scholarly journals An Extended Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction and Cladogenesis

2016 ◽  
Author(s):  
Champak Beeravolu Reddy ◽  
Fabien Condamine
Keyword(s):  
Local Extinction ◽  
Rapid Expansion ◽  
Model Complexity ◽  
Published Data ◽  
Computationally Efficient ◽  
Likelihood Methods ◽  
Origin And Evolution ◽  
Statistical Framework ◽  
Biological Realism

The origin and evolution of species ranges remains a central focus of historical biogeography and the advent of likelihood methods based on phylogenies has revolutionized the way in which range evolution has been studied. A decade ago, the first elements of what turned out to be a popular inference approach of ancestral ranges based on the processes of Dispersal, local Extinction and Cladogenesis (DEC) was proposed. The success of the DEC model lies in its use of a flexible statistical framework known as a Continuous Time Markov Chain and since, several conceptual and computational improvements have been proposed using this as a baseline approach. In the spirit of the original version of DEC, we introduce DEC eXtended (DECX) by accounting for rapid expansion and local extinction as possible anagenetic events on the phylogeny but without increasing model complexity (i.e. in the number of free parameters). Classical vicariance as a cladogenetic event is also incorporated by making use of temporally flexible constraints on the connectivity between any two given areas in accordance with the movement of landmasses and dispersal opportunity over time. DECX is built upon a previous implementation in C/C++ and can analyze phylogenies on the order of several thousand tips in a few minutes. We test our model extensively on Pseudo Observed Datasets and on well-curated and recently published data from various island clades and a worldwide phylogeny of Amphibians (3309 species). We also propose the very first implementation of the DEC model that can specifically account for trees with fossil tips (i.e. non-ultrametric) using the phylogeny of palpimanoid spiders as a case study. In this paper, we argue in favour of the proposed improvements, which have the advantage of being computationally efficient while toeing the line of increased biological realism.

scholarly journals A spatially explicit model for estimating risks of pesticide exposure to bird populations

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252545
Author(s):  
Matthew Etterson ◽  
Nathan Schumaker ◽  
Kristina Garber ◽  
Steven Lennartz ◽  
Andrew Kanarek ◽  
...  
Keyword(s):  
Pesticide Exposure ◽  
Integrated Modeling ◽  
Model Complexity ◽  
Spatially Explicit ◽  
Spatially Explicit Model ◽  
Bird Populations ◽  
Biological Realism ◽  
Agricultural Areas ◽  
Integrated Modeling System

Pesticides are used widely in agriculture and have the potential to affect non-target organisms, including birds. We developed an integrated modeling system to allow for spatially-explicit evaluation of potential impacts to bird populations following exposures to pesticides. Our novel methodology builds upon three existing models: the Terrestrial Investigation Model (TIM), the Markov Chain Nest Productivity Model (MCnest), and HexSim to simulate population dynamics. We parameterized the integrated modeling system using information required under the Federal Insecticide, Fungicide, and Rodenticide Act, together with species habitat and life history data available from the scientific literature as well as landcover data representing agricultural areas and species habitat. Our case study of the federally threatened California Gnatcatcher (Polioptila californica) illustrates how the integrated modeling system can estimate the population-scale consequences of pesticide applications. We simulated impacts from two insecticides applied to wheat: one causing mortality (survival stressor), and the other causing reproductive failure (reproductive stressor). We observed declines in simulated gnatcatcher abundance and changes in the species’ distribution following applications of each pesticide; however, the impacts of the two pesticides were different. Our methodology attempts to strike a balance between biological realism and model complexity and should be applicable to a wide array of species, systems, and stressors.

scholarly journals Lithospheric mantle refertilization by DMM-derived melts beneath the Cameroon Volcanic Line—a case study of the Befang xenolith suite (Oku Volcanic Group, Cameroon)

2021 ◽  
Vol 176 (5) ◽  
Author(s):  
Sylvin S. T. Tedonkenfack ◽  
Jacek Puziewicz ◽  
Sonja Aulbach ◽  
Theodoros Ntaflos ◽  
Mary-Alix Kaczmarek ◽  
...  
Keyword(s):  
Lithospheric Mantle ◽  
Size Variation ◽  
African Plate ◽  
Cameroon Volcanic Line ◽  
Origin And Evolution ◽  
Volcanic Group ◽  
Cenozoic Volcanism ◽  
Composition Of Minerals ◽  
Ree Patterns

