bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian Node Dating based on Probabilities of Fossil Sampling Supports Trans-Atlantic Dispersal of Cichlid Fishes
Authors: Matschiner Michael , Musilová Zuzana , Barth Julia M. I. , Starostová Zuzana , Salzburger Walter , Steel Mike , Bouckaert Remco 
Published: February 2016

AbstractDivergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two non-exclusive alternative approaches have recently been developed, the “fossilized birth-death” model and “total-evidence dating”. While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher-level taxa. We here develop a flexible new approach to Bayesian node dating that combines advantages of traditional node dating and the fossilized birth-death model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated datasets, and compare its performance to that of the fossilized birth-death model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the fossilized birth-death model. By applying our approach to a large dataset including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for trans-oceanic dispersal of cichlids and other groups of teleost fishes. (Keywords: node dating; calibration density; relaxed molecular clock; fossil record; Cichlidae; marine dispersal)
Phenotypic plasticity promotes balanced polymorphism in periodic environments by a genomic storage effect
Authors: Gulisija Davorka , Kim Yuseob , Plotkin Joshua B. 
Published: February 2016

ABSTRACTPhenotypic plasticity is known to evolve in perturbed habitats, where it alleviates the deleterious effects of selection. But the effects of plasticity on levels of genetic polymorphism, an important precursor to adaptation in temporally varying environments, are unclear. Here we develop a haploid, two-locus population-genetic model to describe the interplay between a plasticity modifier locus and a target locus subject to periodically varying selection. We find that the interplay between these two loci can produce a “genomic storage effect” that promotes balanced polymorphism over a large range of parameters, in the absence of all other conditions known to maintain genetic variation. The genomic storage effect arises as recombination allows alleles at the two loci to escape more harmful genetic backgrounds and associate in haplotypes that persist until environmental conditions change. Using both Monte Carlo simulations and analytical approximations we quantify the strength of the genomic storage effect across a range of selection pressures, recombination rates, plasticity modifier effect sizes, and environmental periods.
Variations in MHC-DRB1 exon2 and associations with Brucellosis susceptibility in Chinese Merino sheep
Authors: Chen Yue’e , Xu Wanyun , Chen Chuangfu , Blair Hugh T , Gao Jianfeng 
Published: February 2016

AbstractThe aim of this study was to investigated the association between MHC-DRB1 exon2 and Brucellosis susceptibility in Chinese Merino sheep. MHC-DRB1 exon2 was amplified by polymerase chain reaction (PCR) from 126 healthy and 67 Brucellosis-infected Chinese Merino sheep. PCR products were analyzed using the SSCP technique, and then cloned to allow sequencing of the different alleles. For each SNP, allelic and genotypic frequencies were compared between case and control samples, in addition the association with Brucellosis susceptibility was determined. Haplotypes and their frequencies were established and analyzed by SHEsis online software. There were forty-one single nucleotide polymorphisms (SNPs) in the 270 bp DNA sequence. The distribution of C>T alleles at locus 109 was significantly different between case and control samples. The linkage disequilibrium (LD) analysis showed that there were nine LD blocks in MHC-DRB1 exon2 and strong LD between SNPs existed in every Block. Haplotype analysis identified nine haplotypes with strong LD, but only Hap8 and Hap9 in case-control groups were significantly different (P<0.05); neither haplotype contained the C>T allele at locus 109. In conclusion, genetic variants of MHC-DRB1 gene exon2 demonstrated associations with Brucellosis susceptibility, indicating that further research is warranted.AbbreviationsMHCMajor Histocompatibility ComplexOLAOvine Lymphocyte AntigenSNPSingle Nucleotide Polymorphism
Development of molecular markers for determining continental origin of wood from white oaks (QuercusL. sect.Quercus)
Authors: Schroeder H. , Cronn R. , Yanbaev Y. , Jennings T. , Mader M. , Degen B. , Kersten B. 
Published: February 2016

