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Parsimony
Kinds of Parsimony Terms modified by Parsimony Selected AbstractsWHEN IS PARSIMONY A VIRTUE?THE PHILOSOPHICAL QUARTERLY, Issue 235 2009Michael Huemer Parsimony is a virtue of empirical theories. Is it also a virtue of philosophical theories? I review four contemporary accounts of the virtue of parsimony in empirical theorizing, and consider how each might apply to two prominent appeals to parsimony in the philosophical literature, those made on behalf of physicalism and on behalf of nominalism. None of the accounts of the virtue of parsimony extends naturally to either of these philosophical cases. This suggests that in typical philosophical contexts, ontological simplicity has no evidential value. [source] Limited phylogeographic structure in the flightless ground beetle, Calathus ruficollis, in southern CaliforniaDIVERSITY AND DISTRIBUTIONS, Issue 5 2007Stylianos Chatzimanolis ABSTRACT The California Floristic Province is home to more than 8000 species of beetles, yet their geographical patterns of supra- and infraspecific diversity remain largely unexplored. In this paper, we investigate the phylogeography and population demographics of a flightless ground beetle, Calathus ruficollis (Coleoptera: Carabidae), in southern California. We sampled 136 specimens from 25 localities divided into 10 populations using a fragment of the mitochondrial cytochrome oxidase I gene. We tested several hypotheses, including the association of geography with particular clades and populations, the degree of differentiation among regions, and the expansion of populations. Parsimony and Bayesian phylogenetic analyses along with nested clade analysis and amova indicate a deep split between the southern Sierra Nevada population and populations south and west. This split corresponds closely to the split between subspecies C. ruficollis ignicollis (southern Sierra Nevada) and C. ruficollis ruficollis. Populations otherwise exhibit limited geographical structure, though Fst values indicate some local differentiation. Mismatch distributions and Fu's Fs indicate range expansion of several populations, suggesting that some structure may have been obscured by recent exchange. The population of C. ruficollis on Santa Cruz Island, which might have been expected to be isolated, shares several haplotypes with mainland populations, appearing to represent multiple colonizations. [source] Apparent/spurious multifractality of data sampled from fractional Brownian/Lévy motionsHYDROLOGICAL PROCESSES, Issue 15 2010Shlomo P. Neuman Abstract Many earth and environmental variables appear to be self-affine (monofractal) or multifractal with spatial (or temporal) increments having exceedance probability tails that decay as powers of , , where 1 < , , 2. The literature considers self-affine and multifractal modes of scaling to be fundamentally different, the first arising from additive and the second from multiplicative random fields or processes. We demonstrate theoretically that data having finite support, sampled across a finite domain from one or several realizations of an additive Gaussian field constituting fractional Brownian motion (fBm) characterized by , = 2, give rise to positive square (or absolute) increments which behave as if the field was multifractal when in fact it is monofractal. Sampling such data from additive fractional Lévy motions (fLm) with 1 < , < 2 causes them to exhibit spurious multifractality. Deviations from apparent multifractal behaviour at small and large lags are due to nonzero data support and finite domain size, unrelated to noise or undersampling (the causes cited for such deviations in the literature). Our analysis is based on a formal decomposition of anisotropic fLm (fBm when , = 2) into a continuous hierarchy of statistically independent and homogeneous random fields, or modes, which captures the above behaviour in terms of only E + 3 parameters where E is Euclidean dimension. Although the decomposition is consistent with a hydrologic rationale proposed by Neuman (2003), its mathematical validity is independent of such a rationale. Our results suggest that it may be worth checking how closely would variables considered in the literature to be multifractal (e.g. experimental and simulated turbulent velocities, some simulated porous flow velocities, landscape elevations, rain intensities, river network area and width functions, river flow series, soil water storage and physical properties) fit the simpler monofractal model considered in this paper (such an effort would require paying close attention to the support and sampling window scales of the data). Parsimony would suggest associating variables found to fit both models equally well with the latter. Copyright © 2010 John Wiley & Sons, Ltd. [source] Robust support for tardigrade clades and their ages from three protein-coding nuclear genesINVERTEBRATE BIOLOGY, Issue 2 2004Jerome C. Regier Abstract. Coding sequences (5,334 nt total) from elongation factor-1,, elongation factor-2, and the largest subunit of RNA polymerase II were determined for 6 species of Tardigrada, 2 of Arthropoda, and 2 of Onychophora. Parsimony and likelihood analyses of nucleotides and amino acids yielded strong support for Tardigrada and all internal nodes (i.e., 100% bootstrap support for Tardigrada, Eutardigrada, Parachela, Hypsibiidae, and Macrobiotidae). Results are in agreement with morphology and an earlier molecular study based on analysis of 18S ribosomal sequences. Divergence times have been estimated from amino acid sequence data using an empirical Bayesian statistical approach, which does not assume a strict molecular clock. Divergence time estimates are pre-Vendian for Tardigrada/Arthropoda, Vendian or earlier for Eutardigrada/Heterotardigrada, Silurian to Ordovician for Parachela/Apochela, Permian to Carboniferous for Hypsibiidae and Macrobiotidae, and Mesozoic for Isohypsibius/Thulinia (both within Hypsibiidae) and Macrobiotus/Richtersius (both within Macrobiotidae). [source] Cryptic Neogene vicariance and Quaternary dispersal of the red-spotted toad (Bufo punctatus): insights on the evolution of North American warm desert biotasMOLECULAR ECOLOGY, Issue 10 2005JEF R. JAEGER Abstract We define the geographical distributions of mitochondrial DNA (mtDNA) lineages embedded within a broadly distributed, arid-dwelling toad, Bufo punctatus. These patterns were evaluated as they relate to hypothesized vicariant events leading to the formation of desert biotas within western North America. We assessed mtDNA sequence variation