bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying and addressing methodological incongruence in phylogenomics: A review
Authors: Fleming James F. , Valero‐Gracia Alberto , Struck Torsten H. 
Published: June 2023

AbstractThe availability of phylogenetic data has greatly expanded in recent years. As a result, a new era in phylogenetic analysis is dawning—one in which the methods we use to analyse and assess our data are the bottleneck to producing valuable phylogenetic hypotheses, rather than the need to acquire more data. This makes the ability to accurately appraise and evaluate new methods of phylogenetic analysis and phylogenetic artefact identification more important than ever. Incongruence in phylogenetic reconstructions based on different datasets may be due to two major sources: biological and methodological. Biological sources comprise processes like horizontal gene transfer, hybridization and incomplete lineage sorting, while methodological ones contain falsely assigned data or violations of the assumptions of the underlying model. While the former provides interesting insights into the evolutionary history of the investigated groups, the latter should be avoided or minimized as best as possible. However, errors introduced by methodology must first be excluded or minimized to be able to conclude that biological sources are the cause. Fortunately, a variety of useful tools exist to help detect such misassignments and model violations and to apply ameliorating measurements. Still, the number of methods and their theoretical underpinning can be overwhelming and opaque. Here, we present a practical and comprehensive review of recent developments in techniques to detect artefacts arising from model violations and poorly assigned data. The advantages and disadvantages of the different methods to detect such misleading signals in phylogenetic reconstructions are also discussed. As there is no one‐size‐fits‐all solution, this review can serve as a guide in choosing the most appropriate detection methods depending on both the actual dataset and the computational power available to the researcher. Ultimately, this informed selection will have a positive impact on the broader field, allowing us to better understand the evolutionary history of the group of interest.
Model‐based offline reinforcement learning for sustainable fishery management
Authors: Ju Jun , Kurniawati Hanna , Kroese Dirk , Ye Nan 
Published: June 2023

AbstractFisheries, as indispensable natural resources for human, need to be managed with both short‐term economical benefits and long‐term sustainability in consideration. This has remained a challenge, because the population and catch dynamics of the fisheries are complex and noisy, while the data available is often scarce and only provides partial information on the dynamics. To address these challenges, we formulate the population and catch dynamics as a Partially Observable Markov Decision Process (POMDP), and propose a model‐based offline reinforcement learning approach to learn an optimal management policy. Our approach allows learning fishery management policies from possibly incomplete fishery data generated by a stochastic fishery system. This involves first learning a POMDP fishery model using a novel least squares approach, and then computing the optimal policy for the learned POMDP. The learned fishery dynamics model is useful for explaining the resulting policy's performance. We perform systematic and comprehensive simulation study to quantify the effects of stochasticity in fishery dynamics, proliferation rates, missing values in fishery data, dynamics model misspecification, and variability of effort (e.g., the number of boat days). When the effort is sufficiently variable and the noise is moderate, our method can produce a competitive policy that achieves 85% of the optimal value, even for the hardest case of noisy incomplete data and a misspecified model. Interestingly, the learned policies seem to be robust in the presence of model learning errors. However, non‐identifiability kicks in if there is insufficient variability in the effort level and the fishery system is stochastic. This often results in poor policies, highlighting the need for sufficiently informative data. We also provide a theoretical analysis on model misspecification and discuss the tendency of a Schaefer model to overfit compared with a Beverton–Holt model.
Social harvest control rules for sustainable fisheries
Authors: Barclay Kate M. , Bush Simon R. , Poos Jan Jaap , Richter Andries , van Zwieten Paul A. M. , Hamon Katell G. , Carballo‐Cárdenas Eira , Pauwelussen Annet P. , Groeneveld Rolf A. , Toonen Hilde M. , Schadeberg Amanda , Kraan Marloes , Bailey Megan , van Leeuwen Judith 
Published: June 2023

