Reconciling niche and neutrality: the continuum hypothesis

In this study, we ask if instead of being fundamentally opposed, niche and neutral theories could simply be located at the extremes of a continuum. First, we present a model of recruitment probabilities that combines both niche and neutral processes. From this model, we predict and test whether the relative importance of niche vs. neutral processes in controlling community dynamics will vary depending on community species richness, niche overlap and dispersal capabilities of species (both local and long distance). Results demonstrate that niche and neutrality form ends of a continuum from competitive to stochastic exclusion. In the absence of immigration, competitive exclusion tends to create a regular spacing of niches. However, immigration prevents the establishment of a limiting similarity. The equilibrium community consists of a set of complementary and redundant species, with their abundance determined, respectively, by the distribution of environmental conditions and the amount of immigration.     

Testing neutrality in subdivided populations

Statistical tests of the neutrality hypothesis that are based on the sampling theory of Ewens (1972) require the assumption of panmixia. It is proposed that for a population comprising numerous local populations with weak gene flow among them, tests based on Ewens' theory can be applied separately to samples from each local population. At low levels of gene flow, migration acts primarily like mutation, introducing new alleles to each local population. It is shown with simulation results that, at low levels of migration, correlations in allele frequencies among demes are sufficiently small that the results from the application of Ewens' theory to each deme are statistically independent. It is also shown that, by combining the results of the tests in different demes, some statistical power to detect deviations from neutrality is gained. The method is illustrated with the application to data on a salamander species. At low levels of gene flow, population subdivision must be taken account of in testing neutrality and the proposed test provides one way to do so.     

Testing the geometric clutch hypothesis

The Geometric Clutch hypothesis is based on the premise that transverse forces (t-forces) acting on the outer doublets of the eukaryotic axoneme coordinate the action of the dynein motors to produce flagellar and ciliary beating. T-forces result from tension and compression on the outer doublets when a bend is present on the flagellum or cilium. The t-force acts to pry the doublets apart in an active bend, and push the doublets together when the flagellum is passively bent and thus could engage and disengage the dynein motors. Computed simulations of this working mechanism have reproduced the beating pattern of simple cilia and flagella, and of mammalian sperm. Cilia-like beating, with a clearly defined effective and recovery stroke, can be generated using one uniformly applied switching algorithm. When the mechanical properties and dimensions appropriate to a specific flagellum are incorporated into the model the same algorithm can simulate a sea urchin or bull sperm-like beat. The computed model reproduces many of the observed behaviors of real flagella and cilia. The model can duplicate the results of outer arm extraction experiments in cilia and predicted two types of arrest behavior that were verified experimentally in bull sperm. It also successfully predicted the experimentally determined nexin elasticity. Calculations based on live and reactivated sea urchin and bull sperm yielded a value of 0.5 nN/microm for the t-force at the switch-point. This is a force sufficient to overcome the shearing force generated by all the dyneins on one micron of outer doublet. A t-force of this magnitude should produce substantial distortion of the axoneme at the switch-point, especially in spoke or spoke-head deficient motile flagella. This concrete and verifiable prediction is within the grasp of recent advances in imaging technology, specifically cryoelectron microscopy and atomic force microscopy.     

Testing for neutrality in samples with sequencing errors

Many data sets one could use for population genetics contain artifactual sites, i.e., sequencing errors. Here, we first explore the impact of such errors on several common summary statistics, assuming that sequencing errors are mostly singletons. We thus show that in the presence of those errors, estimators of can be strongly biased. We further show that even with a moderate number of sequencing errors, neutrality tests based on the frequency spectrum reject neutrality. This implies that analyses of data sets with such errors will systematically lead to wrong inferences of evolutionary scenarios. To avoid to these errors, we propose two new estimators of theta that ignore singletons as well as two new tests Y and Y* that can be used to test neutrality despite sequencing errors. All in all, we show that even though singletons are ignored, these new tests show some power to detect deviations from a standard neutral model. We therefore advise the use of these new tests to strengthen conclusions in suspicious data sets.     

