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Erney P Camargo - One of the best experts on this subject based on the ideXlab platform.
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the phylogeography of trypanosomes from south american alligatorids and african crocodilids is consistent with the geological history of south american river basins and the transoceanic dispersal of crocodylus at the miocene
Parasites & Vectors, 2013Co-Authors: Bruno R Fermino, Laerte B Viola, Fernando Paiva, Herakles A Garcia, Catia D Paula, Robinson Boteroarias, Carmen S A Takata, Marta Campaner, Patrick B Hamilton, Erney P CamargoAbstract:Background Little is known about the diversity, phylogenetic relationships, and Biogeography of trypanosomes infecting non-mammalian hosts. In this study, we investigated the influence of host species and Biogeography on shaping the genetic diversity, phylogenetic relationship, and distribution of trypanosomes from South American alligatorids and African crocodilids.
Malte C. Ebach - One of the best experts on this subject based on the ideXlab platform.
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A History of Biogeography for the Twenty-First Century Biogeographer
History Philosophy and Theory of the Life Sciences, 2015Co-Authors: Malte C. EbachAbstract:Most histories written for scientists are aimed at identifying a founder, usually a patriarchal figure from whom all knowledge originates. While this may serve some practitioners of science to unify a field, it is in the most part a political exercise. Twenty-first century Biogeography has multiple origins, most of which are in the twentieth century. Few, if any methodologies, theories and implementations of twenty-first century Biogeography go back to the nineteenth century, let alone the eighteenth. What is more, twenty-first century Biogeography has many different practitioners that hail from different backgrounds, very much like the practitioners in the eighteenth and nineteenth centuries. The calls for unity in Biogeography in twenty-first century are remarkably similar to those in the late nineteenth century. Take any given number of practitioners from different backgrounds (e.g., taxonomy, geography) and allow them to pursue questions about organismal distribution, you will invariably end up with a multidisciplinary field regardless in which century you practise. The aim of this book is to show that eighteenth and nineteenth century plant and animal geography is a multidisciplinary profession and in as much conflict as twentieth and twenty-first century Biogeography. The problems being encountered in Biogeography today (e.g., calls for unification) are the same as those in the past. Origins of Biogeography is a history for twenty-first century biogeographers that detail the confusion of geographical and taxonomic laws (Chap. 2), the conflict between practitioners (Chap. 3), the divergence of classifications (Chap. 4), and the way we implement our plant and animal geographies (Chaps. 5 and 6) in the eighteenth and nineteenth centuries. By the end of the nineteenth century the basic divisions in twentieth century Biogeography are already apparent. The twentieth century has its own unique history, which this book will not cover. Few biogeographers see twentieth century origins in their field.
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The multidisciplinary nature of Biogeography
Australian Systematic Botany, 2015Co-Authors: Malte C. EbachAbstract:Having been appointed as an Associate Editor for Australian Systematic Botany and given the task to specialise in the area of Biogeography, I wish to discuss a slight alteration to the journal scope and guidelines and discuss some of the new, exciting directions for the journal. My hope is that in expanding into Biogeography, we offer both a wider scope and articles of interest to our existing readership. Before revealing this new direction I wish examine the multidisciplinary role of Biogeography.
