Why do we still use stepwise modelling in ecology and behaviour?

1. The biases and shortcomings of stepwise multiple regression are well established within the statistical literature. However, an examination of papers published in 2004 by three leading ecological and behavioural journals suggested that the use of this technique remains widespread: of 65 papers in which a multiple regression approach was used, 57% of studies used a stepwise procedure. 2. The principal drawbacks of stepwise multiple regression include bias in parameter estimation, inconsistencies among model selection algorithms, an inherent (but often overlooked) problem of multiple hypothesis testing, and an inappropriate focus or reliance on a single best model. We discuss each of these issues with examples. 3. We use a worked example of data on yellowhammer distribution collected over 4 years to highlight the pitfalls of stepwise regression. We show that stepwise regression allows models containing significant predictors to be obtained from each year's data. In spite of the significance of the selected models, they vary substantially between years and suggest patterns that are at odds with those determined by analysing the full, 4-year data set. 4. An information theoretic (IT) analysis of the yellowhammer data set illustrates why the varying outcomes of stepwise analyses arise. In particular, the IT approach identifies large numbers of competing models that could describe the data equally well, showing that no one model should be relied upon for inference.

Selection on heritable phenotypic plasticity in a wild bird population

Theoretical and laboratory research suggests that phenotypic plasticity can evolve under selection. However, evidence for its evolutionary potential from the wild is lacking. We present evidence from a Dutch population of great tits (Parus major) for variation in individual plasticity in the timing of reproduction, and we show that this variation is heritable. Selection favoring highly plastic individuals has intensified over a 32-year period. This temporal trend is concurrent with climate change causing a mismatch between the breeding times of the birds and their caterpillar prey. Continued selection on plasticity can act to alleviate this mismatch.

Differential contribution of frugivores to complex seed dispersal patterns

Frugivores are highly variable in their contribution to fruit removal in plant populations. However, data are lacking on species-specific variation in two central aspects of seed dispersal, distance of dispersal and probability of dispersal among populations through long-distance transport. We used DNA-based genotyping techniques on Prunus mahaleb seeds dispersed by birds (small- and medium-sized passerines) and carnivorous mammals to infer each seed's source tree, dispersal distance, and the probability of having originated from outside the study population. Small passerines dispersed most seeds short distances (50% dispersed <51 m from source trees) and into covered microhabitats. Mammals and medium-sized birds dispersed seeds long distances (50% of mammals dispersed seeds >495 m, and 50% of medium-sized birds dispersed seeds to >110 m) and mostly into open microhabitats. Thus, dispersal distance and microhabitat of seed deposition were linked through the contrasting behaviors of different frugivores. When the quantitative contribution to fruit removal was accounted for, mammals were responsible for introducing two-thirds of the immigrant seeds into the population, whereas birds accounted for one-third. Our results demonstrate that frugivores differ widely in their effects on seed-mediated gene flow. Despite highly diverse coteries of mutualistic frugivores dispersing seeds, critical long-distance dispersal events might rely on a small subset of large species. Population declines of these key frugivore species may seriously impair seed-mediated gene flow in fragmented landscapes by truncating the long-distance events and collapsing seed arrival to a restricted subset of available microsites.

Coupling of dispersal and aggression facilitates the rapid range expansion of a passerine bird

Behaviors can facilitate colonization of a novel environment, but the mechanisms underlying this process are poorly understood. On one hand, behavioral flexibility allows for an immediate response of colonizers to novel environments, which is critical to population establishment and persistence. On the other hand, integrated sets of behaviors that display limited flexibility can enhance invasion success by coupling behaviors with dispersal strategies that are especially important during natural range expansions. Direct observations of colonization events are required to determine the mechanisms underlying changes in behavior associated with colonization, but such observations are rare. Here, we studied changes in aggression on a large temporal and spatial scale across populations of two sister taxa of bluebirds (Sialia) to show that coupling of aggression and dispersal strongly facilitated the range expansion of western bluebirds across the northwestern United States over the last 30 years. We show that biased dispersal of highly aggressive males to the invasion front allowed western bluebirds to displace less aggressive mountain bluebirds. However, once mountain bluebirds were excluded, aggression of western bluebirds decreased rapidly across consecutive generations in concordance with local selection on highly heritable aggressive behavior. Further, the observed adaptive microevolution of aggression was accelerated by the link between dispersal propensity and aggression. Importantly, our results show that behavioral changes among populations were not caused by behavioral flexibility and instead strongly implicate adaptive integration of dispersal and aggression in facilitating the ongoing and rapid reciprocal range change of these species in North America.

