Dissertations / Theses on the topic 'Evolutionary tree'
To see the other types of publications on this topic, follow the link: Evolutionary tree.
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'Evolutionary tree.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
1
Barros, Rodrigo Coelho. "Evolutionary model tree induction." Pontifícia Universidade Católica do Rio Grande do Sul, 2009. http://hdl.handle.net/10923/1687.
Full textAbstract:
Made available in DSpace on 2013-08-07T18:43:36Z (GMT). No. of bitstreams: 1
000422461-Texto+Completo-0.pdf: 1656872 bytes, checksum: 4520cf1ef2435e86327deed3e89baed9 (MD5)
Previous issue date: 2009Model trees are a particular case of decision trees employed to solve regression problems, where the variable to be predicted is continuous. They have the advantage of presenting an interpretable output, helping the end-user to get more confidence in the prediction and providing the basis for the end-user to have new insight about the data, confirming or rejecting hypotheses previously formed. Moreover, model trees present an acceptable level of predictive performance in comparison to most techniques used for solving regression problems. Since generating the optimal model tree is a NPComplete problem, traditional model tree induction algorithms make use of a greedy top-down divideand- conquer strategy, which may not converge to the global optimal solution. In this work, we propose the use of the evolutionary algorithms paradigm as an alternate heuristic to generate model trees in order to improve the convergence to global optimal solutions. We test the predictive performance of this new approach using public UCI data sets, and we compare the results with traditional greedy regression/model trees induction algorithms. Results show that our approach presents a good tradeoff between predictive performance and model comprehensibility, which may be crucial in many data mining applications.
Árvores-modelo são um caso particular de árvores de decisão aplicadas na solução de problemas de regressão, onde a variável a ser predita é contínua. Possuem a vantagem de apresentar uma saída interpretável, auxiliando o usuário do sistema a ter mais confiança na predição e proporcionando a base para o usuário ter novos insights sobre os dados, confirmando ou rejeitando hipóteses previamente formadas. Além disso, árvores-modelo apresentam um nível aceitável de desempenho preditivo quando comparadas à maioria das técnicas utilizadas na solução de problemas de regressão. Uma vez que gerar a árvore-modelo ótima é um problema NP-Completo, algoritmos tradicionais de indução de árvores-modelo fazem uso da estratégia gulosa, top-down e de divisão e conquista, que pode não convergir à solução ótima-global. Neste trabalho é proposta a utilização do paradigma de algoritmos evolutivos como uma heurística alternativa para geração de árvores-modelo. Esta nova abordagem é testada por meio de bases de dados de regressão públicas da UCI, e os resultados são comparados àqueles gerados por algoritmos gulosos tradicionais de indução de árvores-modelo. Os resultados mostram que esta nova abordagem apresenta uma boa relação custo-benefício entre desempenho preditivo e geração de modelos de fácil interpretação, proporcionando um diferencial muitas vezes crucial em diversas aplicações de mineração de dados.
2
Paulden, Timothy John. "Combinatorial spanning tree representations for evolutionary algorithms." Thesis, University of Exeter, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.486767.
Full textAbstract:
The research presented in this thesis lies at the interface between two distinct' fields: combinatorial mathematics and evolutionary algorithm design. We examine a number of combinatorial spanning tree representations, and develop theoretical and empirical results to quantify the intrinsic properties of each representation, focusing on properties that encapsulate the representation's suitability for evolutionary search. In Part I of the thesis, we focus on a selectIon of Cayley codes - namely, the Priifer Code, the Blob Code, and the family of Dandelion-like codes (which includes the Dandelion Code, Happy Code, MHappy Code, and Theta Code). Each of these representations is bijective, and so the efficacy of evolutionary search primarily depends on the representation's locality. We develop a number of results which demonstrate that Dandelion-like codes possess highly desirable locality properties (including bounded locality), while those of the Blob Code and Priifer. Code are inferior. We also present linear-time decoding and'encoding algorithms for the various codes, many of which have not previously appeared in the evolutionary algorithms literature. In Part II, the Theta Code is adapted to give bijective spanning tree representations on graph topologies other than the complete graph. These extended representations retain the desirable properties of the Thet'a Code, including its high locality. We then formulate general principles for developing extended representations of this kind. Finally, in Part III, we study the Edge-Window-Decoder (EWD) representation. We find that the EWD representation has several desirable properties for evolutionary search (includi.ng bounded locality), but possesses an intrinsic bi~ towards path-like trees. We also present a number of theoretical advances, including the first method for generating EWD strings uniformly at random, and a new technique for characterising representational bias using the Wiener index.
3
Saka, Esin. "A Comparative Study Of Tree Encodings For Evolutionary Computing." Master's thesis, METU, 2005. http://etd.lib.metu.edu.tr/upload/3/12606317/index.pdf.
Full textAbstract:
One of the most important factors on the success of evolutionary algorithms (EAs) about trees is the representation of them. The representation should exhibit efficiency, locality and heritability to enable effective evolutionary computing. Neville proposed three different methods for encoding labeled trees. The first one is similar with Prüfer'
s encoding. In 2001, it is reported that, the use of Prü
fer numbers is a poor representation of spanning trees for evolutionary search, since it has low locality for random trees. In the thesis Neville'
s other two encodings, namely Neville branch numbers and Neville leaf numbers, are studied. For their performance in EA their properties and algorithms for encoding and decoding them are also examined. Optimal algorithms with time and space complexities of O(n) , where n is the number of nodes, for encoding and decoding Neville branch numbers are given. The localities of Neville'
s encodings are investigated. It is shown that, although the localities of Neville branch and leaf numbers are perfect for star type trees, they are low for random trees. Neville branch and Neville leaf numbers are compared with other codings in EAs and SA for four problems: '
onemax tree problem'
, '
degree-constrained minimum spanning tree problem'
, '
all spanning trees problem'
and '
all degree constrained spanning trees problem'
. It is shown that, neither Neville nor Prü
fer encodings are suitable for EAs. These encodings are suitable for only tree enumeration and degree computation. Algorithms which are timewise and spacewise optimal for '
all spanning trees problem'
(ASTP) for complete graphs, are given by using Neville branch encoding. Computed time and space complexities for solving ASTP of complete graphs are O(nn-2) and O(n) if trees are only enumerated and O(nn-1) and O(n) if all spanning trees are printed , respectively, where n is the number of nodes. Similarly, '
all degree constrained spanning trees problem'
of a complete graph is solvable in O(nn-1) time and O(n) space.
4
vanCort, Tracy. "Computational Evolutionary Linguistics." Scholarship @ Claremont, 2001. https://scholarship.claremont.edu/hmc_theses/137.
Full textAbstract:
Languages and species both evolve by a process of repeated divergences, which can be described with the branching of a phylogenetic tree or phylogeny. Taking advantage of this fact, it is possible to study language change using computational tree building techniques developed for evolutionary biology. Mathematical approaches to the construction of phylogenies fall into two major categories: character based and distance based methods. Character based methods were used in prior work in the application of phylogenetic methods to the Indo-European family of languages by researchers at the University of Pennsylvania. Discussion of the limitations of character-based models leads to a similar presentation of distance based models. We present an adaptation of these methods to linguistic data, and the phylogenies generated by applying these methods to several modern Germanic languages and Spanish. We conclude that distance based for phylogenies are useful for historical linguistic reconstruction, and that it would be useful to extend existing tree drawing methods to better model the evolutionary effects of language contact.
5
Lind, Brandon M. "NATURAL AND ANTHROPOGENIC DRIVERS OF TREE EVOLUTIONARY DYNAMICS." VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5359.
Full textAbstract:
Species of trees inhabit diverse and heterogeneous environments, and often play important ecological roles in such communities. As a result of their vast ecological breadth, trees have become adapted to various environmental pressures. In this dissertation I examine various environmental factors that drive evolutionary dynamics in threePinusspecies in California and Nevada, USA. In chapter two, I assess the role of management influence of thinning, fire, and their interaction on fine-scale gene flow within fire-suppressed populations of Pinus lambertiana, a historically dominant and ecologically important member of mixed-conifer forests of the Sierra Nevada, California. Here, I find evidence that treatment prescription differentially affects fine-scale genetic structure and effective gene flow in this species. In my third chapter, I describe the development of a dense linkage map for Pinus balfouriana which I use in chapter four to assess the quantitative trait locus (QTL) landscape of water-use efficiency across two isolated ranges of the species. I find evidence that precipitation-related variables structure the geographical range of P. balfouriana, that traits related to water-use efficiency are heritable and differentiated across populations, and associated QTLs underlying this phenotypic variation explain large proportions of total variation. In chapter five, I assess evidence for local adaptation to the eastern Sierra Nevada rain shadow within P. albicaulisacross fine spatial scales of the Lake Tahoe Basin, USA. Here, genetic variation of traits related to water availability were structured more so across populations than neutral variation, and loci identified by genome-wide association methods show elevated signals of local adaptation that track soil water availability. In chapter six, I review theory related to polygenic local adaptation and literature of genotype-phenotype associations in trees. I find that evidence suggests a polygenic basis for many traits important to conservation and industry, and I suggest paths forward to best describing such genetic bases in tree species. Overall, my results show that spatial and genetic structure of trees are often driven by their environment, and that ongoing selective pressures driven by environmental change will continue to be important in these systems.
6
Wang, Qiang. "Maximum likelihood estimation of phylogenetic tree with evolutionary parameters." Connect to this title online, 2004. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1083177084.
Full textAbstract:
Thesis (Ph. D.)--Ohio State University, 2004.Title from first page of PDF file. Document formatted into pages; contains xi, 167 p.; also includes graphics Includes bibliographical references (p. 157-167). Available online via OhioLINK's ETD Center
7
Chen, Lei. "Construction of Evolutionary Tree Models for Oncogenesis of Endometrial Adenocarcinoma." Thesis, University of Skövde, School of Humanities and Informatics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-25.
Full textAbstract:
Endometrial adenocarcinoma (EAC) is the fourth leading cause of carcinoma in woman worldwide, but not much is known about genetic factors involved in this complex disease. During the EAC process, it is well known that losses and gains of chromosomal regions do not occur completely at random, but partly through some flow of causality. In this work, we used three different algorithms based on frequency of genomic alterations to construct 27 tree models of oncogenesis. So far, no study about applying pathway models to microsatellite marker data had been reported. Data from genome–wide scans with microsatellite markers were classified into 9 data sets, according to two biological approaches (solid tumor cell and corresponding tissue culture) and three different genetic backgrounds provided by intercrossing the susceptible rat BDII strain and two normal rat strains. Compared to previous study, similar conclusions were drawn from tree models that three main important regions (I, II and III) and two subordinate regions (IV and V) are likely to be involved in EAC development. Further information about these regions such as their likely order and relationships was produced by the tree models. A high consistency in tree models and the relationship among p19, Tp53 and Tp53 inducible
protein genes provided supportive evidence for the reliability of results.