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Biogeography in a Changing World - Biogeography in a Changing World
2006Co-Authors: Malte C. Ebach, Raymond S. TangneyAbstract:Ernst Haeckel and Louis Agassiz: Trees That Bite and Their Geographical Dimension, D.M. Williams Introduction People That Bite: Plagiarism and the Threefold Parallelism The Threefold Parallelism: Its Beginning (Tiedemann, 1808)? Ernst Haeckel and Darwinism Trees That Bite: Haeckel's Genealogical Oaks and Stick 'Trees' Heinrich Georg Bronn: Trunks and Twigs Schleicher, Linguistics and Trees Haeckel and Palaeontological Truth Haeckel's 'Hypotheische Skizze des monophyletischen Ursprungs und der Verbreitung der 12 Menschen-Species von Lemurien aus uber die Erde' and the Concept of Chorology The Development of Chorology Origins Realms, Regions and Provinces Agassiz' (1854) Geographical Realms: The Natural Provinces of Mankind Regions, Homology and Relationships Sclater, Huxley and the Classification of Regions Croizat's Radical Realms: Ocean Basin and Cladograms Summary: The Threefold Parallelism: ... and Its End (Nelson, 1978A?) Acknowledgements References Common Cause and Historical Biogeography, L.R. Parenti Introduction Cladistic vs. Phylogenetic Biogeography Methods of Historical Biogeography Geology and Dispersal Molecules and Time Global Biogeographic Patterns vs. Biogeographic Realms or Regions Conclusions Acknowledgements References A Brief Look at Pacific Biogeography: The Trans-Oceanic Travels of Microseris (Angiosperms: Asteraceae), J.R. Grehan Introduction Molecular Mythology Geology First? A Primer in Biogeography Logic of Dispersal Dispersal through Migration Microseris (Panbio)geography Dispersal through Form-Making Past, Present, Future Acknowledgements References Biotic Element Analysis and Vicariance Biogeography, B. Hausdorf and C. Hennig Introduction The Vicariance Model Tests of the Vicariance Model Determination of Biotic Elements Case Studies Other Biogeographical Tests of the Vicariance Model Conclusions References Evolution of Specific and Genetic Diversity during Ontogeny of Island Floras: The Importance of Understanding Process for Interpreting Island Biogeographic Patterns, T.F. Stuessy Introduction General Aspects of Oceanic Island Ontogeny A Hypothesis for the Ontogeny of Oceanic Island Floras Implications of the Hypothesis Acknowledgements References Event-Based Biogeography: Integrating Patterns, Processes and Time, I. Sanmartin Introduction Parsimony-Based Tree Fitting An Empirical Example: Nothofagus Biogeography Area Biogeography: Southern Hemisphere Biogeographic Patterns Dispersal-Vicariance Analysis An Empirical Example: Holarctic Biogeography Acknowledgements References Phylogeography in Historical Biogeography: Investigating the Biogeographic Histories of Populations, Species, and Young Biotas, B.R. Riddle and D.J. Hafner Introduction Phylogeography vs. Historical Biogeography From Single-Taxon to Comparative Phylogeography Towards an Integration of Phylogeography and Historical Biogeography Future Directions Acknowledgements References Are Plate Tectonic Explanations for Trans-Pacific Disjunctions Plausible? Empirical Tests of Radical Dispersalist Theories, D. McCarthy Introduction / The du Toit Denouement Should Ocean-Crossing Taxa Be Wide-Ranging? Furtive Fossils Dispersal Counts, Biotic Similarity and the Distance Effect Brief Responses Geological Concerns Summary Acknowledgements References Index
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Forum on historical Biogeography: what is cladistic Biogeography?
Journal of Biogeography, 2005Co-Authors: Malte C. Ebach, Juan J. MorroneAbstract:J. J. Morrone: Several papers published recently in this journal have revised and discussed some current different approaches of historical Biogeography. In my opinion, some of their conclusions referring to the objectives and methods of cladistic Biogeography were incorrect and may lead to some confusion. I would like to begin our exchange of opinions by discussing the question, ‘What is cladistic Biogeography?’. Among these contributions, I was particularly surprised when I read van Veller et al. (2003). These authors proposed that the available cladistic biogeographical methods have been developed to implement two different research programmes. A priori methods, which allow modification of the taxon–area cladograms to deal with dispersal, extinction or duplicated lineages, in order to obtain resolved area cladograms and provide the maximum fit to a general area cladogram, are intended to implement cladistic Biogeography. A posteriori methods, which deal with dispersal, extinction or duplicated lineages after the parsimony analysis of a data matrix based on unmodified taxon–area cladograms, are intended to implement phylogenetic Biogeography. The outcome means that cladistic Biogeography, as most biogeographers usually conceive of it, is restricted by van Veller et al. (2003) to include only component analysis, reconciled tree analysis, three area statements analysis, and paralogy-free subtrees analysis, whereas other methods, namely Brooks Parsimony Analysis (BPA) (Wiley, 1987) and component compatibility, really belong to phylogenetic Biogeography. In addition to finding this terminology confusing, because ‘phylogenetic Biogeography’ has been used for decades to refer to Hennig’s (1966) and Brundin’s (1966) cladistic implementation of the dispersalist approach, I am unconvinced about the existence of two different research programmes. It seems that Ebach et al. (2003) also support the distinction between cladistic and phylogenetic Biogeography. But is this view justified? M. C. Ebach: I find the distinction between cladistic and