin, 2008. / Vita. Includes bibliographical references.
2

Comparative phylogenetic approaches to macroevolution methods, models, and marine fishes /

Brock, Chad Daniel. January 2009 (has links) (PDF)
Thesis (M.S. in zoology)--Washington State University, May 2009. / Title from PDF title page (viewed on May 27, 2009). "School of Biological Sciences." Includes bibliographical references.
3

Transitions between Marine and Freshwaters in Fishes: Evolutionary Pattern and Process

Bloom, Devin 19 March 2013 (has links)
Evolutionary transitions between marine and freshwater habitats are rare events that can have profound impacts on aquatic biodiversity. The main goal of my thesis is determining the processes involved in transitions between marine and freshwater biomes, and the resulting patterns of diversity using phylogenetic approaches. To test hypotheses regarding the geography, timing, frequency, and mechanisms regulating biome transitions I generated multi-locus time-calibrated molecular phylogenies for groups of fishes that include both exclusively marine and freshwater species. My analysis of anchovies demonstrated that Neotropical freshwater anchovies represent a monophyletic radiation with a single origin in South American freshwaters. I used a phylogeny of herring and allies (Clupeiformes) to investigate the evolution of diadromy, a migratory behavior in which individuals move between oceans and freshwater habitats for reproduction and feeding. These analyses do not support the hypothesis that differences in productivity between marine and freshwater explain the origins of diadromous lineages. Diadromy has been considered an evolutionary pathway for permanent biome transitions, however I found that diadromy almost never produces a fully marine or freshwater clade. Marine lineages often invade continental freshwaters during episodes of marine incursion. In South America, the rich diversity of marine derived fish lineages invaded during Eocene marine incursions from either the Pacific or the Caribbean, and Oligocene marine incursions from the Caribbean. I falsified the highly cited Miocene marine incursion hypothesis, but found that the Pebas Mega-Wetland catalyzed diversification in some marine derived lineages. Using diversification analyses, I investigated the evolutionary processes that have generated disparate patterns of diversity between continents and oceans. I found that freshwater silversides have higher speciation and extinction rates than marine silversides. Lineages accumulation plots suggest ecological limits are not regulating clade growth in either marine or freshwater biomes. Overall, biome conservatism is a widespread pattern among fishes, and this pattern is largely driven by competition in clades that are physiologically capable of biome transitions. Biome transitions are facilitated by rare paleogeographic events, such as marine incursions. Finally, a difference in net diversification rate is the macroevolutionary mechanism that best explains the difference in diversity between continents and oceans.
4

Understanding the importance of taxonomic sampling for large-scale phylogenetic analyses by simulating evolutionary processes under complex models

Heath, Tracy Ann 12 October 2012 (has links)
Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phylogenetic analyses is improved significantly by thorough taxon sampling efforts. Much of the previous work examining the impact of taxon sampling on phylogenetic accuracy has focused on the effects of random taxon sampling or directed taxon addition/removal. Therefore, the effect of realistic, nonrandom taxon sampling strategies on the accuracy of large-scale phylogenetic reconstruction is not well understood. Typically, broad systematic studies of diverse clades select species according to current classification to span the diversity within the group of interest. I simulated phylogenies under a realistic model of cladogenesis and used these trees to generate sequence data. Using these simulations, I explored the effect of taxonomy-based taxon sampling on the accuracy of maximum likelihood reconstruction. The results demonstrate that taxonomy-based sampling has a stronger, negative, effect on phylogenetic accuracy than random taxon sampling. Therefore, it is recommended that systematists conducting phylogenetic analyses of diverse clades concentrate on improving sampling density within their group of interest by selecting multiple representatives from each taxonomic level. Phylogenetic tree imbalance is often used to make inferences about macroevolutionary processes that generate patterns of tree shape. However these patterns may be obscured by non-biological factors that can bias tree shape. Using published trees inferred from biological data and trees simulated under a realistic branching model; I investigated the affect of random taxon omission on phylogenetic tree imbalance. My results indicate that incomplete taxon sampling in the presence of variable rates of speciation and extinction may be sufficient to explain much of the imbalance observed in empirical phylogenies. Previous research has indicated that some methods of phylogenetic inference can produce biased tree topologies and shapes. Using simulated model tree topologies and sequence data, I investigated the non-biological factors that lead to biases in phylogenetic tree imbalance. Based on my results, I concluded that phylogenetic noise is the primary cause of tree shape bias. Methods that account for unobserved substitutions, such as maximum likelihood, can overcome the systematic bias toward imbalanced topologies. / text
5

