Biological Reviews

Freshwater biodiversity is the over‐riding conservation priority during the International Decade for Action ‐‘Water for Life’ ‐ 2005 to 2015. Fresh water makes up only 0.01% of the World's water and approximately 0.8 % of the Earth's surface, yet this tiny fraction of global water supports at least 100 000 species out of approximately 1.8 million ‐ almost 6% of all described species. Inland waters and freshwater biodiversity constitute a valuable natural resource, in economic, cultural, aesthetic, scientific and educational terms. Their conservation and management are critical to the interests of all humans, nations and governments. Yet this precious heritage is in crisis. Fresh waters are experiencing declines in biodiversity far greater than those in the most affected terrestrial ecosystems, and if trends in human demands for water remain unaltered and species losses continue at current rates, the opportunity to conserve much of the remaining biodiversity in fresh water will vanish before the ‘Water for Life’ decade ends in 2015. Why is this so, and what is being done about it? This article explores the special features of freshwater habitats and the biodiversity they support that makes them especially vulnerable to human activities. We document threats to global freshwater biodiversity under five headings: overexploitation; water pollution; flow modification; destruction or degradation of habitat; and invasion by exotic species. Their combined and interacting influences have resulted in population declines and range reduction of freshwater biodiversity worldwide. Conservation of biodiversity is complicated by the landscape position of rivers and wetlands as ‘receivers’ of land‐use effluents, and the problems posed by endemism and thus non‐substitutability. In addition, in many parts of the world, fresh water is subject to severe competition among multiple human stakeholders. Protection of freshwater biodiversity is perhaps the ultimate conservation challenge because it is influenced by the upstream drainage network, the surrounding land, the riparian zone, and ‐ in the case of migrating aquatic fauna ‐ downstream reaches. Such prerequisites are hardly ever met. Immediate action is needed where opportunities exist to set aside intact lake and river ecosystems within large protected areas. For most of the global land surface, trade‐offs between conservation of freshwater biodiversity and human use of ecosystem goods and services are necessary. We advocate continuing attempts to check species loss but, in many situations, urge adoption of a compromise position of management for biodiversity conservation, ecosystem functioning and resilience, and human livelihoods in order to provide a viable long‐term basis for freshwater conservation. Recognition of this need will require adoption of a new paradigm for biodiversity protection and freshwater ecosystem management ‐ one that has been appropriately termed ‘reconciliation ecology’.

Null hypothesis significance testing (NHST) is the dominant statistical approach in biology, although it has many, frequently unappreciated, problems. Most importantly, NHST does not provide us with two crucial pieces of information: (1) the magnitude of an effect of interest, and (2) the precision of the estimate of the magnitude of that effect. All biologists should be ultimately interested in biological importance, which may be assessed using the magnitude of an effect, but not its statistical significance. Therefore, we advocate presentation of measures of the magnitude of effects (i.e. effect size statistics) and their confidence intervals (CIs) in all biological journals. Combined use of an effect size and its CIs enables one to assess the relationships within data more effectively than the use ofpvalues, regardless of statistical significance. In addition, routine presentation of effect sizes will encourage researchers to view their results in the context of previous research and facilitate the incorporation of results into future meta‐analysis, which has been increasingly used as the standard method of quantitative review in biology. In this article, we extensively discuss two dimensionless (and thus standardised) classes of effect size statistics:dstatistics (standardised mean difference) andrstatistics (correlation coefficient), because these can be calculated from almost all study designs and also because their calculations are essential for meta‐analysis. However, our focus on these standardised effect size statistics does not mean unstandardised effect size statistics (e.g. mean difference and regression coefficient) are less important. We provide potential solutions for four main technical problems researchers may encounter when calculating effect size and CIs: (1) when covariates exist, (2) when bias in estimating effect size is possible, (3) when data have non‐normal error structure and/or variances, and (4) when data are non‐independent. Although interpretations of effect sizes are often difficult, we provide some pointers to help researchers. This paper serves both as a beginner’s instruction manual and a stimulus for changing statistical practice for the better in the biological sciences.

