A brief introduction to niche modellingandrewxhill
Niche modeling attempts to predict a species' fundamental ecological niche and potential geographic distribution by relating known occurrence locations to environmental variables. It samples variables like climate and habitat that could describe a species' presence, builds a model of their relationship, and predicts the conditions that define the species' niche. This allows prediction of a species' potential range beyond just point occurrence data. Niche modeling has become more common due to advances in algorithms, worldwide environmental data availability, and GIS technology, and provides insights into a species' historical, present, and potential future distributions under climate change.
This document discusses agrobiodiversity, which refers to the variety of plants, animals and microorganisms used in agriculture, as well as the ecosystems that support agricultural systems. It notes that agrobiodiversity provides food, medicine, ecosystem services and genetic resources. However, agrobiodiversity is being lost due to factors like habitat loss, deforestation, overgrazing, and climate change. The document recommends best practices to enhance agrobiodiversity such as organic farming, integrated pest management, seed banking systems, and crop diversity.
This document discusses biosphere reserves, which are designated by UNESCO to balance environmental conservation and human development. Biosphere reserves have three zones - a fully protected core area, a buffer zone where limited activities are allowed, and an outer transition zone where sustainable economic activities take place. The document outlines the criteria for designation, functions, and structure of biosphere reserves. It also discusses India's participation in UNESCO's Man and Biosphere Programme through its establishment of 11 biosphere reserves within the country.
The document discusses using genetic techniques like PCR, PCR-RFLP, microsatellites, and gene sequencing to study behavior, species identification, and population sizes in various organisms like parasitoid wasps and grizzly bears. It also examines reproductive behaviors like lekking in buff-breasted sandpipers and monogamy versus polygamy in blue and great tits. Population size and evidence of bottlenecks are investigated using Hardy-Weinberg equilibrium calculations on microsatellite data from Joshua tree populations.
Distribution in global pattern of biodiversitySachin Das
Biodiversity varies based on latitude and altitude, with the most biodiversity found in the tropical regions near the equator and decreasing as one moves further north or south in latitude or to higher altitudes up mountains. Specifically, biodiversity is lowest in the Arctic, moderate in temperate regions, and highest in the tropics between 23.5 degrees north and south latitude, while biodiversity also decreases with increasing altitude as temperature decreases the higher one goes. The document discusses these latitudinal and altitudinal gradients in biodiversity as major global patterns.
Species are organisms that can breed and produce fertile offspring. The International Union for Conservation of Nature (IUCN) classifies species into different categories based on extinction risk. The IUCN Red List evaluates thousands of species and subspecies to convey the urgency of conservation and help reduce extinction. Species are classified into groups including Extinct, Critically Endangered, Endangered, Vulnerable, Near Threatened, Least Concern, Data Deficient, and Not Evaluated based on population decline, size, distribution and other risk factors.
International Union for Conservation of Nature
IUCN
United for Life and Livelihoods
Red List of Threatened Species
Red Data Book
global extinction risk status
Extinct (EX)
EXTINCT IN THE WILD (EW)
CRITICALLY ENDANGERED (CR)
ENDANGERED (EN)
VULNERABLE (VU)
NEAR THREATENED (NT)
LEAST CONCERN (LC)
DATA DEFICIENT (DD)
Wildlife management techniques and methods of wildlife conservationAnish Gawande
Wildlife Conservation is the practice of protecting wild plant and animal species and their habitat. Wildlife plays an important role in balancing the environment and provides stability to different natural processes of nature. The goal of wildlife conservation is to ensure that nature will be around for future generations to enjoy and also to recognize the importance of wildlife and wilderness for humans and other species alike. Many nations have government agencies and NGO's dedicated to wildlife conservation, which help to implement policies designed to protect wildlife. Numerous independent non-profit organizations also promote various wildlife conservation causes.
Wildlife conservation has become an increasingly important practice due to the negative effects of human activity on wildlife. An endangered species is defined as a population of a living species that is in the danger of becoming extinct because the species has a very low or falling population, or because they are threatened by the varying environmental or prepositional parameters.