AbstractFisheries are supposed to be for the benefit of society, producing food, providing livelihoods and enabling cultural continuity. Biological productivity goals for fish stocks operationalised through Harvest Control Rules (HCRs) are central to contemporary fisheries management. While fisheries policies often state socio‐economic objectives, such as enhancing the livelihoods of coastal communities, those are rarely, if ever, incorporated into operationalised management procedures. The lack of articulation of social objectives and lack of monitoring of social outcomes around HCRs amounts to poor public policy. In this article, we explore the potential for social HCRs (sHCRs) with reference points and agreed predefined actions to make the social dimensions of fisheries explicit. sHCRs cannot cover all social dimensions, so should be considered as one tool within a broader framework of fisheries governance. Moreover, successful sHCRs would require sound deliberative and participatory processes to generate legitimate social objectives, and monitoring and evaluation of fisheries management performance against those objectives. We introduce two potential types of sHCRs, one based on allocation of catch within biological limit reference points, and one for when fishing exceeds biological limit reference points. The application of sHCRs, we argue, can foster accountability and help avoid non‐transparent negotiations on size and distribution of the catch. Our proposal is a call to action for policy makers and fisheries managers to properly integrate social criteria into fisheries governance, and for both biophysical fisheries scientists and social scientists to do better in practical collaboration for methods and knowledge development to support this integration.
Why do some fish grow faster than others?
Authors: Goodrich Harriet R. , Clark Timothy D. 
Published: June 2023

AbstractAll animals must acquire food to grow, but there is a vast diversity in how different species and even different individuals approach and achieve this task. Individuals within a species appear to fall along a bold‐shy continuum, whereby some fish acquire food aggressively and with seemingly high risk, while others appear more submissive and opportunistic. Greater food consumption generally results in faster growth, but only if the energy acquired through food is more than enough to compensate for heightened metabolism associated with a more active lifestyle. Fast‐growing phenotypes also tend to have elevated baseline metabolism – at least when food is plentiful – which may be linked with gut morphology and digestive efficiency. The net energy gained from a meal (as calculated from the specific dynamic action (SDA) coefficient) is optimised with larger meal sizes, but the digestion of large meals can erode the aerobic metabolic scope available for other critical activities such as predator avoidance, perhaps at an interindividual level. Thus, complex interactions between an individual's genes and environment are likely to regulate the growth phenotype. This review compiles available knowledge to shed light on the question: Why do some fish grow faster than others? We discuss the elaborate interrelationships between behaviour, physiology and the gut microbiome with a goal to better understand what drives interindividual differences in growth performance.
The North American Monsoon buffers forests against the ongoing megadrought in the Southwestern United States
Authors: Strange Brandon M. , Monson Russell K. , Szejner Paul , Ehleringer Jim , Hu Jia 
Published: June 2023

AbstractThe US Southwest has been entrenched in a two‐decade‐long megadrought (MD), the most severe since 800 CE, which threatens the long‐term vitality and persistence of regional montane forests. Here, we report that in the face of record low winter precipitation and increasing atmospheric aridity, seasonal activity of the North American Monsoon (NAM) climate system brings sufficient precipitation during the height of the summer to alleviate extreme tree water stress. We studied seasonally resolved, tree‐ring stable carbon isotope ratios across a 57‐year time series (1960–2017) in 17 Ponderosa pine forests distributed across the NAM geographic domain. Our study focused on the isotope dynamics of latewood (LW), which is produced in association with NAM rains. During the MD, populations growing within the core region of the NAM operated at lower intrinsic and higher evaporative water‐use efficiencies (WUEi and WUEE, respectively), compared to populations growing in the periphery of the NAM domain, indicating less physiological water stress in those populations with access to NAM moisture. The disparities in water‐use efficiencies in periphery populations are due to a higher atmospheric vapor pressure deficit (VPD) and reduced access to summer soil moisture. The buffering advantage of the NAM, however, is weakening. We observed that since the MD, the relationship between WUEi and WUEE in forests within the core NAM domain is shifting toward a drought response similar to forests on the periphery of the NAM. After correcting for past increases in the atmospheric CO2 concentration, we were able to isolate the LW time‐series responses to climate alone. This showed that the shift in the relation between WUEi and WUEE was driven by the extreme increases in MD‐associated VPD, with little advantageous influence on stomatal conductance from increases in atmospheric CO2 concentration.
Microbial communities in terrestrial surface soils are not widely limited by carbon
Authors: Cui Yongxing , Peng Shushi , Delgado‐Baquerizo Manuel , Rillig Matthias C. , Terrer César , Zhu Biao , Jing Xin , Chen Ji , Li Jinquan , Feng Jiao , He Yue , Fang Linchuan , Moorhead Daryl L. , Sinsabaugh Robert L. , Peñuelas Josep 
Published: June 2023