Temperament describes the idea that individual behavioural differences are repeatable over time and across situations. This common phenomenon covers numerous traits, such as aggressiveness, avoidance of novelty, willingness to take risks, exploration, and sociality. The study of temperament is central to animal psychology, behavioural genetics, pharmacology, and animal husbandry, but relatively few studies have examined the ecology and evolution of temperament traits. This situation is surprising, given that temperament is likely to exert an important influence on many aspects of animal ecology and evolution, and that individual variation in temperament appears to be pervasive amongst animal species. Possible explanations for this neglect of temperament include a perceived irrelevance, an insufficient understanding of the link between temperament traits and fitness, and a lack of coherence in terminology with similar traits often given different names, or different traits given the same name. We propose that temperament can and should be studied within an evolutionary ecology framework and provide a terminology that could be used as a working tool for ecological studies of temperament. Our terminology includes five major temperament trait categories: shyness‐boldness, exploration‐avoidance, activity, sociability and aggressiveness. This terminology does not make inferences regarding underlying dispositions or psychological processes, which may have restrained ecologists and evolutionary biologists from working on these traits. We present extensive literature reviews that demonstrate that temperament traits are heritable, and linked to fitness and to several other traits of importance to ecology and evolution. Furthermore, we describe ecologically relevant measurement methods and point to several ecological and evolutionary topics that would benefit from considering temperament, such as phenotypic plasticity, conservation biology, population sampling, and invasion biology.

1. In analysing the ecological conditions of an animal population we have above all to focus our attention upon the most sensitive stages within the life cycle of the animal, that is, the period of breeding and larval development.

2. Most animal populations on the sea bottom maintain the qualitatively composition of the species composing them, over long periods of time, though the individual species use quite different modes of reproduction and development. This shows that species producing a large number of eggs have a larger wastage of eggs and larvae than those with only a few eggs. The wastage of eggs in the sea is much larger than on the land and in fresh water.

3. In the invertebrate populations on the level sea bottom, large fluctuations in numbers from year to year indicate species with a long pelagic larval life, while a more or less constant occurrence indicates species with a very short pelagic life or a non‐pelagic development.

4. In most marine invertebrates which shed their eggs and sperm freely in the water, either (a) the males are the first to spawn, thus stimulating the females to shed their eggs, or (b) an ‘epidemic spawning’ of a whole population takes place within a few hours. Both methods greatly favour the possibility of fertilization of the eggs spawned and show that the heavy wastage of eggs and larvae takes place after fertilization, during the free swimming pelagic life.

5. Embryos with a non‐pelagic development may originate (a) from large yolky eggs, in which case all the hatching young of the same species will be at the same stage of development, or (b) from small eggs which during their development feed on nurse eggs, when the individual embryos of the same species may vary enormously in size at the stage of hatching.

6. Three types of pelagic larvae are known: (a) Lecithotrophic larvae, originating from large yolky eggs spawned in small numbers by the individual mother animals; they are independent of the plankton as a source of food although growing during pelagic life, are absent from high arctic seas but constitute about 1^o% of the species with pelagic larvae in all other seas, (b) The planktotrophic larvae with a long pelagic life, originating from small eggs spawned in huge numbers by the individual mother animal; they feed from, and grow in, the plankton, constituting less than 5% of high arctic bottom invertebrates, 55–65% of the species in boreal seas, and 8^o‐85 % of the tropical species, (c) The planktotrophic larvae with a short pelagic life having the same size and organization at the moment of hatching and at the moment of settling; these constitute about 5% of the species in all Recent seas.

7. To find out the factors which cause the enormous waste of eggs and larvae, we thus have to study those forms (constituting 7^o% of all species of bottom invertebrates in Recent seas) which have a long planktotrophic pelagic life, as only species reproducing in this way have really large numbers of eggs.

8. The food requirements of the planktotrophic pelagic larvae are much greater than those of the adult animals at the bottom. The adaptability of the larvae to poor food conditions seems, nevertheless, to be greater than hitherto believed. The significance of starvation seems mainly to be an indirect one: poor food conditions cause slow growth, prolong larval life, and give the enemies a longer interval of time to attack and eat the larvae.