A brief introduction to niche modellingandrewxhill
Niche modeling attempts to predict a species' fundamental ecological niche and potential geographic distribution by relating known occurrence locations to environmental variables. It samples variables like climate and habitat that could describe a species' presence, builds a model of their relationship, and predicts the conditions that define the species' niche. This allows prediction of a species' potential range beyond just point occurrence data. Niche modeling has become more common due to advances in algorithms, worldwide environmental data availability, and GIS technology, and provides insights into a species' historical, present, and potential future distributions under climate change.
This document discusses agrobiodiversity, which refers to the variety of plants, animals and microorganisms used in agriculture, as well as the ecosystems that support agricultural systems. It notes that agrobiodiversity provides food, medicine, ecosystem services and genetic resources. However, agrobiodiversity is being lost due to factors like habitat loss, deforestation, overgrazing, and climate change. The document recommends best practices to enhance agrobiodiversity such as organic farming, integrated pest management, seed banking systems, and crop diversity.
This document discusses biosphere reserves, which are designated by UNESCO to balance environmental conservation and human development. Biosphere reserves have three zones - a fully protected core area, a buffer zone where limited activities are allowed, and an outer transition zone where sustainable economic activities take place. The document outlines the criteria for designation, functions, and structure of biosphere reserves. It also discusses India's participation in UNESCO's Man and Biosphere Programme through its establishment of 11 biosphere reserves within the country.
The document discusses using genetic techniques like PCR, PCR-RFLP, microsatellites, and gene sequencing to study behavior, species identification, and population sizes in various organisms like parasitoid wasps and grizzly bears. It also examines reproductive behaviors like lekking in buff-breasted sandpipers and monogamy versus polygamy in blue and great tits. Population size and evidence of bottlenecks are investigated using Hardy-Weinberg equilibrium calculations on microsatellite data from Joshua tree populations.
Distribution in global pattern of biodiversitySachin Das
Biodiversity varies based on latitude and altitude, with the most biodiversity found in the tropical regions near the equator and decreasing as one moves further north or south in latitude or to higher altitudes up mountains. Specifically, biodiversity is lowest in the Arctic, moderate in temperate regions, and highest in the tropics between 23.5 degrees north and south latitude, while biodiversity also decreases with increasing altitude as temperature decreases the higher one goes. The document discusses these latitudinal and altitudinal gradients in biodiversity as major global patterns.
Species are organisms that can breed and produce fertile offspring. The International Union for Conservation of Nature (IUCN) classifies species into different categories based on extinction risk. The IUCN Red List evaluates thousands of species and subspecies to convey the urgency of conservation and help reduce extinction. Species are classified into groups including Extinct, Critically Endangered, Endangered, Vulnerable, Near Threatened, Least Concern, Data Deficient, and Not Evaluated based on population decline, size, distribution and other risk factors.
International Union for Conservation of Nature
IUCN
United for Life and Livelihoods
Red List of Threatened Species
Red Data Book
global extinction risk status
Extinct (EX)
EXTINCT IN THE WILD (EW)
CRITICALLY ENDANGERED (CR)
ENDANGERED (EN)
VULNERABLE (VU)
NEAR THREATENED (NT)
LEAST CONCERN (LC)
DATA DEFICIENT (DD)
Wildlife management techniques and methods of wildlife conservationAnish Gawande
Wildlife Conservation is the practice of protecting wild plant and animal species and their habitat. Wildlife plays an important role in balancing the environment and provides stability to different natural processes of nature. The goal of wildlife conservation is to ensure that nature will be around for future generations to enjoy and also to recognize the importance of wildlife and wilderness for humans and other species alike. Many nations have government agencies and NGO's dedicated to wildlife conservation, which help to implement policies designed to protect wildlife. Numerous independent non-profit organizations also promote various wildlife conservation causes.
Wildlife conservation has become an increasingly important practice due to the negative effects of human activity on wildlife. An endangered species is defined as a population of a living species that is in the danger of becoming extinct because the species has a very low or falling population, or because they are threatened by the varying environmental or prepositional parameters.
Ppt is made vailable for public for scientifc use.
