Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies).

Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, Pyrgilauda theresae. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (Montifringilla nivalis). Our phylogenetic reconstructions unanimously refuted the previously suggested paraphyly of genus Pyrgilauda. Misplacement of one species-level taxon (Onychostruthus tazcanowskii) in previous snowfinch phylogenies was undoubtedly inferred from chimeric mitogenomes that included heterospecific sequence information. Furthermore, comparison of novel and previously generated sequence data showed that the presumed sister-group relationship between M. nivalis and the QTP endemic M. henrici was suggested based on flawed taxonomy. Our phylogenetic reconstructions based on genome-wide SNP data and on mitogenomes were largely congruent and supported reciprocal monophyly of genera Montifringilla and Pyrgilauda with monotypic Onychostruthus being sister to the latter. The Afghan endemic P. theresae likely originated from a rather ancient Pliocene out-of-Tibet dispersal probably from a common ancestor with P. ruficollis. Our extended trans-Palearctic sampling for the white-winged snowfinch, M. nivalis, confirmed strong lineage divergence between an Asian and a European clade dated to 1.5 - 2.7 million years ago (mya). Genome-wide SNP data suggested subtle divergence among European samples from the Alps and from the Cantabrian mountains.

Coping with unpredictable environments: fine-tune foraging microhabitat use in relation to prey availability in an alpine species.

Microhabitat utilisation holds a pivotal role in shaping a species' ecological dynamics and stands as a crucial concern for effective conservation strategies. Despite its critical importance, microhabitat use has frequently been addressed as static, centering on microhabitat preference. Yet, a dynamic microhabitat use that allows individuals to adjust to fine-scale spatio-temporal prey fluctuations, becomes imperative for species thriving in challenging environments. High-elevation ecosystems, marked by brief growing seasons and distinct abiotic processes like snowmelt, winds, and solar radiation, feature an ephemeral distribution of key resources. To better understand species' strategies in coping with these rapidly changing environments, we delved into the foraging behaviour of the white-winged snowfinch Montifringilla nivalis, an emblematic high-elevation passerine. Through studying microhabitat preferences during breeding while assessing invertebrate prey availability, we unveiled a highly flexible microhabitat use process. Notably, snowfinches exhibited specific microhabitat preferences, favoring grass and melting snow margins, while also responding to local invertebrate availability. This behaviour was particularly evident in snow-associated microhabitats and less pronounced amid tall grass. Moreover, our investigation underscored snowfinches' fidelity to foraging sites, with over half located within 10 m of previous spots. This consistent use prevailed in snow-associated microhabitats and high-prey-density zones. These findings provide the first evidence of dynamic microhabitat use in high-elevation ecosystems and offer further insights into the crucial role of microhabitats for climate-sensitive species. They call for multi-faceted conservation strategies that go beyond identifying and protecting optimal thermal buffering areas in the face of global warming to also encompass locations hosting high invertebrate densities.

Spatio-temporal variation in the wintering associations of an alpine bird.

Many animals make behavioural changes to cope with winter conditions, being gregariousness a common strategy. Several factors have been invoked to explain why gregariousness may evolve during winter, with individuals coming together and separating as they trade off the different costs and benefits of living in groups. These trade-offs may, however, change over space and time as a response to varying environmental conditions. Despite its importance, little is known about the factors triggering gregarious behaviour during winter and its change in response to variation in weather conditions is poorly documented. Here, we aimed at quantifying large-scale patterns in wintering associations over 23 years of the white-winged snowfinch Montifringilla nivalis nivalis. We found that individuals gather in larger groups at sites with harsh wintering conditions. Individuals at colder sites reunite later and separate earlier in the season than at warmer sites. However, the magnitude and phenology of wintering associations are ruled by changes in weather conditions. When the temperature increased or the levels of precipitation decreased, group size substantially decreased, and individuals stayed united in groups for a shorter time. These results shed light on factors driving gregariousness and points to shifting winter climate as an important factor influencing this behaviour.

The impact of body mass index and nuclear ß-catenin on survival in locally advanced rectal cancer treated with preoperative radiochemotherapy.

