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Likelihood Framework (likelihood + framework)
Selected AbstractsA LIKELIHOOD FRAMEWORK FOR INFERRING THE EVOLUTION OF GEOGRAPHIC RANGE ON PHYLOGENETIC TREESEVOLUTION, Issue 11 2005Richard H. Ree Abstract At a time when historical biogeography appears to be again expanding its scope after a period of focusing primarily on discerning area relationships using cladograms, new inference methods are needed to bring more kinds of data to bear on questions about the geographic history of lineages. Here we describe a likelihood framework for inferring the evolution of geographic range on phylogenies that models lineage dispersal and local extinction in a set of discrete areas as stochastic events in continuous time. Unlike existing methods for estimating ancestral areas, such as dispersal-vicariance analysis, this approach incorporates information on the timing of both lineage divergences and the availability of connections between areas (dispersal routes). Monte Carlo methods are used to estimate branch-specific transition probabilities for geographic ranges, enabling the likelihood of the data (observed species distributions) to be evaluated for a given phylogeny and parameterized paleogeographic model. We demonstrate how the method can be used to address two biogeographic questions: What were the ancestral geographic ranges on a phylogenetic tree? How were those ancestral ranges affected by speciation and inherited by the daughter lineages at cladogenesis events? For illustration we use hypothetical examples and an analysis of a Northern Hemisphere plant clade (Cercis), comparing and contrasting inferences to those obtained from dispersal-vicariance analysis. Although the particular model we implement is somewhat simplistic, the framework itself is flexible and could readily be modified to incorporate additional sources of information and also be extended to address other aspects of historical biogeography. [source] Rapid and convergent evolution of parental care in hydrobiid gastropods from New ZealandJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2005M. HAASE Abstract Although parental care occurs in most phyla encompassing a wide array of forms, little is known about its evolution in invertebrates. Two types of egg capsules have been known among ovoviviparous New Zealand hydrobiid gastropods, elastic capsules and simple membranes. Based on a phylogenetic analysis using two mtDNA sequence fragments, I asked whether the second state was derived from the first or whether brooding had multiple origins. The evolution of ovoviviparity was also investigated in the context of habitat transition between brackish and freshwater. Maximum parsimony and Markov chain models of character state transformations in a maximum likelihood framework suggested that hydrobiids have invaded freshwater three times independently. Two of these invasions were followed by the evolution of ovoviviparity, probably in adaptation to changing water levels during periods of irregular precipitation. The syntopy of two congeneric species, one oviparous and the other one brooding, indicated that the transition between reproductive modes must have occurred rapidly. [source] A unified maximum likelihood approach to document retrievalJOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY, Issue 10 2001David Bodoff Empirical work shows significant benefits from using relevance feedback data to improve information retrieval (IR) performance. Still, one fundamental difficulty has limited the ability to fully exploit this valuable data. The problem is that it is not clear whether the relevance feedback data should be used to train the system about what the users really mean, or about what the documents really mean. In this paper, we resolve the question using a maximum likelihood framework. We show how all the available data can be used to simultaneously estimate both documents and queries in proportions that are optimal in a maximum likelihood sense. The resulting algorithm is directly applicable to many approaches to IR, and the unified framework can help explain previously reported results as well as guide the search for new methods that utilize feedback data in IR. [source] Using Bayesian inference to understand the allocation of resources between sexual and asexual reproductionJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES C (APPLIED STATISTICS), Issue 2 2009C. Jessica E. Metcalf Summary., We address the problem of Markov chain Monte Carlo analysis of a complex ecological system by using a Bayesian inferential approach. We describe a complete likelihood framework for the life history of the wavyleaf thistle, including missing information and density dependence. We indicate how, to make inference on life history transitions involving both missing information and density dependence, the stochastic models underlying each component can be combined with each other and with priors to obtain expressions that can be directly sampled. This innovation and the principles described could be extended to other species featuring such missing stage information, with potential for improving inference relating to a range of ecological or evolutionary questions. [source] | ||||||||||