Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages

Aims: In ecology and conservation biology, the number of species counted in a biodiversity study is a key metric but is usually a biased underestimate of total species richness because many rare species are not detected. Moreover, comparing species richness among sites or samples is a statistical challenge because the observed number of species is sensitive to the number of individuals counted or the area sampled. For individual-based data, we treat a single, empirical sample of species abundances from an investigator-defined species assemblage or community as a reference point for two estimation objectives under two sampling models: estimating the expected number of species (and its unconditional variance) in a random sample of (i) a smaller number of individuals (multinomial model) or a smaller area sampled (Poisson model) and (ii) a larger number of individuals or a larger area sampled. For sample-based incidence (presence-absence) data, under a Bernoulli product model, we treat a single set of species incidence frequencies as the reference point to estimate richness for smaller and larger numbers of sampling units. Methods: The first objective is a problem in interpolation that we address with classical rarefaction (multinomial model) and Coleman rarefaction (Poisson model) for individual-based data and with sample-based rarefaction (Bernoulli product model) for incidence frequencies. The second is a problem in extrapolation that we address with sampling-theoretic predictors for the number of species in a larger sample (multinomial model), a larger area (Poisson model) or a larger number of sampling units (Bernoulli product model), based on an estimate of asymptotic species richness. Although published methods exist for many of these objectives, we bring them together here with some new estimators under a unified statistical and notational framework. This novel integration of mathematically distinct approaches allowed us to link interpolated (rarefaction) curves and extrapolated curves to plot a unified species accumulation curve for empirical examples. We provide new, unconditional variance estimators for classical, individual-based rarefaction and for Coleman rarefaction, long missing from the toolkit of biodiversity measurement. We illustrate these methods with datasets for tropical beetles, tropical trees and tropical ants. Important Findings: Surprisingly, for all datasets we examined, the interpolation (rarefaction) curve and the extrapolation curve meet smoothly at the reference sample, yielding a single curve. Moreover, curves representing 95% confidence intervals for interpolated and extrapolated richness estimates also meet smoothly, allowing rigorous statistical comparison of samples not only for rarefaction but also for extrapolated richness values. The confidence intervals widen as the extrapolation moves further beyond the reference sample, but the method gives reasonable results for extrapolations up to about double or triple the original abundance or area of the reference sample. We found that the multinomial and Poisson models produced indistinguishable results, in units of estimated species, for all estimators and datasets. For sample-based abundance data, which allows the comparison of all three models, the Bernoulli product model generally yields lower richness estimates for rarefied data than either the multinomial or the Poisson models because of the ubiquity of non-random spatial distributions in nature. © 2012 The Author. Published by Oxford University Press on behalf of the Institute of Botany, Chinese Academy of Sciences and the Botanical Society of China. All rights reserved

Evolution of the latitudinal diversity gradient in the hyperdiverse ant genus Pheidole

AimThe latitudinal diversity gradient is the dominant geographic pattern of life on Earth, but a consensus understanding of its origins has remained elusive. The analysis of recently diverged, hyperâ rich invertebrate groups provides an opportunity to investigate latitudinal patterns with the statistical power of large trees while minimizing potentially confounding variation in ecology and history. Here, we synthesize global phylogenetic and macroecological data on a hyperdiverse (> 1,100 species) ant radiation, Pheidole and test predictions of three general explanations for the latitudinal gradient: variation in diversification rates, tropical conservatism and ecological regulation.LocationGlobal.Time periodThe past 35 million years.Major taxa studiedThe hyperdiverse ant genus Pheidole Westwood.MethodsWe assembled geographic data for 1,499 species and morphospecies, and inferred a dated phylogeny for 449 species of Pheidole, including 167 species newly sequenced for this study. We tested for correlations between diversification rate and latitude with Bayesian analysis of macroevolutionary mixtures (BAMM), hidden state speciation and extinction (HiSSE), geographic state speciation and extinction (GeoSSE), and a nonâ parametric method (FiSSE), evaluated evidence for richness steady state, and examined patterns of diversification as Pheidole spread around the globe.ResultsThere was no evidence of systematic variation of net diversification rates with latitude across any of the methods. We found that Pheidole diversification occurred in bursts when new continents were colonized, followed by a slowdown in each region, but there is no evidence richness has saturated at an equilibrium in any region. Additionally, we found latitudinal affinity is moderately conserved with a Neotropical ancestor and simulations show that phylogenetic inertia alone is sufficient to produce the gradient pattern.Main conclusionsOur results provide no evidence that diversification rates vary systematically with latitude. Richness is far from steady state in each region, contrary to the ecological regulation hypothesis, although there is evidence that ecological opportunity promotes diversification after colonization of new areas. The fact that niche conservatism is strong enough to produce the gradient pattern is in accord with the tropical conservatism hypothesis. Overall, these results shed light on the mechanisms underlying the emergence of the diversity gradient within the past 34 million years, complementing recent work on deeper timeâ scales, and more generally contribute toward muchâ needed invertebrate perspective on global biodiversity dynamics.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148253/1/geb12867-sup-0001-AppendixS1-S2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148253/2/geb12867-sup-0005-TableS3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148253/3/geb12867-sup-0006-Supinfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148253/4/geb12867-sup-0002-FigS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148253/5/geb12867.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148253/6/geb12867_am.pd