8
Mork, Amy Lovejoy. "EVOLUTIONARY MORPHOLOGY OF THE MASTICATORY APPARATUS IN TREE GOUGING MARMOSETS." Kent State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=kent1342796212.
Full text
9
Thompson, Evan Benjamin. "The application of genetic and evolutionary algorithms to spanning tree problems." Thesis, University of Exeter, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.288698.
Full text
10
Kummer, Tyler A. "Assessing and Improving Student Understanding of Tree-Thinking." BYU ScholarsArchive, 2017. https://scholarsarchive.byu.edu/etd/6276.
Full textAbstract:
Evolution is the unifying theory of biology. The importance of understanding evolution by those who study the origins, diversification and diversity life cannot be overstated. Because of its importance, in addition to a scientific study of evolution, many researchers have spent time studying the acceptance and the teaching of evolution. Phylogenetic Systematics is the field of study developed to understand the evolutionary history of organisms, traits, and genes. Tree-thinking is the term by which we identify concepts related to the evolutionary history of organisms. It is vital that those who undertake a study of biology be able to understand and interpret what information these phylogenies are meant to convey. In this project, we evaluated the current impact a traditional study of biology has on the misconceptions students hold by assessing tree-thinking in freshman biology students to those nearing the end of their studies. We found that the impact of studying biology was varied with some misconceptions changing significantly while others persisted. Despite the importance of tree-thinking no appropriately developed concept inventory exists to measure student understanding of these important concepts. We developed a concept inventory capable of filling this important need and provide evidence to support its use among undergraduate students. Finally, we developed and modified activities as well as courses based on best practices to improve teaching and learning of tree-thinking and organismal diversity. We accomplished this by focusing on two key questions. First, how do we best introduce students to tree-thinking and second does tree-thinking as a course theme enhance student understanding of not only tree-thinking but also organismal diversity. We found important evidence suggesting that introducing students to tree-thinking via building evolutionary trees was less successful than introducing the concept via tree interpretation and may have in fact introduced or strengthened a misconception. We also found evidence that infusing tree-thinking into an organismal diversity course not only enhances student understanding of tree-thinking but also helps them better learn organismal diversity.
11
Hartmann, Klaas. "Biodiversity conservation and evolutionary models." Thesis, University of Canterbury. Mathematics and Statistics, 2008. http://hdl.handle.net/10092/1776.
Full textAbstract:
Biodiversity conservation requires a framework for prioritising limited resources to the many endangered species. One such framework that has seen much attention and is considered extensively in this thesis, is the Noah's Ark Problem (NAP). The NAP combines a biodiversity measure (Phylogenetic Diversity; PD) with species survival probabilities and conservation costs. The aim of the NAP is to allocate the limited conservation resources such that the future expected PD is maximised. Obtaining optimal solutions to the NAP is a computationally complex problem to which several efficient algorithms are provided here. An extension to the NAP is also developed which allows uncertainty about the survival probability estimates to be included. Using this extension we show that the NAP is robust to uncertainty in these parameters and that even very poor estimates are beneficial. To justify using or promoting PD, it must produce a significant increase in the amount of biodiversity that is preserved. We show that the increase attainable from the NAP is typically around 20% but may be as high as 150%. An alternative approach to PD and the NAP is to prioritise species using simple species specific indices. The benefit of these indices is that they are easy to calculate, explain and integrate into existing management frameworks. Here we investigate the use of such indices and show that they provide between 60% and 80% of the gains obtainable using PD. To explore the expected behaviours of conservation methods (such as the NAP) a distribution of phylogenetics trees is required. Evolutionary models describe the diversification process by which a single species gives rise to multiple species. Such models induce a probability distribution on trees and can therefore be used to investigate the expected behaviour of conservation methods. Even simple and widely used models, such as the Yule model, remain poorly understood. In this thesis we present some new analytic results and methods for sampling trees from a broad range of evolutionary models. Lastly we introduce a new model that provides a simple biological explanation for a long standing discrepancy between models and trees derived from real data -- the tree balance distribution.
12
Kramis, Marc Yves Maria [Verfasser]. "Evolutionary Tree-Structured Storage : Concepts, Interfaces, and Applications / Marc Yves Maria Kramis." Konstanz : Bibliothek der Universität Konstanz, 2014. http://d-nb.info/1050934040/34.
Full text
13
Fenwick, Allyson. "Beyond building a tree: Phylogeny of pitvipers and exploration of evolutionary patterns." Doctoral diss., University of Central Florida, 2012. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/5205.
Full textAbstract:
As generic and higher-scale evolutionary relationships are increasingly well understood, systematists move research in two directions: 1) understanding species-level relationships with dense taxon sampling, and 2) evaluating evolutionary patterns using phylogeny. In this study I address both foci of systematic research using pitvipers, subfamily Crotalinae. For direction one, I evaluate the relationships of 96% of pitvipers by combining independent sets of molecular and phenotypic data. I find the inclusion of species with low numbers of informative characters (i.e. less than 100) negatively impacts resolution of the phylogeny, and the addition of independent datasets has no effect on or a small benefit to confidence in estimated evolutionary relationships. Combined evidence is extremely useful in evaluating taxonomy; I use it with South American bothropoid pitvipers. Previous work found the genus Bothrops paraphyletic, but no study had included enough species to propose a taxonomic resolution. I resolve the relationships of 90% of bothropoid pitvipers, and support the paraphyly of Bothrops as previously defined, but find it consists of three well-supported clades distinguished by distinct habitats and geographic ranges. I propose the division of Bothrops sensu lato into three genera. To address research direction two, I investigate the change in reproductive mode from egg-laying (oviparity) to livebearing (viviparity) in vipers, as well as the expansion of pitvipers through South America. I resolve the phylogeny and the divergence times for subgroups of interest then use model comparison and ancestral character state or geographic range estimation to trace the evolution of reproductive mode or geographic range across evolutionary history. For vertebrates, the predominant explanation for the evolution of reproductive mode is Dollo's Law of unidirectional evolution. This law has been challenged for a number of characters in different systems, but the phylogenetic methods that found those violations were criticized. I find support for unidirectional evolution in two analyses and rejection of it in others, and therefore do not reject Dollo's Law for the evolution of reproductive mode in vipers. In the case of geographic range, dozens of hypotheses have been proposed to explain the great biodiversity in South America, but tests of these hypotheses are lacking. I define specific time- and space-based predictions for seven hypotheses based on geological and climatic events – uplift of the Andes Mountains, saltwater inundation of inland areas, change in river flow, and Pleistocene climate changes. I find some support for half of the hypotheses, including one allopatric, one parapatric, and one based on climate change. I conclude that the evolution of South American pitvipers is extremely complex. Through fulfillment of both systematic research directions, I generated new knowledge about pitvipers and evolutionary processes. My methods of evaluating evolutionary patterns provide frameworks for different research questions in these areas, and I suggest that other researchers apply similar techniques to evaluate other portions of the Tree of Life.Ph.D.
Doctorate
Biology
Sciences
Conservation Biology; Ecology and Organismal Biology
14
Katzen, Jeffrey Marc. "Optimisation of a tree structured centralized data network using an evolutionary algorithm." Master's thesis, University of Cape Town, 1997. http://hdl.handle.net/11427/21169.
Full textAbstract:
This thesis attempts to solve the problem of optimising the design of tree structured centralized data network using an Evolutionary Algorithm. A centralized data network is also known as a client-server network. In this type of network, the client, which is usually a terminal connected to the network, would send a request for information to the server. The server would then download the reply back to the client. An example of such a network would be a bank's ATM network. Each ATM machine would be a client and the central server would store information relating to all the bank's customers. The idea was that once this was done the fitness function used in the above problem would be modified to suite the design of a network used to interconnect LANs that would also form a tree structure. Each of the nodes in this network would be a LAN connected to the network via a bridge or router. Unfortunately the results obtained in attempting to optimise the topology of the centralized data network were very poor. A heuristic normally used to solve this problem outperformed the Evolutionary Algorithm on all the three counts that the comparison was performed. Therefore another method using an Evolutionary Algorithm that can optimise the network interconnecting LANs was introduced. The first chapter in this thesis is an introduction to the thesis and all the terms and concepts that are used in it. The second chapter explains the heuristic used. The third chapter discusses what particular properties are needed by a coding scheme used in an Evolutionary Algorithm to solve this problem. It introduces a few alternatives that have been used in the past but do not meet all the requirements. Then it introduces the coding scheme that was used in this thesis and the fitness function used to evaluate each candidate solution. The next chapter tabulates the results and draws conclusions from these results. The final chapter discusses areas of future research possibilities. There are also several appendices. The first introduces the Genetic Algorithm (GA) and discusses some hypotheses that attempt to explain why it is so successful at problem solving. The next appendix introduces Population Based Incremental Learning (PBIL). This is the Evolutionary Algorithm that is used in attempting to solve this problem. Appendix C explains a method of converting between real and binary numbers; this method is not used in this thesis but is important to know when dealing with Evolutionary Algorithms that are only capable of manipulating binary values. The next two appendices discuss Prim's algorithm and Competitive Learning. Prim's algorithm is an MST algorithm that is used in the coding scheme. Competitive Learning is a classification technique that PBIL is partly based on. An explanation of each function used to implement the heuristic and PBIL is given in Appendix F. This is followed by a listing of the Matlab code of each function.
15
Shi, Tao. "Impact of Rates of Gene Duplication and Domain Shuffling on Species Tree Inference with Gene Tree Parsimony." Thesis, The University of Arizona, 2013. http://hdl.handle.net/10150/301751.
Full textAbstract:
Genome sequencing technologies are providing huge quantities of data for phylogenetic inference. However, most phylogenomic studies exclude gene families, because many have a complicated history of gene duplication/loss and structural change by domain shuffling, especially in deep phylogenies. Gene tree parsimony (GTP) methods, which seek the species tree that minimizes the cost of gene duplication, have been successfully applied to gene families with frequent duplication history. Their utility and performance in the context of gene families with complex histories of gene duplication and domain reshuffling remains unclear. In this study, we analyzed 4389 gene families from six angiosperm genomes encompassing a wide range of duplication rates, and a broad diversity of domain architecture. Overall species tree inference accuracy increased monotonically with the inclusion of more gene trees, and high accuracy was achieved with 50-100 gene trees. The rate of gene duplication strongly influences species tree inference accuracy, with the highest accuracy at either very low or very high rates of duplication and lowest accuracy centered around one duplication per branch in the unrooted species tree. This is the opposite of the relationship between substitution rates on tree construction accuracy, in which intermediate rates have highest accuracy. Accuracy is generally higher in gene families with high domain architecture diversity but has high variance in families with relatively low domain architecture diversity. The latter is probably due to the high variation of gene duplication number for those gene families. We close with some discussion of potential impacts of domain evolution on phylogenomic reconstruction protocols in general, including its effect on alignment.