phylogenetic Biogeography interesting as it does delimit a theoretical rather than a methodological division in historical Biogeography. As has been pointed out, the phylogenetic Biogeography of Lars Brundin was the beginning of interpreting trees and cladograms from a biogeographical perspective. The taxon–area cladogram, a result of Brundin’s work, was interpreted as two separate things, on one hand as the ‘phylogenetic diversification of geographically and ecologically associated clades coincide[d]’ (Brooks, 1990; p. 16), and on the other as historical connections, that is, relationships between biotas in time (Platnick & Nelson, 1978). The two interpretations of taxon–area cladograms can be stated as thus: 1. The geographical distribution of taxa on a phylogenetic tree. 2. The distribution of areas based on the relationships of taxa on a cladogram or an areagram. Taxon–area cladograms tell us of the evolutionary history of lineages. Areagrams provide a classification of area relationships. Taxon–area cladograms still retain nodes, that is, information about individual taxa and areagrams replace nodes with components that contain information about the terminal branches. Taxon–area cladograms and areagrams tell us different things and the methods that use them have different functions and therefore provide biogeographers with different aims. The differences between taxon–area cladograms and areagrams are theoretical and not methodological. The argument used by van Veller et al. to erect a new ‘biogeographical programme’ based on comparing the validity of methods, rather than on aims or intentions, is confusing. If we wish to ‘classify’ historical Biogeography into groups or research programmes, as has been attempted previously by Spellerberg & Sawyer (1999) and Crisci (2001), surely we need to clarify the theory first? Can we compare different methods if they are applied from opposing or different theoretical intentions? One example of this is in your own work where you use the Parsimony Analysis of Endemicity (PAE) (Rosen, 1984) to conduct panBiogeography (Croizat, 1958; Craw et al., 1999). Can we compare the use of the same method under two different theories, such as the implementation of PAE in BPA to score the absence and presence of areas on a taxon–area cladogram (see Ebach & Humphries, 2003) and the use of BPA in ‘phylogenetic’ and comparative phylogeography (Riddle & Hafner, 2004)?
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Cladistic Biogeography: Component-Based Methods and Paleontological Application
Topics in Geobiology, 2001Co-Authors: Malte C. Ebach, Gregory D. EdgecombeAbstract:In 1985 Jablonski et al reviewed biogeographic methods in paleobiology, observing “The impact of vicariance Biogeography on paleobiogeographic research has been minimal thus far”. They recognized that the cladistic aproach to Biogeography pioneered by Platnick and Nelson (1978) and Rosen (1978) offered explicitness and clarity of hypotheses, and attributed the dearth of cladistically-based studies of Biogeography to the limited number of cladistic phylogenies then available. The ensuing years have witnessed the wide-spread use of cladistic systematic methods in paleontology, yet the biogeographic aspect of cladograms has largely been ignored. Our chapter aims to introduce methods in cladistic Biogeography to a paleontological audience, using examples drawn from fossil distributions. An overview of cladistic Biogeography up to 1994 is provided by Morrone and Crisci (1995), and more comprehensive and updated treatments are given by Humphries and Parenti (1999) and Lieberman (2000).
Dan Simon - One of the best experts on this subject based on the ideXlab platform.
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a probabilistic analysis of a simplified Biogeography based optimization algorithm
Evolutionary Computation, 2011Co-Authors: Dan SimonAbstract:Biogeography-based optimization (BBO) is a population-based evolutionary algorithm (EA) that is based on the mathematics of Biogeography. Biogeography is the study of the geographical distribution of biological organisms. We present a simplified version of BBO and perform an approximate analysis of the BBO population using probability theory. Our analysis provides approximate values for the expected number of generations before the population's best solution improves, and the expected amount of improvement. These expected values are functions of the population size. We quantify three behaviors as the population size increases: first, we see that the best solution in the initial randomly generated population improves; second, we see that the expected number of generations before improvement increases; and third, we see that the expected amount of improvement decreases.
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Markov Models for Biogeography-Based Optimization
IEEE transactions on systems man and cybernetics. Part B Cybernetics : a publication of the IEEE Systems Man and Cybernetics Society, 2010Co-Authors: Dan Simon, Mehmet Ergezer, Rick RarickAbstract:Biogeography-based optimization (BBO) is a population-based evolutionary algorithm that is based on the mathematics of Biogeography. Biogeography is the science and study of the geographical distribution of biological organisms. In BBO, problem solutions are analogous to islands, and the sharing of features between solutions is analogous to the migration of species. This paper derives Markov models for BBO with selection, migration, and mutation operators. Our models give the theoretically exact limiting probabilities for each possible population distribution for a given problem. We provide simulation results to confirm the Markov models.
