bluuebunny/crossref_metadata_2025_split huggingface dataset:
The path to host extinction can lead to loss of generalist parasites
Authors: Farrell Maxwell J. , Stephens Patrick R. , Berrang‐Ford Lea , Gittleman John L. , Davies T. Jonathan 
Published: January 2015

SummaryHost extinction can alter disease transmission dynamics, influence parasite extinction and ultimately change the nature of host–parasite systems. While theory predicts that single‐host parasites are among the parasite species most susceptible to extinction following declines in their hosts, documented parasite extinctions are rare.Using a comparative approach, we investigate how the richness of single‐host and multi‐host parasites is influenced by extinction risk among ungulate and carnivore hosts. Host–parasite associations for free‐living carnivores (orderCarnivora) and terrestrial ungulates (ordersPerissodactyla + Cetartiodactyla minus cetaceans) were merged with host trait data andIUCN RedList status to explore the distribution of single‐host and multi‐host parasites among threatened and non‐threatened hosts.We find that threatened ungulates harbour a higher proportion of single‐host parasites compared to non‐threatened ungulates, which is explained by decreases in the richness of multi‐host parasites. However, among carnivores threat status is not a significant predictor of the proportion of single‐host parasites, or the richness of single‐host or multi‐host parasites.The loss of multi‐host parasites from threatened ungulates may be explained by decreased cross‐species contact as hosts decline and habitats become fragmented. Among carnivores, threat status may not be important in predicting patterns of parasite specificity because host decline results in equal losses of both single‐host parasites and multi‐host parasites through reduction in average population density and frequency of cross‐species contact.Our results contrast with current models of parasite coextinction and highlight the need for updated theories that are applicable across host groups and account for both inter‐ and intraspecific contact.
No apparent benefits of allonursing for recipient offspring and mothers in the cooperatively breeding meerkat
Authors: MacLeod Kirsty J. , McGhee Katie E. , Clutton‐Brock Tim H. 
Published: January 2015

SummaryCooperative behaviours by definition are those that provide some benefit to another individual. Allonursing, the nursing of non‐descendent young, is often considered a cooperative behaviour and is assumed to provide benefits to recipient offspring in terms of growth and survival, and to their mothers, by enabling them to share the lactation load. However, these proposed benefits are not well understood, in part because maternal and litter traits and other ecological and social variables are not independent of one another, making patterns hard to discern using standard univariate analyses.Here, we investigate the potential benefits of allonursing in the cooperatively breeding Kalahari meerkat, where socially subordinate females allonurse the young of a dominant pair without having young of their own.We use structural equation modelling to allow us to account for the interdependence of maternal traits, litter traits and environmental factors.We find no evidence that allonursing provides benefits to pups or mothers. Pups that received allonursing were not heavier at emergence and did not have a higher survival rate than pups that did not receive allonursing. Mothers whose litters were allonursed were not in better physical condition, did not reconceive faster and did not reduce their own nursing investment compared to mothers who nursed their litters alone. These patterns were not significantly influenced by whether mothers were in relatively good, or poor, condition.We suggest that allonursing may persist in this species because the costs to allonurses may be low. Alternatively, allonursing may confer other, more cryptic, benefits to pups or allonurses, such as immunological or social benefits.
Long‐term C, N and P allocation to reproduction in Bornean tropical rain forests
Authors: Kitayama Kanehiro , Tsujii Yuki , Aoyagi Ryota , Aiba Shin‐ichiro 
Published: January 2015

Summary

Tropical rain forests in SE Asia are well known for the occurrence of supra‐annual synchronous reproductive events, masting. Answering the question how trees allocate carbon (C), nitrogen (N) and phosphorus (P) to such irregular but gregarious reproduction requires a long‐term observation. We conducted a 10‐year continuous monitoring of litterfall in eight tropical rain forests, which differ significantly in P (and N) availability on Mount Kinabalu, Borneo.

Mean P concentration in reproductive organ litter decreased significantly with increasing P‐use efficiency of net primary production (PUE), an index of P deficiency. Therefore, P in reproductive organ litter became diluted as the magnitude of P deficiency increased.

Mean annual litterfall (kg ha−1 yr−1) of reproductive organs over the 10 years ranged from 128.5 to 730.9 across the eight forests. Long‐term C allocation ratio to reproductive organs (i.e. C in reproductive organs per C in total litterfall) varied from 2.0% to 7.8% across the eight forests and did not relate with PUE, indicating that long‐term C allocation ratio to reproduction was not controlled by the availability of the most critical soil nutrient.