16
Stephens, Sonia. "Placing birds on a dynamic evolutionary map: Using digital tools to update the evolutionary metaphor of the "tree of life"." Doctoral diss., University of Central Florida, 2012. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/5519.
Full textAbstract:
This dissertation describes and presents a new type of interactive visualization for communicating about evolutionary biology, the dynamic evolutionary map. This web-based tool utilizes a novel map-based metaphor to visualize evolution, rather than the traditional “tree of life.” The dissertation begins with an analysis of the conceptual affordances of the traditional tree of life as the dominant metaphor for evolution. Next, theories from digital media, visualization, and cognitive science research are synthesized to support the assertion that digital media tools can extend the types of visual metaphors we use in science communication in order to overcome conceptual limitations of traditional metaphors. These theories are then applied to a specific problem of science communication, resulting in the dynamic evolutionary map. Metaphor is a crucial part of scientific communication, and metaphor-based scientific visualizations, models, and analogies play a profound role in shaping our ideas about the world around us. Users of the dynamic evolutionary map interact with evolution in two ways: by observing the diversification of bird orders over time and by examining the evidence for avian evolution at several places in evolutionary history. By combining these two types of interaction with a non-traditional map metaphor, evolution is framed in a novel way that supplements traditional metaphors for communicating about evolution. This reframing in turn suggests new conceptual affordances to users who are learning about evolution. Empirical testing of the dynamic evolutionary map by biology novices suggests that this approach is successful in communicating evolution differently than in existing tree-based visualization methods. Results of evaluation of the map by biology experts suggest possibilities for future enhancement and testing of this visualization that would help refine these successes. This dissertation represents an important step forward in the synthesis of scientific, design, and metaphor theory, as applied to a specific problem of science communication. The dynamic evolutionary map demonstrates that these theories can be used to guide the construction of a visualization for communicating a scientific concept in a way that is both novel and grounded in theory. There are several potential applications in the fields of informal science education, formal education, and evolutionary biology for the visualization created in this dissertation. Moreover, the approach suggested in this dissertation can potentially be extended into other areas of science and science communication. By placing birds onto the dynamic evolutionary map, this dissertation points to a way forward for visualizing science communication in the future.Ph.D.
Doctorate
Arts and Humanities
Texts and Technology
17
Johansson, Ted. "Tactical Simulation in Air-To-Air Combat : Evolutionary Algorithms and Behavior Tree Framework." Thesis, Luleå tekniska universitet, Datavetenskap, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:ltu:diva-71334.
Full text
18
Galla, Stephanie J. "Exploring the Evolutionary History of North American Prairie Grouse (Genus: Tympanuchus) Using Multi-locus Coalescent Analyses." Thesis, University of North Texas, 2013. https://digital.library.unt.edu/ark:/67531/metadc271815/.
Full textAbstract:
Conservation biologists are increasingly using phylogenetics as a tool to understand evolutionary relationships and taxonomic classification. The taxonomy of North American prairie grouse (sharp-tailed grouse, T. phasianellus; lesser prairie-chicken, T. pallidicinctus; greater prairie-chicken, T. cupido; including multiple subspecies) has been designated based on physical characteristics, geography, and behavior. However, previous studies have been inconclusive in determining the evolutionary history of prairie grouse based on genetic data. Therefore, additional research investigating the evolutionary history of prairie grouse is warranted. In this study, ten loci (including mitochondrial, autosomal, and Z-linked markers) were sequenced across multiple populations of prairie grouse, and both traditional and coalescent-based phylogenetic analyses were used to address the evolutionary history of this genus. Results from this study indicate that North American prairie grouse diverged in the last 200,000 years, with species-level taxa forming well-supported monophyletic clades in species tree analyses. With these results, managers of the critically endangered Attwater's prairie-chicken (T. c. attwateri) can better evaluate whether outcrossing Attwater's with greater prairie-chickens would be a viable management tool for Attwater's conservation.
19
Ritchie, Andrew Miles. "Evaluating the Performance of Diversification Models for Reconstructing Evolutionary History." Thesis, The University of Sydney, 2017. http://hdl.handle.net/2123/17816.
Full textAbstract:
Understanding the processes that generate diversity is key to interpreting the patterns we see in the present. New developments in modelling these processes have promised unprecedented prospects for unravelling the evolutionary past. However, the empirical behaviour of these models in many of their practical applications is not well understood. This thesis investigates the influence of diversification models in a variety of contexts. First, I consider the Generalised Mixed Yule-Coalescent (GMYC) method for molecular species delimitation. This method identifies transition points between species- and population-level diversification processes on a time-resolved evolutionary tree. I show that this method is sensitive to the choice of mitochondrial marker used, and that the best marker can vary widely across study groups. Next, I investigate the influence of diversification models used to place prior distributions on time-resolved trees in molecular dating. Specifically, I look at the influence of the tree prior in analysing data sets with multiple individuals per species. These data sets can arise by accident where species boundaries are not well understood, and violate the assumptions of both population- and species-level tree priors. I use simulation to show that molecular date estimates can be seriously affected by the choice of tree prior in some circumstances, but are remarkably robust in general. Finally, I extend the analysis of tree prior sensitivity to new methods for dating the origins of human language families. I show that these methods are also robust to the choice of tree prior, and that speciation priors are preferred for language data sets regardless of taxonomic scale. My work will contribute to an improved understanding of the role of diversification models in empirical studies and will increase confidence in these methods across multiple realms of enquiry.
20
Stern, Rebecca. "Evaluating Climate And Environmental Drivers Of Tree Species’ Growth Within The Northern Forest." ScholarWorks @ UVM, 2019. https://scholarworks.uvm.edu/graddis/1169.
Full textAbstract:
Northeastern forests are in a period of immense change. While forests are inherently dynamic ecosystems, a range of environmental challenges may cause unique and uncertain transformations within forests moving forward. How trees in northern forests respond to these environmental and anthropogenic changes remains uncertain; reductions and increases in the growth of various species and shifts in current species’ ranges may take place.
I analyzed associations between tree growth (assessed using xylem increment cores) and a range of site, climate, and pollution deposition variables for seven major tree species in Vermont. First, I looked at red oak (Quercus rubra L.), a species that is projected to expand into the northern hardwood forest. Summer moisture metrics were consistently and positively associated with growth, while higher summer temperatures were often negatively associated with growth. Several pollution metrics were associated with reduced growth – a surprising result for a species not known to be sensitive to inputs of acid deposition.
Second, I examined growth of three tree species emblematic of the northern hardwood forest: sugar maple (Acer saccharum Marsh), American beech (Fagus grandifolia Ehrh.), and yellow birch (Betula alleghaniensis Britton), plus a fourth species, red maple (Acer rubrum L.), whose abundance has increased within the region. Winter moisture (likely snow) was important for all species except for red maple, and either summer moisture (positively associated) or temperature (mostly negatively associated) variables were important for all species, with some differences in relationships based on the elevation or time period evaluated. Pollution metrics were also negatively associated with growth for all species except beech.
Third, I studied correlations of growth and environmental parameters for two temperate conifers: eastern white pine (Pinus strobus L.) and eastern hemlock (Tsuga canadensis (L.) Carrière). For both species, growth was positively associated with warmer spring temperatures but negatively associated with summer temperatures. Negative relationships between pollution deposition and growth for white pine, and to a far lesser extent, eastern hemlock, were also detected. If growing seasons lengthen as projected, temperate conifers may be at a competitive advantage for increased growth if changes in summer temperature and moisture regimes do not add excessive stress that offset possible increases in spring growth. These three studies highlight the importance of considering the distinct seasonal projections for moisture availability and temperature when evaluating the likely growth trajectories of these keystone species.
21
Rokas, Antonis. "Tree-thinking, molecules and gallwasps : analysing evolutionary patterns in European gallwasps using a molecular phylogenetic approach." Thesis, University of Edinburgh, 2001. http://hdl.handle.net/1842/14315.
Full textAbstract:
I have analysed data from nuclear and mitochondrial DNA sequence data in gallwasps and reviewed rare large-scale mutational changes in animals, in an attempt to understand their utility for phylogenetic analysis. Analysis of the sequence data led to the identification of fast and slow-evolving loci for insect phylogenetics. Review of published data on rare large-scale mutations (or Rare Genomic Changes - RGCs for short) suggested that RGCs are likely to be useful and low-homoplasy phylogenetic markers. Using DNA sequence and allozyme data, I studied the phylogeography and post-Pleistocene range expansion of two widely distributed European oak gallwasp species, Andricus quercustozae and Biorhiza pallida. Patterns of genetic diversity in these species have been shaped by their association with their obligate hosts, the oaks (both species), and by the bacterial endosymbiont Wolbachia (B. pallida). These studies revealed the existence of multiple distinct European and Anatolian refuges and suggested that the species’ post-glacial distribution range has been determined by the presence/absence of specific oak species in central and northern Europe. Using mitochondrial DNA sequence data, I generated a phylogeny of the various European gallwasp genera, verifying the existence of various conserved clades and suggesting that many species are non-monophyletic due to lineage sorting of ancestral polymorphisms and / or hybridisation. For a subset of this phylogeny - the genus Andricus - the evolution of shift(s) in the sexual generation oak hosts and host organs galled were analysed, using additional nuclear data. Finally, I surveyed member species of most gallwasp tribes for infection with the bacterial endosymbiont Wolbachia and showed that: (i) the prevalence of Wolbachia differs between lineages with different reproductive modes; (ii) Wolbachia is not associated with thelytoky in the cyclical parthenogenetic gallwasp lineage (in contrast, thelytoky in herb and rose gallwasps is, most likely, Wolbachia-induced); and (iii) horizontal transfer of Wolbachia is likely to have occurred between gall-inducers and their associated inquilines.
22
Öberg, Viktor. "EVOLUTIONARY AI IN BOARD GAMES : An evaluation of the performance of an evolutionary algorithm in two perfect information board games with low branching factor." Thesis, Högskolan i Skövde, Institutionen för informationsteknologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-11175.
Full textAbstract:
It is well known that the branching factor of a computer based board game has an effect on how long a searching AI algorithm takes to search through the game tree of the game. Something that is not as known is that the branching factor may have an additional effect for certain types of AI algorithms. The aim of this work is to evaluate if the win rate of an evolutionary AI algorithm is affected by the branching factor of the board game it is applied to. To do that, an experiment is performed where an evolutionary algorithm known as “Genetic Minimax” is evaluated for the two low branching factor board games Othello and Gomoku (Gomoku is also known as 5 in a row). The performance here is defined as how many times the algorithm manages to win against another algorithm. The results from this experiment showed both some promising data, and some data which could not be as easily interpreted. For the game Othello the hypothesis about this particular evolutionary algorithm appears to be valid, while for the game Gomoku the results were somewhat inconclusive. For the game Othello the performance of the genetic minimax algorithm was comparable to the alpha-beta algorithm it played against up to and including depth 4 in the game tree. After that however, the performance started to decline more and more the deeper the algorithms searched. The branching factor of the game may be an indirect cause of this behaviour, due to the fact that as the depth increases, the search space increases proportionally to the branching factor. This increase in the search space due to the increased depth, in combination with the settings used by the genetic minimax algorithm, may have been the cause of the performance decline after that point.