A BAYESIAN STATE-SPACE FORMULATION OF DYNAMIC OCCUPANCY MODELS

Species occurrence and its dynamic components, extinction and colonization probabilities, are focal quantities in biogeography and metapopulation biology, and for species conservation assessments. It has been increasingly appreciated that these parameters must be estimated separately from detection probability to avoid the biases induced by non-detection error. Hence, there is now considerable theoretical and practical interest in dynamic occupancy models that contain explicit representations of metapopulation dynamics such as extinction, colonization, and turnover as well as growth rates. We describe a hierarchical parameterization of these models that is analogous to the state-space formulation of models in time series, where the model is represented by two components, one for the partially observable occupancy process and another for the observations conditional on that process. This parameterization naturally allows estimation of all parameters of the conventional approach to occupancy models, but in addition, yields great flexibility and extensibility, e.g., to modeling heterogeneity or latent structure in model parameters. We also highlight the important distinction between population and finite sample inference; the latter yields much more precise estimates for the particular sample at hand. Finite sample estimates can easily be obtained using the state-space representation of the model but are difficult to obtain under the conventional approach of likelihood-based estimation. We use R and WinBUGS to apply the model to two examples. In a standard analysis for the European Crossbill in a large Swiss monitoring program, we fit a model with year-specific parameters. Estimates of the dynamic parameters varied greatly among years, highlighting the irruptive population dynamics of that species. In the second example, we analyze route occupancy of Cerulean Warblers in the North American Breeding Bird Survey (BBS) using a model allowing for site-specific heterogeneity in model parameters. The results indicate relatively low turnover and a stable distribution of Cerulean Warblers which is in contrast to analyses of counts of individuals from the same survey that indicate important declines. This discrepancy illustrates the inertia in occupancy relative to actual abundance. Furthermore, the model reveals a declining patch survival probability, and increasing turnover, toward the edge of the range of the species, which is consistent with metapopulation perspectives on the genesis of range edges. Given detection/non-detection data, dynamic occupancy models as described here have considerable potential for the study of distributions and range dynamics.

Noise pollution changes avian communities and species interactions

Humans have drastically changed much of the world's acoustic background with anthropogenic sounds that are markedly different in pitch and amplitude than sounds in most natural habitats. This novel acoustic background may be detrimental for many species, particularly birds. We evaluated conservation concerns that noise limits bird distributions and reduces nesting success via a natural experiment to isolate the effects of noise from confounding stimuli and to control for the effect of noise on observer detection biases. We show that noise alone reduces nesting species richness and leads to different avian communities. Contrary to expectations, noise indirectly facilitates reproductive success of individuals nesting in noisy areas as a result of the disruption of predator-prey interactions. The higher reproductive success for birds within noisy habitats may be a previously unrecognized factor contributing to the success of urban-adapted species and the loss of birds less tolerant of noise. Additionally, our findings suggest that noise can have cascading consequences for communities through altered species interactions. Given that noise pollution is becoming ubiquitous throughout much of the world, knowledge of species-specific responses to noise and the cumulative effects of these novel acoustics may be crucial to understanding and managing human-altered landscapes.

Birdsong and anthropogenic noise: implications and applications for conservation

The dramatic increase in human activities all over the world has caused, on an evolutionary time scale, a sudden rise in especially low-pitched noise levels. Ambient noise may be detrimental to birds through direct stress, masking of predator arrival or associated alarm calls, and by interference of acoustic signals in general. Two of the most important functions of avian acoustic signals are territory defence and mate attraction. Both of these functions are hampered when signal efficiency is reduced through rising noise levels, resulting in direct negative fitness consequences. Many bird species are less abundant near highways and studies are becoming available on reduced reproductive success in noisy territories. Urbanization typically leads to homogenization of bird communities over large geographical ranges. We review current evidence for whether and how anthropogenic noise plays a role in these patterns of decline in diversity and density. We also provide details of a case study on great tits (Parus major), a successful urban species. Great tits show features that other species may lack and make them unsuitable for city life. We hypothesize that behavioural plasticity in singing behaviour may allow species more time to adapt to human-altered environments and we address the potential for microevolutionary changes and urban speciation in European blackbirds (Turdus merula). We conclude by providing an overview of mitigating measures available to abate noise levels that are degrading bird breeding areas. Bird conservationists probably gain most by realizing that birds and humans often benefit from the same or only slightly modified measures.