Long‐term N allocation ratio to reproduction varied from 2.7% to 9.9% and significantly positively related with C allocation ratio. The quotient of N allocation ratio to C allocation ratio ranged from 1.1 to 1.4. Long‐term P allocation ratio to reproduction varied from 9.8% to 16.4%. The quotient of P allocation ratio to C allocation ratio ranged from 1.6 to 5.0. Therefore, tropical trees allocated much greater proportion of P to reproduction than C and N over the 10 years. Moreover, trees disproportionately increased P allocation to reproduction with decreasing C allocation to reproduction. Trees adjusted P allocation relative to C allocation and maintained a narrow range of P allocation ratio to reproduction in the long run in each site.

Synthesis. Reproduction in Bornean tropical rain forests costs more P than C and N. Our results suggest that reproductive events in these forests are regulated by P at the level of overall long‐term mean. Understanding patterns and processes of reproductive events requires a long‐term monitoring of nutrient dynamics.
Niche construction by growth forms is as strong a predictor of species diversity as environmental gradients
Authors: Bråthen Kari Anne , Ravolainen Virve Tuulia 
Published: January 2015

Summary

We present a conceptual framework that describes how species belonging to a growth form collectively can be niche constructors (i.e. modify niches) and affect species diversity in plant communities. We use an empirical assessment of tundra plant communities to illustrate the framework's utility. In doing so, we make a first investigation of collective niche construction in ecological communities.

In tundra plant communities, growth forms differently affect ecosystem process rates and cause environmental modifications; thus, growth forms are strong candidates for being niche constructors. To assess the impact of growth form niche construction on plant species diversity, we excluded the species of the growth form applied as niche constructor when estimating the community species diversity.

We assessed niche construction in 70 tundra meadow communities and 1450 randomly selected tundra plant communities that are distributed along ecological gradients in temperature, resource availability, competitive interference and herbivory. These gradients allowed us to concomitantly assess to what extent the niche construction is independent of environmental conditions.

Growth forms varied from strong positive to neutral predictors of both species richness and Simpson index in the order of forbs, grasses, sedges, deciduous shrubs and evergreen shrubs, suggesting that growth forms have important roles as niche constructors in tundra plant communities. Also, the environmental conditions were strong predictors of species diversity, but they did not interact with or confound the effects of growth forms.

Forbs and grasses were the least abundant growth forms, yet they were the strongest positive predictors of species diversity. Therefore, our results suggest a particular niche‐constructing role of these growth forms for enhancing species diversity in tundra plant communities.

Synthesis. In this study, we provide conceptual and empirical evidence for collective niche construction as a powerful ecological process that affects species diversity and that can act independently of environmental conditions. Species sharing a single trait or species belonging to a growth form can act as collective niche constructors, and as exemplified for growth forms in this study, be important predictors of species diversity in ecological communities.
Measuring quality of life in children with speech and language difficulties: a systematic review of existing approaches
Authors: Gomersall Tim , Spencer Sarah , Basarir Hasan , Tsuchiya Aki , Clegg Judy , Sutton Anthea , Dickinson Kath 
Published: January 2015

AbstractBackgroundChildren's and adolescent's speech and language difficulties (SaLD) can affect various domains of quality of life (QoL), and speech and language therapy interventions are critical to improving QoL. Systematically measuring QoL outcomes in this population is highly complex due to factors such as heterogeneity in impairments and differing targets during intervention. However, measurements of QoL are increasingly required by healthcare commissioners and policy‐makers to inform resource allocation.AimsTo review the use of QoL measures in research involving children (age ≤ 18 years) with SaLD.Methods & ProceduresA systematic review was undertaken. A systematic search across various databases was performed. Information on the methodological details of each relevant study, along with descriptions of the QoL measures employed, were extracted into standardized data extraction forms. Findings were discussed in a narrative synthesis.Outcomes & ResultsTwenty‐one relevant studies were identified that deal with a range of subpopulations of children with SaLD. For the most part, generic QoL measures were used, although there was little convergence on the type of QoL measures employed throughout the literature. Five studies utilized preference‐based QoL measures, including the 16D/17D, HUI3, EQ‐5D and QWB‐SA. Of these measures, the HUI3 demonstrated the most promising discriminant validity, although the preference weights for this measure were generated with adults.Conclusions & ImplicationsQoL among children with SaLD is not yet being captured in a systematic way. The HUI3 measure appears to show some promise for generating relevant preference‐based QoL estimates, although further testing of the measure is required.
AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data
Authors: Sovic Michael G. , Fries Anthony C. , Gibbs H. Lisle 
Published: January 2015