Transitions between Marine and Freshwaters in Fishes: Evolutionary Pattern and Process

Bloom, Devin 19 March 2013 (has links)
Evolutionary transitions between marine and freshwater habitats are rare events that can have profound impacts on aquatic biodiversity. The main goal of my thesis is determining the processes involved in transitions between marine and freshwater biomes, and the resulting patterns of diversity using phylogenetic approaches. To test hypotheses regarding the geography, timing, frequency, and mechanisms regulating biome transitions I generated multi-locus time-calibrated molecular phylogenies for groups of fishes that include both exclusively marine and freshwater species. My analysis of anchovies demonstrated that Neotropical freshwater anchovies represent a monophyletic radiation with a single origin in South American freshwaters. I used a phylogeny of herring and allies (Clupeiformes) to investigate the evolution of diadromy, a migratory behavior in which individuals move between oceans and freshwater habitats for reproduction and feeding. These analyses do not support the hypothesis that differences in productivity between marine and freshwater explain the origins of diadromous lineages. Diadromy has been considered an evolutionary pathway for permanent biome transitions, however I found that diadromy almost never produces a fully marine or freshwater clade. Marine lineages often invade continental freshwaters during episodes of marine incursion. In South America, the rich diversity of marine derived fish lineages invaded during Eocene marine incursions from either the Pacific or the Caribbean, and Oligocene marine incursions from the Caribbean. I falsified the highly cited Miocene marine incursion hypothesis, but found that the Pebas Mega-Wetland catalyzed diversification in some marine derived lineages. Using diversification analyses, I investigated the evolutionary processes that have generated disparate patterns of diversity between continents and oceans. I found that freshwater silversides have higher speciation and extinction rates than marine silversides. Lineages accumulation plots suggest ecological limits are not regulating clade growth in either marine or freshwater biomes. Overall, biome conservatism is a widespread pattern among fishes, and this pattern is largely driven by competition in clades that are physiologically capable of biome transitions. Biome transitions are facilitated by rare paleogeographic events, such as marine incursions. Finally, a difference in net diversification rate is the macroevolutionary mechanism that best explains the difference in diversity between continents and oceans.
6

The Rise and Fall of the Cucullaeidae: Exploring Transitions in Species Richness, Geographic Range, Morphology and Ecology in a Relict Bivalve Family

Buick, Devin P. 22 July 2010 (has links)
No description available.
7

Evolution in biological radiations; insights from the Triassic archosaur radiation

