No evidence of kin bias in dispersion of young‐of‐the‐year Atlantic salmon Salmo salar L. in a natural stream

Ninety‐one young‐of‐the‐year Atlantic salmon Salmo salar were captured using a non‐invasive snorkelling technique in a 38 m section of Catamaran Brook, New Brunswick, Canada, to test whether related fish settle closer to one another than unrelated fish. A maximum likelihood estimate of parentage relationships assessed by genotyping eight microsatellite loci revealed five half‐sibling families in the sample of fish. Related juvenile S. salar were not found closer to one another than unrelated fish in three analyses at two spatial scales: a comparison of the relatedness of focal fish to their nearest neighbour and to their four nearest neighbours, and a correlation of the pair‐wise relatedness and distance matrices for all fish in the sample. The lack of a kin‐biased dispersion pattern may be related to the lower density of fish or the scarcity of full‐siblings at the study site compared to laboratory conditions.     

Influence of social and environmental factors on nesting behaviour in captive gorillas (Gorilla gorilla gorilla)

Field studies on gorilla sleeping sites usually emphasize environmental influences on nest site selection, as individual nesting behaviours are usually not observed directly. In captivity, nesting behaviour and influencing factors are often overlooked. In the present study, the sleeping sites of members of a captive group of 16-21 gorillas were analysed, based on 152 nights over a 5-year period. Subadults tended to sleep apart from adults but clustered around the oldest blackback male. Full siblings and mothers with offspring were often nearest neighbours. Some sleeping dyads notably endured. Neither age of offspring nor rank of adult females influenced neighbour choice or distances; an interadult distance of 1.5-3 m was typical. Group dynamics were reflected in nesting arrangements. We suggest that possibilities for co-nesting and choice of sleeping sites should be provided to improve the welfare of captive gorillas and other great apes.     

An application of canonical correspondence analysis for developing ecological quality assessment metrics for river macrophytes

1. Aquatic macrophyte composition and abundance is required by the European Union's Water Framework Directive for determining ecological status. Five metrics were produced that can be combined to determine the deviation of aquatic macrophytes from reference conditions in Northern Ireland's rivers. 2. Species optima and niche breadths along silt, nitrate, pH, conductivity and dissolved oxygen gradients were generated from aquatic macrophyte and water quality surveys conducted at 273 sites throughout Northern Ireland using Canonical Correspondence Analysis (CCA). Five metric scores based on these environmental gradients were determined at new monitoring sites using the mean optima of the species occurring at the site, weighted by percentage cover and niche breadth of each species. 3. A preliminary reference network of 32 sites of high physico‐chemical and hydromorphological quality, and representative of the range of river types in Northern Ireland, enabled reference metric scores to be produced for each river type. Five unimpacted and twenty impacted sites were used for testing the performance of the metrics. By subtracting reference metric scores from metric scores at a monitoring site measures of ecological impact could be determined along five different impact gradients. Metrics were also combined to give a measure of total ecological change. 4. The metrics system distinguished unimpacted from impacted sites and correctly identified 77% of the known impacts. The metrics distinguished different types of impact, e.g. silt and nitrate. 5. Aquatic macrophyte occurrence and abundance has high natural variability at a site, both temporally and spatially. This method was designed to be sensitive to ecological change whilst reducing noise caused by natural variation.     

Seeking functional homogeneity: A framework for definition and classification of fish assemblage types to support assessment tools on temperate reefs

