A framework for defining livestock ecotypes based on ecological modelling and exploring genomic environmental adaptation: the example of Ethiopian village chicken

AbstractIn evolutionary ecology, an ecotype is a population that is genetically adapted to specific environmental conditions. Environmental and genetic characterisation of livestock ecotypes can play a crucial role in conservation and breeding improvement, particularly to achieve climate resilience. However, livestock ecotypes are often arbitrarily defined without a detailed characterisation of their agro-ecologies. In this study, we employ a novel integrated approach, combining Ecological Niche Modelling (ENM) with genomics, to delineate ecotypes based on environmental characterisation of population habitats and unravel the signatures of adaptive selection in the ecotype genomes. The method was applied on 25 Ethiopian village chicken populations representing diverse agro-climatic conditions. ENM identified six key environmental drivers of adaptation and delineated 12 ecotypes. Within- ecotype selection signature analyses (using Hp and iHS methods) identified 1,056 candidate sweep regions (SRs) associated with diverse biological processes. A few biological pathways were shared amongst most ecotypes and the involved genes showed functions important for scavenging chickens, e.g. neuronal development/processes, immune response, vision development, and learning. Genotype-environment association using Redundancy Analysis (RDA) allowed for correlating ∼33% of the SRs with major environmental drivers. Inspection of some strong candidate genes from selection signature analysis and RDA showed highly relevant functions in relation to the major environmental drivers of corresponding ecotypes. This integrated approach offers a powerful tool to gain insight into the complex processes of adaptive evolution including the genotype x environment (GxE) interactions.

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A Sensitivity Analysis of the SPACSYS Model

Agriculture ◽

10.3390/agriculture11070624 ◽

2021 ◽

Vol 11 (7) ◽

pp. 624

Author(s):

Yan Shan ◽

Mingbin Huang ◽

Paul Harris ◽

Lianhai Wu

Keyword(s):

Sensitivity Analysis ◽

Wheat Yield ◽

Climatic Conditions ◽

Water Dynamics ◽

Ecological Modelling ◽

Soil Conditions ◽

Model Parameters ◽

Nutrient Inputs ◽

Nutrient Pool ◽

Wheat Field

A sensitivity analysis is critical for determining the relative importance of model parameters to their influence on the simulated outputs from a process-based model. In this study, a sensitivity analysis for the SPACSYS model, first published in Ecological Modelling (Wu, et al., 2007), was conducted with respect to changes in 61 input parameters and their influence on 27 output variables. Parameter sensitivity was conducted in a ‘one at a time’ manner and objectively assessed through a single statistical diagnostic (normalized root mean square deviation) which ranked parameters according to their influence of each output variable in turn. A winter wheat field experiment provided the case study data. Two sets of weather elements to represent different climatic conditions and four different soil types were specified, where results indicated little influence on these specifications for the identification of the most sensitive parameters. Soil conditions and management were found to affect the ranking of parameter sensitivities more strongly than weather conditions for the selected outputs. Parameters related to drainage were strongly influential for simulations of soil water dynamics, yield and biomass of wheat, runoff, and leaching from soil during individual and consecutive growing years. Wheat yield and biomass simulations were sensitive to the ‘ammonium immobilised fraction’ parameter that related to soil mineralization and immobilisation. Simulations of CO2 release from the soil and soil nutrient pool changes were most sensitive to external nutrient inputs and the process of denitrification, mineralization, and decomposition. This study provides important evidence of which SPACSYS parameters require the most care in their specification. Moving forward, this evidence can help direct efficient sampling and lab analyses for increased accuracy of such parameters. Results provide a useful reference for model users on which parameters are most influential for different simulation goals, which in turn provides better informed decision making for farmers and government policy alike.

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Environmental Drivers and Age Trends in Site Productivity for Oak in Southern Poland

Forests ◽

10.3390/f12020209 ◽

2021 ◽

Vol 12 (2) ◽

pp. 209

Author(s):

Luiza Tymińska-Czabańska ◽

Jarosław Socha ◽

Marek Maj ◽

Dominika Cywicka ◽

Xo Viet Hoang Duong

Keyword(s):