among 191 samples from 82 sites located throughout much of the species' range. Parsimony-based haplotype networks of major identified lineages were used in nested clade analysis (NCA) to further elucidate and evaluate shallow phylogeographic patterns potentially associated with Quaternary (Pleistocene,Holocene) vicariance and dispersal. Phylogenetic analyses provided strong support for three monophyletic lineages (clades) within B. punctatus. The geographical distributions of the clades showed little overlap and corresponded to the general boundaries of the Peninsular Desert, and two continental desert regions, Eastern (Chihuahuan Desert,Colorado Plateau) and Western (Mojave,Sonoran deserts), geographically separated along the Rocky Mountains and Sierra Madre Occidental. The observed divergence levels and congruence with postulated events in earth history implicate a late Neogene (latest Miocene,early Pliocene) time frame for separation of the major mtDNA lineages. Evaluation of nucleotide and haplotype diversity and interpretations from NCA reveal that populations on the Colorado Plateau resulted from a recent, likely post-Pleistocene, range expansion from the Chihuahuan Desert. Dispersal across historical barriers separating major continental clades appear to be recent, resulting in secondary contacts in at least two areas. Given the observed contact between major clades, we speculated as to why the observed deep phylogeographic structure has not been eroded during the multiple previous interglacials of the Pleistocene. [source] Origin and Evolution of the Lichenized Ascomycete Order Lichinales: Monophyly and Systematic Relationships Inferred from Ascus, Fruiting Body and SSU rDNA EvolutionPLANT BIOLOGY, Issue 2 2001M. Schultz Abstract: The Lichinales are a group of lichenized ascomycetes that almost exclusively possess cyanobacteria as their primary photobiont and are hitherto separated from the Lecanorales, the major group of lichenized ascomycetes, by thallus structure, ascoma ontogeny, ascus structure and ascus function. The relationship of the two families Peltulaceae and Lichinaceae, both placed within the Lichinales, with the Heppiaceae, placed within the Lecanorales, was investigated, as well as a possible sister group relationship of the Lichinales to the Lecanorales. Phylogenetic analyses included non-molecular data as well as 18S rDNA sequence data. The monophyly of the Lichinales including the family Heppiaceae and a sister group relationship of Lichinales and Lecanorales, based on the shared presence of lecanoralean asci, are proposed in a morphological hypothesis. Parsimony and distance analyses of 18S rDNA sequence data strongly support the monophyly of the Lichinales, including all three families. Therefore, the presence of rostrate, lecanoralean asci in Peltula and part of the Lichinaceae suggests that this ascus type is an autapomorphy of the monophyletic Lichinales. Furthermore, the occurrence of prototunicate asci in the Heppiaceae and most of the Lichinaceae is autapomorphic and was gained independently by reduction of the rostrate ascus. The 18S rDNA analysis did not reject the non-molecular hypothesis of a sister group relationship of the Lichinales and the Lecanorales as based on ascus characters. The alternative placement of the Lichinales as the sister group of all inoperculate euascomycetes excluding the Sordariomycetes and most of the Leotiales in the gene tree received unsufficient bootstrap support and no support from any non-molecular data and consequently was rejected. [source] WHEN IS PARSIMONY A VIRTUE?THE PHILOSOPHICAL QUARTERLY, Issue 235 2009Michael Huemer Parsimony is a virtue of empirical theories. Is it also a virtue of philosophical theories? I review four contemporary accounts of the virtue of parsimony in empirical theorizing, and consider how each might apply to two prominent appeals to parsimony in the philosophical literature, those made on behalf of physicalism and on behalf of nominalism. None of the accounts of the virtue of parsimony extends naturally to either of these philosophical cases. This suggests that in typical philosophical contexts, ontological simplicity has no evidential value. [source] Evaluating Theories of Health Behavior Change: A Hierarchy of Criteria Applied to the Transtheoretical ModelAPPLIED PSYCHOLOGY, Issue 4 2008James O. Prochaska The most common criteria recommended by philosophers of science for evaluating theories were organised within a hierarchy ranging from the least to the most risky tests for theories of health behavior change. The hierarchy progressed across: (1) Clarity; (2) Consistency; (3) Parsimony; (4) Testable; (5) Predictive Power; (6) Explanatory Power; (7) Productivity; (8) Generalisable; (9) Integration; (10) Utility; (11) Efficacy; and (12) Impact. The hierarchy was applied to the Transtheoretical Model (TTM) as an example of a health behavior change theory. The application was from the perspective of critics and advocates of TTM. Examples of basic and applied research challenging and supporting TTM across the hierarchy of criteria are presented. The goal is to provide a model for comparing alternative theories and to evaluate progress across the hierarchy within a particular theory. As theories meet criteria at each step in the hierarchy, the research and applications they generate can have increasing impacts on the science and practice of health behavior change. Les critères les plus courants mis en avant par les philosophes des sciences pour l'évaluation des théories ont été structurés dans le cadre d'une hiérarchie allant des épreuves les moins aux plus exigeantes en ce qui concerne les théories portant sur les changements de comportement relatifs à la santé. Cette hiérarchie progresse ainsi: 1) Clarté; 2) Cohérence; 3) Economie; 4) Accès à la vérification; 5) Pouvoir prédictif ; 6) Pouvoir explicatif; 7) Valeur heuristique; 8) Possibilités de généralisation; 9) Intégration; 10) Utilité; 11) Efficacité; 12) Impact. Cette hiérarchie a été appliquée au Modèle Transthéorique (TTM) pris comme exemple de théorie du changement comportemental liéà la santé, aussi bien du point de vue des défenseurs que des critiques du TTM. On présente des exemples de recherches fondamentales et appliquées mettant à l'épreuve ou confirmant le TTM à partir de la hiérarchie des critères. L'objectif est d'avoir un modèle permettant de comparer différentes théories et d'évaluer la progression d'une théorie particulière le long de la hiérarchie. Comme les théories trouvent un critère à chaque échelon de la hiérarchie, les recherches et