AbstractThe origin and evolution of subcontinental lithospheric mantle (SCLM) are important issues of Earth’s chemical and physical evolution. Here, we report detailed textural and chemical analyses on a mantle xenolith suite from Befang (Oku Volcanic Group, Cameroon Volcanic Line), which represents a major tectono-magmatic structure of the African plate. The samples are sourced from spinel-facies mantle and are dominated by lherzolites. Their texture is cataclastic to porphyroclastic, and foliation defined by grain-size variation and alignment of spinel occurs in part of peridotites. Spinel is interstitial and has amoeboidal shape. Clinopyroxene REE patterns are similar to those of Depleted MORB Mantle (DMM) except LREEs, which vary from depleted to enriched. The A-type olivine fabric occurs in the subset of one harzburgite and 7 lherzolites studied by EBSD. Orthopyroxene shows deformation consistent with olivine. The fabric of LREE-enriched clinopyroxene is equivalent to those of orthopyroxene and olivine, whereas spinel and LREE-depleted clinopyroxene are oriented independently of host rock fabric. The textural, chemical and thermobarometric constraints indicate that the Befang mantle section was refertilised by MORB-like melt at pressures of 1.0–1.4 GPa and temperatures slightly above 1200–1275 °C. The olivine-orthopyroxene framework and LREE-enriched clinopyroxene preserve the protolith fabric. In contrast, the LREE-depleted clinopyroxene, showing discordant deformation relative to the olivine-orthopyroxene protolith framework, and amoeboidal spinel crystallized from the infiltrating melt. The major element and REEs composition of minerals forming the Befang peridotites indicate subsequent reequilibration at temperatures 930–1000 °C. This was followed by the formation of websterite veins in the lithospheric mantle, which can be linked to Cenozoic volcanism in the Cameroon Volcanic Line that also brought the xenoliths to the surface. This study therefore supports the origin of fertile SCLM via refertilization rather than by extraction of small melt fractions, and further emphasizes the involvement of depleted melts in this process.

The Xianggu Mushroom Industry in Xixia County, Henan: A Case Study (西峡香菇产业的个案研究)

Rural China ◽  
2017 ◽  
Vol 14 (2) ◽  
pp. 375-404 ◽  
Author(s):  
Chang Liu (刘昶) ◽  
Shiqing Bao (包诗卿) ◽  
Danqing Pei (裴丹青)
Keyword(s):  
Local Government ◽  
Food Consumption ◽  
Rapid Growth ◽  
Rapid Expansion ◽  
Fair Share ◽  
Shiitake Mushroom ◽  
Healthy Development ◽  
Reform And Opening Up ◽  
Opening Up

The xianggu (shiitake) mushroom industry in Xixia county, Henan, emerged and initially experienced rapid growth during the reform and opening up period. It has benefited from both the rapid expansion of the food consumption market in China and the guidance and support of the local government. After thirty years of sustained expansion, the growth of the mushroom market began to slow down and competition within the industry became fierce. Facing rich and powerful mushroom dealers, individual mushroom farmers have had to bear the brunt of market fluctuations. To break the predicament of farmers’ suffering from low prices (because of the bumper harvest paradox) and to help farmers protect their interests and gain a fair share of the industry’s profits, and thus to achieve sustained and healthy development of the mushroom industry, important institutional innovations are needed. 西峡县香菇产业在改革开放时期经历了从零开始的飞速增长，这既得益于食品消费市场的迅速扩张，也得益于地方政府的引导和扶持。在经历了三十年的持续扩张后，香菇市场增速开始放缓，业内竞争压力凸显。面对财大气粗的菇行，势孤力单的个体菇农首当其冲,受到市场的挤压。要破解菇贱伤农的困局，帮助菇农保护自己的利益和分享产业的利润，并实现香菇产业的健康持续发展，就需要在产业组织和制度上进行创新。 (This article is in English.)