Adaptive Phenotypic Plasticity and the Successful Colonization of a Novel Environment

Behavior and other forms of phenotypic plasticity potentially enable individuals to deal with novel situations. This implies that establishment of a population in a new environment is aided by plastic responses, as first suggested by Baldwin (1896). In the early 1980s, a small population of dark-eyed juncos from a temperate, montane environment became established in a Mediterranean climate in coastal San Diego. The breeding season of coastal juncos is more than twice as long as that of the ancestral population, and they fledge approximately twice as many young. We investigated the adaptive significance of the longer breeding season and its consequences for population persistence. Within the coastal population, individuals with longer breeding seasons have higher offspring production and recruitment, with no measured detrimental effects such as higher mortality or lower reproductive success the following year. Population size has remained approximately constant during the 6 years of study (1998-2003). The increase in reproductive effort in the coastal population contributes substantially to the persistence of this population because there is no evidence of density-dependent recruitment, which would otherwise negate the effects of increased fledgling production. These results provide the first quantitative support of Baldwin's proposition that plasticity can be crucial for population persistence during the early stages of colonization.

The Evolution of Infidelity in Socially Monogamous Passerines: The Strength of Direct and Indirect Selection on Extrapair Copulation Behavior in Females

Many studies have been aimed at understanding the maintenance of female infidelity in socially monogamous birds. Because engaging in extrapair copulations (EPCs) is believed to be costly for females, it has been argued that EPC behavior must bring indirect benefits to females by elevating offspring fitness. We use empirical data from the literature to assess the relative strength of indirect and direct selection on female EPC behavior, using quantitative genetic approximations of selection. This analysis confirmed that there is generally negative direct selection on EPC behavior caused by depressed paternal investment by social males. In contrast, there was no significant positive indirect selection on EPC behavior in females. A comparison between the two types of selection suggests that the force of direct negative selection is generally much stronger than that of indirect positive selection. Indirect selection is thus unlikely to maintain EPC behavior in the face of direct selection against it. We suggest that EPCs may instead be the result of antagonistic selection on loci influencing the outcome of male-female encounters and that EPC behavior per se may not be adaptive for females but may reflect sexual conflict due to strong selection in males to achieve extrapair copulations.

Testosterone and oxidative stress: the oxidation handicap hypothesis

Secondary sexual traits (SST) are usually thought to have evolved as honest signals of individual quality during mate choice. Honesty of SST is guaranteed by the cost of producing/maintaining them. In males, the expression of many SST is testosterone-dependent. The immunocompetence handicap hypothesis has been proposed as a possible mechanism ensuring honesty of SST on the basis that testosterone, in addition to its effect on sexual signals, also has an immunosuppressive effect. The immunocompetence handicap hypothesis has received mixed support. However, the cost of testosterone-based signalling is not limited to immunosuppression and might involve other physiological functions such as the antioxidant machinery. Here, we tested the hypothesis that testosterone depresses resistance to oxidative stress in a species with a testosterone-dependent sexual signal, the zebra finch. Male zebra finches received subcutaneous implants filled with flutamide (an anti-androgen) or testosterone, or kept empty (control). In agreement with the prediction, we found that red blood cell resistance to a free radical attack was the highest in males implanted with flutamide and the lowest in males implanted with testosterone. We also found that cell-mediated immune response was depressed in testosterone-treated birds, supporting the immunocompetence handicap hypothesis. The recent finding that red blood cell resistance to free radicals is negatively associated with mortality in this species suggests that benefits of sexual signalling might trade against the costs derived from oxidation.

Parent birds assess nest predation risk and adjust their reproductive strategies

Avian life history theory has long assumed that nest predation plays a minor role in shaping reproductive strategies. Yet, this assumption remains conspicuously untested by broad experiments that alter environmental risk of nest predation, despite the fact that nest predation is a major source of reproductive failure. Here, we examined whether parents can assess experimentally reduced nest predation risk and alter their reproductive strategies. We experimentally reduced nest predation risk and show that in safer environments parents increased investment in young through increased egg size, clutch mass, and the rate they fed nestlings. Parents also increased investment in female condition by increasing the rates that males fed incubating females at the nest, and decreasing the time that females spent incubating. These results demonstrate that birds can assess nest predation risk at large and that nest predation plays a key role in the expression of avian reproductive strategies.

Malarial parasites decrease reproductive success: an experimental study in a passerine bird

Malarial parasites are supposed to have strong negative fitness consequences for their hosts, but relatively little evidence supports this claim due to the difficulty of experimentally testing this. We experimentally reduced levels of infection with the blood parasite Haemoproteus prognei in its host the house martin Delichon urbica, by randomly treating adults with primaquine or a control treatment. Treated birds had significantly fewer parasites than controls. The primaquine treatment increased clutch size by 18%; hatching was 39% higher and fledging 42% higher. There were no effects of treatment on quality of offspring, measured in terms of tarsus length, body mass, haematocrit or T-cell-mediated immune response. These findings demonstrate that malarial parasites can have dramatic effects on clutch size and other demographic variables, potentially influencing the evolution of clutch size, but also the population dynamics of heavily infected populations of birds.