AbstractTo detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of Asian Q. mongolica as a reference, we identified 861 variant sites (672 single nucleotide polymorphisms (SNPs); 189 insertion/deletion (indel) polymorphism) from representative species of three continents (Q. mongolica from Asia; Q. petraea and Q. robur from Europe; Q. alba from North America), and we identified additional chloroplast polymorphisms in pools of 20 individuals each from Q. mongolica (789 variant sites) and Q. robur (346 variant sites). Genome sequences were screened for insertion/deletion (indel) polymorphisms to develop markers that identify continental origin of oak species, and that can be easily evaluated using a variety of detection methods. We identified five indel and one SNP that reliably identify continent-of-origin, based on evaluations of up to 1078 individuals representing 13 white oak species and three continents. Due to the size of length polymorphisms revealed, this marker set can be visualized using capillary electrophoresis or high resolution gel (acrylamide or agarose) electrophoresis. With these markers, we provide the wood trading market with an instrument to comply with the U.S. and European laws that require timber companies to avoid the trade of illegally harvested timber.
Genome-wide association analysis identifies novel loci for chronotype in 100,420 individuals from the UKBiobank
Authors: Lane Jacqueline M. , Vlasac Irma , Anderson Simon G. , Kyle Simon , Dixon William G. , Bechtold David A. , Gill Shubhroz , Little Max A. , Luik Annemarie , Loudon Andrew , Emsley Richard , Scheer Frank AJL. , Lawlor Deborah A. , Redline Susan , Ray David W. , Rutter Martin K. , Saxena Richa 
Published: February 2016

AbstractOur sleep timing preference, or chronotype, is a manifestation of our internal biological clock. Variation in chronotype has been linked to sleep disorders, cognitive and physical performance, and chronic disease. Here, we perform a genome-wide association study of self-reported chronotype within the UKBiobank cohort (n=100,420). We identify 12 new genetic loci that implicate known components of the circadian clock machinery and point to previously unstudied genetic variants and candidate genes that might modulate core circadian rhythms or light-sensing pathways. Pathway analyses highlight central nervous and ocular systems and fear-response related processes. Genetic correlation analysis suggests chronotype shares underlying genetic pathways with schizophrenia, educational attainment and possibly BMI. Further, Mendelian randomization suggests that evening chronotype relates to higher educational attainment. These results not only expand our knowledge of the circadian system in humans, but also expose the influence of circadian characteristics over human health and life-history variables such as educational attainment.
Islamic ethical responsibilities for business and sustainable development
Authors: Hassan Abul 
Published: February 2016

Purpose
– The purpose of this paper is to address the issue of environmental development in view of the Islamic ethical responsibilities, and the extent to which businesses should be involved in environment development activities will be addressed.

Design/methodology/approach
– This study integrates the mainstream and Islamic positions on the subject of the environment and sustainable development based on published literature and argues that whichever definition of environmental development one might subscribe to eventually each arrives at an environmental concern. It takes inspiration from the verses of the Holy Quran and ethics of the sayings of Prophet Muhammad (peace be upon him) in respect of environment and business that indicate a way out of this impasse.

Findings
– This study shows that the Islamic approach is more agreeable to environmental protection, and the issues associated with environmental and sustainable development have moral, ethical and social responsibilities, and the businesses should have on intense commitment to Islamic ethics in justice and welfare of human beings. Because of environmental ethics in Islam, and the value chain of suppliers through customers, businesses should be aware of the environmental aspects and impacts of their companies.

Originality/value
– This paper enhances the understanding of Islamic ethical responsibilities in business, environmental and sustainable development and attempts to show attributes of the various levels of behaviour of an organisation.
Efficiency analysis of Islamic banks in Pakistan
Authors: Majeed Muhammad Tariq , Zanib Abida 
Published: February 2016

Purpose– This paper aims to empirically analyze the efficiency of full-fledged Islamic banks, Islamic branches of conventional banks and conventional banks in Pakistan.Design/methodology/approach– The paper uses data envelopment analysis to measure and compare the efficiency of banks. Three measures of efficiencies such as total technical efficiency, pure technical efficiency and scale efficiency are computed to achieve the objective of the paper.Findings– Overall, full-fledged Islamic banks are less efficient in terms of total technical efficiency and pure technical efficiency than conventional banks. However, Islamic branches of conventional banks are highly scale-efficient than their counterparts.Research limitations/implications– The findings need to be supported by considering production function and risk exposure factors.Originality/value– This paper evaluates and compares the efficiency of Islamic and conventional banks by utilizing the largest available data set during 2007-2014.
Efficiency, effectiveness and performance profile of Islamic and conventional banks in Pakistan
Authors: Abbas Muhammad , Azid Toseef , Hj Besar Mohd Hairul Azrin 
Published: February 2016