Nitrogen Deposition ◽

Management Practices ◽

Additive Model ◽

Climatic Conditions ◽

Environmental Indicators ◽

Environmental Drivers ◽

Site Productivity ◽

Site Factors ◽

Wide Range ◽

Si Model

Site productivity provides critical information for forest management practices and is a fundamental measure in forestry. It is determined using site index (SI) models, which are developed using two primary groups of methods, namely, phytocentric (plant-based) or geocentric (earth-based). Geocentric methods allow for direct site growth modelling, in which the SI is predicted using multiple environmental indicators. However, changes in non-static site factors—particularly nitrogen deposition and rising CO2 concentration—lead to an increase in site productivity, which may be visible as an age trend in the SI. In this study, we developed a geocentric SI model for oak. For the development of the SI model, we used data from 150 sample plots, representing a wide range of local topographic and site conditions. A generalized additive model was used to model site productivity. We found that the oak SI depended predominantly on physicochemical soil properties—mainly nitrogen, carbon, sand, and clay content. Additionally, the oak SI value was found to be slightly shaped by the topography, especially by altitude above sea level, and topographic position. We also detected a significant relationship between the SI and the age of oak stands, indicating the long-term increasing site productivity for oak, most likely caused by nitrogen deposition and changes in climatic conditions. The developed geocentric site productivity model for oak explained 77.2% of the SI variation.

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An Integrated Approach Using Spatial Analysis to Study the Risk Factors for Leishmaniasis in Area of Recent Transmission

BioMed Research International ◽

10.1155/2015/621854 ◽

2015 ◽

Vol 2015 ◽

pp. 1-10 ◽

Cited By ~ 8

Author(s):

Júlia Alves Menezes ◽

Eduardo de Castro Ferreira ◽

José Dilermando Andrade-Filho ◽

Alessandra Mara de Sousa ◽

Mayron Henrique Gomes Morais ◽

...

Keyword(s):

Spatial Analysis ◽

Integrated Approach ◽

Climatic Conditions ◽

Sand Fly ◽

Leishmania Braziliensis ◽

Lutzomyia Longipalpis ◽

Recent Transmission ◽

Current Transmission ◽

Canine Infection ◽

The City

Some epidemiological aspects of leishmaniasis in the municipality of Formiga, Brazil, an important touristic site, were evaluated. Those included phlebotomine sand fly vectors, canine infection, and geoprocessing analysis for determining critical transmission areas. Sand flies (224 insects) belonging to ten different species were captured. The most captured species includedLutzomyia longipalpis(35.3%),Lutzomyia cortelezzii(33.5%), andLutzomyia whitmani(18.3%). A significant correlation between sand fly densities and climatic conditions was detected. Serological diagnosis (DPP and ELISA) was performed in 570 dogs indicating a prevalence of 5.8%. After sequencing the main species circulating in the area wereLeishmania infantumandLeishmania braziliensis. Spatial analysis demonstrated that vegetation and hydrography may be related to sand fly distribution and infected dogs. The municipality of Formiga has proven leishmaniasis vectors and infected dogs indicating the circulation of the parasite in the city. Correlation of those data with environmental and human cases has identified the critical areas for control interventions (south, northeast, and northwest). In conclusion, there is current transmission of visceral and canine human cases and the city is on the risk for the appearance of cutaneous cases.

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An integrated approach to identifying and characterising resilient urban food systems to promote population health in a changing climate

Public Health Nutrition ◽

10.1017/s1368980015000610 ◽

2015 ◽

Vol 18 (13) ◽

pp. 2498-2508 ◽

Cited By ~ 21

Author(s):

Sarah W James ◽

Sharon Friel

Keyword(s):

Population Health ◽

Environmental Sustainability ◽

Mixed Methods Research ◽

Food Systems ◽

Food System ◽

Production Systems ◽

Integrated Approach ◽

Integrated Analysis ◽

Climate Resilience ◽

Urban Food Systems

AbstractObjectiveTo determine key points of intervention in urban food systems to improve the climate resilience, equity and healthfulness of the whole system.DesignThe paper brings together evidence from a 3-year, Australia-based mixed-methods research project focused on climate change adaptation, cities, food systems and health. In an integrated analysis of the three research domains – encompassing the production, distribution and consumption sectors of the food chain – the paper examines the efficacy of various food subsystems (industrial, alternative commercial and civic) in achieving climate resilience and good nutrition.SettingGreater Western Sydney, Australia.SubjectsPrimary producers, retailers and consumers in Western Sydney.ResultsThis overarching analysis of the tripartite study found that: (i) industrial food production systems can be more environmentally sustainable than alternative systems, indicating the importance of multiple food subsystems for food security; (ii) a variety of food distributors stocking healthy and sustainable items is required to ensure that these items are accessible, affordable and available to all; and (iii) it is not enough that healthy and sustainable foods are produced or sold, consumers must also want to consume them. In summary, a resilient urban food system requires that healthy and sustainable food items are produced, that consumers can attain them and that they actually wish to purchase them.ConclusionsThis capstone paper found that the interconnected nature of the different sectors in the food system means that to improve environmental sustainability, equity and population health outcomes, action should focus on the system as a whole and not just on any one sector.

