Pattern detection in null model analysis

Synthesis The identification of distinctive patterns in species x site presence‐absence matrices is important for understanding meta‐community organisation. We compared the performance of a suite of null models and metrics that have been proposed to measure patterns of segregation, aggregation, nestedness, coherence, and species turnover. We found that any matrix with segregated species pairs can be re‐ordered to highlight aggregated pairs, indicating that these seemingly opposite patterns are closely related. Recently proposed classification schemes failed to correctly classify realistic matrices that included multiple co‐occurrence structures. We propose using a combination of metrics and decomposing matrix‐wide patterns into those of individual pairs of species and sites to pinpoint sources of non‐randomness. Null model analysis has been a popular tool for detecting pattern in binary presence–absence matrices, and previous tests have identified algorithms and metrics that have good statistical properties. However, the behavior of different metrics is often correlated, making it difficult to distinguish different patterns. We compared the performance of a suite of null models and metrics that have been proposed to measure patterns of segregation, aggregation, nestedness, coherence, and species turnover. We found that any matrix with segregated species pairs can be re‐ordered to highlight aggregated pairs. As a consequence, the same null model can identify a single matrix as being simultaneously aggregated, segregated or nested. These results cast doubt on previous conclusions of matrix‐wide species segregation based on the C‐score and the fixed‐fixed algorithm. Similarly, we found that recently proposed classification schemes based on patterns of coherence, nestedness, and segregation and aggregation cannot be uniquely distinguished using proposed metrics and null model algorithms. It may be necessary to use a combination of different metrics and to decompose matrix‐wide patterns into those of individual pairs of species or pairs of sites to pinpoint the sources of non‐randomness.     

Statistical challenges in null model analysis

This review identifies several important challenges in null model testing in ecology: 1) developing randomization algorithms that generate appropriate patterns for a specified null hypothesis; these randomization algorithms stake out a middle ground between formal Pearson–Neyman tests (which require a fully‐specified null distribution) and specific process‐based models (which require parameter values that cannot be easily and independently estimated); 2) developing metrics that specify a particular pattern in a matrix, but ideally exclude other, related patterns; 3) avoiding classification schemes based on idealized matrix patterns that may prove to be inconsistent or contradictory when tested with empirical matrices that do not have the idealized pattern; 4) testing the performance of proposed null models and metrics with artificial test matrices that contain specified levels of pattern and randomness; 5) moving beyond simple presence–absence matrices to incorporate species‐level traits (such as abundance) and site‐level traits (such as habitat suitability) into null model analysis; 6) creating null models that perform well with many sites, many species pairs, and varying degrees of spatial autocorrelation in species occurrence data. In spite of these challenges, the development and application of null models has continued to provide valuable insights in ecology, evolution, and biogeography for over 80 years.     

Aggregative structure is the rule in communities of fleas: null model analysis

We used null models to examine patterns of species co‐occurrences in 59 communities of fleas parasitic on small mammals from 4 biogeographic realms (Afrotropics, Nearctic, Neotropics, and Palaearctic). We compared frequencies of co‐occurrences of flea species across host species with those expected by chance, using a null model approach. We used 4 tests for non‐randomness to identify pairs of species (within a community) that demonstrate significant positive or negative co‐occurrence. The majority of flea communities were non‐randomly assembled. Patterns of flea co‐occurrences on the same host species indicated aggregation but not segregation of flea species (except for the flea community of Madagascar). Although only a small fraction of species pairs were associated significantly (264 of 10, 943 species pairs according to the most liberal criterion), most of these associations were positive (except for 2 negatively associated species pairs). Significantly associated pairs were represented mainly by non‐congeneric species. The degree of non‐randomness of the entire flea community was similar among biogeographic regions, but the strength of pair‐wise association varied geographically, being the highest in the Afrotropics and the lowest in the European region of the Palaearctic.     