les applications qu'elles génèrent peuvent avoir des retombées croissantes sur la science et la pratique du changement de comportement relatif à la santé. [source] A phylogenetic supertree of the bats (Mammalia: Chiroptera)BIOLOGICAL REVIEWS, Issue 2 2002KATE E. JONES ABSTRACT We present the first estimate of the phylogenetic relationships among all 916 extant and nine recently extinct species of bats (Mammalia: Chiroptera), a group that accounts for almost one-quarter of extant mammalian diversity. This phylogeny was derived by combining 105 estimates of bat phylogenetic relationships published since 1970 using the supertree construction technique of Matrix Representation with Parsimony (MRP). Despite the explosive growth in the number of phylogenetic studies of bats since 1990, phylogenetic relationships in the order have been studied non-randomly. For example, over one-third of all bat systematic studies to date have focused on relationships within Phyllostomidae, whereas relationships within clades such as Kerivoulinae and Murinae have never been studied using cladistic methods. Resolution in the supertree similarly differs among clades: overall resolution is poor (46.4% of a fully bifurcating solution) but reaches 100% in some groups (e.g. relationships within Mormoopidae). The supertree analysis does not support a recent proposal that Microchiroptera is paraphyletic with respect to Megachiroptera, as the majority of source topologies support microbat monophyly. Although it is not a substitute for comprehensive phylogenetic analyses of primary molecular and morphological data, the bat supertree provides a useful tool for future phylogenetic comparative and macroevolutionary studies. Additionally, it identifies clades that have been little studied, highlights groups within which relationships are controversial, and like all phylogenetic studies, provides preliminary hypotheses that can form starting points for future phylogenetic studies of bats. [source] Phylogeny, evolution and systematics of Moehringia (Caryophyllaceae) as inferred from molecular and morphological data: a case of homology reassessmentCLADISTICS, Issue 4 2007Simone Fior The phylogeny of the genus Moehringia (Caryophyllaceae) is investigated by means of analyzing nuclear (ITS) and chloroplast (matK) sequence data in combination with morphological characters. Parsimony and Bayesian methods yield consistent results, and a common phylogenetic signal is shared by the nuclear and chloroplast data. Morphological characters are affected by a high level of homoplasy, but they provide valuable information when analyzed in combination with the molecular data. Moehringia is paraphyletic to Arenaria with the Iberian taxa belonging to Moehringia sect. Pseudomoehringia McNeill more closely related to Arenaria. This cladistic evidence led us to reinterpret the homology of the key character used in most, if not all, floras, to separate Moehringia from Arenaria, i.e., the seed strophiole. Thorough anatomical studies were carried out to elucidate the ontogeny of the strophiole, which proved different in Moehringia s. str. and the Iberian taxa. Within Moehringia s. str., two sister clades are recognized (i.e., Moehringia sect. Moehringia and M. sect. Latifoliae much as recognized by McNeill, whereas representatives of M. sect. Diversifoliae are assigned to either groups), and biogeographical events related to the Würm glaciation are considered to play a fundamental role in the evolution and present distribution of the genus. The variation of the strophiole is regarded as adaptability to ecological conditions and dispersal agents. We also propose two new combinations and two replacement names: Arenaria glochidisperma (J.M. Mont.) Fior et P.O. Karis, comb. nov., Arenaria tejedensis (Willk.) Fior et P.O. Karis, comb. nov., Arenaria suffruticosa Fior et P.O. Karis, nom. nov. for Moehringia intricata Willk., and Arenaria funiculata Fior et P.O. Karis, nom. nov. for Moehringia fontqueri Pau. © The Willi Hennig Society 2007. [source] Parsimony overcomes statistical inconsistency with the addition of more data from the same geneCLADISTICS, Issue 5 2005Kurt M. Pickett Many authors have demonstrated that the parsimony method of phylogenetic analysis can fail to estimate phylogeny accurately under certain conditions when data follow a model that stipulates homogeneity of the evolutionary process. These demonstrations further show that no matter how much data are added, parsimony will forever exhibit this statistical inconsistency if the additional data have the same distributional properties as the original data. This final component,that the additional data must follow the same distribution as the original data,is crucial to the demonstration. Recent simulations show, however, that if data evolve heterogeneously, parsimony can perform consistently. Here we show, using natural data, that parsimony can overcome inconsistency if new data from the same gene are added to an analysis already exhibiting a condition indistinguishable from inconsistency. © The Willi Hennig Society 2005. [source] Parsimony with and without Scientific JustificationCLADISTICS, Issue 2 2001Arnold G. Kluge Brower's (2000, Cladistics 16, 143,154) pursuit of a nonevolutionary cladistics, like those of others (e.g., Scotland, 2000, Syst. Biol. 49, 480,500), fails for lack of a scientific justification. His operational explication of parsimony does not necessarily rule out the use of other criteria on which to base the identification of a hierarchical branching pattern, nor does he give a compelling reason for why just that one kind of pattern is sought. In the absence of evolutionary theory, such as the descent of species, and the modification of character states, one from another, there is no scientific reason to seek congruence among character hierarchies whose origins, functions, and fates are not necessarily the same. Brower's operational parsimony is no substitute for phylogenetic parsimony, where requirements for ad hoc hypotheses of homoplasy are justifiably minimized, assuming only "descent, with modification." In addition to maximizing explanatory power, that most parsimonious cladogram is the least disconfirmed, most highly corroborated, hypothesis. [source] Panic disorder: a review of DSM-IV panic disorder and proposals for DSM-V,DEPRESSION AND ANXIETY, Issue 2 2010Michelle G. Craske Ph.D Abstract This review covers the literature since the publication of DSM-IV on the diagnostic criteria for panic attacks (PAs) and panic disorder (PD). Specific recommendations are made based on the evidence