Due to their important role in the ecosystem and high economic value, there is a need to assess the effect of anthropogenic impacts on marine fish assemblages. However, this can only be achieved if variations due to natural causes are known. Moreover, while most assessment tools rely on functional traits, bottom-up habitat classification frameworks tend to use species composition. The present study proposes an innovative framework to define fish assemblage types through metric pairwise constrained k-means (MPCK-means) clustering of sites based on functional guild categories and univariate metrics, an approach that takes into account within-site variability due to the sampling method and natural causes. This was followed by a label-based ensemble clustering approach, which finds patterns that minimise information loss when integrating clustering results from individual metrics. In order to test the method, fish assemblages on 14 nearshore rocky reefs along the Portuguese coast were sampled. The final typology configuration achieved through ensemble clustering consisted of three assemblage types and maintained an average normalised mutual information of 0.605 with the individual clustering results. Nested PERMANOVA found differences among types and the most variable metrics in the face of natural variation were identified. Ultimately, a k-nearest neighbours classifier is proposed to label new sites, based only on environmental variables that are unlikely to be directly affected by the presence of anthropogenic impacts. Optimal performance for the classification model was achieved with inverse distance-weighted voting of the 4 nearest neighbours with an average classification accuracy of 96.08%.     

Temporal response of stream benthic macroinvertebrate communities to the synergistic effects of anthropogenic acidification and natural drought events

1. We evaluated whether the surprisingly weak biological recovery associated with declines in acid deposition were related to drought‐induced re‐acidification of streams. We used test site analysis (TSA) to characterise temporal changes (1995–2003) in the degree and nature of impairments to stream benthic macroinvertebrate (BMI) communities influenced by acid deposition and drought. 2. The BMI communities in four historically impacted test streams were compared with communities in 30 minimally impacted reference streams. Six multivariate (e.g. ordination axes scores) and four traditional (e.g. % Diptera) summary metrics were used to describe BMI communities. Using all metrics simultaneously (i.e. Mahalanobis or generalised distance), the TSA provided a single probability that a test community was impaired. If a test community was significantly impaired, a further analysis was done to identify the metric(s) important in distinguishing the test community from reference condition. 3. Results of the TSAs indicated that the generalised distances between test communities and the reference condition were inversely related to stream water pH (n = 36). The TSAs also indicated ordination metrics based on BMI abundance were important in distinguishing significantly impaired communities from reference conditions. Temporal trends indicated that there has been short‐term recovery of these BMI communities, but that overall improvements have been hampered by acid or metal toxicity associated with drought‐induced re‐acidification of the streams. 4. Our use of a variety of summary metrics to obtain a single statistical test of significance within the context of the reference‐condition approach provided a simple and unambiguous framework for evaluating the biological condition of test sites.     

Neighbour tolerance,not suppression,provides competitive advantage to non‐native plants

High competitive ability has often been invoked as a key determinant of invasion success and ecological impacts of non‐native plants. Yet our understanding of the strategies that non‐natives use to gain competitive dominance remains limited. Particularly, it remains unknown whether the two non‐mutually exclusive competitive strategies, neighbour suppression and neighbour tolerance, are equally important for the competitive advantage of non‐native plants. Here, we analyse data from 192 peer‐reviewed studies on pairwise plant competition within a Bayesian multilevel meta‐analytic framework and show that non‐native plants outperform their native counterparts due to high tolerance of competition, as opposed to strong suppressive ability. Competitive tolerance ability of non‐native plants was driven by neighbour's origin and was expressed in response to a heterospecific native but not heterospecific non‐native neighbour. In contrast to natives, non‐native species were not more suppressed by hetero‐ vs. conspecific neighbours, which was partially due to higher intensity of intraspecific competition among non‐natives. Heterogeneity in the data was primarily associated with methodological differences among studies and not with phylogenetic relatedness among species. Altogether, our synthesis demonstrates that non‐native plants are competitively distinct from native plants and challenges the common notion that neighbour suppression is the primary strategy for plant invasion success.     