Purpose– Although there exists a huge pile of literature on the performance of banking sector, a gap exists in developing countries like Pakistan where only limited work has been previously done to evaluate the performance of banking sector. In fact, most of the previous studies are based on traditional ratio analysis. Other studies not only have applied modern techniques of frontier approach like data envelopment analysis (DEA) but also are limited to the measurement and comparison of efficiency scores of various groups of banks. The purpose of this study is to find out the determinant of variation in the performance of banks.Design/methodology/approach– This study computes various elements of performance, including efficiency and effectiveness, and finds out the factors of variation in each component of performance by using the Tobit regression.Findings– Overall performance of Islamic banks was influenced positively by age, capitalization, size, non-markup expenditure, minimum capital requirement and gross domestic product (GDP) growth rate, whereas profitability, concentration and inflation had a negative relationship.Research limitations/implications– Islamic financial institutions are in their infancy stage. With the passage of time, one can find the exact trend in the performance and efficiency of these institutions.Practical implications– This study guides the investors in the process of their decision-making.Social implications– Society can also take the advantage of the moral steps which are taken by these institutions.Originality/value– This is an original study.
Employee motivation an Islamic perspective
Authors: Bhatti Omar K , Aslam Uzma  S , Hassan Arif , Sulaiman Mohamed 
Published: February 2016

Purpose
– This paper aims to provide an understanding of employee motivation from the Islamic perspective. The main objective of this paper is to understand Islamic motivation and to explore if Islamic spirituality, punishment and reward and justice motivate Muslim employees.

Design/methodology/approach
– Qualitative research approach was used to understand and examine the views of the respondents. Semi-structured interviewing technique was adopted, and the respondents were asked to share their own thoughts and understanding for each question provided. A sample of 13 experienced academicians and practitioners from renowned private organizations and academic institutions from Malaysia and Pakistan were selected for the present study.

Findings
– The study found that the conventional viewpoint of motivation varies from Islamic viewpoint in regard to motivation of employees. And significantly, Islamic spirituality, reward and punishment, and justice act more compellingly in improving employee’s motivation.

Originality/value
– This paper clearly highlights that the Western viewpoint of employee motivation is different as compared to the Islamic perspective.
Doping scandals in professional cycling: impact on primary team sponsor’s stock return
Authors: Danylchuk Karen , Stegink Jelmer , Lebel Katie 
Published: February 2016

Purpose– The purpose of this paper is to examine the impact of doping scandals (n=25) in professional cycling Grand Tour events on the primary team sponsor’s daily stock return.Design/methodology/approach– Event study methodology.Findings– Overall it was found that during the time period and events under examination in this study doping scandals had no significant impact on the primary team sponsor’s stock returns.Originality/value– There is limited research to explain the economic impact of widespread doping in cycling and its commercial shareholders. This study addresses this gap by examining the relationship between doping scandals in professional cycling and the daily stock return of the involved team’s primary sponsor.
The economic benefit of time‐varying surveillance effort for invasive species management
Authors: Holden Matthew H. , Nyrop Jan P. , Ellner Stephen P. 
Published: February 2016

SummaryGovernment agencies develop invasive species management programmes assuming early detection is key to successful management. Some theoretical studies confirm this intuition, while others, which restrict sampling effort to be constant in time, suggest managers are investing too heavily in sampling to detect new local invader populations.We explore whether these optimal constant‐effort strategies underplay the importance of early surveillance and determine how much changing sampling effort through time reduces total management costs.Using optimal control theory to calculate time‐dependent surveillance policies that minimize the total cost of sampling, eradication, and damage by the invasive, we find that the best strategies often use intense early sampling, followed by reduced sampling effort.Intense early sampling can drastically reduce costs compared with constant‐effort strategies if propagule pressure from outside the managed area is low. However, if new infestations arise from frequent independent introductions from an outside source, constant strategies are cost‐effective.Synthesis and applications. For invasive species that are initially present, not frequently reintroduced into the managed area, and for which surveillance is reasonably cost‐effective, we recommend a simple three‐phase management programme that deploys intense early surveillance until the majority of undetected populations have been discovered, followed by medium effort until most of the heavily infested areas have been cleared of the invader and finally low long‐term effort to prevent infestations caused by future introductions and spread from populations that escaped surveillance. This programme captures the majority of the economic benefits from varying sampling effort continuously through time.
Impacts of environmental filters on functional redundancy in riparian vegetation
Authors: Bruno Daniel , Gutiérrez‐Cánovas Cayetano , Sánchez‐Fernández David , Velasco Josefa , Nilsson Christer 
Published: February 2016

