pinecone/core-2020-05-10-deduplication huggingface dataset:
Nest trampling and ground nesting birds: quantifying temporal and spatial overlap between cattle activity and breeding redshank

Conservation grazing for breeding birds needs to balance the positive effects on vegetation structure and negative effects of nest trampling. In the UK, populations of Common redshank Tringa totanus breeding on saltmarshes declined by >50% between 1985 and 2011. These declines have been linked to changes in grazing management. The highest breeding densities of redshank on saltmarshes are found in lightly grazed areas. Conservation initiatives have encouraged low-intensity grazing at <1 cattle/ha, but even these levels of grazing can result in high levels of nest trampling. If livestock distribution is not spatially or temporally homogenous but concentrated where and when redshank breed, rates of nest trampling may be much higher than expected based on livestock density alone. By GPS tracking cattle on saltmarshes and monitoring trampling of dummy nests, this study quantified (i) the spatial and temporal distribution of cattle in relation to the distribution of redshank nesting habitats and (ii) trampling rates of dummy nests. The distribution of livestock was highly variable depending on both time in the season and the saltmarsh under study, with cattle using between 3% and 42% of the saltmarsh extent and spending most their time on higher elevation habitat within 500 m of the sea wall, but moving further onto the saltmarsh as the season progressed. Breeding redshank also nest on these higher elevation zones, and this breeding coincides with the early period of grazing. Probability of nest trampling was correlated to livestock density and was up to six times higher in the areas where redshank breed. This overlap in both space and time of the habitat use of cattle and redshank means that the trampling probability of a nest can be much higher than would be expected based on standard measures of cattle density. Synthesis and applications: Because saltmarsh grazing is required to maintain a favorable vegetation structure for redshank breeding, grazing management should aim to keep livestock away from redshank nesting habitat between mid-April and mid-July when nests are active, through delaying the onset of grazing or introducing a rotational grazing system
Effective/census population size ratio estimation: a compendium and appraisal

With an ecological-evolutionary perspective increasingly applied toward the conservation and management of endangered or exploited species, the genetic estimation of effective population size (N e) has proliferated. Based on a comprehensive analysis of empirical literature from the past two decades, we asked: (i) how often do studies link N e to the adult census population size (N)? (ii) To what extent is N e correctly linked to N? (iii) How readily is uncertainty accounted for in both N e and N when quantifying N e/N ratios? and (iv) how frequently and to what degree might errors in the estimation of N e or N affect inferences of N e/N ratios? We found that only 20% of available N e estimates (508 of 2617; 233 studies) explicitly attempted to link N e and N; of these, only 31% (160 of 508) correctly linked N e and N. Moreover, only 7% (41 of 508) of N e/N ratios (correctly linked or not) reported confidence intervals for both N e and N; for those cases where confidence intervals were reported for N e only, 31% of N e/N ratios overlapped with 1, of which more than half also reached below N e/N = 0.01. Uncertainty in N e /N ratios thus sometimes spanned at least two orders of magnitude. We conclude that the estimation of N e/N ratios in natural populations could be significantly improved, discuss several options for doing so, and briefly outline some future research directions
Flower resource and land management drives hoverfly communities and bee abundance in semi-natural and agricultural grasslands

1. Pollination is a key ecosystem service, and appropriate management, particularly in agricultural systems, is essential to maintain a diversity of pollinator guilds. However, management recommendations frequently focus on maintaining plant communities, with the assumption that associated invertebrate populations will be sustained. 2. We tested whether plant community, flower resources and soil moisture would influence hoverfly (Syrphidae) abundance and species richness in floristically-rich semi-natural and floristically-impoverished agricultural grassland communities in Wales (U.K.), and compared these to two Hymenoptera genera, Bombus and Lasioglossum. Interactions between environmental variables were tested using generalised linear modelling, and hoverfly community composition examined using canonical correspondence analysis. 3. There was no difference in hoverfly abundance, species richness, or bee abundance, between grassland types. There was a positive association between hoverfly abundance, species richness and flower abundance in unimproved grasslands. However, this was not evident in agriculturally improved grassland, possibly reflecting intrinsically low flower resource in these habitats, or the presence of plant species with low or relatively inaccessible nectar resources. There was no association between soil moisture content and hoverfly abundance or species richness. 4. Hoverfly community composition was influenced by agricultural improvement and the amount of flower resource. Hoverfly species with semi-aquatic larvae were associated with both semi-natural and agricultural wet grasslands, possibly because of localised larval habitat. Despite the absence of differences in hoverfly abundance and species-richness, distinct hoverfly communities are associated with marshy grasslands, agriculturally improved marshy grasslands and unimproved dry grasslands, but not with improved dry grasslands. 5. Grassland plant community cannot be used as a proxy for pollinator community. Management of grasslands should aim to maximise the pollinator feeding resource, as well as maintain plant communities. Retaining waterlogged ground may enhance the number of hoverflies with semi-aquatic larvae.publishersversionPeer reviewe
Tracing coco de mer's reproductive history: Pollen and nutrient limitations reduce fecundity