Developing a Benthic Index of Biological Integrity and Some Relationships to Environmental Factors in the Subtropical Xiangxi River,China

The aim of this study is to develop a benthic index of biotic integrity (B‐IBI) to help understand how the increasing anthropogenic pressure may impact the subtropical Xiangxi River in China. Benthic macroinvertebrate and environmental surveys were conducted at 77 sites in early summer 2004. Each collection site was categorized as reference or impaired based on physical, chemical, biological, and land‐use information. Six non‐redundant metrics from 35 metrics were used to differentiate between reference and impaired sites. We selected six metrics for the final IBI. The scoring criteria of each metric were normalized based on the quadrisection and 0–10 scaling systems. Both scaling methods were used to assess the aquatic health of each site in the Xiangxi River watershed. The results showed that most sites were in fairly poor condition. Furthermore, we identified the relationship between B‐IBI metrics, water‐quality, and land‐use variables with a principal component analysis. A composite of nutrients and land‐use intensity explained most variances. These results suggest that the B‐IBI may be a suitable method for assessing river conditions within the subtropical Xiangxi River in central China (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Enhancing the performance and interpretation of freshwater biological indices: An application in arid zone streams

We assessed the performance of biological indices developed for invertebrate assemblages occurring in arid zone streams: a multimetric index (MMI) and an O/E index of taxonomic completeness. Our overall goal was to advance our understanding of the factors that affect performance and interpretation of biological indices. Our specific objectives were to (1) develop biological indices that are insensitive to natural environmental gradients, (2) develop a general method to determine if the biological potential of an assessed site is adequately represented by the population of reference sites, (3) develop a robust method to select metrics for inclusion in MMIs that ensures maximum independence of metrics, and (4) determine if a fundamental sample property (the evenness of taxa counts within a sample) affects index performance. Random Forest modeling revealed that both individual metrics and taxa composition were strongly associated with natural environmental heterogeneity, which meant both the MMI and O/E index needed to be based on site-specific expectations. We produced a precise, responsive, and ecologically robust MMI by using principal components analysis to identify 7 statistically independent metrics from a list of 31 candidate assemblage-level metrics. However, the O/E index we developed was relatively imprecise compared with O/E indices developed for other regions. This imprecision may be the consequence of low predictability in local taxa composition associated with the relatively high spatial isolation of aquatic habitats within arid regions. We were also able to assess the likelihood that the biological potential of assessed sites were adequately characterized by the population of reference sites by developing and applying a multivariate, nearest-neighbor test that determined if an assessed site occurred within the environmental space of the reference site network. This approach is robust and applicable to all biological indices. We also demonstrate that the evenness of taxa counts within a sample is positively related to estimates of sample taxa richness and thus the scores of both indices. The relationship between richness and sample evenness can potentially compromise inferences regarding biological condition, and post hoc adjustments for the effects of evenness on index scores might be desirable. Further improvements in the performance and interpretation of biological indices will require simultaneous consideration of the effects of incomplete sampling on characterization of biological assemblages and the physical and biological factors that influence community assembly.     

Inclusive fitness,asymmetric competition and kin selection in plants

The findings that some plants alter their competitive phenotype in response to genetic relatedness of its conspecific neighbour (and presumed competitor) has spurred an increasing interest in plant kin‐interactions. This phenotypic response suggests the ability to assess the genetic relatedness of conspecific competitors, proposing kin selection as a process that can influence plant competitive interactions. Kin selection can favour restrained competitive growth towards kin, if the fitness loss from reducing own growth is compensated by increased fitness in the related neighbour. This may lead to positive frequency dependency among related conspecifics with important ecological consequences for species assemblage and coexistence. However, kin selection in plants is still controversial. First, many studies documenting a plastic response to neighbour relatedness do not estimate fitness consequences of the individual that responds, and when estimated, fitness of individuals grown in competition with kin did not necessarily exceed that of individuals grown in non‐kin groups. Although higher fitness in kin groups could be consistent with kin selection, this could also arise from mechanisms like asymmetric competition in the non‐kin groups. Here we outline the main challenges for studying kin selection in plants taking genetic variation for competitive ability into account. We emphasize the need to measure inclusive fitness in order to assess whether kin selection occurs, and show under which circumstances kin selected responses can be expected. We also illustrate why direct fitness estimates of a focal plant, and group fitness estimates are not suitable for documenting kin selection. Importantly, natural selection occurs at the individual level and it is the inclusive fitness of an individual plant – not the mean fitness of the group – that can capture if a differential response to neighbour relatedness is favoured by kin selection.     