SummaryUnderstanding and predicting ecosystem responses to multiple environmental pressures is a long‐standing interest in ecology and environmental management. However, few studies have examined how the functional features of freshwater biological communities vary along multiple gradients of environmental stress. Furthermore, modelling these functional features for a whole river network constitutes a strong potential basis to improve ecosystem management.We explored how functional redundancy of biological communities (FR, a functional feature related to the stability, resistance and resilience of ecosystems) responds to single and multiple environmental filters. We compared these responses with those of functional richness, evenness and divergence. We used riparian vegetation of a Mediterranean basin, and three of the main environmental filters affecting freshwater communities in such regions, that is drought, flow regulation and agricultural intensity, thus considering the potential effect of natural environmental variability. We also assessed the predictability ofFRand estimated it for the entire river network.We found that all functional measures decreased with increasing environmental filter intensity. However,FRwas more sensitive to single and multiple environmental filters compared to other functional measures. The best‐fitting model explained 59% of theFRvariability and included agriculture, drought and flow regulation and the pairwise interactions of agriculture with drought and flow regulation. The parameters of theFRmodels differed from null model expectations reflecting a non‐random decline along stress gradients.Synthesis and applications. We found non‐random detrimental effects along environmental filters' gradients for riparian functional redundancy (the most sensitive functional index), meaning that increased stress could jeopardize stability, resistance and resilience of these systems. In general, agriculture caused the greatest impact on functional redundancy and functional diversity measures, being the most important stressor for riparian functionality in the study area. Temporary streams flowing through an agricultural, regulated basin had reduced values of functional redundancy, whereas the free‐flowing medium‐sized, perennial water courses flowing through unaltered sub‐basins displayed higher values of functional redundancy and potentially greater stability against human impacts. All these findings along with the predicted basin‐wide variation of functional redundancy can assist environmental managers in improving monitoring and ecosystem management.
Individual resource limitation combined with population‐wide pollen availability drives masting in the valley oak (Quercus lobata)
Authors: Pesendorfer Mario B. , Koenig Walter D. , Pearse Ian S. , Knops Johannes M. H. , Funk Kyle A. 
Published: February 2016

Summary

Masting, the synchronized production of variable seed crops, is widespread among woody plants, but there is no consensus about the underlying proximate mechanisms. To understand this population‐level behaviour, it is necessary to dissect the behaviour of individual trees as well as the interactions that synchronize them.

Here, we test a model of masting in which variability in seed set is driven by resource limitation within trees and synchrony is driven by pollen limitation due to phenological asynchrony in some years.

We used a 35‐year seed set data set and a 12‐year phenological data set to analyse seed production of 84 valley oaks (Quercus lobata) in central coastal California. Individual trees varied tremendously in their seed production patterns; trees with high levels of seed production were less variable over time, but showed stronger negative autocorrelation between years, suggesting that they are more resource‐limited than unproductive trees. In years of more asynchronous flowering, Q. lobata produced fewer seeds, consistent with the importance of phenological synchrony.

We parametrized a model with these results to investigate how individual resource limitation and population‐wide pollen limitation – a consequence of asynchronous flowering during cold spring temperatures – interact to shape annual variation in seed production. The model illustrates that this proximate abiotic driver can synchronize the behaviour of individuals, resulting in population‐wide seed production patterns that closely resemble the field data.

Synthesis. Our findings support the hypothesis that an interaction between two proximate mechanisms, individual resource limitation and environmental variation affecting population‐wide pollen availability, drives masting in this population of Quercus lobata. This combination of internal and external proximate drivers may underlie masting behaviour in many wind‐pollinated plants.