Testing the hypothesis of common ancestry

The hypothesis that all life on earth traces back to a single common ancestor is a fundamental postulate in modern evolutionary theory. Yet, despite its widespread acceptance in biology, there has been comparatively little attention to formally testing this "hypothesis of common ancestry". We review and critically examine some arguments that have been proposed in support of this hypothesis. We then describe some theoretical results that suggest the hypothesis may be intrinsically difficult to test. We conclude by suggesting an approach to the problem based on the Aikaike information criterion.     

Testing the covarion hypothesis of molecular evolution

The covarion hypothesis of molecular evolution states that the fixation of mutations may alter the probability that any given position will fix the next change. Tests of this hypothesis using the divergence of real sequences are compromised because models of rate variation among sites (e.g., the gamma version of the one-parameter equation) predict sequence divergence values similar to those for the covarion process. This study therefore focuses on the extent to which the varied and unvaried codons of two well-diverged taxa are the same, because fewer are expected by the covarion hypothesis than by the gamma model. The data for these tests are the protein sequences of Cu, Zn superoxide dismutase (SOD) for mammals and plants. Simulation analyses show that the covarion hypothesis makes better predictions about the frequencies of varied and unhit positions in common between these two taxa than does the gamma version of the one-parameter model. Furthermore, the analysis of SOD tertiary structure demonstrates that mammal and plant variabilities are distributed differently on the protein. These results support the conclusions that the variable and invariable codons of mammal and plant SODs are different and that the covarion model explains the evolution of this protein better than the gamma version of the one-parameter process. Unlike other models, the covarion hypothesis accounts for rate fluctuations among positions over time, which is an important parameter of molecular evolution.      

Testing Darwin's naturalization hypothesis in the Azores

Invasive species are a threat for ecosystems worldwide, especially oceanic islands. Predicting the invasive potential of introduced species remains difficult, and only a few studies have found traits correlated to invasiveness. We produced a molecular phylogenetic dataset and an ecological trait database for the entire Azorean flora and find that the phylogenetic nearest neighbour distance (PNND), a measure of evolutionary relatedness, is significantly correlated with invasiveness. We show that introduced plant species are more likely to become invasive in the absence of closely related species in the native flora of the Azores, verifying Darwin's 'naturalization hypothesis'. In addition, we find that some ecological traits (especially life form and seed size) also have predictive power on invasive success in the Azores. Therefore, we suggest a combination of PNND with ecological trait values as a universal predictor of invasiveness that takes into account characteristics of both introduced species and receiving ecosystem.     

Testing the productive-space hypothesis: rational and power

Understanding and explaining the causes of variation in food-chain length is a fundamental challenge for community ecology. The productive-space hypothesis, which suggests food-chain length is determined by the combination of local resource availability and ecosystem size, is central to this challenge. Two different approaches currently exist for testing the productive-space hypothesis: (1) the dual gradient approach that tests for significant relationships between food-chain length and separate gradients of ecosystem size (e.g., lake volume) and per-unit-size resource availability (e.g., g C m⁻¹ year⁻²), and (2) the single gradient approach that tests for a significant relationship between food-chain length and the productive space (product of ecosystem size and per-unit-size resource availability). Here I evaluate the efficacy of the two approaches for testing the productive-space hypothesis. Using simulated data sets, I estimate the Type 1 and Type 2 error rates for single and dual gradient models in recovering a known relationship between food-chain length and ecosystem size, resource availability, or the combination of ecosystem size and resource ability, as specified by the productive-space hypothesis. The single gradient model provided high power (low Type 2 error rates) but had a very high Type 1 error rate, often erroneously supporting the productive-space hypothesis. The dual gradient model had a very low Type 1 error rate but suffered from low power to detect an effect of per-unit-size resource availability because the range of variation in resource availability is limited. Finally, I performed a retrospective power analysis for the Post et al. (Nature 405:1047–1049, 2000) data set, which tested and rejected the productive-space hypothesis using the dual gradient approach. I found that Post et al. (Nature 405:1047–1049, 2000) had sufficient power to reject the productive-space hypothesis in north temperate lakes; however, the productive-space hypothesis must be tested in other ecosystems before its generality can be fully addressed.     