BACKGROUND AND OBJECTIVE: We examined the prognostic value of obesity and nuclear ß-catenin in patients with locally advanced rectal cancer. METHODS: We prospectively recruited a total of 98 eligible patients with locally advanced cancer for preoperative radiochemotherapy followed by total mesorectal excision. Patients' height and weight were reaorded before radiochemotherapy, and the immunohistochemical expression of nuclear ß-catenin was analyzed. Disease-free survival (DFS) was analyzed using the Kaplan-Meier method and a Cox regression model was employed for the multivariate analysis. RESULTS: Obese patients were associated with a lower number of recurrences (3.6% vs. 34.3%, P = 0.001), and a higher DFS (95% vs. 53%; HR, 0.09; 95%CI, 0.01-0.64; P = 0.005) than non-obese patients. In the multivariate analysis, body mass index, nuclear ß-catenin expression, and the absence of lymph node metastases showed a significant increase in DFS. CONCLUSIONS: Obesity and nuclear ß-catenin are independent favorable prognostic factors for DFS in locally advanced cancer treated with preoperative radiochemotherapy. J. Surg. Oncol. 2017;115:301-306. © 2017 Wiley Periodicals, Inc.

Quantifying space use of breeders and floaters of a long-lived species using individual movement data.

To date, animal movement studies have mostly analysed the movement behaviours of individuals at specific times of their lives, but we lack detailed information on how individual movements may be affected by the various and different changes that individuals experience throughout their life (e.g. life history phases, experience, age). Here, we attempt to identify differences in home range and movement behaviour between two different statuses, disperser vs. breeder, of a long-lived species (the eagle owl Bubo bubo). Information on home range and movement behaviour between different stages of an individual life are crucial for species conservation and management, as well as for basic knowledge on space use and rhythm of activity. Does the transition from an exploratory stage to moving within more familiar surroundings call for changes in the movement behaviour? We observed notable differences during the two stages of the owls' lives, with individuals having different home range behaviours and rhythms of activity depending on their social status. Significant differences in home range behaviour between the sexes began only with the acquisition of a breeding site. Breeders showed larger home ranges than dispersing individuals, although nightly variation of home ranges size was higher for dispersers than for breeders. Finally, dispersers were active throughout the night, whereas breeders displayed a less active movement phase at both the beginning and end of the night. Our results demonstrate it is important to consider individual variations in space use and movement behaviour due to the different life history phases that they attain during their lifetime. The knowledge of the different needs of a species across life stages may represent an important tool for species conservation because each phase of an individual life may need different requirements.

Preoperative chemoradiotherapy in rectal cancer induces changes in the expression of nuclear ß-catenin: prognostic significance.

BACKGROUND: Preoperative chemoradiotherapy (CRT) is the cornerstone of treatment for locally advanced rectal cancer (LARC). Although high local control is achieved, overall rates of distant control remain suboptimal. Colorectal carcinogenesis is associated with critical alterations of the Wnt/ß-catenin pathway involved in proliferation and survival. The aim of this study was to assess whether CRT induces changes in the expression of ß-catenin/E-cadherin, and to determine whether these changes are associated with survival. METHODS: The Immunohistochemical expression of nuclear ß-catenin and membranous E-cadherin was prospectively analysed in tumour blocks from 98 stage II/III rectal cancer patients treated with preoperative CRT. Tumour samples were collected before and after CRT treatment. All patients were treated with pelvic RT (46-50 Gy in 2 Gy fractions) and 5-fluorouracil (5FU) intravenous infusion (225 mg/m2) or capecitabine (825 mg/m2) during RT treatment, followed by total mesorectal excision (TME). Disease-free survival (DFS) was analysed using the Kaplan-Meier method and a multivariate Cox regression model was employed for the Multivariate analysis. RESULTS: CRT induced significant changes in the expression of nuclear ß-catenin (49% of patients presented an increased expression after CRT, 17% a decreased expression and 34% no changes; p = 0.001). After a median follow-up of 25 months, patients that overexpressed nuclear ß-catenin after CRT showed poor survival compared with patients that experienced a decrease in nuclear ß-catenin expression (3-year DFS 92% vs. 43%, HR 0.17; 95% CI 0.03 to 0.8; p = 0.02). In the multivariate analysis for DFS, increased nuclear ß-catenin expression after CRT almost reached the cut-off for significance (p = 0.06). CONCLUSIONS: In our study, preoperative CRT for LARC induced significant changes in nuclear ß-catenin expression, which had a major impact on survival. Finding a way to decrease CRT resistance would significantly improve LARC patient survival.