AbstractMicrobial communities in soils are generally considered to be limited by carbon (C), which could be a crucial control for basic soil functions and responses of microbial heterotrophic metabolism to climate change. However, global soil microbial C limitation (MCL) has rarely been estimated and is poorly understood. Here, we predicted MCL, defined as limited availability of substrate C relative to nitrogen and/or phosphorus to meet microbial metabolic requirements, based on the thresholds of extracellular enzyme activity across 847 sites (2476 observations) representing global natural ecosystems. Results showed that only about 22% of global sites in terrestrial surface soils show relative C limitation in microbial community. This finding challenges the conventional hypothesis of ubiquitous C limitation for soil microbial metabolism. The limited geographic extent of C limitation in our study was mainly attributed to plant litter, rather than soil organic matter that has been processed by microbes, serving as the dominant C source for microbial acquisition. We also identified a significant latitudinal pattern of predicted MCL with larger C limitation at mid‐ to high latitudes, whereas this limitation was generally absent in the tropics. Moreover, MCL significantly constrained the rates of soil heterotrophic respiration, suggesting a potentially larger relative increase in respiration at mid‐ to high latitudes than low latitudes, if climate change increases primary productivity that alleviates MCL at higher latitudes. Our study provides the first global estimates of MCL, advancing our understanding of terrestrial C cycling and microbial metabolic feedback under global climate change.
Quantifying carbon storage and sequestration by native and non‐native forests under contrasting climate types
Authors: Lázaro‐Lobo Adrián , Ruiz‐Benito Paloma , Cruz‐Alonso Verónica , Castro‐Díez Pilar 
Published: June 2023

AbstractNon‐native trees may have significant impacts on the carbon sink capacity of forested lands. However, large‐scale patterns of the relative capacity of native and non‐native forests to uptake and store carbon remain poorly described in the literature, and this information is urgently needed to support management decisions. In this study, we analyzed 17,065 plots from the Spanish Forest Inventory (covering c. 30 years) to quantify carbon storage and sequestration of natural forests and plantations of native and non‐native trees under contrasting climate types, while controlling for the effects of environmental factors (forest structure, climate, soil, topography, and management). We found that forest origin (non‐native vs. native) highly influenced carbon storage and sequestration, but such effect was dependent on climate. Carbon storage was greater in non‐native than in native forests in both wet and dry climates. Non‐native forests also had greater carbon sequestration than native ones in the wet climate, due to higher carbon gains by tree growth. However, in the dry climate, native forests had greater carbon gains by tree ingrowth and lower carbon loss by tree mortality than non‐native ones. Furthermore, forest type (classified by the dominant species) and natural forests versus tree plantations were important determinants of carbon storage and sequestration. Native and non‐nativePinusspp. forests had low carbon storage, whereas non‐nativeEucalyptusspp. forests and nativeQuercusspp.,Fagus sylvatica, and Eurosiberian mixed forests (especially not planted ones) had high carbon storage. Carbon sequestration was greatest inEucalyptus globulus,Quercus ilex, andPinus pinasterforests. Overall, our findings suggest that the relative capacity of native and non‐native forests to uptake and store carbon depends on climate, and that the superiority of non‐native forests over native ones in terms of carbon sequestration declines as the abiotic filters become stronger (i.e., lower water availability and higher climate seasonality).
Estimation of Aquifer Transmissivity From Analysis of Long‐Term Monitoring With the Thiem Solution
Authors: Henry Joel C. , Neville Christopher J. , Olson Alyssa N. 
Published: June 2023

