PROBLEMS WITH TESTING INBREEDING AVOIDANCE: THE CASE OF THE COLLARED FLYCATCHER

Four year's data on collared flycatchers, Ficedula albicollis, breeding in a nestbox plot on the island of Gotland, Sweden, was used to investigate whether individuals avoid mating with close kin (i.e., parents or sibs). Only one case of close inbreeding (0.5% of all pairs) was observed during the years of study. The observed frequency of close inbreeding was compared to expected frequencies based on two different null models. Assuming no inbreeding avoidance behaviors (e.g., dispersal or kin recognition), but taking into account the fact that mortality, and different arrival and pairing times of individuals reduce the probability of mating with close kin, the expected frequency of close inbreeding is 10% and 15% for female and male recruits (i.e., born in the study plot), respectively. However, assuming mating to be random within the study plot reduced the expected frequency of close inbreeding to 1% or less for both males and females. Consequently, conclusions drawn concerning inbreeding avoidance depend on the null model used. Contrasting estimated costs of tolerating close inbreeding with those of avoiding it (by dispersal to other plots), however, suggests that the costs of avoiding close inbreeding are substantially greater than those of tolerating it. Therefore, although inbreeding avoidance cannot be rejected as a cause of dispersal of this species, it is not the primary cause, and particularly not for sex-biased dispersal. The general problems of investigating inbreeding avoidance are discussed. It is argued that all previous null models based on random mating in finite populations produce expected frequencies of close inbreeding that in fact include inbreeding avoidance, since they implicitly assume random dispersal within a finite population. Thus, comparisons between observed and expected frequencies of close inbreeding based on random mating are inadequate. The most promising method of investigating inbreeding avoidance is to experimentally study individual movements and mating preferences in the presence and absence of close kin.     

Random root movements in weightlessness

The dynamics of root growth was studied in weightlessness. In the absence of the gravitropic reference direction during weightlessness, root movements could be controlled by spontaneous growth processes, without any corrective growth induced by the gravitropic system. If truly random of nature, the bending behavior should follow socalled 'random walk' mathematics during weightlessness. Predictions from this hypothesis were critically tested.
In a Spacelab ESA-experiment, denoted RANDOM and carried out during the IML-2 Shuttle flight in July 1994, the growth of garden cress ( Lepidium sativum ) roots was followed by time lapse photography at 1-h intervals.
The growth pattern was recorded for about 20 h. Root growth was significantly smaller in weightlessness as compared to gravity (control) conditions.
It was found that the roots performed spontaneous movements in weightlessness. The average direction of deviation of the plants consistently stayed equal to zero, despite these spontaneous movements. The average squared deviation increased linearly with time as predicted theoretically (but only for 8–10 h).
Autocorrelation calculations showed that bendings of the roots, as determined from the 1-h photographs, were uncorrelated after about a 2-h interval.
It is concluded that random processes play an important role in root growth. Predictions from a random walk hypothesis as to the growth dynamics could explain parts of the growth patterns recorded. This test of the hypothesis required microgravity conditions as provided for in a space experiment.     

The fecundity patterns of S and L type rotifers of Brachionus plicatilis

Fecundity patterns of S and L type rotifers Brachionus plicatilis, which were previously found to have distinct growth ability, were analyzed using data of age-specific fecundity. The data were obtained by individual cultures of S and L type strains at 17, 24 and 34 °C. The pattern was analyzed by using normal probability functions. When the age was transformed into logarithmic value, the S and L types had an identical pattern of fecundity at every temperature. This fact indicates that the difference of the growth response to the temperature between S and L type strains stemmed only from the differences in net reproduction rate, not from the pattern.     

Early response of herbaceous vegetation to Rhododendron ponticum subsp. baeticum invasion in European Atlantic forests

Questions

Rhododendron ponticum subsp. baeticum is an invasive shrub of growing concern in continental Europe, but little is known about its impact on native plant communities. Here we ask: do environmental conditions differ between forest stands invaded by it and uninvaded stands? Do these differences correlate with R. ponticum's cover? Are these differences associated with differences in taxonomic and functional diversity of vascular plant species of the herb layer? Can these vegetation changes be explained by the sorting of certain life-history traits by R. ponticum-induced environmental changes?

Location

Several forests invaded by R. ponticum in the French Atlantic domain.

Methods

We recorded vegetation composition and a number of environmental variables in 400-m² plots that were established in 64 paired forest stands (32 invaded vs 32 uninvaded). We compiled traits from existing databases. We computed several metrics of taxonomic and functional diversity. We compared environmental variables and diversity metrics between invaded and uninvaded stands. We used correlation and regression analyses to relate them with R. ponticum's cover. We ran RLQ and fourth-corner analyses to explore the relationships between R. ponticum invasion, environmental variables, species traits, and vegetation composition.

Results

Independent of its abundance, R. ponticum invasion was associated with lower light arrival at the forest floor and increased litter thickness. Concomitantly, species richness and diversity and trait diversity were reduced. The major driver of species assemblages was soil pH, which strongly interacted with the invasion gradient. R. ponticum did not sort species according to traits associated with shade tolerance and thick-litter tolerance. However, tree and shrub saplings were more abundant in invaded than uninvaded stands, at the expense of graminoid and fern species.

Conclusions

As R. ponticum becomes the dominant shrub, it exerts new selection forces on life-history traits of extant species, mostly via reduced light availability, increased litter thickness, and physical competition, thereby reducing taxonomic and functional diversity of the herb layer, without impeding tree and shrub self-regeneration, at least in the short term.     