23
Adams, Henry. "Temperature Sensitivity, Physiological Mechanism, and Implications of Drought-Induced Tree Mortality." Diss., The University of Arizona, 2012. http://hdl.handle.net/10150/228494.
Full textAbstract:
Drought-induced tree mortality is an emerging global phenomenon that appears related to climate change and rising temperatures in particular, and may be an early indication of vegetation change. However, vegetation response to climate change is uncertain, particularly for future novel climates. Notably, no current models of vegetation change attempt to mechanistically predict plant mortality, and in particular, mortality of trees, which exerts strong influences on ecological function. Resolving uncertainties surrounding the physiological mechanism and temperatures sensitivity of tree mortality is a current challenge in global change ecology. The objectives of this dissertation were to 1) consider tree mortality consequences for earth system processes related to carbon, water, and energy exchange that include climate regulation; 2) explore tree mortality effects on the water cycle by developing hypotheses and research needs; 3) quantify the temperature sensitivity of drought-induced tree mortality and gain insight into the physiological mechanism of mortality; 4) quantify the relationships among temperature, stored carbohydrate resources, and gas exchange to further elucidate physiological tree mortality mechanisms; and 5) quantify the sensitivity of two species of pine seedlings to progressively elevated temperatures and relate mortality to the effect of temperature on carbon metabolism. Major findings of this dissertation relate to the temperature sensitivity, physiological mechanism, and implications of tree mortality. Assessment of the potential consequences of tree mortality for earth system processes documented the contrasting influences of tree mortality on the terrestrial C cycle and land-surface energy exchange, the balance of which will determine the net effects on climate regulation (Appendix A). Following a survey of the ecohydrology literature, thresholds for tree mortality to cause watershed changes were hypothesized at ~20% loss of canopy cover, ~500 mm of annual precipitation, and whether flows are snowmelt dominated (Appendix B). Elevated temperature (~+4°C) accelerated tree mortality by 28% during experimental drought, a difference related to cumulative respiration dynamics in piñon pine (Appendix C). Stored carbohydrate resources were declined during lethal drought but were not entirely depleted prior to mortality (Appendix D). Seedlings exhibited progressive declines in time-to mortality with increased temperatures, a response related to C metabolism (Appendix E).
24
Bogdan, Vukobratović. "Hardware Acceleration of Nonincremental Algorithms for the Induction of Decision Trees and Decision Tree Ensembles." Phd thesis, Univerzitet u Novom Sadu, Fakultet tehničkih nauka u Novom Sadu, 2017. https://www.cris.uns.ac.rs/record.jsf?recordId=102520&source=NDLTD&language=en.
Full textAbstract:
The thesis proposes novel full decision tree and decision tree ensembleinduction algorithms EFTI and EEFTI, and various possibilities for theirimplementations are explored. The experiments show that the proposed EFTIalgorithm is able to infer much smaller DTs on average, without thesignificant loss in accuracy, when compared to the top-down incremental DTinducers. On the other hand, when compared to other full tree inductionalgorithms, it was able to produce more accurate DTs, with similar sizes, inshorter times. Also, the hardware architectures for acceleration of thesealgorithms (EFTIP and EEFTIP) are proposed and it is shown in experimentsthat they can offer substantial speedups.У овоj дисертациjи, представљени су нови алгоритми EFTI и EEFTI заформирање стабала одлуке и њихових ансамбала неинкременталномметодом, као и разне могућности за њихову имплементациjу.Експерименти показуjу да jе предложени EFTI алгоритам у могућностида произведе драстично мања стабла без губитка тачности у односу напостојеће top-down инкременталне алгоритме, а стабла знатно већетачности у односу на постојеће неинкременталне алгоритме. Такође супредложене хардверске архитектуре за акцелерацију ових алгоритама(EFTIP и EEFTIP) и показано је да је уз помоћ ових архитектура могућеостварити знатна убрзања.
U ovoj disertaciji, predstavljeni su novi algoritmi EFTI i EEFTI zaformiranje stabala odluke i njihovih ansambala neinkrementalnommetodom, kao i razne mogućnosti za njihovu implementaciju.Eksperimenti pokazuju da je predloženi EFTI algoritam u mogućnostida proizvede drastično manja stabla bez gubitka tačnosti u odnosu napostojeće top-down inkrementalne algoritme, a stabla znatno većetačnosti u odnosu na postojeće neinkrementalne algoritme. Takođe supredložene hardverske arhitekture za akceleraciju ovih algoritama(EFTIP i EEFTIP) i pokazano je da je uz pomoć ovih arhitektura mogućeostvariti znatna ubrzanja.
25
Tarawneh, Monther. "A Novel Quartet-Based Method for Inferring Evolutionary Trees from Molecular Data." Thesis, The University of Sydney, 2008. http://hdl.handle.net/2123/2301.
Full textAbstract:
Molecular Evolution is the key to explain the divergence of species and the origin of life on earth. The main task in the study of molecular evolution is the reconstruction of evolutionary trees from sequences data of the current species. This thesis introduces a novel algorithm for inferring evolutionary trees from genetic data using quartet-based approach. The new method recursively merges sub-trees based on a global statistical provided by the global quartet weight matrix. The quarte weights can be computed using several methods. Since the quartet weights computation is the most expensive procedure in this approach, the new method enables the parallel inference of large evolutionary trees. Several techniques developed to deal with quartets inaccuracies. In addition, the new method we developed is flexible in such a way that can combine morphological and molecular phylogenetic analyses to yield more accurate trees. Also, we introduce the concept of critical point where more than one possible merges are possible for the same sub-tree. The critical point concept can provide information about the relationships between species in more details and show how close they are. This enables us to detect other reasonable trees. We evaluated the algorithm on both synthetic and real data sets. Experimental results showed that the new method achieved significantly better accuracy in comparison with existing methods.
26
Tarawneh, Monther. "A Novel Quartet-Based Method for Inferring Evolutionary Trees from Molecular Data." University of Sydney, 2008. http://hdl.handle.net/2123/2301.
Full textAbstract:
octor of Philosophy(PhD)Molecular Evolution is the key to explain the divergence of species and the origin of life on earth. The main task in the study of molecular evolution is the reconstruction of evolutionary trees from sequences data of the current species. This thesis introduces a novel algorithm for inferring evolutionary trees from genetic data using quartet-based approach. The new method recursively merges sub-trees based on a global statistical provided by the global quartet weight matrix. The quarte weights can be computed using several methods. Since the quartet weights computation is the most expensive procedure in this approach, the new method enables the parallel inference of large evolutionary trees. Several techniques developed to deal with quartets inaccuracies. In addition, the new method we developed is flexible in such a way that can combine morphological and molecular phylogenetic analyses to yield more accurate trees. Also, we introduce the concept of critical point where more than one possible merges are possible for the same sub-tree. The critical point concept can provide information about the relationships between species in more details and show how close they are. This enables us to detect other reasonable trees. We evaluated the algorithm on both synthetic and real data sets. Experimental results showed that the new method achieved significantly better accuracy in comparison with existing methods.
27
Hoang, Tuan-Hoa Information Technology & Electrical Engineering Australian Defence Force Academy UNSW. "Evolutionary Developmental Evaluation : the Interplay between Evolution and Development." Awarded by:University of New South Wales - Australian Defence Force Academy. Information Technology & Electrical Engineering, 2009. http://handle.unsw.edu.au/1959.4/44870.
Full textAbstract:
This thesis was inspired by the difficulties of artificial evolutionary systems in finding elegant and well structured, regular solutions. That is that the solutions found are usually highly disorganized, poorly structured and exhibit limited re-use, resulting in bloat and other problems. This is also true of previous developmental evolutionary systems, where structural regularity emerges only by chance. We hypothesise that these problems might be ameliorated by incorporating repeated evaluations on increasingly difficult problems in the course of a developmental process. This thesis introduces a new technique for learning complex problems from a family of structured increasingly difficult problems, Evolutionary Developmental Evaluation (EDE). This approach appears to give more structured, scalable and regular solutions to such families of problems than previous methods. In addition, the thesis proposes some bio-inspired components that are required by developmental evolutionary systems to take full advantage of this approach. The key part of this is the developmental process, in combination with a varying fitness function evaluated at multiple stages of development, generates selective pressure toward generalisation. This also means that parsimony in structure is selected for without any direct parsimony pressure. As a result, the system encourages the emergence of modularity and structural regularity in solutions. In this thesis, a new genetic developmental system called Developmental Tree Adjoining Grammar Guided Genetic Programming (DTAG3P), is implemented, embodying the requirements above. It is tested on a range of benchmark problems. The results indicate that the method generates more regularly-structured solutions than the competing methods. As a result, the system is able to scale, at least on the problem classes tested, to very complex instances the system encourages the emergence of modularity and structural regularity in solutions. In this thesis, a new genetic developmental system called Developmental Tree Adjoining Grammar Guided Genetic Programming (DTAG3P), is implemented, embodying the requirements above. It is tested on a range of benchmark problems. The results indicate that the method generates more regularly-structured solutions than competing methods. As a result, the system is able to scale, at least on the problem classes tested, to very complex problem instances.
28
Fang, Qixun. "Predicting functional alterations caused by non-synonymous variants in CHO using models based on phylogenetic tree and evolutionary preservation." Thesis, University of Sheffield, 2018. http://etheses.whiterose.ac.uk/21624/.
Full textAbstract:
Chinese Hamster Ovary (CHO) cell is a major manufacturing platform for one of the most valuable biopharmaceutical products: monoclonal antibodies. Being an immortal cell line adapted to different environments, CHO has been accumulating massive mutations in its genome. Continuous effort has been invested into building a computational model to predict CHO cell productivity. However, not much attention has been focused on its proteins which are surely effected by the mutations accumulated to some extent. In this project, we focused on the functional effect caused by non-synonymous variants found in CHO genome. A tool was built to firstly identify these variants and then predict their potential function effect by preservation, a concept derived from evolutionary conservation. Firstly, the PANTHER subfamilies, which defined on the base of potential function change within gene trees, were extended by adding proteins from species not covered by PANTHER. Sequences within the same subfamily were then aligned and had Hidden Markov Models (HMMs) built on these alignments. The HMMs were used to identify homologs in CHO proteins. After that preservation were calculated in every site of the alignments, which was then used to predict the function alterations caused by mutations on every site. Our tool was then validated using data from origin PANTHER subfamilies, PANTHER-PSEP which also calculated site preservation and BLAST, a well-accepted homolog searching algorithm. CHO protein sequences were then imported and analysed by our tool. For comparison, protein sequences from Chinese hamster were also analysed alone with two published CHO cell lines: CHO-K1 and CHO-K1GS. The predictions of proteins from these three genomes were then compared by mapping onto Gene Ontology (GO). Some detailed case studies were also demonstrated. Our tool showed good performance in validations, however, they failed to produce useful hypotheses that would motivate further experiments on bench. The potential causes are discussed at the end.