AbstractThe application of the Thiem equation to support the interpretation of comprehensive long‐term monitoring datasets, made possible through modern datalogging technology, is presented as an alternative to constant‐rate aquifer testing to obtain representative transmissivity estimates in settings where controlled hydraulic testing may be impractical. Water levels logged at regular intervals can be readily converted to average water levels over time periods corresponding to periods of known pumping rates. By regressing average water levels during multiple time periods of known but variable withdrawal rates, steady‐state conditions can be approximated and Thiem's solution applied to estimate transmissivity, without performance of a constant‐rate aquifer test. Although the application is limited to settings where changes in aquifer storage are negligible, by regressing long data sets to parse interferences the method may characterize aquifer conditions over a much wider radius than short‐term, non‐equilibrium tests. As with all aquifer testing, informed interpretation is critical to identifying and resolving aquifer heterogeneities and interferences.
Age, geochemistry, mineralization, and tectonic significance of felsic‐intermediate dikes in Shuangqishan Au deposit, Cathaysia block, South China
Authors: Fan Feipeng , Xiao Fan , Zhou Yan , Chen Shizhong 
Published: June 2023

AbstractThe Shuangqishan Au deposit (>15 t) is located in the Dehua‐Youxi‐Yongtai goldfield of the southeastern Cathaysia Block, South China. There are three stages of granites in the Shuangqishan Au deposit, the pre‐mineralization granite porphyry formed in the Middle Jurassic (~166.0 ± 0.8 Ma), the metallogenic granite porphyry and monzonite porphyry formed in the late stage of the Late Jurassic (153–151 Ma), the post‐mineralization granites (granite porphyry, the masanophyre, the dioritic porphyrite) formed in the Early Cretaceous (129.0–120.0 Ma). All rocks are characterized by high‐K calc‐alkaline and shoshonities series, the per‐mineralization granites are enriched in Rb, Th, K, Zr, and Hf, depleted in Ba, P, and Ti, significant negative Eu anomaly and distinctly tetrad effect with highly fractionated I‐type granitoids characteristics. The metallogenic granites and the post‐mineralization granite porphyry are enriched in K, Rb, Th, Ce, Zr, Hf, and Y, enriched in LREE, strongly depleted in Sr, Ba Ta, P, Ti, have moderate negative Eu anomalies with I‐type granites characteristics. However, the post‐mineralization dioritic porphyrite displays strong depletions Sr, Ta, P, and Ti whereas Rb, Th, Ce, and Sm are enriched, enriched in LREE with weakly negative Eu anomalies. The metallogenic granite porphyry is significantly enriched in Au, As, Sb, W, Mo, and Bi, especially enriched in Au. The Lu‐Hf isotopic data indicate that the magma source comes from the partial melting of the Paleoproterozoic crust, the minor part from the mantle in the Early Cretaceous. Therefore, we propose that the granitoids formed in the subducted plate environment from the Middle Jurassic to the Early Cretaceous, the Late Jurassic I‐type granites (~153–146 Ma), The Shuangqishan Au deposit was formed in the stage from compression to extension, the Early Cretaceous granites (~129–114 Ma) mainly formed in the extensional environment and destroyed gold ore bodies.
Sludged! Can financial literacy shield against price manipulation at the shops?
Authors: West Tracey , Butler David , Smith Liam 
Published: June 2023