Caterpillars and fungal pathogens: two co-occurring parasites of an ant-plant mutualism

In mutualisms, each interacting species obtains resources from its partner that it would obtain less efficiently if alone, and so derives a net fitness benefit. In exchange for shelter (domatia) and food, mutualistic plant-ants protect their host myrmecophytes from herbivores, encroaching vines and fungal pathogens. Although selective filters enable myrmecophytes to host those ant species most favorable to their fitness, some insects can by-pass these filters, exploiting the rewards supplied whilst providing nothing in return. This is the case in French Guiana for Cecropia obtusa (Cecropiaceae) as Pseudocabima guianalis caterpillars (Lepidoptera, Pyralidae) can colonize saplings before the installation of their mutualistic Azteca ants. The caterpillars shelter in the domatia and feed on food bodies (FBs) whose production increases as a result. They delay colonization by ants by weaving a silk shield above the youngest trichilium, where the FBs are produced, blocking access to them. This probable temporal priority effect also allows female moths to lay new eggs on trees that already shelter caterpillars, and so to occupy the niche longer and exploit Cecropia resources before colonization by ants. However, once incipient ant colonies are able to develop, they prevent further colonization by the caterpillars. Although no higher herbivory rates were noted, these caterpillars are ineffective in protecting their host trees from a pathogenic fungus, Fusarium moniliforme (Deuteromycetes), that develops on the trichilium in the absence of mutualistic ants. Therefore, the Cecropia treelets can be parasitized by two often overlooked species: the caterpillars that shelter in the domatia and feed on FBs, delaying colonization by mutualistic ants, and the fungal pathogen that develops on old trichilia. The cost of greater FB production plus the presence of the pathogenic fungus likely affect tree growth

The art of being human : a project for general philosophy of science

Throughout the medieval and modern periods, in various sacred and secular guises, the unification of all forms of knowledge under the rubric of ‘science’ has been taken as the prerogative of humanity as a species. However, as our sense of species privilege has been called increasingly into question, so too has the very salience of ‘humanity’ and ‘science’ as general categories, let alone ones that might bear some essential relationship to each other. After showing how the ascendant Stanford School in the philosophy of science has contributed to this joint demystification of ‘humanity’ and ‘science’, I proceed on a more positive note to a conceptual framework for making sense of science as the art of being human. My understanding of ‘science’ is indebted to the red thread that runs from Christian theology through the Scientific Revolution and Enlightenment to the Humboldtian revival of the university as the site for the synthesis of knowledge as the culmination of self-development. Especially salient to this idea is science‘s epistemic capacity to manage modality (i.e. to determine the conditions under which possibilities can be actualised) and its political capacity to organize humanity into projects of universal concern. However, the challenge facing such an ideal in the twentyfirst century is that the predicate ‘human’ may be projected in three quite distinct ways, governed by what I call ‘ecological’, ‘biomedical’ and ‘cybernetic’ interests. Which one of these future humanities would claim today’s humans as proper ancestors and could these futures co-habit the same world thus become two important questions that general philosophy of science will need to address in the coming years

Explicating ways of consensus-making in science and society: distinguishing the academic, the interface and the meta-consensus