Population ecology concept and its characteristics explained by using practical examples in a simple language. data is significant for competitive examinations
This document discusses biodiversity and methods for measuring it. It explains that biodiversity has three main components: species diversity, ecosystem diversity, and genetic diversity. It also describes different categories for measuring diversity within habitats (alpha diversity), between habitats (beta diversity), and across landscapes (gamma diversity). The document focuses on the Simpson index, which measures the probability that two randomly selected individuals belong to the same species. It provides the formula for calculating the Simpson index and discusses how it can be adapted to better represent diversity. An example calculation using species data from a woodland is also included.
- The document discusses endemic species, which are plant and animal species found in a particular geographical region and nowhere else. Some examples of endemic species in India are discussed, including the red-crowned roofed turtle, white-cheeked barbet, forest owlet, grey junglefowl, white-browed gibbon, and others. Threats to endemic species include habitat destruction, increasing human population, introduction of new species, and insularity. Their vulnerability is high due to smaller populations and isolation, so protection of endemic species is important for biodiversity conservation.
This document discusses in situ and ex situ conservation methods. In situ conservation involves protecting species within their natural habitats, such as through nature reserves, while ex situ conservation involves protecting species outside their natural habitats, like in zoos, botanical gardens, and seed banks. Setting up wildlife reserves for in situ conservation requires identifying suitable areas, surveying species, establishing legal protections, managing the habitat, and controlling invasive species and natural succession. Ex situ conservation can be useful when in situ options are no longer viable, but it presents challenges like small gene pools, inbreeding, and an inability for species to evolve with their environments.
The IUCN Red List is the world's most comprehensive inventory of the global conservation status of species. It uses a set of criteria to evaluate the extinction risk of thousands of species and publishes its assessments. Major goals are to convey the urgency of conservation and provide information to guide actions to conserve biological diversity. Key findings from assessments over the years have shown increasing numbers of threatened species, including many moving into critically endangered categories. Major taxonomic groups like corals, amphibians, and mammals are particularly at risk.
Biodiversity refers to the variety of life on Earth at all levels, from genes to ecosystems. There are three main types of biodiversity: genetic diversity within species, species diversity between ecosystems, and ecosystem diversity across landscapes. Maintaining biodiversity is important as each species and ecosystem provides vital services like food, medicine, stable climate, water purification and more, with global economic value estimated at $16.54 trillion annually. Loss of any species or ecosystem impacts these services and reduces nature's ability to adapt over time.
Lecture note on Biodiversity conservationTalemos Seta
Describes about the concept, scope, definition of Biodiversity, threats of biodiversity, centre of Origin/diversity, Biodiversity hotspots, strartegies of BD conservation
Biodiversity indicators: a quick guide to indicator developmentIIED
These slides, presented by Sarah Darrah from the UN Environment Programme World Conservation Monitoring Centre, introduce biodiversity indicator development.
In the presentation, she highlights how the nature of indicators depends on what they are being used for, and explains the Biodiversity Indicator Development Framework which has been drawn up by the Biodiversity Indicators Partnership.
The presentation was given to the ‘Biodiversity mainstreaming’ workshop held in Sogakope, Ghana, from 1-3 November 2016.
More information: www.iied.org/nbsaps
Lecture about Monitoring and Biodiversity Indices, with linkage to on-going CBD programs, and a special focus on species monitoring.Many examples, needs some formatting, hope still useful!
This topic deals with the phenomenon of endemism and classification of endemic animals into various categories with a couple of endemic species to Indian subcontinent. This presentation is useful for the teachers teaching classes at UG and PG levels as well as for the students studying at respective classes. This is exclusively for education purpose.
The document discusses various strategies for conservation, including:
1) Wildlife managers aim to maintain animal populations at or below habitat carrying capacity to avoid damage. They also monitor breeding stock levels.
2) To manage habitats, wildlife managers consider historical trends, current conditions, breeding levels, and projections.
3) International efforts to conserve biodiversity include the 1992 Convention on Biological Diversity, which entered into force in 1993 and now has 166 parties.