Hoffman, Devin Kane Fodor 29 June 2022 (has links)
Adaptive radiations, or evolutionary diversifications, are the evolutionary divergence of a single lineage into many different adaptive forms. They play a critical role in the history of life as groups of organisms speciate and fill new ecological roles over geologically rapid time intervals. There is currently no agreed upon operational unit, timeframe, or amount of divergence for organisms to be considered to have undergone an adaptive radiation. Additionally, the paucity of both comparative and fossil studies has limited the utility of the adaptive radiation in framing macroevolutionary questions, such as, is ecological and morphological diversification simultaneous? An ideal fossil clade to test this question is the Archosauriformes (crocodylians, birds, and their closest relatives). Archosauriforms radiated following the end-Permian mass extinction and their lineage diversification through the Early to Late Triassic is well documented in the literature. Prior to the end-Permian mass extinction, these reptiles were both species poor and ecologically limited, but by the Late Triassic they dominated terrestrial ecosystems in both species abundance and ecological breadth. However, continued environmental instability following the end-Permian extinction has led to the hypothesis that ecological expansion of archosauriforms lagged behind the diversification of lineages. The first chapter of my dissertation uses a Middle Triassic archosauriform tooth assemblage from Tanzania to reconstruct dietary specialization, estimated by morphological disparity of teeth. In addition to comparing tooth disparity of isolated and in situ teeth, this also provides a lens for comparing the timing of dietary specialization and species diversification. I found the archosauriforms to be faunivorous with little morphological disparity amongst the teeth. The second chapter uses an Early Triassic reptile tooth assemblage from South Africa to reconstruct the dietary specialization of archosauriforms early in their radiation to compare the amount of morphological disparity and lineage diversity. I use methods from Chapter 1 and integrate 3D morphometrics to better capture shape. I described several tooth morphotypes including six new to the locality. The morphological and dietary differences were minimal, indicating a greater species diversity than ecological diversity. The third chapter is a description of a new pseudosuchian archosaur taxon from the Middle Triassic of Tanzania. As species descriptions form the basic data unit of macroevolutionary analyses, this assists future studies of the archosauriform radiation. I recover this new taxon as the oldest known aetosaur. This species provides insights into the evolution of an armored carapace in crocodylian-line archosaurs and shows morphology related to armor evolved prior to the evolution of an herbivorous diet. / Doctor of Philosophy / There is an incredible diversity of life on Earth, but this is a small fraction of the life that once existed on our planet. The fossil record provides us a window into the past to reconstruct the history of life on our planet. Two of the patterns we see in the fossil record are rapid drops in biodiversity called mass extinctions, and rapid increases in biodiversity called biological radiations. Both of these events are often related and mass extinctions are followed by biological radiations throughout earth history. A particularly interesting case is the end-Permian mass extinction, not only because it is the largest extinction event, but also because the subsequent radiation was delayed by continuing environmental instability. An ideal group of animals to study in this time period are the archosaurs, the group of reptiles including crocodylians, birds, and their extinct relatives. Archosaur reptiles went from very few species before the extinction, to dominate ecosystems for the next 200 million years. However, we do not know if the radiation of many archosaur species occurred at the same time as they filled new roles in their communities. The first two chapters of my dissertation focus on using fossil teeth to reconstruct the diets of archosaurs at a single location. My first chapter describes teeth from the Middle Triassic (247-237 million years ago) of Tanzania. I measured the shapes of these teeth and used that to help assign them to diets. Doing this I found there were more species than types of diets indicating the radiation of species may have occurred before specialization of life habits. In the second chapter where I describe a reptile tooth assemblage from the Early Triassic (252-247 million years ago) of South Africa. I added additional methods for measuring tooth shape, found several different types of teeth (likely different species) but mostly similar diets, indicating again a delay in life habit specialization. In my third chapter I name a new species of archosaur reptile from the Middle Triassic of Tanzania. This new species helps us to understand how heavily armored plant eaters evolved in early crocodylian relatives during the archosaur radiation.
8

Diversification dynamics of Placentalia (Mammalia): integrating the fossil record with molecular phylogenies / Dinâmica de diversificação de Placentalia (Mammalia): integrando o registro fóssil com filogenias moleculares