AbstractAn increase in studies using restriction site‐associated DNA sequencing (RADseq) methods has led to a need for both the development and assessment of novel bioinformatic tools that aid in the generation and analysis of these data. Here, we report the availability of AftrRAD, a bioinformatic pipeline that efficiently assembles and genotypes RADseq data, and outputs these data in various formats for downstream analyses. We use simulated and experimental data sets to evaluate AftrRAD's ability to perform accurate de novo assembly of loci, and we compare its performance with two other commonly used programs, stacks and pyrad. We demonstrate that AftrRAD is able to accurately assemble loci, while accounting for indel variation among alleles, in a more computationally efficient manner than currently available programs. AftrRAD run times are not strongly affected by the number of samples in the data set, making this program a useful tool when multicore systems are not available for parallel processing, or when data sets include large numbers of samples.
High‐throughput genotyping for species identification and diversity assessment in germplasm collections
Authors: Mason Annaliese S. , Zhang Jing , Tollenaere Reece , Vasquez Teuber Paula , Dalton‐Morgan Jessica , Hu Liyong , Yan Guijun , Edwards David , Redden Robert , Batley Jacqueline 
Published: January 2015

AbstractGermplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high‐throughput genotyping tools can provide a fast, efficient and cost‐effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A‐ and C‐genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crops, high‐throughput molecular genotyping will offer an efficient and cost‐effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers.
When Do Analysts Adjust for Biases in Management Guidance? Effects of Guidance Track Record and Analysts' Incentives
Authors: Tan H.‐T. , Libby R. , Hunton J. E. 
Published: January 2015

The above article has been retracted at the request of authors Robert Libby and Hun‐Tong Tan, in agreement with the Editor‐in‐Chief, Patricia C. O'Brien, the copyright holder, the Canadian Academic Accounting Association (CAAA), and Wiley Periodicals, Inc.Bentley University conducted an investigation confirming that Dr. J. E. Hunton, while a faculty member at Bentley University and without the knowledge of his co‐authors, engaged in research misconduct, specifically data fabrication. Dr. Hunton provided the data used in the above study, and did not respond to a request for comment. Based on Bentley's initial report and further investigation into details specific to this paper, we conclude that the validity of the data cannot be confirmed. To correct the academic literature and maintain standards of academic integrity, we therefore retract the paper.The article was published online in Contemporary Accounting Research on 13 May 2010, in Wiley Online (wileyonlinelibrary.com).ReferenceTan, H.‐T., R. Libby, and J. E. Hunton. 2010. . Contemporary Accounting Research 27 (): 187–208. doi: 10.1111/j.1911‐3846.2010.01006.x
Approximate Bayesian Computation of diversification rates from molecular phylogenies: introducing a new efficient summary statistic, the nLTT
Authors: Janzen Thijs , Höhna Sebastian , Etienne Rampal S. 
Published: January 2015

Summary

Molecular phylogenies form a potential source of information on rates of diversification, and the mechanisms that underlie diversification patterns. Diversification models have become increasingly complex over the past decade, and we have reached a point where the computation of the analytical likelihood of the model given a phylogeny is either unavailable or intractable. For such models, a likelihood‐free approach such as Approximate Bayesian Computation (ABC) offers a solution. ABC is a Bayesian framework that uses one or more summary statistics instead of the likelihood function. Crucial to the performance of an ABC algorithm is the choice of summary statistics.

Here, we analyse the applicability of three traditional and often‐used summary statistics (Gamma statistic, Phylogenetic Diversity and tree size) within an ABC framework and propose a new summary statistic: the normalized Lineages‐Through‐Time (nLTT) statistic.

We find that the traditional summary statistics perform poorly and should not be used as a substitute of the likelihood. By contrast, we find that the nLTT statistic performs on par with the likelihood.

We suggest to include the nLTT statistic in future ABC applications within phylogenetics. We argue that the use of ABC in diversification rate analysis is a promising new approach, but that care should be taken which summary statistics are chosen.
Using species distribution models to select species resistant to climate change for ecological restoration of bowé in West Africa
Authors: Padonou Elie A. , Teka Oscar , Bachmann Yvonne , Schmidt Marco , Lykke Anne Mette , Sinsin Brice 
Published: January 2015

AbstractBowalization is a particular form of land degradation and leads to lateral expansion of ferricrete horizons. The process occurs only in tropical regions. In this study, the most adapted and resistant species towards climate change were identified on bowé. The 15 most common bowé species of the subhumid and semi‐arid climate zones of Benin were submitted together with significant environmental variables (elevation, current bioclimatic variables, soil types) to three ecological niche modelling programmes (Maxent, Domain and GARP). For future prediction (2050), IPCC4/CIAT and IPCC5/CMIP5 climate data were applied. Asparagus africanus, Andropogon pseudapricus and Combretum nigricans were identified as the most resistant species for ecological restoration of bowé in the semi‐arid climate zone and Asparagus africanus, Detarium microcarpum and Lannea microcarpa in the subhumid climate zone. The ‘Pull’ strategies were identified as appropriate for ecological restoration of bowé in Benin.
Parental fat‐free mass is related to the fat‐free mass of infants and maternal fat mass is related to the fat mass of infant girls
Authors: Henriksson Pontus , Löf Marie , Forsum Elisabet 
Published: January 2015

