Are comparisons of species distribution models biased? Are they biologically meaningful?

A major problem in ecology is to understand how environmental requirements change over space and time. To this end, numerous authors have attempted to use comparisons of species’ distributions as a surrogate for comparisons of environmental requirements. Unfortunately, it is currently unclear when comparisons of species’ distributions produce reliable inferences about changes in environmental requirements. To address this problem, I develop an analytic model that identifies the conditions under which a comparison of species’ distribution models can serve as surrogate for a comparison of environmental requirements. This work demonstrates that 1) comparisons of species’ distributions typically produce biased comparisons of environmental requirements, 2) assuming distribution models are fit appropriately, it is possible to compare environmental requirements of distinct taxa, 3) there are multiple biologically relevant questions we can address using comparisons of distribution models, with each question corresponding to a distinct measure of the difference between distribution models. By developing an analytic model for comparisons of species’ distributions this work helps to clarify and remedy poorly understood sources of error associated with existing methods.     

Bias? What bias? The evolution of downstream larval‐feeding in animals

The homology of larval-feeding modes has been a major element in recent discussions about animal phylogeny. 'Downstream-feeding' is one of the two main larval-feeding modes, and is usually equated to an opposed-band system involving ciliary bands called the prototroch and metatroch. Larval-feeding in Spiralia is reviewed here and the homology hypothesis of downstream larval-feeding is expanded, encompassing any feeding involving the prototroch. It is often argued that the presence of planktotrophic larvae using downstream-feeding is plesiomorphic among spiralian animals, and that there is a bias in transformations, such that feeding larvae tend to be lost rather than gained. These hypotheses are assessed in relation to the Spiralia, Trochozoa and particularly polychaete annelids. Cladistic parsimony analyses are performed based on datasets of Rouse & Fauchald (1997) and Rouse (1999) , with an additional character based on downstream larval-feeding. Methods adopted to assess the possibility of a bias in transformations towards loss of downstream larval-feeding include: expanded primary homology arguments, character transformations favouring reversals and polymorphic terminals coded as having downstream larval-feeding. These measures all tend to favour the possibility that downstream larval-feeding will be plesiomorphic, and tends to be lost rather than gained. Nevertheless, all analyses show that downstream larval-feeding is not plesiomorphic, and appears to have evolved multiple times. The results support a conclusion that the prototroch has become associated with feeding a number of times. Hypotheses of metazoan phylogeny that are predicated on the assumption that downstream-feeding larvae are plesiomorphic (e.g. Peterson et al . 1997 ) should be re-assessed.     

Are splicing mutations the most frequent cause of hereditary disease?

Disease-causing point mutations are assumed to act predominantly through subsequent individual changes in the amino acid sequence that impair the normal function of proteins. However, point mutations can have a more dramatic effect by altering the splicing pattern of the gene. Here, we describe an approach to estimate the overall importance of splicing mutations. This approach takes into account the complete set of genes known to be involved in disease and suggest that, contrary to current assumptions, many mutations causing disease may actually be affecting the splicing pattern of the genes.     

Are there physiological and biochemical adaptations of metabolism in deep-sea animals?

From the earliest observations of deep-sea animals, it was obvious that they differed in many ways from shallower-living relatives. Over the years, there has been speculation that deep-sea animals have unusually low rates of biological activity; numerous adaptive scenarios explaining this have ben offered. However, these speculations and scenarios have rarely been tested due to the difficulty of data collection and the inevitable confounding of a number of major variables which covary with depth. In recent years, study of the metabolic properties of animals of several phyla from widely differing deep-sea habitats, including the hydrthermal vents, has made it possible, using comparative approaches, to test hypotheses concerning the metabolic adaptations of deep-sea animals.     

Band reporting rates of waterfowl: does individual heterogeneity bias estimated survival rates?