Sugawara, Mauro Toshiro Caiuby 29 July 2015 (has links)
The effects of intrinsic traits on the diversification dynamics have been extensively investigated, with several traits being associated with increase in diversification. On the other hand, the possible negative effects of traits on the diversification of a lineage have been for the most part overlooked. Here we used both the fossil record and molecular data to study the diversification dynamics of Placentalia, focusing on the orders in decline of diversity, and investigated different mechanisms that might control the evolutionary success of the 21 placental orders. More specifically we: 1- determined which of the 21 orders of Placentalia are in decline of diversity (i.e., Decline model); 2- investigated whether the Decline model has a phylogenetic signal; 3- tested the hypothesis that the differences in body size are related to the Decline model; 4- tested the hypothesis that the orders in Decline have lower morphological disparity; 5- investigated whether the orders in decline of diversity, inferred from the fossil record, are the ones with higher extinction risk nowadays. Our analysis indicate that the majority of the orders of placental mammals have a pattern consistent with the Decline model and, although the Decline model is not equally distributed among the placental superorders, there was no significant phylogenetic signal for the orders in diversity decline. We found a positive correlation between the Decline model and the average body size which is in line with previous studies on body size evolution. We argue that such results suggest a complex evolutionary dynamics: larger body size appears to be an evolutionary attractor with lineages showing a tendency to increase in size, however, the increase in body size would be counterbalanced by a higher propensity to Decline. Moreover, we found a the negative correlation between the Decline model and morphological variation. We suggest that such results could indicate two possible scenario: (i) the low morphological variation would cause lineages to loose diversity; (ii) the low morphological variation would be the product of decrease in diversity through extinction selectivity. Finally, we found no correlation between the extinction risk of extant species and the deep time diversity decline, which suggests that the drivers of the current and the past Decline are not the same / O efeito de caracteres intrínsecos na dinâmica de diversificação foram extensamente investigados e diversos caracteres foram associados com aumentos na diversificação. Contudo, os possíveis efeitos negativos de um caractere sobre a diversificação de uma linhagem foram em grande parte ignorados. No presente trabalho integramos o registro fóssil com dados moleculares para estudar a dinâmica de diversificação de Placentalia, focando nas ordens em declínio de diversidade, e investigamos possíveis mecanismos responsáveis por gerar os padrões de diversificação encontrados. Mais especificamente nós: 1- determinamos quais das 21 ordens de Placentalia estão em declínio de diversidade (i.e., Declínio); 2- investigamos se o Declínio apresenta um sinal filogenético; 3- testamos a hipótese de que o tamanho do corpo está relacionado com o Declínio; 4- testamos a hipótese de que as ordens em Declínio possum menor disparidade morfológica; 5- investigamos se as ordens em Declínio, inferido a partir do registro fóssil, são as mesas com maior risco de extinção na atualidade. Nossas análises indicam que a maioria das ordens de mamíferos placentários apresentam um signal consistente com o Declínio e, embora o Declínio não esteja igualmente distribuído entre as superorderns de Placentalia, não há um signal filogenético significativo para as ordens em Declínio. Nossos resultados indicam uma correlação positiva entre o Declínio e o tamanho corporal médio de cada ordem que está de acordo com estudos prévios sobre evolução do tamanho do corpo. Argumentamos que estes resultados sugerem uma dinâmica de evolução complexa: tamanho corpóreo grande seria um atrator evolutivo que gera a tendência das linhagens aumentarem de tamanho, todavia, o aumento do tamanho do corpo seria contrabalançado pela maior susceptibilidade ao Declínio. Outrossim, encontramos uma correlação negativa entre o Declínio e a variação morfológica. Argumentamos que essa correlação poderia indicar dois possíveis cenários: (i) a baixa variação morfológica seria responsável pela redução no número de linhagens e tornaria as ordens mais susceptíveis ao declínio de diversidade; (ii) a baixa variação morfológica teria sido gerada pela diminuição da diversidade. Por último, o risco de extinção das espécies atuais não está correlacionado com o Declínio, o que sugere que os mecanismos responsáveis pelo Declínio no passado e no presente não são os mesmos.
9

The roles of diet, speciation and extinction on the diversification of birds, and on the assembly of frugivory networks / Os papéis da dieta, especiação e extinção na diversificação de aves e na montagem de redes de frugivoria