In this chapter, we shed new light on the epistemic struggle between establishing consensus and acknowledging plurality, by explicating different ways of consensus-making in science and society and examining the impact hereof on their field of intersection, i.e. consensus conferences (in particular those organized by the National Institute of Health). We draw a distinction between, what we call, academic and interface consensus, to capture the wide appeal to consensus in existing literature. We investigate such accounts - i.e. from Miriam Solomon, John Beatty and Alfred Moore, and Boaz Miller - as to put forth a new understanding of consensus-making, focusing on the meta-consensus. We further defend how (NIH) consensus conferences enable epistemic work, through demands of epistemic adequacy and contestability, contrary to the claim that consensus conferences miss a window for epistemic opportunity (Solomon M, The social epistemology of NIH consensus conferences. In: Kincaid H, McKitrick J (ed) Establishing medical reality: methodological and metaphysical issues in philosophy of medicine. Springer, Dordrecht, 2007). Paying attention to the dynamics surrounding consensus, moreover, allows us to illustrate how the public understanding of science and the public use of the ideal of consensus could be well modified

Deweyan tools for inquiry and the epistemological context of critical pedagogy

This article develops the notion of resistance as articulated in the literature of critical pedagogy as being both culturally sponsored and cognitively manifested. To do so, the authors draw upon John Dewey\u27s conception of tools for inquiry. Dewey provides a way to conceptualize student resistance not as a form of willful disputation, but instead as a function of socialization into cultural models of thought that actively truncate inquiry. In other words, resistance can be construed as the cognitive and emotive dimensions of the ongoing failure of institutions to provide ideas that help individuals both recognize social problems and imagine possible solutions. Focusing on Dewey\u27s epistemological framework, specifically tools for inquiry, provides a way to grasp this problem. It also affords some innovative solutions; for instance, it helps conceive of possible links between the regular curriculum and the study of specific social justice issues, a relationship that is often under-examined. The aims of critical pedagogy depend upon students developing dexterity with the conceptual tools they use to make meaning of the evidence they confront; these are background skills that the regular curriculum can be made to serve even outside social justice-focused curricula. Furthermore, the article concludes that because such inquiry involves the exploration and potential revision of students\u27 world-ordering beliefs, developing flexibility in how one thinks may be better achieved within academic subjects and topics that are not so intimately connected to students\u27 current social lives, especially where students may be directly implicated

Transition from self-supported to supported living: Older people's experiences

To become dependent on professional support to accomplish the daily activities of life can be considered a turning point, involving a range of challenging changes in life. The purpose of the study was to describe the experiences of older home-dwelling individuals in transition from self-supported to supported living from a lifeworld perspective. Five women and five men were interviewed, and a descriptive phenomenological design was used. The findings showed that an attitude of acceptance was an essential characteristic for this group. An attitude of acceptance comprised: flexibility and tolerance, recognition and hopes, and valuation of self and situation. Finding themselves in a situation they had to submit to, they took an attitude of acceptance. An attitude of acceptance implied acknowledgement of the situation as well as positivity and desires to manage. This attitude may represent a significant potential for improvement. Awareness of this is crucial to support older individuals in a healthy way through the transition process. An attitude of acceptance, however, also implied an acceptance of discontinuity in their lives, renunciations, and denigration of own needs. But this aspect of the acceptance was trivialized by the participants and not equally obvious. Insight into this complexity is vital to avoid ignorance of older individuals’ vulnerability in the transition process

Scientific Perspectives, Feminist Standpoints, and Non-silly Relativism

Defences of perspectival realism are motivated, in part, by an attempt to find a middle ground between the realist intuition that science seems to tell us a true story about the world, and the Kuhnian intuition that scientific knowledge is historically and culturally situated. The first intuition pulls us towards a traditional, absolutist scientific picture, and the second towards a relativist one. Thus, perspectival realism can be seen as an attempt to secure situated knowledge without entailing epistemic relativism. A very similar motivation is behind feminist standpoint theory, a view which aims to capture the idea that knowledge is socially situated, whilst retaining some kind of absolutism. Elsewhere I argue that the feminist project fails to achieve this balance; its commitment to situated knowledge unavoidably entails epistemic relativism (though of an unproblematic kind), which allows them to achieve all of their feminist goals. In this paper I will explore whether the same arguments apply to perspectival realism. And so I will be asking whether perspectival realism too is committed to an unproblematic kind of relativism, capable of achieving scientific goals; or, whether it succeeds in carving out a third view, between or beyond the relativism/absolutism dichotomy