AbstractRetailers lure consumers with clever use of choice architecture; examples include “bargains” heavily restricted in the fine print and discounts structured to exaggerate the true saving. Given that financial literacy is a key competency for managing money, good financial literacy may provide protection from these “sludges.” In an exploratory experiment, we measure 48 university students' retail literacy and financial literacy, while concurrently tracking their emotional reactions and decision time using FaceReader software. We then test hypotheses on a larger sample using an online survey. We find that strong financial literacy supports retail literacy and vice versa, but the two constructs are distinct. The differences are identified through mathematical and methodological reasoning, gender, and emotion. While gender remains a factor for financial literacy, it is less prominent in retail literacy, and women respond more positively to retail literacy performance measurement. We recommend future investigation into building women's financial literacy performance using materials that are aesthetically pleasing and based on familiar financial frames and scenarios.
Accumulating human capital: Corporate innovation and firm value
Authors: Wang Xun , Yu Jingwen 
Published: June 2023

AbstractWe empirically document that industries that are more R&D intensive exhibit disproportionately greater innovation quantity and better innovation quality in economies with more human capital. Firm‐level evidence confirms that innovation is an important channel through which firm responds to labor market conditions. Further analyses show that in economies with greater human capital, firms better able to innovate exhibit larger increase in labor productivity and capital–labor ratio, an effect driven by deceases in employment and increase in intangible capital investment. By facilitating the adjustment in input mix and capital structure, human capital accumulation allows firms with high innovation ability to enhance firm equity value and improve firm performance.
Argentina’s Emergency Family Income (IFE): An opportunity for women’s empowerment
Authors: D’Elia Vanesa , Gaiada Julio 
Published: June 2023

AbstractThis article provides empirical evidence regarding the impact of the Emergency Family Income (Ingreso Familiar de Emergencia – IFE), which was implemented in Argentina in 2020. Investigated is the impact of the IFE on women’s role in providing household income and on the distribution of roles within households, as a reflection of women’s empowerment. Drawing on various household surveys, the study compared those women eligible to receive the transfer with those who were not. A difference‐in‐differences (DID) methodology was used to measure the impact. Following the implementation of the IFE, women’s share of couple income and household income is found to have increased by some 8 per cent and 11 per cent, respectively, while the probability of women being solely responsible for household chores has fallen by 4 per cent.
The potential impact of introducing a social security system in the State of Palestine: A computable general equilibrium approach
Authors: Sadeq Tareq , Ismael Mohanad , Jabarin Ali , Mitik Lulit 
Published: June 2023

AbstractThis article assesses the potential impact for the State of Palestine (West Bank and Gaza) of enforcing the enactment of the currently suspended Social Security Law (No. 19 of 2016). Using a computable general equilibrium model, we simulate different scenarios associated with the enactment of the social security system on key macroeconomic variables, such as GDP, private consumption, government spending, investment and employment, for the period 2020–2030. We evaluate the influence on the economy of introducing a social security system for private‐sector workers, as set out in the 2016 law, and compare the simulation results of each scenario to the baseline. In each scenario, we consider different options concerning severance payment duration and different options for the investment strategy of social security contributions. However, for employees in Gaza, the article does not consider severance payments due to economic difficulties and the Israeli closure policy.
Work histories and workers’ failure to satisfy pension contribution requirements: A comparison of Mexico and Uruguay
Authors: Apella Ignacio , Zunino Gonzalo 
Published: June 2023

AbstractComparing Mexico and Uruguay, this article examines the work history of workers and the challenges they face to satisfy the minimum contribution period for eligibility to receive a contributory old‐age pension. Administrative data on work histories is used to formulate a survival model aimed at estimating hazard rates of entering and transitioning out of a given contribution status. This model is then used to perform a Monte Carlo simulation to forecast contribution histories. Results suggest that the hazard rate is negatively associated with the length of a worker’s spell in his or her current status and warn that, both in Mexico and Uruguay, a significant group of workers will find it difficult to gain entitlement to a contributory pension in old age. The manner in which each of these national systems has addressed the challenges associated with low contribution densities may explain the two countries’ very different coverage results.