Ferreira, Gustavo Burin 02 October 2017 (has links)
To understand how diversity varies through time and/or space we need to understand speciation and extinction dynamics, and ultimately which factors (biotic or abiotic) affect such dynamics. It has been argued that biological interactions play an important role on the diversification of organisms, but macroevolutionary studies have usually adopted a simple characterization of species interactions. On the other hand ecological studies usually focus on well-characterized interactions of very few species. A network approach can augment our understanding of the ecological roles played by different species but it still lacks an evolutionary perspective preventing us to fully understand how ecological interactions are assembled. Using the available phylogeny, dietary data for virtually all bird species (approximately 9965 species) and a large collection of frugivory net- works, we tested the effect of diet on the diversification of birds, and the relationship between ecological roles within interaction networks and diversification dynamics of frugivorous species. Lastly, using computational simulations, we assessed the per- formance of two state-of-the-art methods to estimate diversification rates using molecular phylogenies. We suggest that omnivory acts as macroevolutionary sink where its ephemeral nature is retrieved through transitions from other guilds rather than from omnivore speciation. We propose that these dynamics result from competition within and among dietary guilds, influenced by the deep-time availability and predictability of food resources. We also observed that in the temperate zone, lineages with high-paced evolutionary dynamics (e.g. higher turn- over rates) typically do not occupy central roles in frugivory net- works, and that these restrictions are modulated by water avail- ability/predictability. Lastly, we found that the two state-of-the art phylogenetic methods perform equally well in diversity de- cline scenarios when estimating current rates, but both fail to detect the true diversification trajectory when extinction rates vary in time. This dissertation contributes to the understanding of biotic and abiotic mechanisms driving both the diversification and the assembly of interaction networks, and also provides important information on the reliability of diversification rate estimates by current, widely used methods / Para entendermos como a biodiversidade varia no tempo e/ou no espaço precisamos entender a dinâmcia de especiação e extinção, e quais fatores (bióticos ou abióticos) afetam essa dinâmica. Acredita-se que as interações biológicas desempen- ham um papel importante na diversificação de organismos, porém estudos macroevolutivos usualmente adotam caracter- izações simples de interações entre espécies. Por outro lado, estudos ecológicos comumente focam na descrição detalhada de interações entre poucas espécies. Uma abordagem de re- des pode aumentar a compreensão dos papéis ecológicos de- sempenhados por diferentes espécies, mas a pouca ênfase em abordagens evolutivas em estudos de redes biológicas nos im- pedem de compreender completamente como essas redes são montadas. Usando a filogenia e dados de dieta disponíveis para virtualmente todas as espécies de aves (aprox. 9965 espécies), e uma grande coleção de redes de frugivoria, investigamos o efeito da dieta na diversificação de aves, e testamos a relação en- tre papéis ecológicos em redes de interação e a dinâmica da di- versificação de espécies frugívoras. Ainda, usando simulações computacionais, avaliamos a performance de dois métodos am- plamente utilizados para estimar taxas de diversificação usando filogenias moleculares. Sugerimos que onivoria atua como um ralo macroevolutivo, onde sua natureza efêmera é recuperada através de transições de outras guildas de dieta ao invés de através da especiação de espécies onívoras. Nós sugerimos que essa dinâmica resulta da competição intra- e entre guildas, in- fluenciada pela disponibilidade e previsibilidade de recursos em ampla escalas de tempo. Nós também observamos que em regiões temperadas, linhagens com uma dinâmica evolutiova mais rápida (maiores taxas de substituição de espécies) em geral não ocupam papéis centrais em redes de frugivoria, e que es- sas restrições são principalmente modificadas por disponibili- dade/previsibilidade hídricas. Por fim, observamos que ambos os métodos filogenéticos testados tem desempenho igualmente bom para estimar taxas atuais, porém ambos falham em detectar a trajetória da diversificação quando as taxas de extinção variam no tempo. Essa tese contribui para o conhecimento de mecanis- mos bióticos e abióticos que afetam tanto a diversificação quanto a montagem de redes de interação, e também provê informações importantes acerca da confiabilidade das estimativas de taxas de diversificação advindas dos métodos atuais amplamente utilizados
10

Major evolutionary trends

Hughes, Martin January 2013 (has links)
Palaeontological data are essential for determining patterns of biological diversity through geological time, enabling the investigation of important macroevolutionary events such as mass extinctions and explosive radiations. Most studies utilise proxies of taxonomic diversity. A more complex undertaking is to assess patterns of morphological variety (disparity) through time, revealing the manner in which groups evolved through their ‘design space’. Many published studies indicate clades tend to reach their maximum disparity early in their evolutionary history. Whether this is a real biological pattern has yet to be tested. Chapter 1 tackles the evolution of disparity in metazoans across the Phanerozoic. The results of a meta-analysis of disparity in 98 extinct clades indicate early high disparity is the most prevalent pattern across the Phanerozoic but finds no clear trends through the Phanerozoic. Mass extinction ended clades were the exception, tending to result in late high disparity. Chapters 2-4 focus on the clade Bivalvia for disparity and diversity analysis. Bivalves are ecologically and taxonomically diverse and have an excellent fossil record but have not been scrutinised using the latest diversity techniques, and have been untouched by disparity analysis. Chapter 2 uses the most up to date stratigraphic ranges and techniques to revise the bivalve Phanerozoic diversity curve. The results show bivalve Phanerozoic diversity is robust to the sampling and fossil record biases examined. Chapter 3 uses data provided as part of collaboration between Martin Hughes, Dr Joseph Carter (University of North Carolina) and Dr Matthew Wills (University of Bath) to address the disparity of bivalves across the Palaeozoic. The results find disparity rises across time but not decreased by mass extinctions. Chapter 4 conducts the first large scale analysis of disparity across latitude. The results find that bivalve disparity across latitude is unchanging and stable compared to the steep gradient of bivalve diversity.

Page generated in 0.1288 seconds