In capture–recapture studies, the estimation accuracy of demographic parameters is essential to the efficacy of management of hunted animal populations. Dead recovery models based upon the reporting of rings or bands are often used for estimating survival of waterfowl and other harvested species. However, distance from the ringing site or condition of the bird may introduce substantial individual heterogeneity in the conditional band reporting rates (r), which could cause bias in estimated survival rates (S) or suggest nonexistent individual heterogeneity in S. To explore these hypotheses, we ran two sets of simulations (n = 1000) in MARK using Seber''s dead recovery model, allowing time variation on both S and r. This included a series of heterogeneity models, allowing substantial variation on logit(r), and control models with no heterogeneity. We conducted simulations using two different values of S: S = 0.60, which would be typical of dabbling ducks such as mallards (Anas platyrhynchos), and S = 0.80, which would be more typical of sea ducks or geese. We chose a mean reporting rate on the logit scale of −1.9459 with SD = 1.5 for the heterogeneity models (producing a back-transformed mean of 0.196 with SD = 0.196, median = 0.125) and a constant reporting rate for the control models of 0.196. Within these sets of simulations, estimation models where σ_S = 0 and σ_S > 0 (σ_S is SD of individual survival rates on the logit scale) were incorporated to investigate whether real heterogeneity in r would induce apparent individual heterogeneity in S. Models where σ_S = 0 were selected approximately 91% of the time over models where σ_S > 0. Simulation results showed < 0.05% relative bias in estimating survival rates except for models estimating σ_S > 0 when true S = 0.8, where relative bias was a modest 0.5%. These results indicate that considerable variation in reporting rates does not cause major bias in estimated survival rates of waterfowl, further highlighting the robust nature of dead recovery models that are being used for the management of harvested species.     

Bias in vegetation databases? A comparison of stratified‐random and preferential sampling

Aim: Vegetation plots collected since the early 20th century and stored in large vegetation databases are an important source of ecological information. These databases are used for analyses of vegetation diversity and estimation of vegetation parameters, however such analyses can be biased due to preferential sampling of the original data. In contrast, modern vegetation survey increasingly uses stratified‐random instead of preferential sampling. To explore how these two sampling schemes affect vegetation analyses, we compare parameters of vegetation diversity based on preferentially sampled plots from a large vegetation database with those based on stratified‐random sampling. Location: Moravian Karst and Silesia, Czech Republic. Methods: We compared two parallel analyses of forest vegetation, one based on preferentially sampled plots taken from a national vegetation database and the other on plots sampled in the field according to a stratified‐random design. We repeated this comparison for two different regions in the Czech Republic. We focussed on vegetation properties commonly analysed using data from large vegetation databases, including alpha (within‐plot) diversity, cover and participation of different species groups, such as endangered and alien species within plots, total species richness of data sets, beta diversity and ordination patterns. Results: The preferentially sampled data sets obtained from the database contained more endangered species and had higher beta diversity, whereas estimates of alpha diversity and representation of alien species were not consistently different between preferentially and stratified‐randomly sampled data sets. In ordinations, plots from the preferential samples tended to be more common at margins of plot scatters. Conclusions: Vegetation data stored in large databases are influenced by researcher subjectivity in plot positioning, but we demonstrated that not all of their properties necessarily differ from data sets obtained by stratified‐random sampling. This indicates the value of vegetation databases for use in biodiversity studies; however, some analyses based on these databases are clearly biased and their results must be interpreted with caution.     

Age differences in blue tit Parus caeruleus plumage colour: within‐individual changes or colour‐biased survival?

In many species of passerine birds yearlings display a less elaborate version of the adult secondary sexual traits, but the causes of such differences in ornamentation are not always well understood. We studied age-related changes in blue tit Parus caeruleus UV/blue structural crown coloration, a sexually selected trait. In our Austrian study population, older blue tits, irrespective of sex, displayed on average a more ultraviolet (lower hue, higher UV chroma), more chromatic and brighter crown coloration than yearlings. This age dichromatism was caused by within-individual changes in the expression of crown coloration between years since males and females became more UV, more chromatic and brighter as they aged. Colour biased survival did not contribute to the observed pattern of age dichromatism since crown coloration was largely unrelated to overwinter survival. Between-year repeatability of crown colour was significant for most colour variables but low in general, and lower for females than for males. In the blue tit, yearling males might benefit from being less ornamented by avoiding adult aggression but at the expense of sexual attractiveness. Adaptive explanations of blue tit age dichromatism should however take into account that age effects were of similar magnitude in males and females. This suggests that both male and female yearlings could benefit from being less ornamented and hence that sexual selection might be acting on both sexes simultaneously in this species.     

Are there genetically controlled habitat-specific differences in spatial aggregation of drosophilids?

