Form,function and consequences of density dependence in a long‐distance migratory bird

The density dependence of demographic parameters and its implications for population regulation have long been recognized. Recent work has revealed potential effects of density on mating systems and sexual selection, but few studies concurrently assess the consequences of density on both demography and sexual selection. Such an approach is important because population processes and individual behaviors can interact to influence population growth and evolutionary trajectories. In this study, we tested the density dependence of breeding success, extra‐pair paternity, and the opportunity for sexual selection in a population of American redstarts Setophaga ruticilla using two different measures of density. To evaluate temporal patterns, we analyzed annual territory density, based on the total number of territories at our study site each year. To evaluate spatial patterns, we analyzed local territory density within years, based on the number of territories surrounding a focal territory. Greater annual density was associated with fewer offspring fledged per female, a reduced mean population rate of fledging success, and a lower relative contribution of extra‐pair paternity to male fitness. Greater local density was associated with fewer offspring fledged, reduced fledgling success, higher rates of nest loss, and higher rates of paternity loss on focal territories. Interestingly, greater local density was also associated with greater nestling mass on focal territories, which could imply that more densely‐packed territories contain superior resources. Overall, our results suggest that the effects of crowding via greater territory density reduce fecundity through increased nest predation, rather than reduced food availability, and increase rates of extra‐pair paternity. Thus, the selective pressures faced by individuals and their reproductive behaviors are likely to differ based on the annual and local density they experience, which may then feed back into population demography.     

Large‐scale,long‐term ecosystem monitoring: Interview with David Lindenmayer

David Lindenmayer leads six large‐scale, long‐term research programmes in south‐eastern Australia to help conserve biodiversity in restored areas on farmland as well as conservation in reserves, national parks, wood production forests and plantations. What makes this award‐winning researcher tick and how is the research influencing biodiversity management and policy?     

Relationships among timing of moult,moult duration and feather mass in long‐distance migratory passerines

Moult is a costly but necessary process in avian life, which displays two main temporal patterns within the annual cycle of birds (summer and winter moult). Timing of moult can affect its duration and consequently the amount of material invested in feathers, which could have a considerable influence on feather structure and functionality. In this study, we used two complementary approaches to test whether moult duration and feather mass vary in relation to the timing of moult. Firstly, we conducted a comparative study between a sample of long‐distance migratory passerine species which differ in moult pattern. Secondly, we took advantage of the willow warbler's Phylloscopus trochilus biannual moult, for which it is well‐known that winter moult takes longer than summer moult, to assess between‐moult variation in feather mass. Our comparative analysis showed that summer moulting species performed significantly shorter moults than winter moulters. We also detected that feathers produced in winter were comparatively heavier than those produced in summer, both in between‐species comparison and between moults of the willow warbler. These results suggest the existence of a trade‐off between moult speed and feather mass mediated by timing of moult, which could contribute to explain the diversity of moult patterns in passerines.     

Metabolic consequences of overlapping food restriction and cell‐mediated immune response in a long‐distance migratory shorebird,the little ringed plover Charadrius dubius

Investment in immunity is commonly viewed as an energetically costly activity in birds. Although several studies have focused on the energy cost of mounting an immune response and its concomitant physiological trade‐offs, nothing is known about the metabolic adjustments experienced by immunochallenged birds under resource limitation, or about the basal metabolism cost of mounting cell‐mediated immune (CMI) responses in bird species other than non‐migratory passerines. Here we measured the basal metabolic rate (BMR), inflammatory response, and body mass in ad libitum fed and food‐restricted little ringed plovers Charadrius dubius challenged with phytohemagglutinin (PHA) in order to assess the energy cost, the strength, and the time course of the CMI response in a long‐distance migratory bird in different nutritional states. We found that ad libitum birds injected with PHA significantly increased both mass‐independent BMR and inflammatory response, whereas birds with an induced food restriction‐immune response overlap experienced a mass‐independent BMR downregulation and decreased inflammatory response relative to ad libitum birds. We suggest that both the BMR downregulation and the diminished inflammatory response observed in birds facing such an overlap could be energy‐saving mechanisms to maintain the body mass above a critical level and maximize fitness.     