29
Brantner, Emily K. "Regional evolutionary distinctiveness and endangerment as a means of prioritizing protection of endangered species." FIU Digital Commons, 2015. http://digitalcommons.fiu.edu/etd/2267.
Full textAbstract:
Conservation is costly, and choices must be made about where to best allocate limited resources. I propose a regional evolutionary diversity and endangerment (RED-E) approach to prioritization of endangered species. It builds off of the evolutionary diversity and global endangerment (EDGE) approach, but will allow conservation agencies to focus their efforts on species in specific regions. I used the RED-E approach to prioritize mammal and bird species listed under the U.S. Endangered Species Act (ESA), as well as to make a ranking of species without ESA critical habitat (CH), as a practical application. Regional conservation approaches differ significantly from global approaches. The RED-E approach places a high significance on the level of endangerment of a species, but also allows for very distinct species to have increased prioritization on the RED-E list. Using the CH RED-E list, the U.S. government could begin focusing resources toward endangered and genetically diverse species.
30
Gibson, Jacob R. "Individualistic Response of Piñon and Juniper Tree Species Distributions to Climate Change in North America's Arid Interior West." DigitalCommons@USU, 2011. https://digitalcommons.usu.edu/etd/908.
Full textAbstract:
Piñon and juniper tree species have species-specific climatic requirements, resulting in unique distributions and differential responses to climate change. Piñons and junipers co-dominate the arid woodlands of North America as groups with widespread hybridization. Two piñons, Pinus edulis; P. monophylla, and four junipers, Juniperus deppeana var. deppeana; J. monosperma; J. occidentalis; J. osteosperma, are endemic to the midlatitude interior west and form three groups of hybridizing sister species, P. edulis-P. monophylla; J. deppeana var. deppeana-J. monosperma; J. occidentalis-J. osteosperma. Recent droughts have caused widespread mortality among piñons, but have had less impact on junipers and indicate shifts in co-occurrence have already begun in response to global climate change. Within these groups hybridization likely plays an important role in such distribution changes.
The central objective of this thesis is to forecast the distributions of piñons and junipers endemic to the US under modeled climate change for the 21st century. Species distribution models are built with an emphasis placed on aligning the life cycle dynamics of the species within the temporal and spatial resolution of predictor variables, and within the modeling technique. Two concerns surrounding species distribution modeling are addressed. First, concerns regarding the extent to which species are at equilibrium with the current climate are addressed by incorporating dispersal into the model building process. Second, concerns regarding the potential role of hybridization between closely related species are addressed by building distribution models for each of the three sister species groups as well as the six component species.
Species distribution models exhibited individualistic responses to modeled climate change. Modeled areal loss was greater than gain for all species, which is reflected in changes of co-occurrence. Piñon-juniper richness is forecast to increase in the northern Colorado Plateau, eastern Great Basin, and Rocky Mountains. The sister-species models forecast greater areal gain, and less areal loss, along hybridization zones for P. edulis-P. monophylla and for J. occidentalis-J. osteosperma, but forecast greater areal loss along the periphery of the component species distributions. The sister-species model for J. deppeana var. deppeana-J. monosperma forecasts overall greater areal loss than the component species. In general, forecast changes in latitude and elevation are about one third of the changes inferred, from the fossil record, to have occurred following the transition to the current interglacial ~10,000 years ago.
31
Kosiba, Alexandra M. "Quantifying tree response to alterations in pollution deposition and climate change in the northeastern US." ScholarWorks @ UVM, 2017. http://scholarworks.uvm.edu/graddis/733.
Full textAbstract:
Understanding tree physiological responses to climate change is critical for quantifying forest carbon, predicting species' range change, and forecasting growth trajectories. Continued increases in temperature could push trees into conditions to which they are ill adapted -- such as decreased depth of winter snow cover, altered water regimes, and a lengthened effective growing season. A complicating factor is that in the northeastern United States, climate change is occurring on a backdrop of acid deposition and land-use change. In this dissertation, I used three studies to investigate the spatiotemporal nuances of resultant tree and sapling physiology to environmental change.
First, I compared annual growth of co-occurring tree species (sugar maple, red spruce, red maple, yellow birch, and balsam fir) along an elevational gradient on Vermont's tallest peak: Mt. Mansfield. I found baseline differences in growth among species, and many annual variations were associated with species-specific events. Yet, protracted growth patterns, such as recent increases for red spruce and red maple, were correlated with increased temperature and cooling degree days (a heat index). For most species, temperature was positively associated with current growth, but negatively associated with growth the following year. This work demonstrated species' differences in response to change and the complex relationships between growth and temperature.
Next, I analyzed how climate, environmental parameters, and site and tree factors related to recent, regional increases in red spruce growth. While there was variability in response to climate and acid deposition by elevation and location, site and tree factors did not adequately explain growth. Higher temperatures outside the traditional growing season were positively related to growth, while nitrogen deposition was strongly negative. However, if nitrogen inputs decline as projected then the strength of this relationship may decrease over time. These results suggest continued favorable conditions for red spruce in the near term as acid deposition declines and temperatures increase, provided precipitation remains adequate to support growth.
Lastly, I used a replicated micro-catchment study to examine how four species of tree saplings (paper birch, quaking aspen, American chestnut and black cherry) responded to experimentally elevated temperature (2-4C above control) and reduced early winter snow (first six weeks of winter), depending on soil type. Soil and species characteristics strongly influenced sapling response. However, natural weather patterns during the treatment period were highly variable and muted or exacerbated results. Heating increased the potential photosynthetic period in the fall, causing an overall increase in leaf area. Many two- and three-way interactions of treatment factors were also detected. These outcomes demonstrate the variability in sapling response to a changing climate, as well as the complex interactions that occur among soil, species, and weather parameters.
32
Michael, Skevi. "Studying two different stochastic models : on the study of a random coloured tree and on the generalization of an evolutionary model." Thesis, University of Bristol, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.546186.
Full text
33
Celemín, Amaro Enrique. "The common meadow EuropeanGrasshopper (Chorthippus parallelus)as a window to the process ofspecies formation." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-412206.
Full textAbstract:
Despite more than 50 years of research on the genetic basis of speciation, we still know very little about the early stages of this process. A general rule of speciation is the Haldane’s Rule, which states that postzygotic isolation is expressed earlier in the heterogametic sex: sterility and inviability in hybrids is much more likely to occur in the heterogametic sex. However, it is still unknown how long hybrid sterility takes to be established in the heterogametic sex, since most studies have focused on highly divergent species that no longer hybridize in nature. The meadow grasshopper (Chorthippus parallelus) is a suitable system to shed light on this matter because hybrid male sterility exists between subspecies that show low divergence and are still able to hybridize readily in nature. C. p. parallelus is distributed throughout Northern, Central and Eastern Europe while C. p. erythropus is restricted to the Iberian Peninsula. Both subspecies meet in the Pyrenees, where they form a narrow hybrid zone. Yet, it is unknown 1) how long ago have these subspecies diverged and 2) how have they expanded to form the hybrid zone where these incompatibilities take place. Here, we applied phylogenomic methods to estimate the time of divergence of the subspecies and to study its phylogeographic history. Using the mitogenome and known mitochondrial rates of evolution, we dated the diversification of the subspecies ≈100,000 years ago and found six ancient mitochondrial haplotypes. Implementing coalescent theory to estimate a nuclear species tree, we found evidence of sub-refugia within two or three main refugia and that the hybrid zone originated from a recent post-glacial expansion from one sub-refugia. Haldane’s rule evolved rapidly in C. parallelus, within ≈100,000 years, with demographic processes, such as population expansion. Founder effect reduced genetic diversity in C. parallelus parallelus, with the possibility of fixing incompatible alleles with C. parallelus erythropus resulting in hybrid male sterility.
34
Keen, Rachel M. "Using Tree-Ring Growth and Stable Isotopes to Explore Ponderosa Pine Ecophysiological Responses to Climate Variability and the 2012-2015 California Drought." DigitalCommons@USU, 2019. https://digitalcommons.usu.edu/etd/7511.
Full textAbstract:
Climate warming in recent decades has resulted in more frequent and severe drought events in the western United States. These changes are projected to continue, making it exceedingly important to understand how forests respond to severe drought stress, and how we can manage these forests to reduce mortality during future events. The 2012-2015 California drought is a recent example of a severe, multi-year drought that was coupled with an epidemic-scale outbreak of western pine beetle, killing nearly 90% of ponderosa pines in the central and southern Sierra Nevadas. In the first portion of this study, we compared pairs of surviving and dead ponderosa pines following this drought event to determine how the surviving trees were able to survive. We were also interested in how closely ponderosa pine tree-rings were recording ecosystem responses to this drought event. In the second portion of this study, we compared tree-ring growth rates and stable isotopes to data from an on-site flux tower to determine whether tree-rings were recording important information regarding ecosystem carbon and water fluxes during this severe drought event. Overall, we sought to better understand how the 2012- 2015 California drought event affected ponderosa pines to inform future management practices in forests of the western United States.
35
Logan, Samuel Alexander. "Ancient relicts in the limelight : an evolutionary study of diversity and demographic history in species of the broad-leaved temperate forest tree genus Tilia." Thesis, University of Newcastle upon Tyne, 2016. http://hdl.handle.net/10443/3312.
Full textAbstract:
Tilia L. is a temperate-forest tree genus with a wide northern hemisphere distribution. Several species within the genus are affected by forest fragmentation. Three species were the focus of this study, T. cordata Mill. (small-leaved lime) and T. platyphyllos Scop. (large-leaved lime) from the UK, Austria, Poland, and western Siberia and T. sibirica Bayer (Siberian lime) from southern Siberia. Tilia specific microsatellite markers were used to assess various population genetics indices. Genetic diversity and structure of UK T. cordata and T. platyphyllos populations were estimated. To determine the genetic and demographic history of T. sibirica and T. cordata, Approximate Bayesian Computation (ABC) analyses were used. An investigation into the clonal architecture of the three species was carried out to assess the level of clonality and the impact of clonal reproduction on genetic diversity. In addition, Next Generation Sequencing of the Tilia leaf transcriptome was carried out using direct RNA sequencing Results confirm that the three species are diploid and outcrossing. Although hybridisation occurs among T. cordata and T. platyphyllos, the two are distinct biological units with high genetic diversity and intra-specific population structure. Significant genetic differentiation was observed between T. sibirica and T. cordata and low genetic diversity in the Siberian lime was revealed. ABC analysis suggests a relatively recent (Early Holocene) divergence between the Siberian lime and the small-leaved lime. The Holocene split coincided with a westerly migration of Tilia genotypes that may have contributed to the recolonization of T. cordata in Europe. Fewer clones were observed in T. platyphyllos than the other two species and range-edge populations experience greater clonality than central European populations. Clonal occurrence does not appear to have had a negative effect on genetic diversity. A method for the de novo assembly and annotation of the leaf transcriptome from T. cordata and T. platyphyllos is provided. Potentially thousands of simple sequence repeats (SSRs) from each species have been identified.