9. At the temperatures to which they are normally exposed, northern as well as tropical larvae seem on an average to spend a similar time (about 3 weeks) in the plankton. The length of the pelagic life of the individual species may, however, vary significantly in nature. In the Sound (Denmark) the larvae are never exposed to temperatures outside the range which they are able to endure. The wastage caused by temperature, like that due to starvation, seems mainly to be an indirect one: low temperatures postpone growth and metamorphosis, and give the enemies a longer time to feed on the larvae.

1^o. When a larva feeding on a pure algal diet metamorphoses into a carnivorous bottom stage, a ‘physiological revolution’ occurs and a huge waste of larvae might be expected. Experiments have, however, shown that this is not the case.

11. Young pelagic larvae are photopositive and crowd near the surface; larvae about to metamorphose are photonegative. Larval polychaetes, echinoderms, and presumably also prosobranchs, may prolong their pelagic life for days or weeks until they find a suitable substratum. Forced towards the bottom by their photonegativity and transported by currents over wide bottom areas, testing the substratum at intervals, their chance of finding a suitable place for settling is much better than hitherto believed.

12. Continuous currents from the continental shelf towards the open ocean may transport larvae from the coast to the deep sea where they will perish. Such conditions may (for instance in the Gulf of Guinea) deeply influence the composition of the fauna, while in other areas (European western coast, southern California) they seem to be only of small significance.

13. The toll levied by enemies appears to be the most essential source of waste among the larvae. A list of such enemies, comprising other pelagic larvae, holoplank‐tonic animals and bottom animals, is given on p. 2^o. A medium‐sized Mytilus edulis, filtering 1–4 1. of water per hour, may retain and kill about 100,000 pelagic lamellibranch larvae in 24 hr. during the maximum breeding season in a Danish fjord.

14. Species reproducing in a vegetative way, by fission, laceration, budding, etc., might be expected to have good chances of competition in such areas where conditions for sexual reproduction are unfavourable. Nevertheless, they only supply a rather small percentage of the animal populations of all Recent seas, probably because their intensity of reproduction is low and because they are unable to spread to new areas. Most forms reproducing in a vegetative way have sexual reproduction as well.

15. Pelagic development is nearly or totally suspended in the deep sea, and is restricted to the shelf faunas. In the arctic and antarctic seas pelagic development is nearly or totally suppressed, even in the shelf faunas, but starting from here the percentage of forms with pelagic larvae gradually increases as we pass into warmer water, reaching its summit on the tropic shelves.

16. In order to survive in high arctic areas a planktotrophic, pelagic larva has to complete its development from hatching to metamorphosis within I–I ½ months (i.e. the period during which phytoplankton production takes place) at a temperature below 2–4^o C. Most larvae, that is in 95% of the species, are unable to do so and have a non‐pelagic development, but if a pelagic larva is able to develop under these severe conditions the planktotrophic pelagic life seems to afford good opportunities even in the Arctic. Thus the 5 % of arctic invertebrates reproducing in this way comprise several of the species which quantitatively are most common within the area.

17. The antarctic shore fauna has poor conditions similar to those of the Arctic. The longest continuous periods of phytoplankton production are 2 and 3 weeks respectively, and pelagic larvae have, in order to survive, to complete their development within this short space of time at a temperature between 1 and 4^o C. Accordingly, non‐pelagic development is the rule, but most arctic species are able to support their non‐pelagic development by means of much smaller eggs than the antarctic species, where brood protection and viviparity is dominant. The antarctic fauna has apparently had a longer time to develop its tendency to abandon a pelagic life. The greater the size of the individual born, the smaller its relative food requirements and the better its chance of competing under poor food conditions.

18. The relatively few data on reproduction in deep sea invertebrates point to a non‐pelagic development. The larvae of such forms, in order to develop through a planktotrophic pelagic stage, would have to rise by the aid of their own locomotory organs through a water column 2000–4000 m. high or more (often with counteracting currents) to the food producing surface layer, and to cover the same distance when descending to metamorphose and settle.

19. The ecological features common to the deep sea, the arctic and the antarctic seas, which enable the same animals to live and to reproduce there, contribute to explain the ‘equatorial submergence’ of many arctic and antarctic coastal forms.