The role of migratory ducks in the long‐distance dispersal of native plants and the spread of exotic plants in Europe

Little is known about the role of migratory waterfowl in the long‐distance dispersal (LDD) of seeds. We studied the gut contents of 42 teals Anas crecca collected in the Camargue, southern France, and found intact seeds of 16 species. There was no relationship between the probability that a given seed species was found intact in the lower gut, and the seed hardness or size. The number of seeds found in the oesophagus and gizzard (a measure of ingestion rate) was the only significant predictor of the occurrence of intact seeds in the lower gut, so studies of waterfowl diet can be used as surrogates of dispersal potential. In a literature review, we identified 223 seed species recorded in 25 diet studies of teal, pintail Anas acuta, wigeon A. penelope or mallard A. platyrhynchos in Europe. We considered whether limited species distribution reduces the chances that a seed can be carried to suitable habitat following LDD. Overall, 72% of plant species recorded in duck diets in southern Europe (36 of 50) were also recorded in the north, whereas 97% of species recorded in duck diets in the north (137 of 141) were also recorded in the south. This suggests a great potential for LDD, since most dispersed plants species occur throughout the migratory range of ducks. Migratory ducks are important vectors for both terrestrial and aquatic plant species, even those lacking the fleshy fruits or hooks typically used to identify seeds dispersed by birds. Finally, we show ducks are important vectors of exotic plant species. We identified 14 alien to Europe and 44 native to Europe but introduced to some European countries whose seeds have been recorded in duck diet.     

Behavioural response of a migratory songbird to geographic variation in song and morphology

Introduction

Sexually selected traits contribute substantially to evolutionary diversification, for example by promoting assortative mating. The contributing traits and their relevance for reproductive isolation differ between species. In birds, sexually selected acoustic and visual signals often undergo geographic divergence. Clines in these phenotypes may be used by both sexes in the context of sexual selection and territoriality. The ways conspecifics respond to geographic variation in phenotypes can give insights to possible behavioural barriers, but these may depend on migratory behaviour. We studied a migratory songbird, the Stonechat, and tested its responsiveness to geographic variation in male song and morphology. The traits are acquired differently, with possible implications for population divergence. Song can evolve quickly through cultural transmission, and thus may contribute more to the establishment of geographic variation than inherited morphological traits. We first quantified the diversity of song traits from different populations. We then tested the responses of free-living Stonechats of both sexes to male phenotype with playbacks and decoys, representing local and foreign stimuli derived from a range of distances from the local population.

Results

Both sexes discriminated consistently between stimuli from different populations, responding more strongly to acoustic and morphological traits of local than foreign stimuli. Time to approach increased, and time spent close to the stimuli and number of tail flips decreased consistently with geographic distance of the stimulus from the local population. Discriminatory response behaviour was more consistent for acoustic than for morphological traits. Song traits of the local population differed significantly from those of other populations.

Conclusions

Evaluating an individual’s perception of geographic variation in sexually selected traits is a crucial first step for understanding reproductive isolation mechanisms. We have demonstrated that in both sexes of Stonechats the responsiveness to acoustic and visual signals decreased with increasing geographic distance of stimulus origin. These findings confirm consistent, fine discrimination for both learned song and inherited morphological traits in these migratory birds. Maintenance or further divergence in phenotypic traits could lead to assortative mating, reproductive isolation, and potentially speciation.

     

Large‐scale molecular genetic analysis in plant‐pathogenic fungi: a decade of genome‐wide functional analysis

Plant‐pathogenic fungi cause diseases to all major crop plants world‐wide and threaten global food security. Underpinning fungal diseases are virulence genes facilitating plant host colonization that often marks pathogenesis and crop failures, as well as an increase in staple food prices. Fungal molecular genetics is therefore the cornerstone to the sustainable prevention of disease outbreaks. Pathogenicity studies using mutant collections provide immense function‐based information regarding virulence genes of economically relevant fungi. These collections are rich in potential targets for existing and new biological control agents. They contribute to host resistance breeding against fungal pathogens and are instrumental in searching for novel resistance genes through the identification of fungal effectors. Therefore, functional analyses of mutant collections propel gene discovery and characterization, and may be incorporated into disease management strategies. In the light of these attributes, mutant collections enhance the development of practical solutions to confront modern agricultural constraints. Here, a critical review of mutant collections constructed by various laboratories during the past decade is provided. We used Magnaporthe oryzae and Fusarium graminearum studies to show how mutant screens contribute to bridge existing knowledge gaps in pathogenicity and fungal–host interactions.     