available. In particular, slight changes are proposed for the wording of the diagnostic criteria for PAs to ease the differentiation between panic and surrounding anxiety; simplification and clarification of the operationalization of types of PAs (expected vs. unexpected) is proposed; and consideration is given to the value of PAs as a specifier for all DSM diagnoses and to the cultural validity of certain symptom profiles. In addition, slight changes are proposed for the wording of the diagnostic criteria to increase clarity and parsimony of the criteria. Finally, based on the available evidence, no changes are proposed with regard to the developmental expression of PAs or PD. This review presents a number of options and preliminary recommendations to be considered for DSM-V. Depression and Anxiety, 2010. © 2010 Wiley-Liss, Inc. [source] BIODIVERSITY RESEARCH: Genetic diversity in two introduced biofouling amphipods (Ampithoe valida & Jassa marmorata) along the Pacific North American coast: investigation into molecular identification and cryptic diversityDIVERSITY AND DISTRIBUTIONS, Issue 5 2010Erik M. Pilgrim Abstract Aim, We investigated patterns of genetic diversity among invasive populations of Ampithoe valida and Jassa marmorata from the Pacific North American coast to assess the accuracy of morphological identification and determine whether or not cryptic diversity and multiple introductions contribute to the contemporary distribution of these species in the region. Location, Native range: Atlantic North American coast; Invaded range: Pacific North American coast. Methods, We assessed indices of genetic diversity based on DNA sequence data from the mitochondrial cytochrome c oxidase subunit I (COI) gene, determined the distribution of COI haplotypes among populations in both the invasive and putative native ranges of A. valida and J. marmorata and reconstructed phylogenetic relationships among COI haplotypes using both maximum parsimony and Bayesian approaches. Results, Phylogenetic inference indicates that inaccurate species-level identifications by morphological criteria are common among Jassa specimens. In addition, our data reveal the presence of three well supported but previously unrecognized clades of A. valida among specimens in the north-eastern Pacific. Different species of Jassa and different genetic lineages of Ampithoe exhibit striking disparity in geographic distribution across the region as well as substantial differences in genetic diversity indices. Main conclusions, Molecular genetic methods greatly improve the accuracy and resolution of identifications for invasive benthic marine amphipods at the species level and below. Our data suggest that multiple cryptic introductions of Ampithoe have occurred in the north-eastern Pacific and highlight uncertainty regarding the origin and invasion histories of both Jassa and Ampithoe species. Additional morphological and genetic analyses are necessary to clarify the taxonomy and native biogeography of both amphipod genera. [source] Inferring historical introduction pathways with mitochondrial DNA: the case of introduced Argentine ants (Linepithema humile) into New ZealandDIVERSITY AND DISTRIBUTIONS, Issue 5 2007Steve E. Corin ABSTRACT The threat imposed by invasive species and difficulties associated with control and management places more impetus on trying to prevent their introduction. The identification of introduction pathways is a vital component towards this goal. In this study, we use a genetic marker-based approach to retrospectively investigate the pathway of origin of the invasive Argentine ant (Linepithema humile) into New Zealand. We intensively sample the mitochondrial gene cytochrome b, from the entire known range of Argentine ants in New Zealand. No genetic variation was found in New Zealand. In order to identify likely introduction pathways, we use two alternative genetic analyses and suggest that a tcs approach that collapses identical haplotypes and calculates the probability of parsimony is superior to standard phylogenetic tree-building algorithms. A minimum spanning network allowed relationships to be examined among sequences collated from previous international studies. The cytochrome b sequence, when compared to a global database, matched that from an Australian population. That Australia is the potential source of Argentine ants is in agreement with the New Zealand interception record, as goods from Australia have the highest number of interception records of Argentine ants. Our approach can easily be duplicated for other organisms and the methodology can be more widely applied to help aid further efforts to identify the routes of transmission for other invasive species and allow us to efficiently direct our biosecurity monitoring effort. [source] Integrating DNA data and traditional taxonomy to streamline biodiversity assessment: an example from edaphic beetles in the Klamath ecoregion, California, USADIVERSITY AND DISTRIBUTIONS, Issue 5 2006Ryan M. Caesar ABSTRACT Conservation and land management decisions may be misguided by inaccurate or misinterpreted knowledge of biodiversity. Non-systematists often lack taxonomic expertise necessary for an accurate assessment of biodiversity. Additionally, there are far too few taxonomists to contribute significantly to the task of identifying species for specimens collected in biodiversity studies. While species level identification is desirable for making informed management decisions concerning biodiversity, little progress has been made to reduce this taxonomic deficiency. Involvement of non-systematists in the identification process could hasten species identification. Incorporation of DNA sequence data has been recognized as one way to enhance biodiversity assessment and species identification. DNA data are now technologically and economically feasible for most scientists to apply in biodiversity studies. However, its use is not widespread and means of its application has not been extensively addressed. This paper illustrates how such data can be used to hasten biodiversity assessment of species using a little-known group of edaphic beetles. Partial mitochondrial cytochrome oxidase I was sequenced for 171 individuals of feather-wing beetles (Coleoptera: Ptiliidae) from the Klamath ecoregion, which is part of a biodiversity hotspot, the California Floristic Province. A phylogram of these data was reconstructed via parsimony and the strict consensus of 28,000 equally parsimonious trees was well resolved except for peripheral nodes. Forty-two voucher specimens were selected