Succession ,its types ,causes and theories SalmaAjmal
This document discusses plant succession, including the causes, types, and theories of succession. It provides details on primary and secondary succession. There are two main types of succession: primary succession, which occurs in newly exposed bare areas, and secondary succession, which occurs in areas where vegetation has been disturbed but soil remains. Succession proceeds through a series of plant communities called seral stages and over time progresses toward a climax community. Major theories of succession include the monoclimax theory, polyclimax theory, and climax pattern theory. The document also outlines the main stages of hydrosere and xerosere, or aquatic and dry land succession.
This document discusses the concept of a gene pool. It begins by defining the gene pool as the set of all genes in a population, usually of a particular species. It then provides a brief history of the term and how it was formulated by geneticists in the 1920s. The document goes on to explain the rational behind the gene pool concept, including how genetic diversity within a population allows for greater adaptability. It then discusses how the gene pool concept is applied to crop breeding, dividing plant materials into primary, secondary, and tertiary gene pools based on their genetic relationship and the ease of gene transfer. Key aspects of each gene pool type are outlined. The document concludes by discussing gene pool centers and the importance of studying the gene
This document discusses the basis and classification of forest types. It begins by outlining seven bases for forest classification: physiognomy, structure, function, floristics, habitat, physiography, and history. It then describes the four major forest categories: tropical forests, subtropical forests, temperate forests, and northern coniferous forests. For each category, it provides details on location, climate characteristics, and examples of forest types. The document concludes by summarizing Champion and Seth's revised 1968 classification of forests in India, which divides forests into five major groups.
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
This document discusses biodiversity conservation through the establishment of protected areas like national parks, wildlife refuges, biosphere reserves, and conservation corridors. It explains that national parks protect natural landscapes and species while prohibiting activities like grazing and cultivation. Wildlife refuges provide sanctuary for species from threats. Biosphere reserves integrate biodiversity conservation with sustainable development and include core protected zones surrounded by buffer and transition areas where limited human activities are permitted. Conservation corridors help share genetic information between protected populations.
Population counting method line transect, point count, mark and recaptureTarique Bin Aziz
Line transect, point count, and mark-recapture are three common population counting methods. Line transect involves walking or flying along a straight transect line and recording sightings and their perpendicular distances. Point count involves recording all birds seen and heard from count stations for a set time period. Mark-recapture involves capturing and marking a sample of the population, releasing them, then capturing another sample to estimate the total population size based on the proportion that were marked. Each method makes assumptions about animal behavior and has advantages such as being economical or applicable throughout the year as well as disadvantages like missing rare species.
This document discusses island biogeography and provides examples of continental and oceanic islands. It describes how continental islands like Great Britain and Borneo have fauna more similar to nearby mainland areas due to past connections, while oceanic islands have fauna that arrived by air/water and is often endemic. It discusses species-area relationships and how larger islands support more species due to lower extinction rates. It summarizes Robert MacArthur and E.O. Wilson's equilibrium theory of island biogeography.
Ecological niche modeling uses species occurrence data and environmental data to build a model predicting a species' probability of presence in a given area. However, the process is more complicated than simply combining the two data sources. It involves carefully preparing and quality checking the data, choosing an appropriate area and method for model calibration, evaluating the model, and assessing whether the model can be extrapolated to other times or places. Many steps are required to produce an accurate ecological niche model.
The document discusses concepts and methodology in ecological niche modeling and species distribution modeling. It addresses issues like spatial autocorrelation, study design, and scenarios in the background area of modeling (BAM). It presents methods for calibrating models, evaluating models and comparing different modeling algorithms. Maps of distributions of disease vectors in Brazil are shown and factors influencing distributions are examined.
Ppt is made vailable for public for scientifc use.
Population ecology concept and its characteristics explained by using practical examples in a simple language. data is significant for competitive examinations
This document discusses biodiversity and methods for measuring it. It explains that biodiversity has three main components: species diversity, ecosystem diversity, and genetic diversity. It also describes different categories for measuring diversity within habitats (alpha diversity), between habitats (beta diversity), and across landscapes (gamma diversity). The document focuses on the Simpson index, which measures the probability that two randomly selected individuals belong to the same species. It provides the formula for calculating the Simpson index and discusses how it can be adapted to better represent diversity. An example calculation using species data from a woodland is also included.