Assortative Mating as a Mechanism for Rapid Evolution of a Migratory Divide

There have been numerous recent observations of changes in the behavior and dynamics of migratory bird populations, but the plasticity of the migratory trait and our inability to track small animals over large distances have hindered investigation of the mechanisms behind migratory change. We used habitat-specific stable isotope signatures to show that recently evolved allopatric wintering populations of European blackcaps Sylvia atricapilla pair assortatively on their sympatric breeding grounds. Birds wintering further north also produce larger clutches and fledge more young. These findings describe an important process in the evolution of migratory divides, new migration routes, and wintering quarters. Temporal segregation of breeding is a way in which subpopulations of vertebrates may become isolated in sympatry.

Food-caching western scrub-jays keep track of who was watching when

Western scrub-jays (Aphelocoma californica) hide food caches for future consumption, steal others' caches, and engage in tactics to minimize the chance that their own caches will be stolen. We show that scrub-jays remember which individual watched them during particular caching events and alter their recaching behavior accordingly. We found no evidence to suggest that a storer's use of cache protection tactics is cued by the observer's behavior.

Predation risk induces changes in nest-site selection and clutch size in the Siberian jay

Life-history theory predicts that an individual should reduce its reproductive efforts by laying a smaller clutch size when high risk of nest predation reduces the value of current reproduction. Evidence in favour of this 'nest predation hypothesis', however, is scarce and based largely on correlative analyses. Here, we manipulated perceived risk of nest predation in the Siberian jay Perisoreus infaustus using playback involving a mixture of calls by corvid nest predators in the vicinity of nest sites. In response to being exposed to this acoustic cue simulating increased risk of nest predation, the jays chose a nest site offering more protective covering and reduced clutch size. This is the first experimental demonstration of clutch size adjustment and nest site selection as a result of phenotypic plasticity in an open nesting passerine reflecting a facultative response to the perceived risk of nest predation.

Sperm morphology and sperm velocity in passerine birds

Sperm velocity is one of the main determinants of the outcome of sperm competition. Since sperm vary considerably in their morphology between and within species, it seems likely that sperm morphology is associated with sperm velocity. Theory predicts that sperm velocity may be increased by enlarged midpiece (energetic component) or flagellum length (kinetic component), or by particular ratios between sperm components, such as between flagellum length and head size. However, such associations have rarely been found in empirical studies. In a comparative framework in passerine birds, we tested these theoretical predictions both across a wide range of species and within a single family, the New World blackbirds (Icteridae). In both study groups, sperm velocity was influenced by sperm morphology in the predicted direction. Consistent with theoretical models, these results show that selection on sperm morphology and velocity are likely to be concomitant evolutionary forces.

Urbanization and its effects on personality traits: a result of microevolution or phenotypic plasticity?

Human-altered environmental conditions affect many species at the global scale. An extreme form of anthropogenic alteration is the existence and rapid increase of urban areas. A key question, then, is how species cope with urbanization. It has been suggested that rural and urban conspecifics show differences in behaviour and personality. However, (i) a generalization of this phenomenon has never been made; and (ii) it is still unclear whether differences in personality traits between rural and urban conspecifics are the result of phenotypic plasticity or of intrinsic differences. In a literature review, we show that behavioural differences between rural and urban conspecifics are common and taxonomically widespread among animals, suggesting a significant ecological impact of urbanization on animal behaviour. In order to gain insight into the mechanisms leading to behavioural differences in urban individuals, we hand-raised and kept European blackbirds (Turdus merula) from a rural and a nearby urban area under common-garden conditions. Using these birds, we investigated individual variation in two behavioural responses to the presence of novel objects: approach to an object in a familiar area (here defined as neophilia), and avoidance of an object in a familiar foraging context (defined as neophobia). Neophilic and neophobic behaviours were mildly correlated and repeatable even across a time period of one year, indicating stable individual behavioural strategies. Blackbirds from the urban population were more neophobic and seasonally less neophilic than blackbirds from the nearby rural area. These intrinsic differences in personality traits are likely the result of microevolutionary changes, although we cannot fully exclude early developmental influences.