Responses of a top and a meso predator and their prey to moon phases.

We compared movement patterns and rhythms of activity of a top predator, the Iberian lynx Lynx pardinus, a mesopredator, the red fox Vulpes vulpes, and their shared principal prey, the rabbit Oryctolagus cuniculus, in relation to moon phases. Because the three species are mostly nocturnal and crepuscular, we hypothesized that the shared prey would reduce its activity at most risky moon phases (i.e. during the brightest nights), but that fox, an intraguild prey of lynx, would avoid lynx activity peaks at the same time. Rabbits generally moved further from their core areas on darkest nights (i.e. new moon), using direct movements which minimize predation risk. Though rabbits responded to the increased predation risk by reducing their activity during the full moon, this response may require several days, and the moon effect we observed on the rabbits had, therefore, a temporal gap. Lynx activity patterns may be at least partially mirroring rabbit activity: around new moons, when rabbits moved furthest and were more active, lynxes reduced their travelling distances and their movements were concentrated in the core areas of their home ranges, which generally correspond to areas of high density of rabbits. Red foxes were more active during the darkest nights, when both the conditions for rabbit hunting were the best and lynxes moved less. On the one hand, foxes increased their activity when rabbits were further from their core areas and moved with more discrete displacements; on the other hand, fox activity in relation to the moon seemed to reduce dangerous encounters with its intraguild predator.

Superpredation increases mercury levels in a generalist top predator, the eagle owl.

Superpredation can increase the length of the food chain and potentially lead to mercury (Hg) bioaccumulation in top predators. We analysed the relationship of Hg concentrations in eagle owls Bubo bubo to diet composition and the percentage of mesopredators in the diet. Hg levels were measured in the adult feathers of eagle owls from 33 owl territories in the south-western Iberian Peninsula, and in three trophic levels of their prey: primary consumers, secondary consumers and mesopredators. In addition, we studied 6,181 prey in the eagle owl diet. Hg concentrations increased along the food chain, but the concentrations in eagle owls showed considerable variation. The Hg concentration in eagle owls increased when the percentage of mesopredators in the diet increased and the percentage of primary consumers decreased. Superpredation is often related to food stress, and the associated increase in accumulation of Hg may cause additional negative effects on vertebrate top predators. Hg levels in these eagle owl populations are relatively low, but future monitoring is recommended.

Assessing the benefits of composting poultry manure in reducing antimicrobial residues, pathogenic bacteria, and antimicrobial resistance genes: a field-scale study.

The poultry industry in the European Union produces 13 million tons of manure annually, which represents a major health and environmental challenge. Composting is an environmental-friendly technique for the management of manure, but there are few studies about antibiotic residues and antimicrobial resistances at a field scale. The goal of this study was to determine if the composting of poultry manure at a field scale would result in the reduction of antibiotic residues, pathogenic bacteria, and antibiotic resistance genes (ARGs) in the final fertilizer product. A 10-week composting of poultry manure spiked with enrofloxacin, doxycycline, and ciprofloxacin was performed. The determination of antibiotics residues and 22 selected ARGs was carried out together with the identification of bacteria by metagenomics. In the case of ciprofloxacin and doxycycline, a 90% decrease was observed after composting for 3 weeks. Sixteen ARGs were detected at the beginning of the experiment; 12 of them decreased from week 0 to week 10 (reduction of 73.7-99.99%). The presence of potentially pathogenic bacteria, such as, Campylobacter coli or commensal bacteria such as Escherichia coli decreases along the composting process. In conclusion, 10-week composting of poultry manure promotes the reduction of antibiotic residues and most of the ARGs and pathogenic bacteria.

Behavioral states help translate dispersal movements into spatial distribution patterns of floaters.