Defining null expectations for animal site fidelity

Site fidelity—the tendency to return to previously visited locations—is widespread across taxa. Returns may be driven by several mechanisms, including memory, habitat selection, or chance; however, pattern-based definitions group different generating mechanisms under the same label of ‘site fidelity’, often assuming memory as the main driver. We propose an operational definition of site fidelity as patterns of return that deviate from a null expectation derived from a memory-free movement model. First, using agent-based simulations, we show that without memory, intrinsic movement characteristics and extrinsic landscape characteristics are key determinants of return patterns and that even random movements may generate substantial probabilities of return. Second, we illustrate how to implement our framework empirically to establish ecologically meaningful, system-specific null expectations for site fidelity. Our approach provides a conceptual and operational framework to test hypotheses on site fidelity across systems and scales.     

Maximal ecological diversity exceeds evolutionary diversity in model ecosystems

Understanding community saturation is fundamental to ecological theory. While investigations of the diversity of evolutionary stable states (ESSs) are widespread, the diversity of communities that have yet to reach an evolutionary endpoint is poorly understood. We use Lotka–Volterra dynamics and trait-based competition to compare the diversity of randomly assembled communities to the diversity of the ESS. We show that, with a large enough founding diversity (whether assembled at once or through sequential invasions), the number of long-time surviving species exceeds that of the ESS. However, the excessive founding diversity required to assemble a saturated community increases rapidly with the dimension of phenotype space. Additionally, traits present in communities resulting from random assembly are more clustered in phenotype space compared to random, although still markedly less ordered than the ESS. By combining theories of random assembly and ESSs we bring a new viewpoint to both the saturation and random assembly literature.     

Individual risk prediction: Comparing random forests with Cox proportional-hazards model by a simulation study

With big data becoming widely available in healthcare, machine learning algorithms such as random forest (RF) that ignores time-to-event information and random survival forest (RSF) that handles right-censored data are used for individual risk prediction alternatively to the Cox proportional hazards (Cox-PH) model. We aimed to systematically compare RF and RSF with Cox-PH. RSF with three split criteria [log-rank (RSF-LR), log-rank score (RSF-LRS), maximally selected rank statistics (RSF-MSR)]; RF, Cox-PH, and Cox-PH with splines (Cox-S) were evaluated through a simulation study based on real data. One hundred eighty scenarios were investigated assuming different associations between the predictors and the outcome (linear/linear and interactions/nonlinear/nonlinear and interactions), training sample sizes (500/1000/5000), censoring rates (50%/75%/93%), hazard functions (increasing/decreasing/constant), and number of predictors (seven, 15 including noise variables). Methods' performance was evaluated with time-dependent area under curve and integrated Brier score. In all scenarios, RF had the worst performance. In scenarios with a low number of events (⩽70), Cox-PH was at least noninferior to RSF, whereas under linearity assumption it outperformed RSF. Under the presence of interactions, RSF performed better than Cox-PH as the number of events increased whereas Cox-S reached at least similar performance with RSF under nonlinear effects. RSF-LRS performed slightly worse than RSF-LR and RSF-MSR when including noise variables and interaction effects. When applied to real data, models incorporating survival time performed better. Although RSF algorithms are a promising alternative to conventional Cox-PH as data complexity increases, they require a higher number of events for training. In time-to-event analysis, algorithms that consider survival time should be used.     

Bayesian tests for random mating in polyploids

Hardy–Weinberg proportions (HWP) are often explored to evaluate the assumption of random mating. However, in autopolyploids, organisms with more than two sets of homologous chromosomes, HWP and random mating are different hypotheses that require different statistical testing approaches. Currently, the only available methods to test for random mating in autopolyploids (i) heavily rely on asymptotic approximations and (ii) assume genotypes are known, ignoring genotype uncertainty. Furthermore, these approaches are all frequentist, and so do not carry the benefits of Bayesian analysis, including ease of interpretability, incorporation of prior information, and consistency under the null. Here, we present Bayesian approaches to test for random mating, bringing the benefits of Bayesian analysis to this problem. Our Bayesian methods also (i) do not rely on asymptotic approximations, being appropriate for small sample sizes, and (ii) optionally account for genotype uncertainty via genotype likelihoods. We validate our methods in simulations and demonstrate on two real datasets how testing for random mating is more useful for detecting genotyping errors than testing for HWP (in a natural population) and testing for Mendelian segregation (in an experimental S1 population). Our methods are implemented in Version 2.0.2 of the hwep R package on the Comprehensive R Archive Network https://cran.r-project.org/package=hwep .     

Homology among RAPD fragments in interspecific comparisons

The use of RAPDs for comparative purposes relies on the assumption that similarity of fragment size is a dependable indicator of homology. To test the validity of this assumption, homology among 220 pairs of comigrating fragments from three wild sunflower species was determined. Ninety-one per cent cross-hybridized and/or displayed congruent restriction fragment profiles suggestive of homology. However, comparative linkage mapping data indicated that 13% of the homologous loci mapped to genomic locations that were incongruent with the majority of loci, suggestive of paralogous rather than orthologous relationships. Thus, of the 220 pairwise comparisons, only 174 (79.1%) identified loci that are useful for comparative genetic studies. These problems, as well as several other factors discussed in the text, will introduce noise into RAPD data sets and thereby reduce the probability of generating accurate estimates of genetic relationships. Recommended methods for reducing noise in RAPD data sets include increasing gel resolution and/or testing fragment homology. However, implementation of these approaches will not eliminate all uncertainties, and it is also recommended that RAPD data sets be tested for structure and reliability.