Nearest-neighbour interactions in species-rich shrublands: the roles of abundance, spatial patterns and resources

We explored pairwise nearest‐neighbour interactions in four species‐rich shrubland plant communities, asking the question: how often is an individual of species j the nearest‐neighbour of species i? In the observed data and null models, less than 35% of the maximum possible number of nearest‐neighbour species pairs was present, and at three of the four sites the number of observed nearest‐neighbour pairs were significantly less than those occurring in simulated null communities. Many of the missing pairs included woody shrubs whose absence might be interpreted as evidence of site‐specific competition between larger growth forms for soil resources or space. Less than 5% of the pairs of species that occurred did so at frequencies different from that expected under random mixing, and many of these pairs were conspecific. Of the heterospecific pairs whose frequency differed significantly from random mixing there was a weak bias towards pairs occurring at higher rather than lower frequencies than expected. There was no evidence for asymmetry (interaction of species j with species i but not the reverse) in the frequency of species pairs. Nearest‐neighbour relationships are species‐specific rather than between plant functional types. The four sites form a soil nutrient and water availability gradient, and, according to the stress gradient hypothesis, positive species interactions should be most prevalent at the most stressful sites. However, we found the opposite: the site with the highest availability of resources had both proportionally the most heterospecific pairs, and the most conspecific and heterospecific species pairs with frequencies departing significantly from that expected under random mixing.     

Gene dispersal and outbreeding in a philopatric mammal

Extensive mark-recapture data from banner-tailed kangaroo rats, Dipodomys spectabilis, have shown that both males and females are highly philopatric and suggest the possibility of close inbreeding. However, indirect analyses based on genetic structure appear to contradict direct observations, suggesting longer dispersal distances. Using microsatellite genotypes from most members of a banner-tailed kangaroo rat population during five successive breeding seasons, we ask how relatedness is influenced by dispersal and how it in turn influences mating patterns. The data confirm that, because of philopatry, neighbours are often close relatives. However, patterns of parentage also show that the average distance between mates is large relative to natal dispersal distances and larger than the average distance between nearest opposite-sexed neighbours. Females' mates were often not their nearest male neighbour and many were less related than the nearest male neighbour. We detected multiple paternity in some females' litters; both sexes produce offspring with multiple mates within and between breeding seasons. At the population level, heterozygosities were high and estimates of F were low, indicating that levels of inbreeding were low. Using individual inbreeding coefficients of all juveniles to estimate their parents' relatedness, we found that parental relatedness was significantly lower than relatedness between nearest opposite-sexed adult neighbours. Thus in philopatric populations, long breeding forays can cause genes to move further than individuals disperse, and polyandry may serve to reduce relatedness between mates.     

Phylogenetic community structure metrics and null models: a review with new methods and software

Competitive exclusion and habitat filtering influence community assembly, but ecologists and evolutionary biologists have not reached consensus on how to quantify patterns that would reveal the action of these processes. Currently, at least 22 α‐diversity and 10 β‐diversity metrics of community phylogenetic structure can be combined with nine null models (eight for β‐diversity metrics), providing 278 potentially distinct approaches to test for phylogenetic clustering and overdispersion. Selecting the appropriate approach for a study is daunting. First, we describe similarities among metrics and null models across variance in phylogeny size and shape, species abundance, and species richness. Second, we develop spatially explicit, individual‐based simulations of neutral, competitive exclusion, or habitat filtering community assembly, and quantify the performance (type I and II error rates) of all 278 metric and null model combinations against each assembly process. Many α‐diversity metrics and null models are at least functionally equivalent, reducing the number of truly unique metrics to 12 and the number of unique metric + null model combinations to 72. An even smaller subset of metric and null model combinations showed robust statistical performance. For α‐diversity metrics, phylogenetic diversity and mean nearest taxon distance were best able to detect habitat filtering, while mean pairwise phylogenetic distance‐based metrics were best able to detect competitive exclusion. Overall, β‐diversity metrics tended to have greater power to detect habitat filtering and competitive exclusion than α‐diversity metrics, but had higher type 1 error in some cases. Across both α‐ and β‐diversity metrics, null model selection affected type I error rates more than metric selection. A null model that maintained species richness, and approximately maintained species occurrence frequency and abundance across sites, exhibited low type I and II error rates. This regional null model simulates neutral dispersal of individuals into local communities by sampling from a regional species pool. We introduce a flexible new R package, metricTester, to facilitate robust analyses of method performance.     