36
Johns, Jason W. "Araucaria in the Urban Landscape: A Novel Leaning Pattern and Evidence of Cultivated Hybridization." DigitalCommons@CalPoly, 2017. https://digitalcommons.calpoly.edu/theses/1784.
Full textAbstract:
Our understanding of the natural world is constantly evolving and strengthening as more observations are made and experiments are performed. For example, we understand that tree stems grow toward the light (positive phototropism; Darwin 1880, Loehle 1986, Christie et al. 2013) and against gravity (negative gravitropism; Knight 1806, Hashiguchi et al. 2013). We also know that plants respond to mechanical stimulus and perturbation (thigmotropism; Braam 2005). Genes and their resulting proteins have been described to uncover some of the mechanisms for these environmental responses, but relatively speaking, we have just scratched the surface (Wyatt et al. 2013). While the discovery of the molecular mechanisms responsible for these behaviors is certainly dependent on the ever-improving lab technology available, every molecular discovery is dependent on a macroscopic observation.
In this manuscript I present the two novel macroscopic observations I made on members of Araucaria in the urban forest. The first describes a hemisphere-dependent lean in A. columnaris, and the second provides genetic and morphological evidence that hybrids exist between A. columnaris and A. heterophylla.
Araucaria columnaris (J.R. Forst.) Hooker, or the Cook Pine is a conifer with a narrow native range that has been cultivated worldwide and grows unlike any other tree known. The initial observation we made was that trees in California and Hawaii lean south, and trees in California lean to a greater extent than trees in Hawaii. Measuring 250 trees in 16 regions worldwide, however, produced statistically significant evidence for a hemisphere dependent directional leaning pattern. Trees in the northern hemisphere lean south, and trees in the southern hemisphere lean north. Additionally, the lean becomes more pronounced at greater distances from the equator.
We also gathered morphological and genetic evidence in the California urban forest that A. columnaris and A. heterophylla (Salisb.) Franco are hybridizing. Many individuals have intermediate characteristics of both species, which originally led me to believe that hybrids exist in cultivation. After analyzing several individuals with microsatellite genetic markers, I have enough evidence to conclude that hybrids between A. columnaris and A. heterophylla exist. This is an important observation mainly for municipalities and arborists interested in properly identifying trees in the urban forest. Knowing the proper identity of trees is imperative to informing decisions about their protection or removal.
As we continue to ask questions about the inner workings of nature we will continue to gain a better appreciation for what we still do not know. The evidence provided in this manuscript better informs our future questions about a leaning pattern in A. columnaris and about the history of the cultivation of Araucaria.
37
Jack, Steven B. "Forest Canopies: Form and Functional Relationships." DigitalCommons@USU, 1990. https://digitalcommons.usu.edu/etd/6484.
Full textAbstract:
Forest canopy structure is strongly influenced by stand density due to changing competitive interactions among the individual trees and in turn directly influences stemwood volume production. The structure and dynamics of forest canopies, particularly in relation to the production of stemwood, were examined in unmanaged, even-aged stands of two dissimilar tree species, Pinus contorta var. latifolia Engelm. and Abies lasiocarpa (Hook.) Nutt. The analysis of structure-production relationships was guided by a conceptual model which generated hypotheses and led to examination of assumptions incorporated in the model.
Mean crown dimensions were related to stand density through a negative exponential function for both species, but because of differing shade-tolerances, mean crown size of lodgepole pine was affected more by increasing density than was mean crown size of subalpine fir. More importantly, examination of the model assumptions indicated that adequate characterization of canopy structure should account for the influence of both crown shyness and stand height.
Stand density also influenced the amount and distribution of leaf area in these forest stands. The more plastic mean leaf area of lodgepole pine led to a constant leaf area index over a range of density and, thus, was consistent with conventional wisdom which assumes closed canopied forest stands support stable leaf area indices across a wide range of densities. The less plastic mean leaf area of subalpine fir, however, led to positive correlation between leaf area index and density.
Changes in mean crown dimensions and mean leaf area influenced the production of stemwood volume such that large mean crown sizes were less efficient than small mean crown sizes. The decrease in efficiency was attributed to accumulation of large branch biomass in large crowns to support foliage far from the stem. Increased support costs were indicated by the increasing proportion of crown volume which was nonfoliated as mean crown size increased. The assumption that accumulated branch biomass was responsible for the observed declines in efficiency for forest trees was reinforced by a comparison of structure-production relationships for lodgepole pine and the annual Helianthus annuus L.
38
Edin, Martin. "Learning stationary tasks using behavior trees and genetic algorithms." Thesis, Uppsala universitet, Avdelningen för systemteknik, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-415121.
Full textAbstract:
The demand for collaborative, easy to use robots has increased during the last decades in hope of incorporating the use of robotics in smaller production scales, with easier and faster programming. Artificial intelligence (AI) and Machine learning (ML) are showing promising potential in robotics and this project has attempted to automatically solve a specific assembly task with Behavior trees (BTs). BTs can be used to elegantly divide a problem into different subtasks, while being modular and easy to modify. The main focus is put towards developing a Genetic algorithm (GA), that uses the fundamentals of biological evolution to produce BTs that solves the problem at hand. As a comparison to the GA result, a so-called Automated planner was developed to solve the problem and produce a benchmark BT. With a realistic physics simulation, this project automatically generated BTs that builds a tower of Duplo-like bricks and achieved successful results. The results produced by the GA showed a variety of possible solutions, a portion resembling the automated planner's results but also alternative, perhaps more elegant, solutions. As a conclusion, the approach used in this project shows promising signs and has many possible improvements for future research.
39
Urbini, Laura. "Models and algorithms to study the common evolutionary history of hosts and symbionts." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSE1214/document.
Full textAbstract:
Lors de cette thèse, je me suis intéressée aux modèles et aux algorithmes pour étudier l'histoire évolutive commune des hôtes et des symbiotes. Le premier objectif était d'analyser la robustesse des méthodes de réconciliation des arbres phylogénétiques, qui sont très utilisées dans ce type d'étude. Celles-ci associent (ou lient) un arbre, d'habitude celui des symbiotes, à l'autre, en utilisant un modèle dit basé sur des évènements. Les évènements les plus utilisés sont la cospéciation, la duplication, le saut et la perte. Les phylogénies des hôtes et des symbiotes sont généralement considérés comme donnés, et sans aucune erreur. L'objectif était de comprendre les forces et les faiblesses du modèle parcimonieux utilisé et comprendre comment les résultats finaux peuvent être influencés en présence de petites perturbations ou d'erreurs dans les données en entrée. Ici deux cas sont considérés, le premier est le choix erroné d'une association entre les feuilles des hôtes et des symbiotes dans le cas où plusieurs existent, le deuxième est lié au mauvais choix de l'enracinement de l'arbre des symbiotes. Nos résultats montrent que le choix des associations entre feuilles et le choix de l'enracinement peuvent avoir un fort impact sur la variabilité de la réconciliation obtenue. Nous avons également remarqué que l'evènement appelé “saut” joue un rôle important dans l'étude de la robustesse, surtout pour le problème de l'enracinement. Le deuxième objectif de cette thèse était d'introduire certains evènements peu ou pas formellement considérés dans la littérature. L'un d'entre eux est la “propagation”, qui correspond à l'invasion de différents hôtes par un même symbiote. Dans ce cas, lorsque les propagations ne sont pas considérés, les réconciliations optimales sont obtenues en tenant compte seulement des coûts des évènements classiques (cospeciation, duplication, saut, perte). La nécessité de développer des méthodes statistiques pour assigner les coûts les plus appropriés est toujours d'actualité. Deux types de propagations sont introduites : verticaux et horizontaux. Le premier type correspond à ce qu'on pourrait appeler aussi un gel, à savoir que l'évolution du symbiote s'arrête et “gèle” alors que le symbiote continue d'être associé à un hôte et aux nouvelles espèces qui descendent de cet hôte. Le second comprend à la fois une invasion, du symbiote qui reste associé à l'hôte initial, mais qui en même temps s'associe (“envahit”) un autre hôte incomparable avec le premier, et un gel par rapport à l'évolution des deux l'hôtes, celui auquel il était associé au début et celui qu'il a envahi. Nos résultats montrent que l'introduction de ces evènements rend le modèle plus réaliste, mais aussi que désormais il est possible d'utiliser directement des jeux de données avec un symbiote qui est associé plusieurs hôtes au même temps, ce qui n'était pas faisable auparavantIn this Ph.D. work, we proposed models and algorithms to study the common evolutionary history of hosts and symbionts. The first goal was to analyse the robustness of the methods of phylogenetic tree reconciliations, which are a common way of performing such study. This involves mapping one tree, most often the symbiont’s, to the other using a so-called event-based model. The events considered in general are cospeciation, duplication, host switch, and loss. The host and the symbiont phylogenies are usually considered as given and without any errors. The objective here was to understand the strengths and weaknesses of the parsimonious model used in such mappings of one tree to another, and how the final results may be influenced when small errors are present, or are introduced in the input datasets. This may correspond either to a wrong choice of present-day symbiont-host associations in the case where multiple ones exist, or to small errors related to a wrong rooting of the symbiont tree. Our results show that the choice of leaf associations and of root placement may have a strong impact on the variability of the reconciliation output. We also noticed that the host switch event has an important role in particular for the rooting problem. The second goal of this Ph.D. was to introduce some events that are little or not formally considered in the literature. One of them is the spread, which corresponds to the invasion of different hosts by a same symbiont. In this case, as when spreads are not considered, the optimal reconciliations obtained will depend on the choice made for the costs of the events. The need to develop statistical methods to assign the most appropriate ones therefore remains of actuality. Two types of spread are introduced: vertical and horizontal. The first case corresponds to what could be called also a freeze in the sense that the evolution of the symbiont “freezes” while the symbiont continues to be associated with a host and with the new species that descend from this host. The second includes both an invasion, of the symbiont which remains with the initial host but at the same time gets associated with (“invades”) another one incomparable with the first, and a freeze, actually a double freeze as the evolution of the symbiont “freezes” in relation to the evolution of the host to which it was initially associated and in relation to the evolution of the second one it “invaded”. Our results show that the introduction of these events makes the model more realistic, but also that it is now possible to directly use datasets with a symbiont that is associated with more than one host at the same time, which was not feasible before
40
Martijn, Joran. "Exploration of microbial diversity and evolution through cultivation independent phylogenomics." Doctoral thesis, Uppsala universitet, Molekylär evolution, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-327310.