Variation in spatial patterns of competing organisms is of fundamental importance for community and population processes. Yet the mechanisms controlling subjects like the degree of spatial aggregation in competing insect larvae across fragmented resources have rarely been addressed. In the present study, we tested for systematic differences in the spatial distribution patterns of Drosophila subobscura in natural fly communities, and found significant differences in two habitats that differ in the availability of breeding substrate types (decaying fruits). Assuming that the spatial egg-laying behaviour of drosophilids is under genetic control, and that different breeding substrates mediate different density-dependent larval fitness consequences, we tested whether adaptive genotypic variability is involved in the local variation of egg distribution patterns. We extracted isofemale lines from both habitats and analysed the spatial distribution of eggs achieved by single female flies under controlled laboratory conditions. This is a reasonable first test, because spatial patterns at the fly population level can be attributed to individual egg-laying behaviour. The degree of individual egg aggregation significantly depended on fly line identity, which indicates the existence of behavioural variants in natural populations. Based on habitat-dependent differences in the degree of spatial aggregation, we discuss to what extent our findings may reflect a behavioural adaptation to local breeding conditions.     

The current state of GMO governance: Are we ready for GM animals?

Given the history of GMO conflict and debate, the GM animal future is dependent on the response of the regulatory landscape and its associated range of interest groups at national, regional and international levels. Focusing on the EU and the USA, this article examines the likely form of that multi-level response, the increased role of cultural values, the contribution of new and existing interest groups and the consequent implications for the commercialization of both green and red GM animal biotechnology.     

Does random blood glucose sampling outdate testing for glycosuria in the detection of diabetes during pregnancy?

A random blood glucose concentration was determined in 2403 pregnant women attending an antenatal clinic at between 28 and 32 weeks'' gestation. The calculated 99% cut off values were 6.1 mmol/l (110 mg/100 ml) within two hours after a meal and 5.6 mmol/l (101 mg/100 ml) more than two hours after a meal. Patients with a blood glucose concentration in excess of these values were referred for a 75 g oral glucose tolerance test. Of 59 referred, four were found to have previously unsuspected but unequivocal diabetes mellitus and another four to have impaired glucose tolerance on the basis of the World Health Organisation''s criteria. Screening all antenatal patients by randomly measuring blood glucose concentrations is not only cheap and efficient but also does not interfere with the routine of busy antenatal clinics.     

Are sweep net sampling and pitfall trapping compatible with molecular analysis of predation?

Molecular analysis of predation enables accurate and reliable elucidation of trophic linkages in complex food webs, but identifying the strength of such interactions can be subject to error. Currently two techniques dominate: monoclonal antibody-based enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR). Although the optimization and characterization of these systems ensures their sensitivity and specificity, predator collection protocols such as sweep-netting and vacuum sampling could overestimate feeding rates because of surface-level contamination, yielding positive reactivity or predation within the sampling device. Therefore, two sampling techniques (sweep-net sampling and hand collection) were compared within an alfalfa agroecosystem using a monoclonal antibody-based ELISA to test the hypothesis that cross-contamination is a source of error, i.e., significantly more predators (linyphiid spiders) would test positive for prey (Diptera) proteins. A concurrent study examining the viability of trapping predators into saline solution was also undertaken. No significant differences were found between the proportions of spiders screening positive for Diptera when collected by sweep-net versus hand collection, rejecting the hypothesis that sweep-netting predators for subsequent molecular gut content analysis overestimates predation frequency. ELISA was also capable of detecting prey proteins in predator guts from pitfall traps containing phosphate-buffered saline, indicating the suitability of this approach for the collection and analysis of epigeal predators. Although these results indicate that sweep netting and pitfall trapping into solution is appropriate in this predator-prey and ELISA analysis system, caution should be exercised with other interactions and PCR-based analysis. The likelihood for false-positive reactivity should therefore be considered on a case-by-case basis.     

Are genetic differences in foraging behaviour of laying hen chicks paralleled by hybrid-specific differences in feather pecking?