The Role of Neighbours Selection on Cohesion and Order of Swarms

We introduce a multi-agent model for exploring how selection of neighbours determines some aspects of order and cohesion in swarms. The model algorithm states that every agents'' motion seeks for an optimal distance from the nearest topological neighbour encompassed in a limited attention field. Despite the great simplicity of the implementation, varying the amplitude of the attention landscape, swarms pass from cohesive and regular structures towards fragmented and irregular configurations. Interestingly, this movement rule is an ideal candidate for implementing the selfish herd hypothesis which explains aggregation of alarmed group of social animals.     

Herbarium records identify the role of long‐distance spread in the spatial distribution of alien plants in New Zealand

Aim To use herbarium records to characterize important correlates of spatial spread, areal occupancy and clustering of 100 alien plant species of conservation concern in the North and South Islands of New Zealand. Location New Zealand. Methods Using herbarium data of 6294 records representing 100 alien plant species, we assessed spatial heterogeneity in the distribution of alien species by examining the role of major urban areas as sources of sampling bias. A novel method to account for spatial biases in sampling effort was developed and applied to two simple distance metrics: nearest‐ and furthest‐neighbour spread rate. The relative importance of these two distance metrics in determining the range, areal extent and dispersion of alien species across both the North and South Islands of New Zealand was also assessed. Results The spatial distribution of herbarium records was highly clustered with a significant bias towards the more populated regions. Once sampling bias was taken into account, there was no indication that species were found closer to these urban centres than might be expected based on sampling effort. The nearest‐neighbour spread rates were usually 1–5 km yr^?1 and correlated positively with the furthest‐neighbour spread rates that were an order of magnitude higher. Range and area increased and clustering decreased with higher spread rates and longer recording time span. The spread rates divided species into five groups that were clearly distinguishable in terms of the extent of their distribution and the degree of clustering. Species occurring on both islands did not exhibit similar spread rates or spatial patterns. Main conclusions The nearest‐ and furthest‐neighbour spread rates from herbarium records can explain the area and pattern of alien plant distributions and improve the understanding of the dynamics of their spread. Five groups emerge from the spread rates in relation to a null model. Fast‐spreading plants had the widest, least clustered distribution, which suggests widespread chronic problems; slow‐spreading plants had localized, but dense, clustered distributions, indicating acutely problematic weeds. These patterns appear robust and may be useful in predicting the future patterns of spread and in planning long‐term management strategies in New Zealand.     

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.     

Genetic variation in tolerance of competition and neighbour suppression in Arabidopsis thaliana

Intraspecific competitive interactions can profoundly influence phenotypic evolution. However, prior studies have rarely evaluated the evolutionary potential of the two components of competitive ability, tolerance of competition and suppression of neighbours. Here, we grow a set of 20 Arabidopsis thaliana recombinant inbred lines in three competitive treatments (noncompetitive, intra‐genotypic competition and inter‐genotypic competition) to examine if there is genetic variation for the components of competitive ability and whether neighbour relatedness has an effect on fitness. We find evidence for genetic variation in tolerance of competition and neighbour suppression and that these two competitive strategies are correlated, such that genotypes that tolerate competition will also strongly suppress neighbours. We further observe that the effect of neighbour relatedness on fitness of target individuals depends on neighbour identity, i.e. whether target individuals perform better when competing against self vs. nonself individuals depends on the genotypic identity of the nonself neighbour. The results are particularly relevant to evolutionary responses under multi‐level selection.     