Full textAbstract:
Our understanding of microbial evolution is largely dependent on available genomic data of diverse organisms. Yet, genome-sequencing efforts have mostly ignored the diverse uncultivable majority in favor of cultivable and sociologically relevant organisms. In this thesis, I have applied and developed cultivation independent methods to explore microbial diversity and obtain genomic data in an unbiased manner. The obtained genomes were then used to study the evolution of mitochondria, Rickettsiales and Haloarchaea. Metagenomic binning of oceanic samples recovered draft genomes for thirteen novel Alphaproteobacteria-related lineages. Phylogenomics analyses utilizing the improved taxon sample suggested that mitochondria are not related to Rickettsiales but rather evolved from a proteobacterial lineage closely related to all sampled alphaproteobacteria. Single-cell genomics and metagenomics of lake and oceanic samples, respectively, identified previously unobserved Rickettsiales-related lineages. They branched early relative to characterized Rickettsiales and encoded flagellar genes, a feature once thought absent in this order. Flagella are most likely an ancestral feature, and were independently lost during Rickettsiales diversification. In addition, preliminary analyses suggest that ATP/ADP translocase, the marker for energy parasitism, was acquired after the acquisition of type IV secretion systems during the emergence of the Rickettsiales. Further exploration of the oceanic samples yielded the first draft genomes of Marine Group IV archaea, the closest known relatives of the Haloarchaea. The halophilic and generally aerobic Haloarchaea are thought to have evolved from an anaerobic methanogenic ancestor. The MG-IV genomes allowed us to study this enigmatic evolutionary transition. Preliminary ancestral reconstruction analyses suggest a gradual loss of methanogenesis and adaptation to an aerobic lifestyle, respectively. The thesis further presents a new amplicon sequencing method that captures near full-length 16S and 23S rRNA genes of environmental prokaryotes. The method exploits PacBio's long read technology and the frequent proximity of these genes in prokaryotic genomes. Compared to traditional partial 16S amplicon sequencing, our method classifies environmental lineages that are distantly related to reference taxa more confidently. In conclusion, this thesis provides new insights into the origins of mitochondria, Rickettsiales and Haloarchaea and illustrates the power of cultivation independent methods with respect to the study of microbial evolution.
41
Stark, Scott C. "On the Mechanistic Connection of Forest Canopy Structure with Productivity and Demography in the Amazon." Diss., The University of Arizona, 2012. http://hdl.handle.net/10150/265347.
Full textAbstract:
Canopy structure has long been thought to influence the productivity and ecological dynamics of tropical forests by altering the availability of light to leaves. Theories and methods that can connect detailed quantitative observations of canopy structure with forest dynamics, however, have been lacking. There is urgent need to resolve this uncertainty because human-caused climate change may alter canopy structure and function in the Amazon. This work addresses this problem by, first, developing methods based on LiDAR remote sensing of fine-scale structural variation to predict the spatial structure of leaf area and light in forest canopies of the central Amazon (Appendices B&C). I show that LiDAR-based leaf area and light estimates can be used to predict the productivity of tree size groups and one-hectare forest plots--as well as differences between 2 sites separated by 500km (App. B). Sites also differed in canopy structure and the distribution of tree frequencies over size (size or diameter distribution). A model based on tree architecture, however, was able to connect observed differences in canopy architecture with size distributions to predict plot and site differences (App. D). This model showed that tree architecture is plastic in different light environments. While plasticity may increase light absorption, the smallest size groups appeared light limited. Absorption over size groups in one site, but not the other, agreed with the hypothesis of energetic equivalence across size structure. Ultimately, the performance of individual trees of different sizes in different canopy environments links forest demography with canopy structure and ecosystem function--I present a study aimed at improving tests of individual level theories for the role of light dependence in tree growth (App. A). Together, this work quantitatively connects canopy structure with forest carbon dynamics and demographic structure and further develops LiDAR as premier tool for studying forest ecological dynamics. Assessing variation in biomass growth and demographic structure over tropical landscapes with remote sensing will improve understanding of ecosystem function and the role of the Amazon in global Carbon dynamics.
42
Shaffer, James D. "FACTORS INFLUENCING THE ESTABLISHMENT AND SURVIVAL OF NATIVE HARDWOOD TREE SEEDLINGS OF THE KENTUCKY INNER BLUEGRASS BLUE ASH-OAK SAVANNA-WOODLAND." UKnowledge, 2013. http://uknowledge.uky.edu/biology_etds/15.
Full textAbstract:
Historically, the Kentucky Inner Bluegrass blue ash-oak savanna-woodland was the primary ecosystem of the Inner Bluegrass Region (IBR) of Kentucky. After European settlement, the majority (>99%) of Bluegrass savanna was converted to agricultural and urban land uses. Currently remnant savanna tree species are failing to recruit. Therefore, a long-term restoration ecology project researching competition and disturbance on seedling establishment, survival, and growth has been established at Griffith Woods (the largest remaining savanna in Kentucky) in Harrison Co., KY. Fourteen native hardwood tree species (a total of 6,168 seedlings) have been experimentally planted. Light, soil, surrounding vegetation, and herbivory, factors thought to influence seedling survival, have been initially assessed. Results show that soils differed spatially in P, Ca, Mg, Zn, pH, N percent and soil organic matter percent. Light was significantly reduced by diffusive filtering through vegetation. Vegetation biomass was influenced by pH and Mg. Initial seedling survival was high, but significantly differed by species type, location, and soil pH, Mg, and Zn. This research demonstrates that under a similar range of conditions, native hardwood tree seedling establishment is possible. Therefore, the potential exists to restore Bluegrass savanna-woodland in order to return proper ecological functioning into a degraded landscape.
43
Russell, Monica G. "Abundance, distribution and habitat requirements of the tree-stem trapdoor spider, Aganippe castellum (Arachnida : Idiopidae) in the eastern West Australian wheatbelt." Thesis, Edith Cowan University, Research Online, Perth, Western Australia, 2008. https://ro.ecu.edu.au/theses/183.
Full textAbstract:
The rare and endemic Trapdoor spider Aganippe castellum (Main, 1986) is currently distributed across the north-eastern West Australian wheatbelt. The sedentary nature of A castellum makes it susceptible to changes in soil and litter, and specifically to sheet flooding and fire events. Studies have shown that spider abundances, species richness and composition are strongly influenced by ve1etation density (Hatley & MacMahon, 1980), and the depth and complexity of the leaf litter layer (Uetz, 1991). Therefore, although all known populations of A. castellum are closed to grazing, any alterations to these vegetation characteristics (in addition to the previous large-scale clearing in Western Australia) may threaten the success of the populations. With most of the remaining populations found in remnant bushland areas either on nature reserves, road verges or private property and these populations suspected to be in decline it was essential that the species' ecology be investigated in order to facilitate a management plan. This was attempted during this study through first establishing the current distribution and abundances of populations of A. castellum which required the development of a method which determined spider presence, and then sampling of the habitat and microhabitat within the four study populations and the one extinct population.
44
Perkins, Dana Lee. "Ecology of Treeline Whitebark Pine (Pinus albicaulis) Populations in Central Idaho: Successional Status, Recruitment, and Mortality, and A Spring Temperature Reconstruction from Whitebark Pine Tree Rings." DigitalCommons@USU, 2001. https://digitalcommons.usu.edu/etd/6591.
Full textAbstract:
T his research investigated the successional status of treeline whitebark pine (Pinus albicaulis) populations on 14 stands in central Idaho and used empirical statistical models to determine the principal factors affecting recruitment and mortality. The longest lived whitebark pines from four additional high-elevation sites were used to develop a tree-ring chronology to reconstruct over 1,000 years of average April-May temperature.
The assessment of stand structures using size-frequency distributions generally provides evidence that treeline whitebark pine populations are currently self-sustaining in areas of low to nonexistent incidence of white pine blister rust (Cronartium ribicola). However the presence of subalpine fir (Abies lasiocarpa) in all size classes on sample plots suggests potential replacement of, or codominant climax with whitebark pine.
Inference from Poisson regression models suggests that stand structure variables are important to whitebark pine establishment, which may be constrained by interference competition and available growing space. Subalpine fir establishment appears to be constrained by distance to seed source at lower elevations and by favorable site water-balance effects on northly aspects.
Inferences from logistic regression models calibrated from pre-epidemic stand conditions and post-epidemic mortality levels surrounding a historic mountain pine beetle (Dendroctonus ponderosae) outbreak suggest that density and tree size variables are significant predictors of stand and individual tree attack. The significance of the predictor variables in these models corroborates the susceptible host characteristics identified in other pine-mountain pine beetle system risk assessments.
A composite whitebark pine tree-ring chronology from 24 trees from four sites was used to develop a 1028-year long reconstruction of spring temperature for the Sawtooth-Salmon River region of central Idaho. The chronology was calibrated against Ketchum and New Meadows, Idaho US Historical Stations, April-May average monthly temperature using half-sample calibration-verification tests for the period that contained historic climate data, 1909-1992. The chronology accounted for 41% of the variability in the climatic data and successfully simulated medium to high frequency trends. A 19th century cold period coincides with the "Little Ice Age." Neither the instrumental nor the proxy temperature records show evidence of warming in the 20th century.
45
Teytaud, Fabien. "Introduction of statistics in optimization." Phd thesis, Université Paris Sud - Paris XI, 2011. http://tel.archives-ouvertes.fr/tel-00655731.
Full textAbstract:
In this thesis we study two optimization fields. In a first part, we study the use of evolutionary algorithms for solving derivative-free optimization problems in continuous space. In a second part we are interested in multistage optimization. In that case, we have to make decisions in a discrete environment with finite horizon and a large number of states. In this part we use in particular Monte-Carlo Tree Search algorithms. In the first part, we work on evolutionary algorithms in a parallel context, when a large number of processors are available. We start by presenting some state of the art evolutionary algorithms, and then, show that these algorithms are not well designed for parallel optimization. Because these algorithms are population based, they should be we well suitable for parallelization, but the experiments show that the results are far from the theoretical bounds. In order to solve this discrepancy, we propose some rules (such as a new selection ratio or a faster decrease of the step-size) to improve the evolutionary algorithms. Experiments are done on some evolutionary algorithms and show that these algorithms reach the theoretical speedup with the help of these new rules.Concerning the work on multistage optimization, we start by presenting some of the state of the art algorithms (Min-Max, Alpha-Beta, Monte-Carlo Tree Search, Nested Monte-Carlo). After that, we show the generality of the Monte-Carlo Tree Search algorithm by successfully applying it to the game of Havannah. The application has been a real success, because today, every Havannah program uses Monte-Carlo Tree Search algorithms instead of the classical Alpha-Beta. Next, we study more precisely the Monte-Carlo part of the Monte-Carlo Tree Search algorithm. 3 generic rules are proposed in order to improve this Monte-Carlo policy. Experiments are done in order to show the efficiency of these rules.