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Biogeography-based optimization
IEEE Transactions on Evolutionary Computation, 2008Co-Authors: Dan SimonAbstract:Biogeography is the study of the geographical distribution of biological organisms. Mathematical equations that govern the distribution of organisms were first discovered and developed during the 1960s. The mindset of the engineer is that we can learn from nature. This motivates the application of Biogeography to optimization problems. Just as the mathematics of biological genetics inspired the development of genetic algorithms (GAs), and the mathematics of biological neurons inspired the development of artificial neural networks, this paper considers the mathematics of Biogeography as the basis for the development of a new field: Biogeography-based optimization (BBO). We discuss natural Biogeography and its mathematics, and then discuss how it can be used to solve optimization problems. We see that BBO has features in common with other biology-based optimization methods, such as GAs and particle swarm optimization (PSO). This makes BBO applicable to many of the same types of problems that GAs and PSO are used for, namely, high-dimension problems with multiple local optima. However, BBO also has some features that are unique among biology-based optimization methods. We demonstrate the performance of BBO on a set of 14 standard benchmarks and compare it with seven other biology-based optimization algorithms. We also demonstrate BBO on a real-world sensor selection problem for aircraft engine health estimation.
Christopher John Humphries - One of the best experts on this subject based on the ideXlab platform.
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Historical Biogeography, the natural science
TAXON, 2004Co-Authors: Lynne R. Parenti, Christopher John HumphriesAbstract:0 INTRODUCTION Twenty years ago we wrote a monograph on historical Biogeography that was published in 1986 in the Oxford University Press Monograph Series on Biogeography (Humphries & Parenti, 1986). We summarized and interpreted the field of cladistic Biogeography as it stood at the time for the undergraduate, graduate student and professional biologist, and as it had developed in concert with the cladistic revolution in phylogenetic methods (i.e., Hennig, 1966; Nelson & Platnick, 1981; Wiley, 1981). During the following decade, Biogeography enjoyed a renaissance, particularly in methodology, and we wrote a second edition of our book in large part to summarize advances made during the 1990s (Humphries & Parenti, 1999). A challenge facing biologists today is to understand the enormous amount and variety of information that is being generated and archived in databases, particularly those in systematics collections documenting global species diversity over time for discovering a pattern. Biogeographic patterns provide an organizing framework within which we may interpret biological data, as well as provide the basic information for understanding relationships among areas. Well-corroborated biogeographic patterns have a high predictive value. They may inform other phylogenetic studies, by predicting where a primitive sister group may live; reinforce conservation studies, by identifying species, endemic areas and complementary hot spots; or simplify our understanding of, hence our explanations for, patterns of diversity, by proposing a common cause of our observations in the sense of Life and Earth evolving together rather than a series of unrelated events, such as dispersal scenarios. Biogeography is more relevant now than it has perhaps ever been, and it is time for yet another renaissance. Many terms have been coined that pull together diverse bits of biological information: biodiversity, bioinformatics, biocomplexity, and so on. None of these can replace the power of "historical Biogeography" that asks a simple question: What lives where, and why? And, the subject is bold enough to suggest some answers to that ques1\1 DRE,
Bruno R Fermino - One of the best experts on this subject based on the ideXlab platform.
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the phylogeography of trypanosomes from south american alligatorids and african crocodilids is consistent with the geological history of south american river basins and the transoceanic dispersal of crocodylus at the miocene
Parasites & Vectors, 2013Co-Authors: Bruno R Fermino, Laerte B Viola, Fernando Paiva, Herakles A Garcia, Catia D Paula, Robinson Boteroarias, Carmen S A Takata, Marta Campaner, Patrick B Hamilton, Erney P CamargoAbstract:Background Little is known about the diversity, phylogenetic relationships, and Biogeography of trypanosomes infecting non-mammalian hosts. In this study, we investigated the influence of host species and Biogeography on shaping the genetic diversity, phylogenetic relationship, and distribution of trypanosomes from South American alligatorids and African crocodilids.