20. In the tropical coastal zones where the percentage of species with pelagic larvae reaches its maximum, the production of food for the larvae takes place much more continuously than in temperate and arctic seas, because light conditions enable the phytoplankton to assimilate all the year round. The tropical species of marine invertebrates breed (in contrast to temperate and arctic species) within such different seasons that their larval stock, taken as a whole, is more or less equally distributed in the plankton all the year round. This makes the competition in the plankton less keen.

21. The fact that a mode of reproduction and development, well fit for an arctic area, is unfit in a temperate or tropical area of the sea is probably one of the main reasons for the restricted distribution of species.

22. In most groups of marine invertebrates the individual species have only one mode of reproduction and development, which accordingly restricts their area of distribution. In the polychaetes, however, the individual species often show an astonishing lability in their mode of reproduction and development which enables them to compete in wide areas of the sea. Thus, out of the Western European species of polychaetes, 28‐4% have been found also in the Indian Ocean, and 18%, at least, along the Californian coast, while the corresponding number of Western European echinoderms, prosobranchs and lamellibranchs found also in the Indian Ocean and California amounts to less than 2%.

23. The pelagic or non‐pelagic development of marine prosobranchs has proved to be a very fine ‘barometer’ for ecological conditions. Recent observations, still not elaborated, seem to indicate that the shape of the top whorls, the apex, of the adult shells of prosobranchs may show whether the species in question has a pelagic or a non‐pelagic development. This discovery may also give us valuable information about the larval development in fossil species, and help us to form an idea about ecological conditions in sea areas from earlier geological periods.

Repeatability (more precisely the common measure of repeatability, the intra‐class correlation coefficient, ICC) is an important index for quantifying the accuracy of measurements and the constancy of phenotypes. It is the proportion of phenotypic variation that can be attributed to between‐subject (or between‐group) variation. As a consequence, the non‐repeatable fraction of phenotypic variation is the sum of measurement error and phenotypic flexibility. There are several ways to estimate repeatability for Gaussian data, but there are no formal agreements on how repeatability should be calculated for non‐Gaussian data (e.g. binary, proportion and count data). In addition to point estimates, appropriate uncertainty estimates (standard errors and confidence intervals) and statistical significance for repeatability estimates are required regardless of the types of data. We review the methods for calculating repeatability and the associated statistics for Gaussian and non‐Gaussian data. For Gaussian data, we present three common approaches for estimating repeatability: correlation‐based, analysis of variance (ANOVA)‐based and linear mixed‐effects model (LMM)‐based methods, while for non‐Gaussian data, we focus on generalised linear mixed‐effects models (GLMM) that allow the estimation of repeatability on the original and on the underlying latent scale. We also address a number of methods for calculating standard errors, confidence intervals and statistical significance; the most accurate and recommended methods are parametric bootstrapping, randomisation tests and Bayesian approaches. We advocate the use of LMM‐ and GLMM‐based approaches mainly because of the ease with which confounding variables can be controlled for. Furthermore, we compare two types of repeatability (ordinary repeatability and extrapolated repeatability) in relation to narrow‐sense heritability. This review serves as a collection of guidelines and recommendations for biologists to calculate repeatability and heritability from both Gaussian and non‐Gaussian data.

In the 12 years since Dudgeon et al. (2006) reviewed major pressures on freshwater ecosystems, the biodiversity crisis in the world's lakes, reservoirs, rivers, streams and wetlands has deepened. While lakes, reservoirs and rivers cover only 2.3% of the Earth's surface, these ecosystems host at least 9.5% of the Earth's described animal species. Furthermore, using the World Wide Fund for Nature's Living Planet Index, freshwater population declines (83% between 1970 and 2014) continue to outpace contemporaneous declines in marine or terrestrial systems. The Anthropocene has brought multiple new and varied threats that disproportionately impact freshwater systems. We document 12 emerging threats to freshwater biodiversity that are either entirely new since 2006 or have since intensified: (i) changing climates; (ii) e‐commerce and invasions; (iii) infectious diseases; (iv) harmful algal blooms; (v) expanding hydropower; (vi) emerging contaminants; (vii) engineered nanomaterials; (viii) microplastic pollution; (ix) light and noise; (x) freshwater salinisation; (xi) declining calcium; and (xii) cumulative stressors. Effects are evidenced for amphibians, fishes, invertebrates, microbes, plants, turtles and waterbirds, with potential for ecosystem‐level changes through bottom‐up and top‐down processes. In our highly uncertain future, the net effects of these threats raise serious concerns for freshwater ecosystems. However, we also highlight opportunities for conservation gains as a result of novel management tools (e.g. environmental flows, environmental DNA) and specific conservation‐oriented actions (e.g. dam removal, habitat protection policies, managed relocation of species) that have been met with varying levels of success. Moving forward, we advocate hybrid approaches that manage fresh waters as crucial ecosystems for human life support as well as essential hotspots of biodiversity and ecological function. Efforts to reverse global trends in freshwater degradation now depend on bridging an immense gap between the aspirations of conservation biologists and the accelerating rate of species endangerment.