Assessing feeding electivity in Acanthaster planci: a null model analysis

Feeding electivity was investigated in a non-outbreaking population of the crown-of-thorns starfish Acanthaster planci (L.) from North Sulawesi, Indonesia. A null model-based approach was used to assess the feeding pattern of Acanthaster in relation to the availability of coral prey in the field. Of a total of 70 species of corals recorded as prey, massive species, particularly of Faviidae, tended to be more frequently consumed than would be expected under the assumption of random feeding by A. planci. Branched and encrusting/laminar forms of corals that occurred in relatively exposed sites were apparently not preferred, pointing to the importance of non-acroporan massive species of corals in cryptic habitats as prey for A. planci. The null model-based electivity index Z introduced here directly measured the deviation from random feeding, while two common indices (Ivlev’s and Vanderploeg and Scavia’s) only partially reflected such deviations (hence, prey selection cannot be accurately demonstrated by these). Electivity values (Z) for poritid species and Acropora palifera, the most common Acropora species in the study site, were significantly negative, indicating apparent avoidance of them by Acanthaster. Our results indicate that accessibility to different coral species and the choice/avoidance of certain species are the important elements of feeding in non-outbreaking populations of Acanthaster inhabiting spatially variable reef environments. A similar consideration may apply to the feeding patterns of other corallivores that possess superior/inferior mobility to Acanthaster. The present study emphasizes the merit of testing the observed patterns, using null models for a rigorous assessment of feeding preferences.     

Evaluating thermoregulation in reptiles: an appropriate null model

Established indexes of thermoregulation in ectotherms compare body temperatures of real animals with a null distribution of operative temperatures from a physical or mathematical model with the same size, shape, and color as the actual animal but without mass. These indexes, however, do not account for thermal inertia or the effects of inertia when animals move through thermally heterogeneous environments. Some recent models have incorporated body mass, to account for thermal inertia and the physiological control of warming and cooling rates seen in most reptiles, and other models have incorporated movement through the environment, but none includes all pertinent variables explaining body temperature. We present a new technique for calculating the distribution of body temperatures available to ectotherms that have thermal inertia, random movements, and different rates of warming and cooling. The approach uses a biophysical model of heat exchange in ectotherms and a model of random interaction with thermal environments over the course of a day to create a null distribution of body temperatures that can be used with conventional thermoregulation indexes. This new technique provides an unbiased method for evaluating thermoregulation in large ectotherms that store heat while moving through complex environments, but it can also generate null models for ectotherms of all sizes.     

Microsatellite null alleles in parentage analysis

Highly polymorphic microsatellite markers are widely employed in population genetic analyses (eg, of biological parentage and mating systems), but one potential drawback is the presence of null alleles that fail to amplify to detected levels in the PCR assays. Here we examine 233 published articles in which authors reported the suspected presence of one or more microsatellite null alleles, and we review how these purported nulls were detected and handled in the data analyses. We also employ computer simulations and analytical treatments to determine how microsatellite null alleles might impact molecular parentage analyses. The results indicate that whereas null alleles in frequencies typically reported in the literature introduce rather inconsequential biases on average exclusion probabilities, they can introduce substantial errors into empirical assessments of specific mating events by leading to high frequencies of false parentage exclusions.     

Partial and full agonism in endomorphin derivatives: comparison by null and operational model

The partial mu-opioid receptor pool inactivation strategy in isolated mouse vas deferens was used to determine partial agonism of endomorphins and their analogs (endomorphin-1-ol, 2',6'-dimethyltyrosine (Dmt)-endomorphin-1, endomorphin-2-ol and (D-Met2)-endomorphin-2) using morphine, normorphine, morphiceptin, (D-Ala2,MePhe4,Gly5-ol)-enkephalin (DAMGO) and its amide (DAMGA) as reference opioid agonists. Agonist affinities (KA) and efficacies were assessed both by the "null" and the "operational" method. The KA values determined by the two methods correlated significantly with each other and also with the displacing potencies against 3H-naloxone in the receptor binding assay in the presence of Na+. DAMGO and DAMGA were full agonist prototypes, morphine, endomorphin-1, endomorphin-1-ol, Dmt-endomorphin-1, endomorphin-2-ol and (D-Met2)-endomorphin-2 were found by both methods to be partial agonists whereas the parameters for normorphine, morphiceptin and endomorphin-2 were intermediate.     