This is the final version of the article. Available from Wiley Open Access via the DOI in this record.Habitat degradation can reduce or even prevent the reproduction of previously abundant plant species. To develop appropriate management strategies, we need to understand the reasons for reduced recruitment in degraded ecosystems. The dioecious coco de mer palm (Lodoicea maldivica) produces by far the largest seeds of any plant. It is a keystone species in an ancient palm forest that occurs only on two small islands in the Seychelles, yet contemporary rates of seed production are low, especially in fragmented populations. We developed a method to infer the recent reproductive history of female trees from morphological evidence present on their inflorescences. We then applied this method to investigate the effects of habitat disturbance and soil nutrient conditions on flower and fruit production. The 57 female trees in our sample showed a 19.5-fold variation in flower production among individuals over a seven-year period. Only 77.2% of trees bore developing fruits (or had recently shed fruits), with the number per tree ranging from zero to 43. Flower production was positively correlated with concentrations of available soil nitrogen and potassium and did not differ significantly between closed and degraded habitat. Fruiting success was positively correlated with pollen availability, as measured by numbers and distance of neighboring male trees. Fruit set was lower in degraded habitat than in closed forest, while the proportion of abnormal fruits that failed to develop was higher in degraded habitat. Seed size recorded for a large sample of seeds collected by forest wardens varied widely, with fresh weights ranging from 1 to 18 kg. Synthesis: Shortages of both nutrients and pollen appear to limit seed production of Lodoicea in its natural habitat, with these factors affecting different stages of the reproductive process. Flower production varies widely amongst trees, while seed production is especially low in degraded habitat. The size of seeds is also very variable. We discuss the implications of these findings for managing this ecologically and economically important species.Deutsche Forschungsgemeinschaft. Grant Number: KA 3349/2‐1. Eidgenössische Technische Hochschule Zürich. Grant Number: ETH‐37 12‐
Marine protected area restricts demographic connectivity: Dissimilarity in a marine environment can function as a biological barrier

The establishment of marine protected areas (MPAs) can often lead to environmental differences between MPAs and fishing zones. To determine the effects on marine dispersal of environmental dissimilarity between an MPA and fishing zone, we examined the abundance and recruitment patterns of two anemonefishes (Amphiprion frenatus and A.perideraion) that inhabit sea anemones in different management zones (i.e., an MPA and two fishing zones) by performing a field survey and a genetic parentage analysis. We found lower levels of abundance per anemone in the MPA compared to the fishing zones for both species (n=1,525 anemones, p=.032). The parentage analysis also showed that lower numbers of fishes were recruited from the fishing zones and outside of the study area into each anemone in the MPA than into each anemone in the fishing zones (n=1,525 anemones, p<.017). However, the number of self-recruit production per female did not differ between the MPA and fishing zones (n=384 females, p=.516). Because the ocean currents around the study site were unlikely to cause a lower settlement intensity of larvae in the MPA, the ocean circulation was not considered crucial to the observed abundance and recruitment patterns. Instead, stronger top-down control and/or a lower density of host anemones in the MPA were potential factors for such patterns. Our results highlight the importance of dissimilarity in a marine environment as a factor that affects connectivity
Close and distant : contrasting the metabolism of two closely related subspecies of Scots pine under the effects of folivory and summer drought

Imbalance-P paper. contact with Jordi Sardans: j.sardans@creaf.uab.catMetabolomes, as chemical phenotypes of organisms, are likely not only shaped by the environment but also by common ancestry. If this is the case, we expect that closely related species of pines will tend to reach similar metabolomic solutions to the same environmental stressors. We examined the metabolomes of two sympatric subspecies of Pinus sylvestris in Sierra Nevada (southern Iberian Peninsula), in summer and winter and exposed to folivory by the pine processionary moth. The overall metabolomes differed between the subspecies but both tended to respond more similarly to folivory. The metabolomes of the subspecies were more dissimilar in summer than in winter, and iberica trees had higher concentrations of metabolites directly related to drought stress. Our results are consistent with the notion that certain plant metabolic responses associated with folivory have been phylogenetically conserved. The larger divergence between subspecies metabolomes in summer is likely due to the warmer and drier conditions that the northern iberica subspecies experience in Sierra Nevada. Our results provide crucial insights into how iberica populations would respond to the predicted conditions of climate change under an increased defoliation in the Mediterranean Basin
Incorporating ecological functions in conservation decision making