Testing the depth-differentiation hypothesis in a deepwater octocoral

The depth-differentiation hypothesis proposes that the bathyal region is a source of genetic diversity and an area where there is a high rate of species formation. Genetic differentiation should thus occur over relatively small vertical distances, particularly along the upper continental slope (200–1000 m) where oceanography varies greatly over small differences in depth. To test whether genetic differentiation within deepwater octocorals is greater over vertical rather than geographical distances, Callogorgia delta was targeted. This species commonly occurs throughout the northern Gulf of Mexico at depths ranging from 400 to 900 m. We found significant genetic differentiation (F_ST = 0.042) across seven sites spanning 400 km of distance and 400 m of depth. A pattern of isolation by depth emerged, but geographical distance between sites may further limit gene flow. Water mass boundaries may serve to isolate populations across depth; however, adaptive divergence with depth is also a possible scenario. Microsatellite markers also revealed significant genetic differentiation (F_ST = 0.434) between C. delta and a closely related species, Callogorgia americana, demonstrating the utility of microsatellites in species delimitation of octocorals. Results provided support for the depth-differentiation hypothesis, strengthening the notion that factors covarying with depth serve as isolation mechanisms in deep-sea populations.     

Testing the rate isomorphy hypothesis using five statistical methods

Abstract Organisms are said to be in developmental rate isomorphy when the proportions of developmental stage durations are unaffected by temperature. Comprehensive stage‐specific developmental data were generated on the cabbage beetle, Colaphellus bowringi Baly (Coleoptera: Chrysomelidae), at eight temperatures ranging from 16°C to 30°C (in 2°C increments) and five analytical methods were used to test the rate isomorphy hypothesis, including: (i) direct comparison of lower developmental thresholds with standard errors based on the traditional linear equation describing developmental rate as the linear function of temperature; (ii) analysis of covariance to compare the lower developmental thresholds of different stages based on the Ikemoto‐Takai linear equation; (iii) testing the significance of the slope item in the regression line of versus temperature, where p is the ratio of the developmental duration of a particular developmental stage to the entire pre‐imaginal developmental duration for one insect or mite species; (iv) analysis of variance to test for significant differences between the ratios of developmental stage durations to that of pre‐imaginal development; and (v) checking whether there is an element less than a given level of significance in the p‐value matrix of rotating regression line. The results revealed no significant difference among the lower developmental thresholds or among the aforementioned ratios, and thus convincingly confirmed the rate isomorphy hypothesis.     

Testing specialization hypothesis on a stress gradient

Specialization can allow plants to perform well in their home environments at the expense of poor performance in other habitats. A great difference in performance across habitats is observed as high phenotypic plasticity in performance traits and a by‐product of selection. However, phenotypic plasticity (particularly adaptive plasticity) can be an active response to the selection by allowing the maintenance of performance. Therefore, specialization and adaptive plasticity delineate two opposing strategies. The specialization hypothesis presents a non‐adaptive interpretation of plasticity and predicts that phenotypic plasticity of performance traits is greater in specialization to good habitats, whereas bad habitat specialists express low plasticity in performance traits. We tested the specialization hypothesis using plants adapted to extremely stressful mine‐site habitats (sites with highly acidic soil and heavy metal contamination). Seeds of five herbaceous species were collected from high stress (mine site) and low stress habitats. We established a glasshouse experiment where seedlings from high and low stress habitats were grown under near neutral pH and acid soil treatments. We compared performance trait plasticity (e.g. biomass) from high stress and low stress populations and found that there was no significant difference in performance traits between high and low stress populations across treatments. The overall result did not support the specialization hypothesis. Moreover, our results suggest that the species invaded the mine sites are either extreme generalists or the surrounding populations retain some stress tolerant genotypes that are capable of invading the mine sites.     

Testing the hybrid superiority hypothesis in crested and marbled newts

We tested the hybrid superiority hypothesis in the zone of overlap and hybridization of the newts Triturus cristatus and T. marmoratus. To do so, we compared size, age, and growth-related parameters in F₁ hybrids and both parental species in Mayenne, France. We found significant differences in snout-vent length (SVL), body mass and average lifespan between the parental species and hybrids, increasing from T. cristatus – T. marmoratus – hybrids. The relation between age and SVL fitted von Bertalanffy's growth model and showed that SVL_max was significantly larger in hybrids than in the parental species, while the growth coefficient was lower in hybrids and T. marmoratus than in T. cristatus. Triturus cristatus appears to be the better competitor, since it attains sexual maturity faster and thus achieves more annual breeding opportunities. At the evolutionary level, the observed heterosis appears not to have further consequences as the hybrids are largely infertile. Our results support the hypothesis raised for the genus Triturus, that infertile hybrids allocate resources to growth.     