for further identification from clades that were associated with many synonymous and non-synonymous nucleotide changes. A ptiliid taxonomic expert identified nine species that corresponded to monophyletic groups. These results allowed for a more accurate assessment of ptiliid species diversity in the Klamath ecoregion. In addition, we found that the number of amino acid changes or percentage nucleotide difference did not associate with species limits. This study demonstrates that the complementary use of taxonomic expertise and molecular data can improve both the speed and the accuracy of species-level biodiversity assessment. We believe this represents a means for non-systematists to collaborate directly with taxonomists in species identification and represents an improvement over methods that rely solely on parataxonomy or sequence data. [source] Fossils provide better estimates of ancestral body size than do extant taxa in fishesACTA ZOOLOGICA, Issue 2009James S. Albert Abstract The use of fossils in studies of character evolution is an active area of research. Characters from fossils have been viewed as less informative or more subjective than comparable information from extant taxa. However, fossils are often the only known representatives of many higher taxa, including some of the earliest forms, and have been important in determining character polarity and filling morphological gaps. Here we evaluate the influence of fossils on the interpretation of character evolution by comparing estimates of ancestral body size in fishes (non-tetrapod craniates) from two large and previously unpublished datasets; a palaeontological dataset representing all principal clades from throughout the Phanerozoic, and a macroecological dataset for all 515 families of living (Recent) fishes. Ancestral size was estimated from phylogenetically based (i.e. parsimony) optimization methods. Ancestral size estimates obtained from analysis of extant fish families are five to eight times larger than estimates using fossil members of the same higher taxa. These disparities arise from differential survival of large-bodied members of early branching lineages, and are not statistical or taphonomic artefacts. Estimates of ancestral size obtained from a limited but judicious selection of fossil fish taxa are more accurate than estimates from a complete dataset of extant fishes. [source] Corporate Governance and Competitive Advantage in Family-Controlled FirmsENTREPRENEURSHIP THEORY AND PRACTICE, Issue 3 2005Michael Carney Recent attempts to identify the basis of family-controlled firms' competitive advantage have drawn upon the resource-based view of the firm. This article supplements these efforts and advances the argument that family-controlled firms' competitive advantage arises from their system of corporate governance. Systems of corporate governance embody incentives, authority patterns, and norms of legitimation that generate particular organizational propensities to create competitive advantages and disadvantages. For comparative purposes, the characteristics of managerial, alliance, and family governance are reviewed. The impact of a family's control rights over a firm's assets generates three dominant propensities (parsimony, personalism, and particularism). These propensities give advantages in scarce environments, facilitate the creation and utilization of social capital, and engender opportunistic investment processes. The experience of family-controlled firms in emerging markets is drawn upon to illustrate the argument. [source] Six independent factors of personality variation: a response to SaucierEUROPEAN JOURNAL OF PERSONALITY, Issue 1 2002Michael C. Ashton We address the concerns raised by Saucier about our proposed six-factor structure of personality. First, we dispute Saucier's new interpretation of the Negative Valence factor as a meaningful dimension of personality variation. We explain that Negative Valence terms may distort the structure of personality-descriptive terms, and that the substantive variance of Honesty is weakly correlated with Negative Valence. Also, we point out that our proposed six factors are (like the Big Five) roughly orthogonal, and that the occurrence of rotational variants within this six-dimensional space is not problematic. We argue that in terms of comprehensiveness, parsimony, independence of factors, and replicability across languages, our proposed six-factor model so far seems to be the optimal structure of personality characteristics. Copyright © 2002 John Wiley & Sons, Ltd. [source] The Causal Exclusion PuzzleEUROPEAN JOURNAL OF PHILOSOPHY, Issue 1 2002David Pineda The article is divided into two parts. The first part offers a careful reconstruction and detailed discussion of the argument of causal exclusion, as well as of the implications it has for physicalism. In its second part the article examines two important objections to the causal exclusion argument: the generalization objection, which holds that the argument is unacceptable since it confers causal efficacy only to ultimate basic properties, which arguably might not exist; and Yablo's objection, according to which underlying the argument of causal exclusion there is a principle of causal parsimony which leads to strong counterintuitive results and should therefore be abandoned. The article offers grounds for rejecting both objections as well as a new diagnosis of the problem for mental causation generated by the causal exclusion argument. [source] EVOLUTION OF SCAPULA SIZE AND SHAPE IN DIDELPHID MARSUPIALS (DIDELPHIMORPHIA: DIDELPHIDAE)EVOLUTION, Issue 9 2009Diego Astúa The New World family Didelphidae, the basal lineage within marsupials, is commonly viewed as morphologically conservative, yet includes aquatic, terrestrial, scansorial, and arboreal species. Here, I quantitatively estimated the existing variability in size and shape of the Didelphidae scapula (1076 specimens from 56 species) using geometric morphometrics, and compared size and shape differences to evolutionary and ecologic distances. I found considerable variation in the scapula morphology, most of it related to size differences between species. This results in morphologic divergence between different locomotor habits in larger species (resulting from increased mechanical loads), but most smaller species present similarly shaped scapulae. The only exceptions are the water opossum and the short-tailed opossums, and the functional explanations for these differences remain unclear. Scapula size and shape were mapped onto a molecular phylogeny for 32 selected taxa