- The document discusses endemic species, which are plant and animal species found in a particular geographical region and nowhere else. Some examples of endemic species in India are discussed, including the red-crowned roofed turtle, white-cheeked barbet, forest owlet, grey junglefowl, white-browed gibbon, and others. Threats to endemic species include habitat destruction, increasing human population, introduction of new species, and insularity. Their vulnerability is high due to smaller populations and isolation, so protection of endemic species is important for biodiversity conservation.
This document discusses in situ and ex situ conservation methods. In situ conservation involves protecting species within their natural habitats, such as through nature reserves, while ex situ conservation involves protecting species outside their natural habitats, like in zoos, botanical gardens, and seed banks. Setting up wildlife reserves for in situ conservation requires identifying suitable areas, surveying species, establishing legal protections, managing the habitat, and controlling invasive species and natural succession. Ex situ conservation can be useful when in situ options are no longer viable, but it presents challenges like small gene pools, inbreeding, and an inability for species to evolve with their environments.
The IUCN Red List is the world's most comprehensive inventory of the global conservation status of species. It uses a set of criteria to evaluate the extinction risk of thousands of species and publishes its assessments. Major goals are to convey the urgency of conservation and provide information to guide actions to conserve biological diversity. Key findings from assessments over the years have shown increasing numbers of threatened species, including many moving into critically endangered categories. Major taxonomic groups like corals, amphibians, and mammals are particularly at risk.
Biodiversity refers to the variety of life on Earth at all levels, from genes to ecosystems. There are three main types of biodiversity: genetic diversity within species, species diversity between ecosystems, and ecosystem diversity across landscapes. Maintaining biodiversity is important as each species and ecosystem provides vital services like food, medicine, stable climate, water purification and more, with global economic value estimated at $16.54 trillion annually. Loss of any species or ecosystem impacts these services and reduces nature's ability to adapt over time.
Lecture note on Biodiversity conservationTalemos Seta
Describes about the concept, scope, definition of Biodiversity, threats of biodiversity, centre of Origin/diversity, Biodiversity hotspots, strartegies of BD conservation
Biodiversity indicators: a quick guide to indicator developmentIIED
These slides, presented by Sarah Darrah from the UN Environment Programme World Conservation Monitoring Centre, introduce biodiversity indicator development.
In the presentation, she highlights how the nature of indicators depends on what they are being used for, and explains the Biodiversity Indicator Development Framework which has been drawn up by the Biodiversity Indicators Partnership.
The presentation was given to the ‘Biodiversity mainstreaming’ workshop held in Sogakope, Ghana, from 1-3 November 2016.
More information: www.iied.org/nbsaps
Lecture about Monitoring and Biodiversity Indices, with linkage to on-going CBD programs, and a special focus on species monitoring.Many examples, needs some formatting, hope still useful!
This topic deals with the phenomenon of endemism and classification of endemic animals into various categories with a couple of endemic species to Indian subcontinent. This presentation is useful for the teachers teaching classes at UG and PG levels as well as for the students studying at respective classes. This is exclusively for education purpose.
The document discusses various strategies for conservation, including:
1) Wildlife managers aim to maintain animal populations at or below habitat carrying capacity to avoid damage. They also monitor breeding stock levels.
2) To manage habitats, wildlife managers consider historical trends, current conditions, breeding levels, and projections.
3) International efforts to conserve biodiversity include the 1992 Convention on Biological Diversity, which entered into force in 1993 and now has 166 parties.
Succession ,its types ,causes and theories SalmaAjmal
This document discusses plant succession, including the causes, types, and theories of succession. It provides details on primary and secondary succession. There are two main types of succession: primary succession, which occurs in newly exposed bare areas, and secondary succession, which occurs in areas where vegetation has been disturbed but soil remains. Succession proceeds through a series of plant communities called seral stages and over time progresses toward a climax community. Major theories of succession include the monoclimax theory, polyclimax theory, and climax pattern theory. The document also outlines the main stages of hydrosere and xerosere, or aquatic and dry land succession.