AbstractAimExisting studies suggest that weight and body composition of parents influence the size and body composition of their offspring, but are often inconclusive and conducted by means of inappropriate body composition methodology. Our aim was to study infant size and body composition variables in relation to body composition variables of their mothers and fathers in a well‐nourished population using an accurate methodology.MethodsBetween 2008 and 2011, we used air displacement plethysmography to measure the body composition of 209 parent–infant units. Parents were measured when women were in gestational week 32. Their healthy, singleton, full‐term infants were measured at 1 week.ResultsInfant fat‐free mass in grams was positively related (p ≤ 0.007) to the fat‐free mass in kilograms of the mothers (15.6 g/kg) and the fathers (9.1 g/kg). Furthermore, the fat mass of the daughters, but not of the sons, was positively related to the fat mass of the mothers (5.8 g/kg, p = 0.007).ConclusionThis study found associations between the fat‐free mass of parents and infants and an association between the fat mass of mothers and their infant girls. These findings may help to understand early life factors behind overweight and obesity.
The incidence of type 1 diabetes is still increasing in the Netherlands, but has stabilised in children under five (Young DUDEs‐1)
Authors: Spaans Engelina A. J. M. , Gusdorf Lisette M. A. , Groenier Klaas H. , Brand Paul L. P. , Veeze Henk J. , Reeser Hans M. , Bilo Henk J. G. , Kleefstra Nanne 
Published: January 2015

AbstractAimThis study described the incidence and prevalence of type 1 diabetes in children in the Netherlands in 2010–2011 and to compare these results with earlier studies.MethodsThis was a retrospective nationwide cohort study of Dutch children aged 14 years or younger. Patients were identified using health insurance reimbursement registries for hospital care and invoices for insulin. In the Netherlands, all children with diabetes are treated by hospital‐based paediatricians and health care for all Dutch citizens is covered by law.ResultsThe incidence of type 1 diabetes almost doubled between 1978–1980 and 2010–2011, from 11.1 to 21.4 per 100 000. In the youngest age group, who were under 5 years, the incidence rate doubled between 1996 and 1999 and remained stable after that. There were no relevant incidence differences between the sexes. The overall prevalence of type 1 diabetes in the Netherlands during 2009–2011 was 143.6 (95% confidence interval 141.1–146.2) per 100 000 children and was similar for boys and girls.ConclusionThe incidence of type 1 diabetes in children in the Netherlands almost doubled between 1978–1980 and 2010–2011, but the incidence in children under 5 years appeared to stabilise between 1996 and 1999. There were no statistical differences between the sexes.
Condition‐dependence, pleiotropy and the handicap principle of sexual selection in melanin‐based colouration
Authors: Roulin Alexandre 
Published: January 2015

ABSTRACTThe signalling function of melanin‐based colouration is debated. Sexual selection theory states that ornaments should be costly to produce, maintain, wear or display to signal quality honestly to potential mates or competitors. An increasing number of studies supports the hypothesis that the degree of melanism covaries with aspects of body condition (e.g. body mass or immunity), which has contributed to change the initial perception that melanin‐based colour ornaments entail no costs. Indeed, the expression of many (but not all) melanin‐based colour traits is weakly sensitive to the environment but strongly heritable suggesting that these colour traits are relatively cheap to produce and maintain, thus raising the question of how such colour traits could signal quality honestly. Here I review the production, maintenance and wearing/displaying costs that can generate a correlation between melanin‐based colouration and body condition, and consider other evolutionary mechanisms that can also lead to covariation between colour and body condition. Because genes controlling melanic traits can affect numerous phenotypic traits, pleiotropy could also explain a linkage between body condition and colouration. Pleiotropy may result in differently coloured individuals signalling different aspects of quality that are maintained by frequency‐dependent selection or local adaptation. Colouration may therefore not signal absolute quality to potential mates or competitors (e.g. dark males may not achieve a higher fitness than pale males); otherwise genetic variation would be rapidly depleted by directional selection. As a consequence, selection on heritable melanin‐based colouration may not always be directional, but mate choice may be conditional to environmental conditions (i.e. context‐dependent sexual selection). Despite the interest of evolutionary biologists in the adaptive value of melanin‐based colouration, its actual role in sexual selection is still poorly understood.