Fitting a line to a bivariate dataset can be a deceptively complex problem, and there has been much debate on this issue in the literature. In this review, we describe for the practitioner the essential features of line‐fitting methods for estimating the relationship between two variables: what methods are commonly used, which method should be used when, and how to make inferences from these lines to answer common research questions.

A particularly important point for line‐fitting in allometry is that usually, two sources of error are present (which we call measurement and equation error), and these have quite different implications for choice of line‐fitting method. As a consequence, the approach in this review and the methods presented have subtle but important differences from previous reviews in the biology literature.

Linear regression, major axis and standardised major axis are alternative methods that can be appropriate when there is no measurement error. When there is measurement error, this often needs to be estimated and used to adjust the variance terms in formulae for line‐fitting. We also review line‐fitting methods for phylogenetic analyses.

Methods of inference are described for the line‐fitting techniques discussed in this paper. The types of inference considered here are testing if the slope or elevation equals a given value, constructing confidence intervals for the slope or elevation, comparing several slopes or elevations, and testing for shift along the axis amongst several groups. In some cases several methods have been proposed in the literature. These are discussed and compared. In other cases there is little or no previous guidance available in the literature.

Simulations were conducted to check whether the methods of inference proposed have the intended coverage probability or Type I error. We identified the methods of inference that perform well and recommend the techniques that should be adopted in future work.

Understanding how landscape characteristics affect biodiversity patterns and ecological processes at local and landscape scales is critical for mitigating effects of global environmental change. In this review, we use knowledge gained from human‐modified landscapes to suggest eight hypotheses, which we hope will encourage more systematic research on the role of landscape composition and configuration in determining the structure of ecological communities, ecosystem functioning and services. We organize the eight hypotheses under four overarching themes. Section A: ‘landscape moderation of biodiversity patterns' includes (1) the landscape species pool hypothesis—the size of the landscape‐wide species pool moderates local (alpha) biodiversity, and (2) the dominance of beta diversity hypothesis—landscape‐moderated dissimilarity of local communities determines landscape‐wide biodiversity and overrides negative local effects of habitat fragmentation on biodiversity. Section B: ‘landscape moderation of population dynamics' includes (3) the cross‐habitat spillover hypothesis—landscape‐moderated spillover of energy, resources and organisms across habitats, including between managed and natural ecosystems, influences landscape‐wide community structure and associated processes and (4) the landscape‐moderated concentration and dilution hypothesis—spatial and temporal changes in landscape composition can cause transient concentration or dilution of populations with functional consequences. Section C: ‘landscape moderation of functional trait selection’ includes (5) the landscape‐moderated functional trait selection hypothesis—landscape moderation of species trait selection shapes the functional role and trajectory of community assembly, and (6) the landscape‐moderated insurance hypothesis—landscape complexity provides spatial and temporal insurance, i.e. high resilience and stability of ecological processes in changing environments. Section D: ‘landscape constraints on conservation management' includes (7) the intermediate landscape‐complexity hypothesis—landscape‐moderated effectiveness of local conservation management is highest in structurally simple, rather than in cleared (i.e. extremely simplified) or in complex landscapes, and (8) the landscape‐moderated biodiversity versus ecosystem service management hypothesis—landscape‐moderated biodiversity conservation to optimize functional diversity and related ecosystem services will not protect endangered species. Shifting our research focus from local to landscape‐moderated effects on biodiversity will be critical to developing solutions for future biodiversity and ecosystem service management.