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Acoustic Performance of Louvred Facades for Brisbane Domestic Airport: An Integrated Approach

ASME 2012 Noise Control and Acoustics Division Conference ◽

10.1115/ncad2012-1393 ◽

2012 ◽

Author(s):

Frank Butera ◽

Keith Hewett

Keyword(s):

Natural Ventilation ◽

Transmission Loss ◽

Internal Noise ◽

Building Design ◽

Integrated Approach ◽

External Noise ◽

Climatic Conditions ◽

Sustainable Building ◽

Heating And Cooling ◽

Airport Terminals

Maximising cross ventilation is a low energy method of naturally ventilating and providing heating and cooling to deep plan spaces. Significant reduction in the emission of greenhouse gases can be achieved through minimising the use of mechanical systems in regions with climatic conditions that support the use of natural ventilation. Arup has provided input into the design of a louvered facade for the control of external noise for Brisbane Domestic Airport. A full scale prototype facade was constructed and noise transmission loss measurements were undertaken. The results indicate that significant noise reduction can be achieved to enable compliance with the internal noise limits for airport terminals, whilst using natural ventilation. The findings from this research will directly benefit building designers and innovators in the pursuit of achieving sustainable building design.

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Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens

10.1101/2020.08.19.257212 ◽

2020 ◽

Cited By ~ 1

Author(s):

Almas A. Gheyas ◽

Adriana Vallejo Trujillo ◽

Adebabay Kebede ◽

Maria Lozano-Jaramillo ◽

Tadelle Dessie ◽

...

Keyword(s):

Environmental Adaptation ◽

Environmental Drivers ◽

Integrative Approach ◽

Niche Modelling ◽

Environmental Pressures ◽

Cold Temperatures ◽

Association Analyses ◽

Indigenous Chickens ◽

Environmental Selection ◽

Signatures Of Selection

AbstractElucidating the genetic basis of environmental adaptation in indigenous livestock populations has important implications for sustainable breeding improvement. It requires a detailed untangling of relevant environmental pressures and fine resolution detection of genomic signatures of selection associated with these environmental parameters. Here, we uniquely employed an integrative approach, combining Ecological Niche Modelling (ENM) with (i) genome-wide analyses of positive signatures of selection (SSA) and (ii) genotype-environment association (GEA) analyses to unravel the environmental adaptation of Ethiopian indigenous chickens. We first examined 34 agro-ecological and climatic variables and identified six main environmental selection drivers (one temperature - strongly correlated to elevation, three precipitation, and two soil/land variables). We then performed genomic analyses using high-density SNP data from whole-genome sequencing of 245 Ethiopian chickens from 25 different populations. Environmental genomic association analyses (SSA and GEA) identify a few strongly supported selected genomic regions, often with clusters of candidate genes, related to altitude-induced stresses (hypoxia, thrombosis, and cold temperatures), water scarcity, and the challenges of scavenging feeding behaviour. These analyses support a predominantly oligogenic control of environmental adaptation and possible regulation by one or few genetic elements only. Our study shows that the pre-identification of the key environmental drivers of adaptation, followed by a detailed genomic investigation of the associated genetic mechanisms provides a powerful new approach for elucidating the effect of natural selection in domestic animals. These results represent new landmarks to inform sustainable poultry breeding improvement.

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A General Lake Model (GLM 3.0) for linking with high-frequency sensor data from the Global Lake Ecological Observatory Network (GLEON)

Geoscientific Model Development ◽

10.5194/gmd-12-473-2019 ◽

2019 ◽

Vol 12 (1) ◽

pp. 473-523 ◽

Cited By ~ 24

Author(s):

Matthew R. Hipsey ◽

Louise C. Bruce ◽

Casper Boon ◽

Brendan Busch ◽

Cayelan C. Carey ◽

...