Systematic conservation planning has become a standard approach globally, but prioritization of conservation efforts hardly considers species traits in decision making. This can be important for species persistence and thus adequacy of the conservation plan. Here, we developed and validated a novel approach of incorporating trophic information into a systematic conservation planning framework. We demonstrate the benefits of this approach using fish data from Europe's second largest river, the Danube. Our results show that adding trophic information leads to a different spatial configuration of priority areas at no additional cost. This can enhance identification of priority refugia for species in the lower position of the trophic web while simultaneously identifying areas that represent a more diverse species pool. Our methodological approach to incorporating species traits into systematic conservation planning is generally applicable, irrespective of realm, geographical area, and species composition and can potentially lead to more adequate conservation plans.Griffith Sciences, Australian Rivers InstituteFull Tex
Inbreeding depression is high in a self-incompatible perennial herb population but absent in a self-compatible population showing mixed mating.

High inbreeding depression is thought to be one of the major factors preventing evolutionary transitions in hermaphroditic plants from self-incompatibility (SI) and outcrossing toward self-compatibility (SC) and selfing. However, when selfing does evolve, inbreeding depression can be quickly purged, allowing the evolution of complete self-fertilization. In contrast, populations that show intermediate selfing rates (a mixed-mating system) typically show levels of inbreeding depression similar to those in outcrossing species, suggesting that selection against inbreeding might be responsible for preventing the transition toward complete self-fertilization. By implication, crosses among populations should reveal patterns of heterosis for mixed-mating populations that are similar to those expected for outcrossing populations. Using hand-pollination crosses, we compared levels of inbreeding depression and heterosis between populations of Linaria cavanillesii (Plantaginaceae), a perennial herb showing contrasting mating systems. The SI population showed high inbreeding depression, whereas the SC population displaying mixed mating showed no inbreeding depression. In contrast, we found that heterosis based on between-population crosses was similar for SI and SC populations. Our results are consistent with the rapid purging of inbreeding depression in the derived SC population, despite the persistence of mixed mating. However, the maintenance of outcrossing after a transition to SC is inconsistent with the prediction that populations that have purged their inbreeding depression should evolve toward complete selfing, suggesting that the transition to SC in L. cavanillesii has been recent. SC in L. cavanillesii thus exemplifies a situation in which the mating system is likely not at an equilibrium with inbreeding depression
Survival of a specialist natural enemy experiencing resource competition with an omnivorous predator when sharing the invasive prey #Tuta absoluta#

Can specialist natural enemies persist in ecosystems when competing with omnivorous natural enemies for their shared prey? The consequences of omnivory have been studied theoretically, but empirical studies are still lacking. Omnivory is nevertheless common in nature and omnivorous predators coexist with specialists in many ecosystems, even when they are intraguild predators. This type of association is also common in agroecosystems in which biological control strategies are used. Our study provides an example of the outcome of such an association in the context of biological control of the invasive pest Tuta absoluta (Lepidoptera) in a tomato agroecosystem. The two natural enemies involved, that is, a specialist (Stenomesius japonicus (Hymenoptera) parasitoid) and an omnivore (Macrolophus pygmaeus (Hemiptera) predator), were able to coexist for 3 months in our experimental cages in the absence of metacommunity mechanisms (i.e., emigration and recolonization), contrary to theoretical expectations. However, they negatively affected each other's population dynamics. We found that spatial resource segregation was not a mechanism that promoted their coexistence. Regarding pest control, the specialist and omnivorous natural enemies were found to exhibit complementary functional traits, leading to the best control when together. Mechanisms that may have promoted the coexistence of the two species as well as consequences with regard to the inoculative biological control program are discussed. (Résumé d'auteur
Seasonal variation in daily patterns of social contacts in the European badger Meles meles