Testing the enemy release hypothesis: a review and meta-analysis

One of the most cited hypotheses explaining the inordinate success of a small proportion of introduced plants that become pests is the ‘natural enemies hypothesis’. This states that invasive introduced plants spread rapidly because they are liberated from their co-evolved natural enemies. This hypothesis had not been properly tested until recently. Previous reviews on this topic have been narrative and vote counting in nature. In this review, we carried out quantitative synthesis and meta-analysis using existing literature on plants and their herbivores to test the different components of the enemy release hypothesis. We found supporting evidence in that (1) insect herbivore fauna richness is significantly greater in the native than introduced ranges, and the reduction is skewed disproportionally towards specialists and insects feeding on reproductive parts; and (2) herbivore damage levels are greater on native plants than on introduced invasive congeners. However, herbivore damage levels are only marginally greater for plants in native than in introduced ranges, probably due to the small numbers of this type of study. Studies quantifying herbivore impacts on plant population dynamics are too scarce to make conclusions for either comparison of plants in native vs introduced ranges or of co-occurring native and introduced congeners. For future research, we advocate that more than two-way comparisons between plants in native and introduced ranges, or native and introduced congeners are needed. In addition, the use of herbivore exclusions to quantify the impacts of herbivory on complete sets of population vital rates of native vs introduced species are highly desirable. Furthermore, three-way comparisons among congeners of native plants, introduced invasive, and introduced non-invasive plants can also shed light on the importance of enemy release. Finally, simultaneously testing the enemy release hypothesis and other competing hypotheses will provide significant insights into the mechanisms governing the undesirable success of invasive species.     

Anomalies in sedimentation. II. Testing the entanglement hypothesis

Zones of T2 DNA were sedimented through uniform solutions of T7 DNA to determine if the smaller DNA molecules would become entangled in the larger. No entanglement could be demonstrated even at high DNA concentrations. It is suggested that molecular entanglement is not responsible for the sudden loss of DNA from solution which occurs in high centrifugal fields. This communication also includes observations on the effects of rotor speed on the sedimentation behavior of DNA in high centrifugal fields, distortion of zone shape at high concentrations, and hydrodynamic interactions between DNA and MS2 bacteriophage particles.     

Testing the immunocompetence handicap hypothesis: a review of the evidence

The immunocompetence handicap hypothesis was formulated 12 years ago in an attempt to offer a proximate mechanism by which female choice of males could be explained by endocrine control of honest signalling. The hypothesis suggested that testosterone has a dual effect in males of controlling the development of sexual signals while causing immunosuppression. Our purpose in this review is to examine the empirical evidence to date that has attempted to test the hypothesis, and to conduct a meta-analysis on two of the assumptions of the hypothesis, that testosterone reduces immunocompetence and increases parasitism, to ascertain any statistical trend in the data. There is some evidence to suggest that testosterone is responsible for the magnitude of trait expression or development of sexual traits, but this is by no means conclusive. The results of many studies attempting to find evidence for the supposed immunosuppressive qualities of testosterone are difficult to interpret since they are observational rather than experimental. Of the experimental studies, the data obtained are ambiguous, and this is reflected in the result of the meta-analysis. Overall, the meta-analysis found a significant suppressive effect of testosterone on immunity, in support of the hypothesis, but this effect disappeared when we controlled for multiple studies on the same species. There was no effect of testosterone on direct measures of immunity, but it did increase ectoparasite abundance in several studies, in particular in reptiles. A funnel analysis indicated that the results were robust to a publication bias. Alternative substances that interact with testosterone, such as glucocorticoids, may be important. Ultimately, a greater understanding is required of the complex relationships that exist both within and between the endocrine and immune systems and their consequences for mate choice decision making.