Keyword(s):

Vertical Mixing ◽

Scientific Basis ◽

Climatic Conditions ◽

Ecological Modelling ◽

Sensor Data ◽

Environmental Models ◽

Community Model ◽

Lake Model ◽

Surface Heat Exchange ◽

Distributed Cloud

Abstract. The General Lake Model (GLM) is a one-dimensional open-source code designed to simulate the hydrodynamics of lakes, reservoirs, and wetlands. GLM was developed to support the science needs of the Global Lake Ecological Observatory Network (GLEON), a network of researchers using sensors to understand lake functioning and address questions about how lakes around the world respond to climate and land use change. The scale and diversity of lake types, locations, and sizes, and the expanding observational datasets created the need for a robust community model of lake dynamics with sufficient flexibility to accommodate a range of scientific and management questions relevant to the GLEON community. This paper summarizes the scientific basis and numerical implementation of the model algorithms, including details of sub-models that simulate surface heat exchange and ice cover dynamics, vertical mixing, and inflow–outflow dynamics. We demonstrate the suitability of the model for different lake types that vary substantially in their morphology, hydrology, and climatic conditions. GLM supports a dynamic coupling with biogeochemical and ecological modelling libraries for integrated simulations of water quality and ecosystem health, and options for integration with other environmental models are outlined. Finally, we discuss utilities for the analysis of model outputs and uncertainty assessments, model operation within a distributed cloud-computing environment, and as a tool to support the learning of network participants.

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EXPLICIT AND TACIT KNOWLEDGE IN CONSTRUCTION OF PASSIVE HOUSING, KNOWLEDGE MODELS IN LITHUANIA / IŠREIKŠTINĖS IR NEIŠREIKŠTINĖS ŽINIOS PASYVIŲJŲ NAMŲ STATYBOJE, ŽINIŲ MODELIAI PASAULYJE IR LIETUVOJE

Mokslas - Lietuvos ateitis ◽

10.3846/mla.2011.024 ◽

2011 ◽

Vol 3 (2) ◽

pp. 12-16

Author(s):

Jevgenija Rutė

Keyword(s):

Organizational Performance ◽

Tacit Knowledge ◽

Construction Industry ◽

Practical Knowledge ◽

Initial Step ◽

Integrated Approach ◽

Climatic Conditions ◽

Knowledge Generation ◽

Factors Affecting ◽

Building Maintenance

Optimization of building maintenance expenditure becomes really an urgent issue in Lithuania. People prefer a warmer housing and show interest in recent decisions of engineering systems. They are looking for the best decision of heating costs optimization to price down heating costs not 10-20%, but a number of times. The results of passive houses scientific research as well as models of passive housing are discussed in the article. They ascertain and compare features of passive housing construction in different countries which depends on climatic conditions. Most countries support traditional housing. Remarkable thermal resistance and cost efficient maintenance of passive housing may be reached through an integrated approach of using proper architectural, constructional and engineering resolution, as well as applying the most relevant material usage and elaborating and accumulating practical knowledge. Lithuania, as well as other countries in the world, reveals that the concept of tacit knowledge still lacks sufficient attention within the construction industry, despite the fact that proper understanding and management of this resource is of immense importance for the achievement of better organizational performance. As the initial step towards the management of tacit knowledge, this paper examines the factors affecting tacit knowledge generation and utilization in the construction industry.

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Advances in Agronomic Management of Indian Mustard (Brassica juncea(L.) Czernj. Cosson): An Overview

International Journal of Agronomy ◽

10.1155/2012/408284 ◽

2012 ◽

Vol 2012 ◽

pp. 1-14 ◽

Cited By ~ 69

Author(s):

Kapila Shekhawat ◽

S. S. Rathore ◽

O. P. Premi ◽

B. K. Kandpal ◽

J. S. Chauhan

Keyword(s):

Nutrient Management ◽

Cropping Systems ◽

Indian Mustard ◽

Cropping System ◽

Integrated Approach ◽

Climatic Conditions ◽

Agronomic Management ◽

Management Techniques ◽

Seedbed Preparation ◽

Crop Geometry

India is the fourth largest oilseed economy in the world. Among the seven edible oilseeds cultivated in India, rapeseed-mustard contributes 28.6% in the total oilseeds production and ranks second after groundnut sharing 27.8% in the India’s oilseed economy. The mustard growing areas in India are experiencing the vast diversity in the agro climatic conditions and different species of rapeseed-mustard are grown in some or other part of the country. Under marginal resource situation, cultivation of rapeseed-mustard becomes less remunerative to the farmers. This results in a big gap between requirement and production of mustard in India. Therefore site-specific nutrient management through soil-test recommendation based should be adopted to improve upon the existing yield levels obtained at farmers field. Effective management of natural resources, integrated approach to plant-water, nutrient and pest management and extension of rapeseed-mustard cultivation to newer areas under different cropping systems will play a key role in further increasing and stabilizing the productivity and production of rapeseed-mustard. The paper reviews the advances in proper land and seedbed preparation, optimum seed and sowing, planting technique, crop geometry, plant canopy, appropriate cropping system, integrated nutrient management and so forth to meet the ever growing demand of oil in the country and to realize the goal of production of 24 million tonnes of oilseed by 2020 AD through these advanced management techniques.

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