46
Pucko, Carolyn Ann. "The Impacts of Multiple Anthropogenic Disturbances on the Montane Forests of the Green Mountains, Vermont, USA." ScholarWorks @ UVM, 2014. http://scholarworks.uvm.edu/graddis/315.
Full textAbstract:
How and why species’ ranges shift has long been a focus of ecology but is now becoming increasingly important given the current rate of climatic and environmental change. In response to global warming, species will need to migrate northward or upward to stay within their climatic tolerances. The ability of species to migrate will determine their fate and affect the community compositions of the future. However, to more accurately predict the future extent of species, we must identify and understand their responses to past and current climatic and environmental changes. The first place change is expected to occur is within ecotones where the ranges of many species converge and individuals exist at the limits of their environmental tolerances. In montane regions, these boundaries are compressed, creating a situation in which even relatively small changes in conditions can lead to shifts in the elevational ranges of species.
In this dissertation, I examine the responses of forests in the Green Mountains of Vermont to recent climatic and environmental change in an attempt to understand how future climate change will affect their location and composition. I focus on the Boreal-Deciduous Ecotone (BDE), where the high elevation spruce-fir forests converge with the lower elevation northern hardwoods. In addition to investigating adult trees within the BDE, I also examine the responses of understory herbs and tree seedlings to changes in environmental and climatic factors. Factors considered in these investigations include temperature, soil environment, light environment, invasive species, competition, disturbance and many others. I will examine the complex range of responses in forest species that results from prolonged exposure to these forces alone and in combination.
I have attempted to identify the responses of forest species to environmental changes by resurveying historic vegetation plots (Chapter 2), experimentally manipulating the growing environment of tree seedlings (Chapter 3) and performing dendrochronological analyses on tree rings (Chapter 4). Through my resurvey of historic vegetation plots, I determined the degree to which understory species have shifted as individuals or as groups. I also identified a set of novel understory communities that have developed since the 1960's in response to recent climate change, acid deposition and invasive species (Chapter 2). By transplanting and artificially warming tree seedlings, I identified factors responsible for limiting the growth and survival of northern hardwood species above the BDE. Temperature was the primary factor limiting sugar maple (Acer saccharum) at high elevations, while yellow birch (Betula alleghaniensis) was limited almost exclusively by light (Chapter 3). Dendrochronological studies of sugar maples indicated that prolonged exposure to acidified soils has only recently caused growth declines and has altered their relationship to climate (Chapter 4). Together, these studies have produced a cohesive picture of how northeastern montane forests have responded to recent climate change and other anthropogenic impacts. These findings can be used to help predict future species' ranges and identify species that may not be capable of migrating fast enough on their own to keep pace with changes in climatic conditions.
47
Le, Roux Candice. "Nocturnal roost tree, roost site and landscape characteristics of Carnaby's Black-Cockatoo (Calyptorynchus latirostris) on the Swan Coastal Plain." Thesis, Edith Cowan University, Research Online, Perth, Western Australia, 2017. https://ro.ecu.edu.au/theses/2017.
Full textAbstract:
There is limited information on communal roosting in parrot species of Western Australia and other parts of the world. Carnaby’s Black-Cockatoo is an endangered species that forms large nocturnal communal roosts, and for this reason they are an ideal model species to test the characteristics or factors that are associated with roost sites. Known roost sites distributed across the Swan Coastal Plain were identified and selected through the Great Cocky Count project. A minimum of five and maximum of ten individual trees were assessed at 11 roost sites with an overall total of 95 roost trees sampled. I determined the tree species composition and vegetation structural arrangement, as well as the roost site location properties of each of the selected roosts. A total of 18 widely dispersed roost sites on the Swan Coastal Plain were chosen for spatial analysis of landscape characteristics at three scales, namely 1, 6 and 12 km radii around each roost. Landscape characteristics were derived from data layers using a geographical information system. Generalized linear modelling was used to investigate which landscape variables best explain the roost count numbers and fidelity of Carnaby’s Black-Cockatoo at the three spatial scales. Landscape variables were broadly categorised into urban pressures, tree characteristics, and, food and water availability.
I found that at the roost tree scale, the cockatoos utilised a wide range of native and non-native trees, situated within a variety of land-use types. Results showed that bird’s roosted in tall (average of > 25 m) tree species that have relatively thick trunks (average DBH of 1 m) and medium foliage density (average of 50 %), and that are not too densely forested amongst other trees (average tree crown connectivity was 20.58 %). Carnaby’s Black-Cockatoos showed no preferences for any particular tree species or bark colour across the study sites. At the landscape scale, models (based on Akaike Information Criterion) showed that variables associated with bird abundance and roost fidelity varied with scale. The models highlighted the importance of a 1 km radius of potential roost trees (tall trees i.e. ≥ 8 m) across all scales, and food (Banksia and pine) and water sources, particularly within a 1 and 6 km radius. Study sites surrounded by more urban pressure may be driving greater numbers of Carnaby’s Black-Cockatoo at such sites because the formation of larger flocks can increase resource location in fragmented landscapes. Reduced density of roads and non-native ground cover vegetation, over the greater landscape, indicated that restricting the amount of densely urbanised structures should be considered when further developing around roost sites across the Swan Coastal Plain.
The nocturnal roost study sites had greater fidelity and numbers of cockatoos with a combination of landscape variables at different scales, which are based on habitat structure, food availability and water availability. The understanding of the characteristics of communal roosts, roost site choice, and the surrounding matrix developed in this thesis provides managers with insights on how best to conserve this species.
48
Hansen, Christopher Felix. "Lidar Remote Sensing Of Forest Canopy Structure: An Assessment Of The Accuracy Of Lidar And Its Relationship To Higher Trophic Levels." ScholarWorks @ UVM, 2015. http://scholarworks.uvm.edu/graddis/356.
Full textAbstract:
Light detection and ranging (LiDAR) data can provide detailed information about three-dimensional forest horizontal and vertical structure that is important to forest productivity and wildlife habitat. Indeed, LiDAR data have been shown to provide accurate estimates to forest structural parameters and measures of higher trophic levels (e.g., avian abundance and diversity). However, links between forest structure and tree function have not been evaluated using LiDAR. This study was designed and scaled to assess the relationship of LiDAR to multiple aspects of forest structure and higher trophic levels (arthropod and bird populations), which included the ground-based collection of percent crown and understory closure, as well as arthropod and avian abundance and diversity data. Additional plot-based measures were added to assess the relationship of LiDAR to forest health and productivity. High-resolution discrete-return LiDAR data (flown summer of 2009) were acquired for the Hubbard Brook Experimental Forest (HBEF) in New Hampshire, USA. LiDAR data were classified into four canopy structural categories: 1) high crown and high understory closure, 2) high crown and low understory closure, 3) low crown and high understory closure, and 4) low crown and low understory closure. Nearby plots from each of the four LiDAR categories were grouped into "blocks" to assess the spatial consistency of data. Ground-based measures of forest canopy structure, site, stand and individual tree measures were collected on nine 50 m-plots from each LiDAR category (36 plots total), during summer of 2012. Analysis of variance was used to assess the relationships between LiDAR and a suite of tree function measures. Our results show the novel ability of LiDAR to assess forest health and productivity at the stand and individual tree level. We found significant correspondence between LiDAR categories and our ground-based measures of tree function, including xylem increment growth, foliar nutrition, crown health, and stand mortality. Furthermore, we found consistent reductions in xylem increment growth, decreases in foliar nutrition and crown health, and increases in stand mortality related to high understory closure. This suggests that LiDAR measures can reflect competitive interactions, not just among overstory trees for light, but also interactions between overstory trees and understory vegetation for resources other than light (e.g., nutrients). High-resolution LiDAR data show promise in the assessment of forest health and productivity related to tree function.
49
Goldman, Nicholas. "Statistical estimation of evolutionary trees." Thesis, University of Cambridge, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.239234.
Full text
50
McKenzie, Andy. "Stochastic speciation models for evolutionary trees." Thesis, University of Canterbury. Mathematics and Statistics, 2000. http://hdl.handle.net/10092/5597.
Full textAbstract:
Phylogenetic trees are widely used in biology to represent evolutionary relationships between species. As the details of the evolutionary process are mostly unknown, modelling work on the shapes of these trees has had to incorporate a random component. Two null models introduced for this purpose are the uniform model and the Yule model. A third model, the comb model, is useful for giving bounds on theoretical results. We investigate some mathematical properties of these three models.
Let the distance between two nodes be the number of edges separating them. We find exact formulae for the mean distance of a randomly chosen leaf from the root, and for the mean distance between two randomly chosen leaves of a rooted tree. In addition, for the Yule model we find the probability distribution for the distance of randomly chosen leaf from the root.
A cherry is a pair of leaves which are adjacent to a common node. By realising the process of cherry formation by extended Polya urn models we show that the number of cherries is asymptotically normal. This allows us to develop simple statistical tests for the Yule and uniform null hypotheses for the growth of rooted trees. A triplet is a cherry and a pendant edge that are adjacent to a common node. We also show that the asymptotic distribution of triplets is normal for the Yule model, and put forward a conjecture for the distribution under the uniform model.
The construction of an evolutionary tree is generally a two stage process: an unrooted tree is constructed, then it is rooted. We investigate a method for rooting a tree based on the shape of the tree and the Yule model for the growth of rooted trees. We show that even for trees with large number of leaves the approximate location of the root can be located with high probability.
Let S be a set of two rooted binary trees for which the leaf sets L1, L2 form a partition of the set {l, 2, ... ,n}. We derive a recursion for the number of trees on n leaves that are compatible with the set S. We extend this recursion for a set S of three trees, but show that the numbers of terms required in the recursion grows at least exponentially with the number of trees in the set S.
Let S be a set of rooted binary trees. A tree which is a sub-tree of each of the trees in the set is called an agreement sub-tree, and such a tree with the maximum number of possible leaves is called a maximum agreement sub-tree (MAST). We derive an upper bound for the probability that two randomly generated trees have a MAST with number of leaves greater than or equal to a given value s. We find the form the upper bound takes when the trees are generated according to the uniform and Yule models.
The entropy of a probability distribution is equal to the mean information, where the information of an event E is - log P (E). We derive exact and asymptotic formulae for the entropy of the comb, uniform and Yule probability distributions. We show that the comb, uniform, and Yule models satisfy a property called group elimination. A special case of the property of group elimination is sampling consistency.
We show that for any probability distribution on trees that satisfies sampling consistency there is an upper bound on the probability of the fully symmetric tree shapes.
We introduce a modification of the Yule model in which the speciation rate is a function of the time since the last speciation event of a lineage. Using analytical methods we investigate the probability (conditional and unconditional) of the symmetric tree on four leaves under this modified model. If the speciation rate is constant then the probability of the symmetric tree is the same as in the Yule model. Making the speciation rate zero for a period after a speciation event, then constant afterwards, is found to make the symmetric tree more probable. If the speciation rate is constant for some period after a speciation event, then subsequently zero, the symmetric tree is found to be less probable.