and ancestral size and shapes were reconstructed using squared-changed parsimony. Results indicate that the Didelphidae evolved from a medium- to small-sized ancestor with a generalized scapula, slightly more similar to arboreal ones, but strikingly different from big-bodied present arboreal species, suggesting that the ancestral Didelphidae was a small scansorial animal with no particular adaptations for arboreal or terrestrial habits, and these specializations evolved only in larger-bodied clades. [source] THE PHYLOGENETIC PATTERN OF SPECIATION AND WING PATTERN CHANGE IN NEOTROPICAL ITHOMIA BUTTERFLIES (LEPIDOPTERA: NYMPHALIDAE)EVOLUTION, Issue 7 2006Chris D. Jiggins Abstract Species level phylogenetic hypotheses can be used to explore patterns of divergence and speciation. In the tropics, speciation is commonly attributed to either vicariance, perhaps within climate-induced forest refugia, or ecological speciation caused by niche adaptation. Mimetic butterflies have been used to identify forest refugia as well as in studies of ecological speciation, so they are ideal for discriminating between these two models. The genus Ithomia contains 24 species of warningly colored mimetic butterflies found in South and Central America, and here we use a phylogenetic hypothesis based on seven genes for 23 species to investigate speciation in this group. The history of wing color pattern evolution in the genus was reconstructed using both parsimony and likelihood. The ancestral pattern for the group was almost certainly a transparent butterfly, and there is strong evidence for convergent evolution due to mimicry. A punctuationist model of pattern evolution was a significantly better fit to the data than a gradualist model, demonstrating that pattern changes above the species level were associated with cladogenesis and supporting a model of ecological speciation driven by mimicry adaptation. However, there was only one case of sister species unambiguously differing in pattern, suggesting that some recent speciation events have occurred without pattern shifts. The pattern of geographic overlap between clades over time shows that closely related species are mostly sympatric or, in one case, parapatric. This is consistent with modes of speciation with ongoing gene flow, although rapid range changes following allopatric speciation could give a similar pattern. Patterns of lineage accumulation through time differed significantly from that expected at random, and show that most of the extant species were present by the beginning of the Pleistocene at the latest. Hence Pleistocene refugia are unlikely to have played a major role in Ithomia diversification. [source] EVOLUTION OF MOUTHBROODING AND LIFE-HISTORY CORRELATES IN THE FIGHTING FISH GENUS BETTAEVOLUTION, Issue 4 2004Lukas Rüber Abstract The origin of and evolutionary transitions among the extraordinary diverse forms of parental care in teleost fish remain largely unknown. The "safe harbor" hypothesis predicts that the evolution from a "guarding" to a "brooding" form of care in teleost fish is associated with shifts in reproductive and life-history features such as reduced fecundity, and increased egg volume with higher parental investment. Robust phylogenetic hypotheses may help to identify evolutionary changes in key traits associated with differences in the form of parental care. Here, we used reconstruction of ancestral character states to study the evolution of the two forms of parental care, bubble nesting and mouthbrooding in the fighting fish genus Betta. We also applied a comparative analysis using the phylogenetic generalized least-squares method to test the "safe harbor" hypothesis by evaluating differences between the two forms of parental care in standard length, life-history traits, and three habitat variables. Evolutionary hypotheses were derived from the first molecular phylogeny (nuclear and mitochondrial DNA sequence data; 4448 bp) of this speciose group. Ancestral character state reconstructions of the evolution of the form of parental care in the genus Betta, using the methods of unweighted parsimony and maximum likelihood, are uncertain and further indicate a high rate of evolutionary transitions. Applying different weights for the suspected directionality of changes, based on the consistent phenotypic and behavioral differences found between bubble nesters and mouthbrooders, recurrent origin of mouthbrooding in the genus Betta is favored using parsimony. Our comparative analyses further demonstrate that bubble nesters and mouthbrooders do not have a consistent set of life-history correlates. The form of parental care in Betta is correlated only with offspring size, with mouthbrooders having significantly bigger offspring than bubble nesters, but is not correlated with egg volume, clutch size, and broodcare duration, nor with any of the three habitat variables tested. Our results thus challenge the general predictions of the "safe harbor" hypothesis for the evolution of alternative brood care forms in the fighting fish genus Betta. [source] Geobiological analysis using whole genome-based tree building applied to the Bacteria, Archaea, and EukaryaGEOBIOLOGY, Issue 1 2003Christopher H. House ABSTRACT We constructed genomic trees based on the presence and absence of families of protein-encoding genes observed in 55 prokaryotic and five eukaryotic genomes. There are features of the genomic trees that are not congruent with typical rRNA phylogenetic trees. In the bacteria, for example, Deinococcus radiodurans associates with the Gram-positive bacteria, a result that is also seen in some other phylogenetic studies using whole genome data. In the Archaea, the methanogens plus Archaeoglobus form a united clade and the Euryarchaeota are divided with the two Thermoplasma genomes and Halobacterium sp. falling below the Crenarchaeota. While the former appears to be an accurate representation of methanogen-relatedness, the misplacement of Halobacterium may be an artefact of parsimony. These results imply the last common ancestor of the Archaea was not a methanogen, leaving sulphur reduction as the most geochemically plausible metabolism for the base of the archaeal crown group. It also suggests that methanogens were not a component of the Earth's earliest biosphere and that their origin occurred sometime during the Archean. In the Eukarya, the parsimony analysis of five Eukaryotes using the Crenarchaeota as an outgroup seems to counter the Ecdysozoa hypothesis, placing Caenorhabditis elegans (Nematoda) below the common ancestor of Drosophila melanogaster (Arthropoda) and