scholarly journals Comparison of two individual-based model simulators for HIV epidemiology in a population with HSV-2 using as case study Yaoundé-Cameroon, 1980-2005

2019 ◽  
Author(s):  
Diana M Hendrickx ◽  
João Dinis Sousa ◽  
Pieter J.K. Libin ◽  
Wim Delva ◽  
Jori Liesenborgs ◽  
...  
Keyword(s):  
Model Complexity ◽  
Individual Based Model ◽  
Policy Makers ◽  
Basic Model ◽  
Hiv Epidemiology ◽  
Hiv Epidemic ◽  
Simplex Virus ◽  
Evidence For Policy ◽  
The Impact

ABSTRACTModel comparisons have been widely used to guide intervention strategies to control infectious diseases. Agreement between different models is crucial for providing robust evidence for policy-makers because differences in model properties can influence their predictions. In this study, we compared models implemented by two individual-based model simulators for HIV epidemiology in a population with Herpes simplex virus type 2 (HSV-2). For each model simulator, we constructed four models, starting from a simplified basic model and stepwise including more model complexity. For the resulting eight models, the predictions of the impact of behavioural interventions on the HIV epidemic in Yaoundé (Cameroon) were compared. The results show that differences in model assumptions and model complexity can influence the size of the predicted impact of the intervention, as well as the predicted qualitative behaviour of the HIV epidemic after the intervention. Moreover, two models that agree in their predictions of the HIV epidemic in the absence of intervention can have different outputs when predicting the impact of interventions. Without additional data, it is impossible to determine which of these two models is the most reliable. These findings highlight the importance of making more data available for the calibration and validation of epidemiological models.

New Christian Family Networks in the First Visitation of the Inquisition to Brazil

2020 ◽  
Author(s):  
Jessica O’Leary
Keyword(s):  
Rapid Expansion ◽  
Northeastern Brazil ◽  
Family Networks ◽  
The Social ◽  
Sugar Trade ◽  
Colonial Brazil ◽  
Christian Family ◽  
Commercial Network

This chapter provides a case study of João and Diogo Nunes during the First Visitation of the Inquisition to Brazil (1591–1595). The Nunes brothers were part of a broader commercial network of New Christian merchant families who controlled the sugar trade in northeastern Brazil during its rapid expansion in the late sixteenth and early seventeenth centuries. However, the social ascendency of New Christians in colonial Brazil threatened the existing elite who used the Inquisition to banish them via spurious denunciations. Using Inquisition testimony, this chapter will underscore the importance of New Christian networks to the sugar trade. It was their success, which both brought them to the attention of the Inquisition and saved them by virtue of royal intervention.

scholarly journals Examining Equitable Online Federal Food Assistance during the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Case Study in 2 Regions

2020 ◽  
Vol 4 (10) ◽  
Author(s):  
Melanie D Hingle ◽  
Carmen Byker Shanks ◽  
Courtney Parks ◽  
Joseph Prickitt ◽  
Kyung E Rhee ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Low Income ◽  
Food Assistance ◽  
Rapid Expansion ◽  
Policy Changes ◽  
Assistance Program ◽  
Federal Food ◽  
Hispanic Adults ◽  
Nutrition Assistance

ABSTRACT The USDA Supplemental Nutrition Assistance Program (SNAP) provides food and financial assistance to food-insecure individuals and families. In the midst of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, SNAP benefits evolved. Policy changes and federal legislation expanded SNAP eligibility, raised benefit levels, and introduced program waivers that enabled online ordering to reduce participants’ exposure to community-acquired SARS-CoV-2. Although rapid expansion of SNAP benefits in the online space represents significant progress for federal food assistance, changes also introduced unforeseen partiality in how benefits and services were accessed and utilized, as illustrated by 2 populations and regions in the early months of the SARS-CoV-2 pandemic: low-income older adults in rural Alabama and low-income Hispanic adults in urban California. Opportunities exist to build on the recent progress in SNAP, while also ensuring continued inclusiveness of eligible persons. Efforts should be informed by evidence that supports equitable access to federal food assistance.

scholarly journals Investigating spatiotemporal dynamics and trade-off/synergy of multiple ecosystem services in response to land cover change: a case study of Nanjing city, China