This document discusses the concept of a gene pool. It begins by defining the gene pool as the set of all genes in a population, usually of a particular species. It then provides a brief history of the term and how it was formulated by geneticists in the 1920s. The document goes on to explain the rational behind the gene pool concept, including how genetic diversity within a population allows for greater adaptability. It then discusses how the gene pool concept is applied to crop breeding, dividing plant materials into primary, secondary, and tertiary gene pools based on their genetic relationship and the ease of gene transfer. Key aspects of each gene pool type are outlined. The document concludes by discussing gene pool centers and the importance of studying the gene
This document discusses the basis and classification of forest types. It begins by outlining seven bases for forest classification: physiognomy, structure, function, floristics, habitat, physiography, and history. It then describes the four major forest categories: tropical forests, subtropical forests, temperate forests, and northern coniferous forests. For each category, it provides details on location, climate characteristics, and examples of forest types. The document concludes by summarizing Champion and Seth's revised 1968 classification of forests in India, which divides forests into five major groups.
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
This document discusses biodiversity conservation through the establishment of protected areas like national parks, wildlife refuges, biosphere reserves, and conservation corridors. It explains that national parks protect natural landscapes and species while prohibiting activities like grazing and cultivation. Wildlife refuges provide sanctuary for species from threats. Biosphere reserves integrate biodiversity conservation with sustainable development and include core protected zones surrounded by buffer and transition areas where limited human activities are permitted. Conservation corridors help share genetic information between protected populations.
Population counting method line transect, point count, mark and recaptureTarique Bin Aziz
Line transect, point count, and mark-recapture are three common population counting methods. Line transect involves walking or flying along a straight transect line and recording sightings and their perpendicular distances. Point count involves recording all birds seen and heard from count stations for a set time period. Mark-recapture involves capturing and marking a sample of the population, releasing them, then capturing another sample to estimate the total population size based on the proportion that were marked. Each method makes assumptions about animal behavior and has advantages such as being economical or applicable throughout the year as well as disadvantages like missing rare species.
This document discusses island biogeography and provides examples of continental and oceanic islands. It describes how continental islands like Great Britain and Borneo have fauna more similar to nearby mainland areas due to past connections, while oceanic islands have fauna that arrived by air/water and is often endemic. It discusses species-area relationships and how larger islands support more species due to lower extinction rates. It summarizes Robert MacArthur and E.O. Wilson's equilibrium theory of island biogeography.
Ecological niche modeling uses species occurrence data and environmental data to build a model predicting a species' probability of presence in a given area. However, the process is more complicated than simply combining the two data sources. It involves carefully preparing and quality checking the data, choosing an appropriate area and method for model calibration, evaluating the model, and assessing whether the model can be extrapolated to other times or places. Many steps are required to produce an accurate ecological niche model.
The document discusses concepts and methodology in ecological niche modeling and species distribution modeling. It addresses issues like spatial autocorrelation, study design, and scenarios in the background area of modeling (BAM). It presents methods for calibrating models, evaluating models and comparing different modeling algorithms. Maps of distributions of disease vectors in Brazil are shown and factors influencing distributions are examined.
This document summarizes research on discovering spatial co-location patterns from geospatial data. It discusses how spatial data mining differs from classical data mining by considering attribute relationships between neighboring spatial objects. The paper focuses on extracting frequent co-occurrence rules between boolean spatial features from ecological datasets. It presents three approaches for modeling co-location rules problems - reference feature centric, window centric, and event centric. The Co-location Miner algorithm is introduced for mining co-location rules that satisfy minimum prevalence and conditional probability thresholds from the data.