Homo sapiens (Chordata) even when efforts are made to counter the possible effects of a faster rate of sequence evolution for the C. elegans genome. Further analysis, however, suggests that the gene loss of ,animal' genes is highest in C. elegans and is obscuring the relationships of these organisms. [source] Global evidence that deforestation amplifies flood risk and severity in the developing worldGLOBAL CHANGE BIOLOGY, Issue 11 2007COREY J. A. BRADSHAW Abstract With the wide acceptance of forest-protection policies in the developing world comes a requirement for clear demonstrations of how deforestation may erode human well-being and economies. For centuries, it has been believed that forests provide protection against flooding. However, such claims have given rise to a heated polemic, and broad-scale quantitative evidence of the possible role of forests in flood protection has not been forthcoming. Using data collected from 1990 to 2000 from 56 developing countries, we show using generalized linear and mixed-effects models contrasted with information-theoretic measures of parsimony that flood frequency is negatively correlated with the amount of remaining natural forest and positively correlated with natural forest area loss (after controlling for rainfall, slope and degraded landscape area). The most parsimonious models accounted for over 65% of the variation in flood frequency, of which nearly 14% was due to forest cover variables alone. During the decade investigated, nearly 100 000 people were killed and 320 million people were displaced by floods, with total reported economic damages exceeding US$1151 billion. Extracted measures of flood severity (flood duration, people killed and displaced, and total damage) showed some weaker, albeit detectable correlations to natural forest cover and loss. Based on an arbitrary decrease in natural forest area of 10%, the model-averaged prediction of flood frequency increased between 4% and 28% among the countries modeled. Using the same hypothetical decline in natural forest area resulted in a 4,8% increase in total flood duration. These correlations suggest that global-scale patterns in mean forest trends across countries are meaningful with respect to flood dynamics. Unabated loss of forests may increase or exacerbate the number of flood-related disasters, negatively impact millions of poor people, and inflict trillions of dollars in damage in disadvantaged economies over the coming decades. This first global-scale empirical demonstration that forests are correlated with flood risk and severity in developing countries reinforces the imperative for large-scale forest protection to protect human welfare, and suggests that reforestation may help to reduce the frequency and severity of flood-related catastrophes. [source] Molecular phylogeny of Diabrotica beetles (Coleoptera: Chrysomelidae) inferred from analysis of combined mitochondrial and nuclear DNA sequencesINSECT MOLECULAR BIOLOGY, Issue 4 2001T. L. Clark Abstract The phylogenetic relationships of thirteen Diabrotica (representing virgifera and fucata species groups) and two outgroup Acalymma beetle species (Coleoptera: Chrysomelidae) were inferred from the phylogenetic analysis of a combined data set of 1323 bp of mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (COI) and the entire second internal transcribed spacer region (ITS-2) of nuclear ribosomal DNA of 362 characters. Species investigated were D. adelpha, D. balteata, D. barberi, D. cristata, D. lemniscata, D. longicornis, D. porracea, D. speciosa, D. undecimpunctata howardi, D. u. undecimpunctata, D. virgifera virgifera, D. v. zeae, D. viridula, and outgroup A. blandulum and A. vittatum. Maximum parsimony (MP), minimum evolution (ME), and maximum likelihood (ML) analyses of combined COI and ITS-2 sequences clearly place species into their traditional morphological species groups with MP and ME analyses resulting in identical topologies. Results generally confer with a prior work based on allozyme data, but within the virgifera species group, D. barberi and D. longicornis strongly resolve as sister taxa as well as monophyletic with the neotropical species, D. viridula, D. cristata and D. lemniscata also resolve as sister taxa. Both relationships are not in congruence with the prior allozyme-based hypothesis. Within the fucata species group, D. speciosa and D. balteata resolve as sister taxa. Results also strongly supported the D. virgifera and D. undecimpunctata subspecies complexes. Our proposed phylogeny provides some insight into current hypotheses regarding distribution status and evolution of various life history traits for Diabrotica. [source] On parameter estimation of a simple real-time flow aggregation modelINTERNATIONAL JOURNAL OF COMMUNICATION SYSTEMS, Issue 7 2006Huirong Fu Abstract There exists a clear need for a comprehensive framework for accurately analysing and realistically modelling the key traffic statistics that determine network performance. Recently, a novel traffic model, sinusoid with uniform noise (SUN), has been proposed, which outperforms other models in that it can simultaneously achieve tractability, parsimony, accuracy (in predicting network performance), and efficiency (in real-time capability). In this paper, we design, evaluate and compare several estimation approaches, including variance-based estimation (Var), minimum mean-square-error-based estimation (MMSE), MMSE with the constraint of variance (Var+MMSE), MMSE of autocorrelation function with the constraint of variance (Var+AutoCor+MMSE), and variance of secondary demand-based estimation (Secondary Variance), to determining the key parameters in the SUN model. Integrated with the SUN model, all the proposed methods are able to capture the basic behaviour of the aggregation reservation system and closely approximate the system performance. In addition, we find that: (1) the Var is very simple to operate and provides both upper and lower performance bounds. It can be integrated into other methods to provide very accurate approximation to the aggregation's performance and thus obtain an accurate solution; (2) Var+AutoCor+MMSE is superior to other proposed methods in the accuracy to determine system performance; and (3) Var+MMSE and Var+AutoCor+MMSE differ from the other three methods in that both adopt an experimental analysis method, which helps to improve the prediction accuracy while reducing computation complexity. Copyright © 2005 John Wiley & Sons, Ltd. [source] Developing Clinical Terms for Health Visiting in the United KingdomINTERNATIONAL JOURNAL