Risk taking by singing males

The distance at which an individual flees from a potential predatorrepresents a measure of risk taking. If individuals are engagedin another activity that might affect fitness, trade-offs betweenthe fitness benefits of flight and the other activity shoulddetermine the nearest distance of approach by a predator. Ina comparative analysis of birds, flight distance representeda reliable measure of risk of predation by the sparrowhawk Accipiternisus that increased with decreasing flight distance acrossspecies. To test the hypothesis that singing males adjustedtheir risk taking to the costs and benefits of early flight,we compared the flight distance of singing and nonsinging birdsto an approaching human observing with a binocular. Singingbirds on average fled at a greater distance than nonsingingbirds, implying that singing birds took small risks. We useda standardized measure of difference in flight distance betweensinging and nonsinging individuals to investigate factors affectinginterspecific variation in risk taking. Species that used moreexposed song posts (sites used for singing) took smaller risksthan species with less exposed song posts. Species that sufferedfrom higher levels of parasitism as reflected by the prevalenceof Plasmodium, but not by 3 other genera of blood parasites,took greater risks during singing compared with nonsinging activities.Likewise, species with high circulating levels of natural antibodies,and hence a history of natural selection caused by bacteriatook relatively greater risks during singing than species withfew natural antibodies. These findings suggest that risks takenby singing birds have been molded by natural and sexual selection,and that risk taking represents a compromise between the costsand benefits of flight from a potential predator.     

The three-dimensional structure of schools in the minnow, Phoxinus phoxinus (L.)

A photographic technique is described for determining the three-dimensional position of fish schooling in front of a mirror in a flow tank. School structure is discussed in terms of the distance, horizontal bearing, and elevation of nearest neighbours. Nearest neighbour distances were measured snout-to-snout. A technique of analysis is described which considers the probability distribution of nearest neighbours in space. At speeds of flow 0 to 0·125 metres per second it was possible to show that Phoxinus, a facultative schooler, tended to maintain a school structure as previously reported for obligate schooling species. The structure was present only in a dynamic statistical sense and not in the sense of a rigid crystal lattice. Minnows maintained themselves at approximately 0·9 of their body length from each other under normal conditions and the bearings of neighbour fish suggested an attempt to maintain an optimum packing at this distance. At high speeds of flow the school structure tended to break up as fish sought areas of refuge from the current. All minnow schools were ellipsoidal in shape. The strategic and tactical methods by which schooling fish derive anti-predator advantage are discussed in relation to the school structure.     

Social cohesion in groups of sheep: Effect of activity level, sex composition and group size

We investigated the effects of activity, group size and sex composition on the cohesion of merino sheep (Ovis aries) groups. Mixed-sex (50% of each sex) and single-sex groups of 2, 4, 6 and 8 sheep were placed within 491-m² arenas located in natural pastures and were video recorded during 6 daily hours. The behaviour, orientation and location of each sheep were then extracted from the films at 1-s intervals. We analysed the polarisation of individual orientations, mean inter-individual and nearest neighbours’ distances, as well as the frequency of pairs of nearest neighbours according to their sex within mixed-sex groups. Sheep were more aggregated than predicted under the null hypothesis of random spatial distribution for all group compositions and sizes. Sheep were more spread out and less aligned in half-active than in all-active groups, showing that social cohesion was reduced by a lack of activity synchronisation. The highest proximity between individuals was found in resting groups, yet alignment was low. The polarisation peaked in all-active groups. Mean inter-individual distance did not vary and the nearest neighbour distance decreased as group size increased. When sheep were all-active or all-resting, mixed-sex groups were more spread out than single-sex ones, with a greater distance between opposite than between same-sex individuals. Nearest neighbours of the same sex were also more frequent than random. Our results show that social cohesion can be modulated by activity synchrony but also by social affinity.