Differentiating between stopover and staging sites: functions of the southern and northern Yellow Sea for long‐distance migratory shorebirds

Evidence‐based protection of migratory birds at flyway levels requires a solid understanding of their use of ‘stopping sites’ during migration. To characterize the site use of northward‐migration great knots Calidris tenuirostris in China, we compared length of stay and fuel deposition during northward migration at areas in the south and the north of the Yellow Sea, a region critical for migrating shorebirds. Radio‐tracking showed that at the southern site great knots stayed for only short periods (2.3 ± 1.9 d, n = 40), and bird captures showed that they did not increase their mean body mass while there. In the north birds stayed for 1 month (31.0 ± 13.6 d, n = 22) and almost doubled their mean body mass. Fuel consumption models suggest that great knots departing from the northern Yellow Sea should be able to fly nonstop to the breeding grounds, whereas those from the south would require a refueling stop further north. These results indicate that the study sites in the northern and southern Yellow Sea serve different roles: the southern site acts as a temporary stopover area that enables birds with low fuel stores to make it to main staging areas further north, while the northern site serves as the critical staging site where birds refuel for the next leg of their migration. The rapid turnover rate in the southern Yellow Sea indicates that many more birds use that area than are indicated by peak counts. Differential use of the southern and northern sites indicates that both play crucial roles in the ability of great knots to migrate successfully.     

Implications of long‐distance movements of frugivorous rain forest hornbills

Long‐distance seed dispersal influences many critical ecological processes by improving chances of gene flow and maintaining genetic diversity among plant populations. Accordingly, large‐scale movements by frugivores may have important conservation implications as they provide an opportunity for long‐distance seed dispersal. We studied movement patterns, resource tracking, and potential long‐distance seed dispersal by two species of Ceratogymna hornbills, the black‐casqued hornbill C. atrata, and the white‐thighed hornbill C. cylindricus, in lowland tropical forests of Cameroon. We determined fruiting phenology of 24 tree species important in hornbill diet at monthly intervals and compared these patterns to monthly hornbill census data. After capture and radio‐tagging of 16 hornbills, we used radio telemetry by vehicle and fixed wing aircraft to determine the extent of long‐distance movements. Hornbills exhibited up to 20‐fold changes in numbers in response to fruit availability in our 25 km² study area. Also, hornbills made large‐scale movements up to 290 km, which are larger than any movement previously reported for large avian frugivores. Together, these observations provide direct evidence that hornbills are not resident and that hornbills track available fruit resources. Our results suggest that Ceratogymna hornbills embark on long‐distance movements, potentially dispersing seeds and contributing to rain forest regeneration and diversity.     

Large‐scale image‐based profiling of single‐cell phenotypes in arrayed CRISPR‐Cas9 gene perturbation screens

High‐content imaging using automated microscopy and computer vision allows multivariate profiling of single‐cell phenotypes. Here, we present methods for the application of the CISPR‐Cas9 system in large‐scale, image‐based, gene perturbation experiments. We show that CRISPR‐Cas9‐mediated gene perturbation can be achieved in human tissue culture cells in a timeframe that is compatible with image‐based phenotyping. We developed a pipeline to construct a large‐scale arrayed library of 2,281 sequence‐verified CRISPR‐Cas9 targeting plasmids and profiled this library for genes affecting cellular morphology and the subcellular localization of components of the nuclear pore complex (NPC). We conceived a machine‐learning method that harnesses genetic heterogeneity to score gene perturbations and identify phenotypically perturbed cells for in‐depth characterization of gene perturbation effects. This approach enables genome‐scale image‐based multivariate gene perturbation profiling using CRISPR‐Cas9.     

Large‐scale analysis of secondary structure changes in proteins suggests a role for disorder‐to‐order transitions in nucleotide binding proteins

Conformational changes in proteins often involve secondary structure transitions. Such transitions can be divided into two types: disorder‐to‐order changes, in which a disordered segment acquires an ordered secondary structure (e.g., disorder to α‐helix, disorder to β‐strand), and order‐to‐order changes, where a segment switches from one ordered secondary structure to another (e.g., α‐helix to β‐strand, α‐helix to turn). In this study, we explore the distribution of these transitions in the proteome. Using a comprehensive, yet highly conservative method, we compared solved three‐dimensional structures of identical protein sequences, looking for differences in the secondary structures with which they were assigned. Protein chains in which such secondary structure transitions were detected, were classified into two sets according to the type of transition that is involved (disorder‐to‐order or order‐to‐order), allowing us to characterize each set by examining enrichment of gene ontology terms. The results reveal that the disorder‐to‐order set is significantly enriched with nucleotide binding proteins, whereas the order‐to‐order set is more diverse. Remarkably, further examination reveals that >22% of the purine nucleotide binding proteins include segments which undergo disorder‐to‐order transitions, suggesting that such transitions play an important role in this process. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Large‐scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis

Protein phosphorylation regulates a wide range of cellular processes. Here, we report the proteome‐wide mapping of in vivo phosphorylation sites in Arabidopsis by using complementary phosphopeptide enrichment techniques coupled with high‐accuracy mass spectrometry. Using unfractionated whole cell lysates of Arabidopsis, we identified 2597 phosphopeptides with 2172 high‐confidence, unique phosphorylation sites from 1346 proteins. The distribution of phosphoserine, phosphothreonine, and phosphotyrosine sites was 85.0, 10.7, and 4.3%. Although typical tyrosine‐specific protein kinases are absent in Arabidopsis, the proportion of phosphotyrosines among the phospho‐residues in Arabidopsis is similar to that in humans, where over 90 tyrosine‐specific protein kinases have been identified. In addition, the tyrosine phosphoproteome shows features distinct from those of the serine and threonine phosphoproteomes. Taken together, we highlight the extent and contribution of tyrosine phosphorylation in plants.     

Heritability of arrival date in a migratory bird

The behaviour of long-distance migratory birds is assumed to partly be under the influence of genes, as demonstrated by selection experiments. Furthermore, competition for early arrival among males may lead to condition-dependent migration associated with fitness benefits of early arrival achieved by individuals in prime condition. Here I present field data on the repeatability and the heritability of arrival date in a trans-equatorial migratory bird, the barn swallow Hirundo rustica, and I test for a genetic correlation between arrival date and the expression of a condition-dependent secondary sexual character. The repeatability was statistically significant and the heritability of arrival date was estimated to be 0.54 (s.e. = 0.15). There was no significant evidence of this estimate being inflated by environmental or maternal condition during rearing. Arrival date and migration are condition dependent in the barn swallow, with males with the most exaggerated secondary sexual characters also arriving the earliest. There was a significant genetic correlation between arrival date and tail length in male barn swallows, providing indirect evidence for a genetic basis of this condition dependence. Given the high level of heritability, arrival date could readily respond to selection caused by environmental change.     

Large‐scale patterns in genetic variation,gene flow and differentiation in five species of European Coenagrionid damselfly provide mixed support for the central‐marginal hypothesis

Recently, an increased effort has been directed towards understanding the distribution of genetic variation within and between populations, particularly at central and marginal areas of a species’ distribution. Much of this research is centred on the central‐marginal hypothesis, which posits that populations at range margins are sparse, small and genetically diminished compared to those at the centre of a species’ distribution range. We tested predictions derived from the central‐marginal hypothesis for the distribution of genetic variation and population differentiation in five European Coenagrionid damselfly species. We screened genetic variation (microsatellites) in populations sampled in the centre and margins of the species’ latitudinal ranges, assessed genetic diversity (H_S) in the populations and the distribution of this genetic diversity between populations (F_ST). We further assessed genetic substructure and migration with Bayesian assignment methods, and tested for significant associations between genetic substructure and bioclimatic and spatial (altitude and latitude) variables, using general linearized models. We found no general adherence to the central‐marginal hypothesis; instead we found that other factors such as historical or current ecological factors often better explain the patterns uncovered. This was illustrated in Coenagrion mercuriale whose colonisation history and behaviour most likely led to the observation of a high genetic diversity in the south and lower genetic diversity with increasing latitude, and in C. armatum and C. pulchellum whose patterns of low genetic diversity coupled with the weakest genetic differentiation at one of their range margins suggested, respectively, possible range shifts and recent, strong selection pressure.     

Effects of long‐distance running on serum opsonic activity measured by chemiluminescence

Exhaustive exercise such as long‐distance running has been shown to increase susceptibility to infection. In order to investigate whether serum opsonic activity plays a role in such conditions, we utilized luminol‐dependent and lucigenin‐dependent chemiluminescence (LmCL and LgCL). We took serum samples from 24 male marathon runners before and after running 30 km. Neutrophils were isolated from the peripheral blood of healthy volunteers. Serum opsonic activity was examined by measuring neutrophil ROS stimulated with zymosan particles opsonized by the serum samples. Immunoglobulin and complement levels in the serum were also measured. After a 30 km run, the maximum light emission was increased and the time to reach the maximum light emission was shortened significantly (p < 0.05) in LmCL. However, there were no significant changes in the immunoglobulin and complement levels. The increase of ROS production may suggest that serum opsonic activity is accelerated after running 30 km. Thus, serum opsonic activity might not play a significant role in the susceptibility to infection after long‐distance running. Copyright © 2003 John Wiley & Sons, Ltd.     