Within the field of spatial ecology, it is important to study animal movements in order to better understand population dynamics. Dispersal is a nonlinear process through which different behavioral mechanisms could affect movement patterns. One of the most common approaches to analyzing the trajectories of organisms within patches is to use random-walk models to describe movement features. These models express individual movements within a specific area in terms of random-walk parameters in an effort to relate movement patterns to the distributions of organisms in space. However, only using the movement trajectories of individuals to predict the spatial spread of animal populations may not fit the complex distribution of individuals across heterogeneous environments. When we empirically tested the results from a random-walk model (a residence index) used to predict the spatial equilibrium distribution of individuals, we found that the index severely underestimated the spatial spread of dispersing individuals. We believe this is because random-walk models only account for the effects of environmental conditions on individual movements, completely overlooking the crucial influence of behavior changes over time. In the future, both aspects should be accounted for when predicting general rules of (meta)population abundance, distribution, and dynamics from patterns of animal movements.

The environmental footprint of an organic peri-urban orchard network.

Over the past years, the implementation of urban and peri-urban orchards in cities has increased and so has the environmental awareness regarding these systems. This study applied the environmental extended multi-regional input-output analysis to obtain the Environmental Footprint associated with an organic peri-urban orchard network in Spain. The total environmental impacts were calculated for seven organic peri-urban orchards identified as PUO1 to PUO7. PUO1, PUO4 and PUO6 presented the highest environmental impacts due to a higher consumption of (1) fuel, (2) plastics and (3) electricity in comparison to the other orchards. Approximately 70% of the overall impacts were indirect impacts generated in the supply chain. A more in-depth study of climate change impacts in the supply chain of the organic peri-urban orchard network revealed that the major hotspots were the sectors "extraction of crude petroleum" (29%) and "production of electricity by gas and coal" (31%) located in Spain, China and Middle East countries. The Environmental Footprint serves as a useful indicator to provide the environmental performance of an organic peri-urban orchard network and foster greener and more sustainable cities.

The importance of individual variation in the dynamics of animal collective movements.

Animal collective movements are a key example of a system that links two clearly defined levels of organization: the individual and the group. Most models investigating collective movements have generated coherent collective behaviours without the inclusion of individual variability. However, new individual-based models, together with emerging empirical information, emphasize that within-group heterogeneity may strongly influence collective movement behaviour. Here we (i) review the empirical evidence for individual variation in animal collective movements, (ii) explore how theoretical investigations have represented individual heterogeneity when modelling collective movements and (iii) present a model to show how within-group heterogeneity influences the collective properties of a group. Our review underscores the need to consider variability at the level of the individual to improve our understanding of how individual decision rules lead to emergent movement patterns, and also to yield better quantitative predictions of collective behaviour.This article is part of the theme issue 'Collective movement ecology'.

Genetics of dispersal.

Dispersal is a process of central importance for the ecological and evolutionary dynamics of populations and communities, because of its diverse consequences for gene flow and demography. It is subject to evolutionary change, which begs the question, what is the genetic basis of this potentially complex trait? To address this question, we (i) review the empirical literature on the genetic basis of dispersal, (ii) explore how theoretical investigations of the evolution of dispersal have represented the genetics of dispersal, and (iii) discuss how the genetic basis of dispersal influences theoretical predictions of the evolution of dispersal and potential consequences. Dispersal has a detectable genetic basis in many organisms, from bacteria to plants and animals. Generally, there is evidence for significant genetic variation for dispersal or dispersal-related phenotypes or evidence for the micro-evolution of dispersal in natural populations. Dispersal is typically the outcome of several interacting traits, and this complexity is reflected in its genetic architecture: while some genes of moderate to large effect can influence certain aspects of dispersal, dispersal traits are typically polygenic. Correlations among dispersal traits as well as between dispersal traits and other traits under selection are common, and the genetic basis of dispersal can be highly environment-dependent. By contrast, models have historically considered a highly simplified genetic architecture of dispersal. It is only recently that models have started to consider multiple loci influencing dispersal, as well as non-additive effects such as dominance and epistasis, showing that the genetic basis of dispersal can influence evolutionary rates and outcomes, especially under non-equilibrium conditions. For example, the number of loci controlling dispersal can influence projected rates of dispersal evolution during range shifts and corresponding demographic impacts. Incorporating more realism in the genetic architecture of dispersal is thus necessary to enable models to move beyond the purely theoretical towards making more useful predictions of evolutionary and ecological dynamics under current and future environmental conditions. To inform these advances, empirical studies need to answer outstanding questions concerning whether specific genes underlie dispersal variation, the genetic architecture of context-dependent dispersal phenotypes and behaviours, and correlations among dispersal and other traits.