Brain death and brain life: rethinking the connection

The connection between brain life and brain death is neither as simple nor as defensible as it might at first appear. The problem rests with the two dominant competing definitions of death:...the loss of that which is necessary for the organism to continue to function as a whole;....the loss of that which is essentially significant to the nature of the organism... If death is understood as the loss of that which is necessary for the continued functioning of the organism as whole, then the apparent symmetry breaks down. If...death could be understood as the loss of that which is essentially significant to the nature of the organism....consciousness, then the symmetry would hold. However, that definition of death is indefensible. Therefore...statements about the status of anencephalic infants and early human embryos based upon a connection between brain death and brain life are unfounded.     

Behavioral drive versus behavioral inertia in evolution: a null model approach

Some biologists embrace the classical view that changes in behavior inevitably initiate or drive evolutionary changes in other traits, yet others note that behavior sometimes inhibits evolutionary changes. Here we develop a null model that quantifies the impact of regulatory behaviors (specifically, thermoregulatory behaviors) on body temperature and on performance of ectotherms. We apply the model to data on a lizard (Anolis cristatellus) and show that thermoregulatory behaviors likely inhibit selection for evolutionary shifts in thermal physiology with altitude. Because behavioral adjustments are commonly used by ectotherms to regulate physiological performance, regulatory behaviors should generally constrain rather than drive evolution, a phenomenon we call the "Bogert effect." We briefly review a few other examples that contradict the classical view of behavior as the inevitable driving force in evolution. Overall, our analysis and brief review challenge the classical view that behavior is invariably the driving force in evolution, and instead our work supports the alternative view that behavior has diverse--and sometimes conflicting--effects on the directions and rates at which other traits evolve.     

Force and compliance: rethinking morphogenesis in walled cells

In the turgid cells of plants, protists, fungi, and bacteria, walls resist swelling; they also confer shape on the cell. These two functions are not unrelated: cell physiologists have generally agreed that morphogenesis turns on the deformation of existing wall and the deposition of new wall, while turgor pressure produces the work of expansion. In 1990, I summed up consensus in a phrase: "localized compliance with the global force of turgor pressure." My purpose here is to survey the impact of recent discoveries on the traditional conceptual framework. Topics include the recognition of a cytoskeleton in bacteria; the tide of information and insight about budding in yeast; the role of the Spitzenk?rper in hyphal extension; calcium ions and actin dynamics in shaping a tip; and the interplay of protons, expansins and cellulose fibrils in cells of higher plants.     

An efficient null model for conformational fluctuations in proteins

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Highlights? TYPHON explores a protein's conformational space under given nonlocal restraints ? TYPHON's advanced probabilistic models ensure protein-like local structure ? TYPHON can reproduce a range of experimental results ? TYPHON's computational efficiency makes large scale screening efforts possible     

AGRA: analysis of gene ranking algorithms

Often, the most informative genes have to be selected from different gene sets and several computer gene ranking algorithms have been developed to cope with the problem. To help researchers decide which algorithm to use, we developed the analysis of gene ranking algorithms (AGRA) system that offers a novel technique for comparing ranked lists of genes. The most important feature of AGRA is that no previous knowledge of gene ranking algorithms is needed for their comparison. Using the text mining system finding-associated concepts with text analysis. AGRA defines what we call biomedical concept space (BCS) for each gene list and offers a comparison of the gene lists in six different BCS categories. The uploaded gene lists can be compared using two different methods. In the first method, the overlap between each pair of two gene lists of BCSs is calculated. The second method offers a text field where a specific biomedical concept can be entered. AGRA searches for this concept in each gene lists' BCS, highlights the rank of the concept and offers a visual representation of concepts ranked above and below it. AVAILABILITY AND IMPLEMENTATION: Available at http://agra.fzv.uni-mb.si/, implemented in Java and running on the Glassfish server. CONTACT: simon.kocbek@uni-mb.si.     

Measuring potential fertility through null segments: An exploratory analysis

Abstract

Procedures are presented for estimating from null segments the natural fecundability of couples who may be practicing contraception. The procedures include an assessment of bias. Also presented is a new measure designed to bring out the implications for residual fertility of the pregnancy outcome probabilities and fecundability functions recorded for given five‐year age classes of respondents. Application is made to two Taiwan samples featuring segment coded data.     