Effects of landscape corridors on seed dispersal by birds

Habitat fragmentation threatens biodiversity by disrupting dispersal. The mechanisms and consequences of this disruption are controversial, primarily because most organisms are difficult to track. We examined the effect of habitat corridors on long-distance dispersal of seeds by birds, and tested whether small-scale (<20 meters) movements of birds could be scaled up to predict dispersal of seeds across hundreds of meters in eight experimentally fragmented landscapes. A simulation model accurately predicted the observed pattern of seed rain and revealed that corridors functioned through edge-following behavior of birds. Our study shows how models based on easily observed behaviors can be scaled up to predict landscape-level processes.

Components of variance underlying fitness in a natural population of the great tit Parus major

Traits that are closely associated with fitness tend to have lower heritabilities (h2) than those that are not. This has been interpreted as evidence that natural selection tends to deplete genetic variation more rapidly for traits more closely associated with fitness (a corollary of Fisher's fundamental theorem), but Price and Schluter (1991) suggested the pattern might be due to higher residual variance in traits more closely related to fitness. The relationship between 10 different traits for females, seven traits for males, and overall fitness (lifetime recruitment) was quantified for great tits (Parus major) studied in their natural environment of Wytham Wood, England, using data collected over 39 years. Heritabilities and the coefficients of additive genetic and residual variance (CVA and CVR, respectively) were estimated using an "animal model." For both males and females, a trait's correlation (r) with fitness was negatively related to its h2 but positively related to its CVR. The CVA was not related to the trait's correlation with fitness in either sex. This is the third study using directly measured fitness in a wild population to show the important role of residual variation in determining the pattern of lower heritabilities for traits more closely related to fitness.

Brain size, innovative propensity and migratory behaviour in temperate Palaearctic birds

The evolution of migration in birds remains an outstanding, unresolved question in evolutionary ecology. A particularly intriguing question is why individuals in some species have been selected to migrate, whereas in other species they have been selected to be sedentary. In this paper, we suggest that this diverging selection might partially result from differences among species in the behavioural flexibility of their responses to seasonal changes in the environment. This hypothesis is supported in a comparative analysis of Palaearctic passerines. First, resident species tend to rely more on innovative feeding behaviours in winter, when food is harder to find, than in other seasons. Second, species with larger brains, relative to their body size, and a higher propensity for innovative behaviours tend to be resident, while less flexible species tend to be migratory. Residence also appears to be less likely in species that occur in more northerly regions, exploit temporally available food sources, inhabit non-buffered habitats and have smaller bodies. Yet, the role of behavioural flexibility as a response to seasonal environments is largely independent of these other factors. Therefore, species with greater foraging flexibility seem to be able to cope with seasonal environments better, while less flexible species are forced to become migratory.

Western scrub-jays anticipate future needs independently of their current motivational state

Planning for the future has been considered to be a uniquely human trait [1-3]. However, recent studies challenge this hypothesis by showing that food-caching Western scrub-jays (Aphelocoma californica) can relate their previous experience as thieves to the possibility of future cache theft by another bird [4], are sensitive to the state of their caches at recovery ([5] and S. De Kort, S.P.C.C., D. Alexis, A.D., and N.S.C., unpublished data), and can plan for tomorrow's breakfast [6]. Although these results suggest that scrub-jays are capable of future planning, the degree to which these birds act independently of their current motivational state is a matter of contention. The Bischof-Köhler hypothesis [1] holds that nonhuman animals cannot anticipate and act toward the satisfaction of a future need not currently experienced or cued by their present motivational state. Using specific satiety to control for the jays' current and future motivational states, here we specifically test this hypothesis by dissociating current and future motivational states. We report that Western scrub-jays anticipate the recovery of their caches, as well as their own future needs, by acting independently of their current motivational state and immediate needs. The fact that the birds act in favor of a future need as opposed to the current one challenges the hypothesis that this ability is unique to humans.

Background-matching and disruptive coloration, and the evolution of cryptic coloration

Cryptic prey coloration typically bears a resemblance to the habitat the prey uses. It has been suggested that coloration which visually matches a random sample of the background maximizes background matching. We studied this previously untested hypothesis, as well as another, little studied principle of concealment, disruptive coloration, and whether it could, acting in addition to background matching, provide another plausible means of achieving camouflage. We presented great tits (Parus major) with artificial background-matching and disruptive prey (DP), and measured detection times. First, we studied whether any random sample of a background produces equally good crypsis. This turned out to not be the case. Next, we compared the DP and the best background-matching prey and found that they were equally cryptic. We repeated the tests using prey with all the coloration elements being whole, instead of some of them being broken by the prey outline, but this did not change the result. We conclude that resemblance of the background is an important aspect of concealment, but that coloration matching a random visual sample of the background is neither sufficient nor necessary to minimize the probability of detection. Further, our study lends empirical support to the principle of disruptive coloration.