Feather pecking is a behavioural disorder in laying hens which consists of pecking the feathers of conspecifics, causing feather damage or even injuries to the skin. Its development can be explained by redirection of foraging behaviour. While the occurrence of feather pecking strongly depends on the kind of housing condition, it is also known that there are strain differences in the tendency to feather peck. From the inverse relation between feather pecking and foraging behaviour found earlier, we hypothesised that genetically determined differences in foraging behaviour could be responsible for the observed differences in feather pecking between strains.In a first experiment we tested whether there are differences in the foraging behaviour of two hybrids. As hybrids, we used Lohman selected leghorn (LSL) and Dekalb; eight groups of 20 1-day old chicks each. They were kept in enriched pens (265cmx90cm) with a litter area (200cmx90cm) consisting of wood-shavings, chaff, straw, polystyrene blocks, sand area (65cmx90cm) and elevated perches. Behavioural observations were carried out in week 4. In a subsequent experiment with the same birds we tested how the foraging behaviour of the two hybrids differed when housing conditions were changed from enriched to restricted and to what extent they developed feather pecking. A 2x2 factorial design with hybrid (LSL, Dekalb) and housing condition (restricted, enriched) as factors and with four replicates of each factor combination was used. Half of the pens of each hybrid were changed from enriched to restricted housing conditions by covering the litter area with slats. Behavioural observations were carried out in weeks 5 and 6.In experiment 1, LSL and Dekalb spent the same amount of time foraging, but Dekalb spent significantly more of that time with pecking and hacking at the polystyrene blocks. On the other hand, LSL spent significantly more time at the feeding troughs and rested significantly less than Dekalb. In the restricted environment of experiment 2, again, the total foraging time did not differ between hybrids, but LSL chicks spent significantly less time scratching, while Dekalb spent significantly more time moving. Both hybrids developed feather pecking but LSL showed significantly higher rates than Dekalb.Our results demonstrate genetic differences in the foraging behaviour and in the way hybrids cope with the change in housing condition from enriched to an environment that is restricted in relation to foraging possibilities. We conclude that the results support the hypothesis put forward that genetic differences in foraging behaviour could be the basis for the genetic influence in the development of feather pecking.     

Are age differences in sleep due to phase differences in the output of the circadian timing system?

Our aim was to evaluate whether age-related changes in the phase of the output of the circadian timing system (CTS) can explain age differences in habitual bedtime/wake time and in sleep consolidation parameters. Analyses focused on a group of healthy elderly people (older than 70 years) with no sleep problems and with similar subjective sleep quality as a young control group. The 2-week sleep diary data and 24h laboratory temperature recordings were examined for 70 subjects (22 young men [YM], 19 old men [OM], 29 old women [OW]). Polysomnographic (PSG) sleep data recorded during temperature data acquisition were also available for 62 subjects. These analyses made use of our recently developed technique to demask temperature rhythm data. As expected, compared to the young subjects, older subjects showed earlier habitual bedtime and wake time, more disturbed sleep, and a tendency for an earlier minimum of the circadian temperature rhythm. Despite sleep consolidation differences, the groups showed very similar habitual phase-angle differences (interval between the time occurrence of the fitted temperature minimum and habitual wake time). Both elderly and young subjects woke up on average 3h after the temperature minimum. After controlling for the effects of age group, habitual bedtime and wake time were related to clock time phase of the circadian temperature rhythm, with an earlier phase associated with earlier habitual bedtime and wake time. None of the sleep consolidation parameters were linked to the temperature phase angle. In conclusion, sleep consolidation changes associated with healthy aging do not appear to be related to changes in the phase-angle difference between the output signal from the CTS and sleep.     

Are there age-related differences in the song repertoire size of Eurasian blackbirds?

Most oscine bird species possess a repertoire of different song patterns, and repertoire size is thought to signal aspects of male quality. As age is assumed to be related to male quality in terms of experience and/or viability, repertoire size may be expected to reflect male age. Here, we investigated the relationship between repertoire size and age (yearlings or older) in Eurasian blackbirds, Turdus merula, a species with a large repertoire delivered in a highly variable manner. We found that older males tended to have larger repertoires than yearlings though the two age groups overlapped considerably. Thus, compared to other species with large repertoires, age-related differences in repertoire size seem rather small in male Eurasian blackbirds. We also compared repertoires of three individuals in two successive years (as yearlings and in the year following) and found a large element turnover. Our investigation revealed that this turnover was almost complete in the quiet terminating twitter part of the song. Such turnover may allow a young bird to adjust his repertoire to his neighbours?? repertoires, which could be useful for song matching interactions.     

Are most of the domoic acid-producing species of the diatom genus Pseudo-nitzschia cosmopolites?

Records from all oceans, most of them published during 1990–2000, and personal unpublished observations of nine Pseudo-nitzschia taxa known as potential domoic acid (DA) producers have been used to outline their geographical distribution. Pseudo-nitzschia seriata f. seriata as the only taxon was found in the North Atlantic Ocean exclusively. The records of P. multistriata were too few and the identification of P. turgidula from the North Atlantic too unreliable to provide an idea about their distribution. Pseudo-nitzschia pungens and the less frequently recorded P. fraudulenta, P. multiseries and P. australis appeared to be cosmopolites. The wide distribution of the apparently most efficient DA producers, P. australis and P. multiseries, is especially noteworthy. The records of P. delicatissima and P. pseudodelicatissima also indicate a cosmopolitan distribution although with the qualification of certain taxonomic and identification ambiguities. Hence, the question of whether most DA-producing Pseudo-nitzschia species are cosmopolites may be answered with a tentative “yes”.     