OF NURSING TERMINOLOGIES AND CLASSIFICATION, Issue 2003June Clark BACKGROUND The UK health visiting service provides a universalist preventive health service that focuses mainly on families with young children and the elderly or vulnerable, but anyone who wishes can access the services. The principles of health visiting have been formally defined as the search for health needs, the stimulation of awareness of health needs, influencing policies that affect health, and the facilitation of health-enhancing activities. The project is currently in its fourth phase. In phase 1, 17 health visitors recorded their encounters with families with new babies over a period of 3 months; in phase 2, 27 health visitors recorded their encounters with a wider range of clients (769 encounters with 205 families) over a period of 9 months; in phase 3, the system is being used by a variety of healthcare professionals in a specialist program that provides intensive parenting support; phase 4 is developing a prototype of an automated version for point-of-contact recording. UK nursing has no tradition of standardized language and the concept of nursing diagnosis is almost unknown. Over the past decade, however, the government has initiated the development of a standardized terminology (Read codes) to cover all disciplines and all aspects of health care, and it is likely that the emerging SNOMED-CT terminology (a merger of the Read codes with the SNOMED terminology) will be mandated for use throughout the National Health Service (NHS). MAIN CONTENT POINTS The structure and key elements of the Omaha System were retained but the terminology was modified to take account of the particular field of practice and emerging UK needs. Modifications made were carefully tracked. The Problem Classification Scheme was modified as follows: ,All terms were anglicized. ,Some areas , notably relating to antepartum/postpartum, neonatal care, child protection, and growth and development,were expanded. ,The qualifiers "actual,""potential," and "health promotion" were changed to "problem,""risk," and "no problem." ,Risk factors were included as modifiers of "risk" alongside the "signs and symptoms" that qualify problems. The Intervention Classification was modified by substituting synonymous terms for "case management" and "surveillance" and dividing "health teaching, guidance, and counseling" into two categories. The Omaha System "targets" were renamed "focus" and a new axis of "recipient" was introduced in line with SNOMED-CT. The revised terminologies were tested in use and also sent for review to 3 nursing language experts and 12 practitioners, who were asked to review them for domain completeness, appropriate granularity, parsimony, synonymy, nonambiguity, nonredundancy, context independence, and compatibility with emerging multiaxial and combinatorial nomenclatures. Review comments were generally very favourable and modifications suggested are being incorporated. CONCLUSIONS The newly published government strategy for information management and technology in the NHS in Wales requires the rapid development of an electronic patient record, for which the two prerequisites are structured documentation and the use of standardized language. The terminology developed in this project will enable nursing concepts to be incorporated into the new systems. The experiences of the project team also offer many lessons that will be useful for developing the necessary educational infrastructure. [source] A Review of Statistical Methods for Genome MappingINTERNATIONAL STATISTICAL REVIEW, Issue 1 2000Hywel B. Jones Summary Framework maps of the human genome are an important staging post in the on-going effort to sequence the entire genome. The existence of high quality maps is also a prerequistite for studies attempting to determine the location of genes involved in common diseases. The basic experimental approaches to constructing both genetic and physical maps are briefly described as well as their respective uses. A variety of statistical approaches to map construction are outlined including parsimony, maximum likelihood and Bayesian methodologies. The mostly widely used of these, the method of maximum likelihood, is discussed in detail, particularly in the context of physical mapping using radiation hybrids. Finally, current statistical issues and problems in the field of genome mapping are described. Résumé Des cartes squelette du génome humain sont une étape, important dans l'effort actuel pour séquecer, le génome tout entier. L'existence de cartes de bonne qualité est aussi la condition d'études visant à localiser les génes, interwenant dans des maladies courantes. Les approches expérimentales de base pour construire tant des cartes génétigues, que physiques sont briévement, décrites ainsi que leurs usages respectifs. Plusieurs méthodes, statistiques de cartographie sont mises en relief: notamment celles de parcimonie, du maximum de vraisemblance et bayésiennce.La plus largement utilisée-laméthode, du maximum de vraisemblance-est examinéen détail, particuliérement pour la cartographue physique utilisant des phybrides d'irradiation Enfin sont abordés, divers questions et probémes, courants on matiéde cartographie génétique. [source] The pure parsimony haplotyping problem: overview and computational advancesINTERNATIONAL TRANSACTIONS IN OPERATIONAL RESEARCH, Issue 5 2009Daniele Catanzaro Abstract Haplotyping estimation from aligned single-nucleotide polymorphism fragments has attracted more and more attention in recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range from mapping of complex disease genes to inferring population histories, passing through designing drugs, functional genomics, and pharmacogenetics. The literature proposes a number of estimation criteria to select a set of haplotypes among possible alternatives. Usually, such criteria can be expressed under the form of objective functions, and the sets of haplotypes that optimize them are referred to as optimal. One of the most important estimation criteria is the pure parsimony, which states that the optimal set of haplotypes for a given set of genotypes is that having minimal cardinality. Finding the minimal number of haplotypes necessary to explain a given set of genotypes involves solving an optimization problem, called the pure parsimony haplotyping (PPH) estimation problem, which is notoriously -hard. This article provides an overview of PPH, and discusses the different approaches to solution that occur in the literature. [source] | |||||||||||||||||||||||||||||||||||||||||||||||||||||||