2020 ◽  
Vol 192 (11) ◽  
Author(s):  
Jie Zhao ◽  
Cheng Li
Keyword(s):  
Ecosystem Services ◽  
Urban Development ◽  
Crop Production ◽  
Spatiotemporal Dynamics ◽  
Rapid Expansion ◽  
Trade Off ◽  
Spatiotemporal Trends ◽  
Production Values ◽  
Nanjing City

AbstractInvestigating the spatiotemporal trends and trade-off/synergy relationships among ecosystem services can provide effective support for urban planning and decision making toward sustainable development. With Nanjing city in China as a case study, this study assessed the spatiotemporal dynamics of six key ecosystem services from 2005 to 2030. Integration of Markov-cellular automata and ecosystem services models was realized to analyze the potential impacts of future urbanization on ecosystem services by simulating business-as-usual (BAU), cropland protection (CP), and ecological restoration (ER) scenarios. Furthermore, an innovative trade-off/synergy degree was developed to quantify the magnitude of the complex relationship among the multiple ecosystem services under the different scenarios. Due to the rapid expansion of built-up land, carbon storage, habitat quality, and air purification decreased 2.92%, 5.80%, and 7.91%, respectively. The CP scenario exhibited the highest crop production values, and the ER scenario was a better urban development strategy that enhanced the regulating ecosystem services at the expense of crop production. To promote urban ecosystem services and minimize trade-offs, we proposed certain future urban development strategies, including ecological corridor construction and compact development. The study could provide a scientific reference for the effective ecosystem management of Nanjing and other rapidly urbanized regions.

Bayesian analysis of longitudinal and multidimensional functional data

Biostatistics ◽  
2020 ◽  
Author(s):  
John Shamshoian ◽  
Damla Şentürk ◽  
Shafali Jeste ◽  
Donatello Telesca
Keyword(s):  
Functional Data ◽  
Observational Studies ◽  
Children With Autism ◽  
Autism Spectrum ◽  
Computationally Efficient ◽  
Modeling Framework ◽  
Simulated Environment ◽  
First Case ◽  
Low Dimensional

Summary Multi-dimensional functional data arises in numerous modern scientific experimental and observational studies. In this article, we focus on longitudinal functional data, a structured form of multidimensional functional data. Operating within a longitudinal functional framework we aim to capture low dimensional interpretable features. We propose a computationally efficient nonparametric Bayesian method to simultaneously smooth observed data, estimate conditional functional means and functional covariance surfaces. Statistical inference is based on Monte Carlo samples from the posterior measure through adaptive blocked Gibbs sampling. Several operative characteristics associated with the proposed modeling framework are assessed comparatively in a simulated environment. We illustrate the application of our work in two case studies. The first case study involves age-specific fertility collected over time for various countries. The second case study is an implicit learning experiment in children with autism spectrum disorder.

The relational work of international teachers: A case study of a Sino-foreign school

2019 ◽  
Vol 3 (2) ◽  
pp. 127-144 ◽  
Author(s):  
Alex Kostogriz ◽  
Gary Bonar
Keyword(s):  
Rapid Expansion ◽  
Teacher Mobility ◽  
International Teachers ◽  
Theory Of Practice ◽  
Relational Work ◽  
Practice Architectures ◽  
English Speaking ◽  
Linguistic Challenges ◽  
International Teacher

Abstract In the context of a rapid expansion of 'internationalized' schools around the world, and the subsequent demands for a teaching workforce, teachers are increasingly on the move. It is, however, no longer sufficient to represent international teacher mobility merely as a movement of predominantly English-speaking teachers who can deliver American, British, Canadian or Australian curricula. The increase in schools that offer bilingual and dual curricula has resulted in the mobility of local teachers who work alongside English-speaking ones. Although these schools are attractive to many international and local teachers, they also present certain professional, cultural and linguistic challenges. Drawing on the theory of practice architectures, this article identifies and discusses the relational tensions between foreign and local teachers as they grapple to build a new professional culture of collaboration ‐ one that demands the transformation of dispositions, professional knowledge, actions and judgements to 'fit in' to the internationalized school.

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