Are Ichthyosporea animals or fungi? Bayesian phylogenetic analysis of elongation factor 1alpha of Ichthyophonus irregularis

Ichthyosporea is a recently recognized group of morphologically simple eukaryotes, many of which cause disease in aquatic organisms. Ribosomal RNA sequence analyses place Ichthyosporea near the divergence of the animal and fungal lineages, but do not allow resolution of its exact phylogenetic position. Some of the best evidence for a specific grouping of animals and fungi (Opisthokonta) has come from elongation factor 1alpha, not only phylogenetic analysis of sequences but also the presence or absence of short insertions and deletions. We sequenced the EF-1alpha gene from the ichthyosporean parasite Ichthyophonus irregularis and determined its phylogenetic position using neighbor-joining, parsimony and Bayesian methods. We also sequenced EF-1alpha genes from four chytrids to provide broader representation within fungi. Sequence analyses and the presence of a characteristic 12 amino acid insertion strongly indicate that I. irregularis is a member of Opisthokonta, but do not resolve whether I. irregularis is a specific relative of animals or of fungi. However, the EF-1alpha of I. irregularis exhibits a two amino acid deletion heretofore reported only among fungi.     

Are the antiarrhythmic-defibrillating effects of D-sotalol due to or despite the prolongation of the action potential duration?

These results support our hypothesis that class III compounds, with a positive inotropic effect, increase intercellular coupling and synchronization, mainly by preventing intracellular Ca overload. They act as defibrillating compound, similar to cAMP and adrenaline, most probably due to their so called sympathomimetic effect. In our opinion, their cardioprotective effects, resembling cardioversion, are not related to their ability to prolong APD and ERP. Moreover, we suggest that any compound that possesses these sympathomimetic effects, but without inducing the arrhythmogenic prolongation of APD, may exhibit a potent, safety and more efficient antiarrhythmic - defibrillating ability.     

The Index of Biological Integrity and the bootstrap: Can random sampling error affect stream impairment decisions?

Multimetric indices, such as the Index of Biological Integrity (IBI), are increasingly used by management agencies to determine whether surface water quality is impaired. However, important questions about the variability of these indices have not been thoroughly addressed in the scientific literature. In this study, we used a bootstrap approach to quantify variability associated with fish IBIs developed for streams in two Minnesota river basins. We further placed this variability into a management context by comparing it to impairment thresholds currently used in water quality determinations for Minnesota streams. We found that 95% confidence intervals ranged as high as 40 points for IBIs scored on a 0–100 point scale. However, on average, 90% of IBI scores calculated from bootstrap replicate samples for a given stream site yielded the same impairment status as the original IBI score. We suggest that sampling variability in IBI scores is related to both the number of fish and the number of rare taxa in a field collection. A comparison of the effects of different scoring methods on IBI variability indicates that a continuous scoring method may reduce the amount of bias in IBI scores.     

Reference Valence Effects of Affective S–R Compatibility: Are Visual and Auditory Results Consistent?

Humans may be faster to avoid negative words than to approach negative words, and faster to approach positive words than to avoid positive words. That is an example of affective stimulus–response (S–R) compatibility. The present study identified the reference valence effects of affective stimulus–response (S–R) compatibility when auditory stimulus materials are used. The researchers explored the reference valence effects of affective S–R compatibility using a mixed-design experiment based on visual words, visual pictures and audition. The study computed the average compatibility effect size. A t-test based on visual pictures showed that the compatibility effect size was significantly different from zero, t (22) = 2.43, p<.05 (M = 485 ms). Smaller compatibility effects existed when switching the presentation mode from visual stimuli to auditory stimuli. This study serves as an important reference for the auditory reference valence effects of affective S–R compatibility.     

Hox transcriptional specificity despite a single class of cofactors: Are flexible interaction modes the key?

Editor's suggested further reading in BioEssays ftz Evolution: Findings, hypotheses and speculations (response to DOI 10.1002/bies.201100019 ) Abstract On the border of the homeotic function: Re‐evaluating the controversial role of cofactor‐recruiting motifs Abstract Control of DNA replication: A new facet of Hox proteins? Abstract Classification of sequence signatures: a guide to Hox protein function Abstract