Measuring potential fertility through null segments: an exploratory analysis

The demographic effectiveness of a family planning program must measure the difference between actual fertility and the "gross" potential fertility, i.e., the natural fertility which would have been achieved without use of contraception. The various methods of measuring "gross" fertility which have been used are described. It is understood that users of contraception are never a random sampling of the general population; they tend to be higher in fecundability and lower in proportion of sterile. For this reason, the best strategm of measurement involves utilization of preacceptance fertility rates over some given period of time among those reporting no contraceptive usage during that period. A procedure of measurement is proposed whereby natural fecundability is estimated from null segments. Possible biases are taken into account. Application of the method is made to 2 sets of data collected in Taiwan. Results of the application of the method to the Taiwanese data are tabulated. Fecundability functions derived from unrestricted null segments are different from those constructed from restricted subsets of "closed" null segments. Choice of whether to use restricted or unrestricted null segments will depend on the nature of the data available.     

Phylogeny can make the mid-domain effect an inappropriate null model

The mid-domain effect (MDE), a bias in species richness towards the midpoint of a given geographical dimension, has been used as a null model in macro-ecological studies. Departures from a MDE are often thought of as interesting. The MDE is a product of the interaction between geometric boundaries and range locations, with species being forced to occupy more central positions in proportion to their range size. We criticize this mechanism for assuming species' locations to be wholly independent from their evolutionary past. We present a simple simulation model that shows how range locations arising as part of a phylogenetic process depart from a MDE. The amount of departure is positively correlated with phylogenetic imbalance (tree shape), but a deviation from an equal-rates Markov speciation model is not necessary to negate a MDE. We suggest that the MDE is an appropriate ecological null model only when phylogenetic influence on range location is demonstrably low or non-existent.     

On nestedness analyses: rethinking matrix temperature and anti-nestedness

The analysis of nested structures in sets of species assemblages across different sites or in networks of interspecific interactions has become common practice in ecological studies. Although new analyses and metrics have been proposed, few studies have scrutinized the concepts that subtend nestedness analysis. We note two important conceptual problems that can lead to terminological inconsistencies and flawed interpretations. First, the thermodynamic analogy that underlies the most common metric of nestedness, matrix temperature, is flawed and has led some authors to incorrect interpretations. Second, the term anti-nestedness is a potential source of confusion and inconsistencies. We review four concepts for anti-nestedness and examine how distinct they are. Anti-nested matrices, i.e. less nested than expected by chance, may result from different ecological processes and show distinct structural patterns. Thus, there is no single unequivocal opposite of nestedness to be represented as anti-nestedness. A more profitable approach is to designate and test each distinct non-nested pattern according to its specific assumptions and mechanistic hypotheses.     

Evolutionary medicine at twenty: rethinking adaptationism and disease

Two decades ago, the eminent evolutionary biologist George C. Williams and his physician coauthor, Randolph Nesse, formulated the evolutionary medicine research program. Williams and Nesse explicitly made adaptationism a core component of the new program, which has served to undermine the program ever since, distorting its practitioners’ perceptions of evidentiary burdens and in extreme cases has served to warp practitioner’s understandings of the relationship between evolutionary benefits/detriments and medical ones. I show that the Williams and Nesse program more particularly embraces the panselectionist variety of adaptationism (the empirical assumption that non-adaptive evolutionary processes are causally unimportant compared to natural selection), and argue that this has harmed the field. Panselectionism serves to conceal the enormous evidentiary hurdles that evolutionary medicine hypotheses face, making them appear stronger than they are. I use two examples of evolutionary medicine texts, on neonatal jaundice and on asthma, to show that some evolutionary medicine practitioners have allowed their fervent panselectionism to directly shape their recommendations for clinical practice. I argue that this escalation of panselectionism’s influence is inappropriate under Williams’ and Nesse original stated standards, despite being inspired by their program. I also show that the examples’ conflation of clinical and evolutionary considerations is inappropriate even under Christopher Boorse’s controversial evolution-rooted concepts of disease and health.