Natural selection on body size traits in a long‐lived bird,the snow petrel Pagodroma nivea

I consider the possibility of selection favouring large body size in a population of snow petrels (Pagodroma nivea), a long‐lived seabird species. I measured natural selection on body size traits in a population from 1987 to 1998. There was evidence of selection on body size associated with fecundity and survival. Directional selection on bill length and stabilizing selection on tarsus length associated with reproductive success were detected among males. Selection associated with survival favoured males with longer bills. However, selection was weak in all cases. No evidence of selection acting on female body size traits was detected. Offspring–parents regression suggested that bill length and tarsus length were heritable. Although I was able to identify the targets of selection in this population, I could not demonstrate the ecological implications of both tarsus length and bill length variation. The selection on male, but not on female, body size traits suggests factors such as intrasexual competition for nests and/or mates rather than factors such as feeding efficiency as mechanisms of selection on bill size.     

Comparing short and long‐distance dispersal: modelling and field case studies

Dispersal is a factor of great importance in determining a species spatial distribution. Short distance dispersal (SDD) and long distance dispersal (LDD) strategies yield very different spatial distributions. In this paper we compare spatial spread patterns from SDD and LDD simulations, contrast them with patterns from field data, and assess the significance of biological and population traits. Simulated SDD spread using an exponential function generates a single circular patch with a well‐defined invasion front showing a travelling‐wave structure. The invasive spread is relatively slow as it is restricted to reproductive individuals occupying the outer zone of the circular patch. As a consequence of this dispersal dynamics, spread is slower than spread generated by LDD. In contrast, the early and fast invasion of the entire habitat mediated by power law LDD not only involves a significantly greater invasion velocity, but also an entirely different habitat occupation. As newly dispersed individuals soon reach very distant portions of the habitat as well as the vicinity of the original dispersal focus, new growing patches are generated while the main patch increases its own growth absorbing the closest patches. As a consequence of both dispersal and lower density dependence, growth of the occupied area is much faster than with SDD. SDD and LDD also differ regarding pattern generation. With SDD, fractal patterns appear only in the border of the invasion front in SDD when competitive interaction with residents is included. In contrast, LDD patterns show fractality both in the spatial arrangements of patches as well as in patch borders. Moreover, values of border fractal dimension inform on the dispersal process in relation with habitat heterogeneity. The distribution of patch size is also scale‐free, showing two power laws characteristic of small and large patch sizes directly arising from the dispersal and reproductive dynamics. Ecological factors like habitat heterogeneity are relevant for dispersal, although its importance is greater for SDD, lowering the invasion velocity. Among the life history traits considered, adult mortality, the juvenile bank and mean dispersal distance are the most relevant for SDD. For LDD, habitat heterogeneity and changes in life history traits are not so relevant, causing minor changes in the values of the scale‐free parameters. Our work on short and long distance dispersal shows novel theoretical differences between SDD and LDD in invasive systems (mechanisms of pattern formation, fractal and scaling properties, relevance of different life history traits and habitat variables) that correspond closely with field examples and were not analyzed, at least in this degree of detail, by the previously existing models.     

Nematodes surfing the waves: long‐distance dispersal of soil‐borne microfauna via sea swept rhizomes

Dispersal mechanisms of soil‐borne microfauna have hitherto received little attention. Understanding dispersal mechanisms of these species is important to unravel their basic life history traits, biogeography, exchange of individuals between populations, and local adaptation. Soil‐borne nematodes and root‐feeding nematodes in particular occupy a key position in soil‐food webs and can be determinants for plant growth and vegetation structure and succession. However, their dispersal abilities have been scarcely addressed, predominantly focusing on species of agricultural importance. Still, root‐feeding nematodes are usually considered as being extremely limited and bound to the rhizosphere of plants. We investigated a mechanism for long distance dispersal of root‐feeding nematodes associated to two widespread coastal dune grasses. The nematodes are known to be crucial for the functioning of these grasses. We experimentally tested the hypothesis that root‐feeding nematodes are able to move across long distances inside rhizome fragments that are dispersed by seawater. We also tested the survival capacities of the host plants in seawater. Our study demonstrates that root‐feeding nematodes and plants are able to survive immersion in seawater, providing a mechanism for long distance dispersal of root feeding nematodes together with their host plant. Drifting rhizome fragments enable the exchange of plant material and animals between dune systems. These results provide new insights to understand the ecology of dune vegetation, the interaction with soil‐borne organisms and more importantly, re‐set the scale of spatial dynamics of a group of organisms considered extremely constrained in its dispersal capacities.