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.Social interactions among hosts influence the persistence and spread of infectious pathogens. Daily 20 and seasonal variation in the frequency and type of social interactions will play an important role in 21 disease epidemiology, and alongside other factors may have an influence on wider disease dynamics 22 by causing seasonal forcing of infection, especially if the seasonal variation experienced by a 23 population is considerable. We explored temporal variation in within-group contacts in a high-24 density population of European badgers Meles meles naturally-infected with bovine tuberculosis. 25 Summer contacts were more likely and of longer duration during the daytime, while the frequency 26 and duration of winter contacts did not differ between day and night. In spring and autumn within-27 group contacts peaked at dawn and dusk, corresponding with when they were of shortest duration 28 with reduced potential for aerosol transmission of pathogens. Summer and winter could be critical 29 for bovine tuberculosis transmission in badgers, due to the high frequency and duration of contacts 30 during resting periods, and we discuss the links between this result and empirical data. This study 31 reveals clear seasonality in daily patterns of contact frequency and duration in species living in stable 32 social groups, suggesting that changes in social contacts could drive seasonal forcing of infection in 33 wildlife populations even when the number of individuals interacting remains similar.MJS is funded by NERC grant NE/M004546/1 awarded to RAM, DPC, DJH and MB, with RJD and the 386 APHA team at Woodchester Park, UK as project partners. Data were collected for NW’s PhD, funded 387 by Defra. We thank Jared Wilson-Aggarwal and two anonymous reviewers for useful comments and 388 Keith Silk for providing the photograph for Figure 1
Intraspecific trait variation can weaken interspecific trait correlations when assessing the whole-plant economic spectrum

This research was supported by a grant (UOW1201) from the Royal Society of New Zealand Marsden Fund (DCL), Australian Research Council Discovery Grant DP1094606 (CHL), core funding to Landcare Research from New Zealand's Ministry for Business, Innovation and Employment's Science and Innovation Group and a Hayward Fellowship (PJB and DFRPB), and University of Waikato Scholarships (AHS, KRK-W). DATA ACCESSIBILITY All data used in this study, including all plant traits, by species, for cultivated juveniles, wild juveniles, and wild mature trees are available online at Landcare Research Datastore, https://doi.org/10.7931/j2qn64wd (Laughlin et al., 2017).Peer reviewedPublisher PD
Genome comparisons indicate recent transfer of wRi‐like Wolbachia between sister species Drosophila suzukii and D. subpulchrella

Wolbachia endosymbionts may be acquired by horizontal transfer, by introgression through hybridization between closely related species, or by cladogenic retention during speciation. All three modes of acquisition have been demonstrated, but their relative frequency is largely unknown. Drosophila suzukii and its sister species D. subpulchrella harbor Wolbachia, denoted wSuz and wSpc, very closely related to wRi, identified in California populations of D. simulans. However, these variants differ in their induced phenotypes: wRi causes significant cytoplasmic incompatibility (CI) in D. simulans, but CI has not been detected in D. suzukii or D. subpulchrella. Our draft genomes of wSuz and wSpc contain full-length copies of 703 of the 734 single-copy genes found in wRi. Over these coding sequences, wSuz and wSpc differ by only 0.004% (i.e., 28 of 704,883 bp); they are sisters relative to wRi, from which each differs by 0.014%–0.015%. Using published data from D. melanogaster, Nasonia wasps and Nomada bees to calibrate relative rates of Wolbachia versus host nuclear divergence, we conclude that wSuz and wSpc are too similar—by at least a factor of 100—to be plausible candidates for cladogenic transmission. These three wRi-like Wolbachia, which differ in CI phenotype in their native hosts, have different numbers of orthologs of genes postulated to contribute to CI; and the CI loci differ at several nucleotides that may account for the CI difference. We discuss the general problem of distinguishing alternative modes of Wolbachia acquisition, focusing on the difficulties posed by limited knowledge of variation in absolute and relative rates of molecular evolution for host nuclear genomes, mitochondria, and Wolbachi
The role of species-specific sensory cues in male responses to mating rivals in D. melanogaster fruitflies

Complex sets of cues can be important in recognising and responding to conspecific mating competitors and avoiding potentially costly heterospecific competitive interactions. Within Drosophila. melanogaster, males can detect sensory inputs from conspecifics to assess the level of competition. They respond to rivals by significantly extending mating duration and gain significant fitness benefits from doing so. Here, we tested the idea that the multiple sensory cues used by D. melanogaster males to detect conspecifics also function to minimise ‘off-target’ responses to heterospecific males that they might encounter (D. simulans, D. yakuba. D. pseudoobscura or D. virilis). Focal D. melanogaster males exposed to D. simulans or D. pseudoobscura subsequently increased mating duration, but to a lesser extent than following exposure to conspecific rivals. The magnitude of rivals responses expressed by D. melanogaster males did not align with genetic distance between species and none of the sensory manipulations caused D. melanogaster to respond to males of all other species tested. However, when we removed or provided ‘false’ sensory cues, D. melanogaster males became more likely to show increased mating duration responses to heterospecific males. We suggest that benefits of avoiding inaccurate assessment of the competitive environment may shape the evolution of recognition cues