Autocorrelation_kriging_techniques for Hydrologysmartwateriitrk
This document provides an introduction to spatial autocorrelation and kriging. It discusses Tobler's first law of geography, which states that nearby locations tend to be more related than distant locations. Spatial autocorrelation refers to the correlation of a variable with itself over space as a function of distance. The document outlines common tests for spatial autocorrelation like Moran's I and variograms. It explains how kriging uses a variogram model and nearest neighbor distances to interpolate values at unsampled locations. Kriging aims to provide the best linear unbiased predictions and estimates of uncertainty. The history of variograms, kriging, and their development by mathematicians like Matheron and geologist Krige are
1. Models are simplified representations of phenomena or systems that retain significant features and relationships.
2. Spatial models can be descriptive or prescriptive, static or dynamic, and deductive or inductive.
3. Developing a spatial model involves defining the goal, identifying variables, implementing the model, and calibrating it using empirical data. Models can then be used to predict future conditions, impacts of actions, and for planning and risk assessment.
A data-intensive assessment of the species abundance distributionElita Baldridge
Doctoral defense for Elita Baldridge from the Weecology lab at Utah State University. Slides for the talk (defense_pres.pdf) and a transcript are available on GitHub with the analysis code to fully reproduce the analyses presented. In addition, a fully closed captioned video of the talk is available on YouTube.
https://github.com/weecology/sad-comparison
https://www.youtube.com/watch?v=tkXUD0MSRCo#t=202
In this study various techniques for exploratory spatial data analysis are reviewed : spatial autocorrelation, Moran's I statistic, hot spots analysis, spatial lag and spatial error models.
Prote-OMIC Data Analysis and VisualizationDmitry Grapov
Introductory lecture to multivariate analysis of proteomic data.
Material from the UC Davis 2014 Proteomics Workshop.
See more at: http://sourceforge.net/projects/teachingdemos/files/2014%20UC%20Davis%20Proteomics%20Workshop/
Finding Meaning in Points, Areas and Surfaces: Spatial Analysis in RRevolution Analytics
Everything happens somewhere and spatial analysis attempts to use location as an explanatory variable. Such analysis is made complex by the very many ways we habitually record spatial location, the complexity of spatial data structures, and the wide variety of possible domain-driven questions we might ask. One option is to develop and use software for specific types of spatial data, another is to use a purpose-built geographical information system (GIS), but determined work by R enthusiasts has resulted in a multiplicity of packages in the R environment that can also be used.
This document discusses the concept of equifinality in complex environmental systems modeling. Equifinality refers to the idea that there are many different model structures and parameter sets that can produce similar and acceptable results when modeling system behavior. The generalized likelihood uncertainty estimation (GLUE) methodology is described as a way to account for equifinality by using ensembles of behavioral models weighted by their likelihood to estimate prediction uncertainties. An example application to rainfall-runoff modeling is used to illustrate the GLUE methodology.
1) Models like AMMI and GGE are commonly used to analyze genotype by environment interactions and identify patterns in the data. These models combine ANOVA with principal component analysis.
2) Biplots from AMMI and GGE models help visualize relationships between genotypes and environments and can identify genotypes with broad or specific adaptation.
3) Other models like PLS and FR incorporate additional environmental and genetic data to help explain sources of genotype by environment interaction.
The document discusses best practices for estimating ecological niches and producing species distribution models. It recommends using multiple modeling approaches rather than a single "best" algorithm, and fitting simple, convex models of the fundamental niche rather than complex models of the realized niche which risk overfitting. The document also discusses incorporating factors like dispersal limitations, land use change, and human effects that can't be included directly in niche models.
This document discusses different types of models used for modeling spatial processes in GIS for decision support. It describes natural and scale analogue models which use real-world events or objects as analogues. Conceptual models represent processes visually using diagrams. Mathematical models include deterministic, stochastic, and optimization models. Deterministic models show direct relationships while stochastic models use probabilities. Optimization models maximize or minimize outputs. The document argues that combining different modeling techniques in GIS allows for complex spatial process modeling to support decisions.
Curso Lichos - MOP and (separately) Niche conservatism 201606Town Peterson
MODEL TRANSFERS AND MOP
- MESS and MOP are methods for detecting extrapolative situations in species distribution models. MESS compares areas to the centroid of calibration data, while MOP compares to the nearest calibration data.
- MOP better characterizes similarities between calibration and transfer regions, making it more optimistic about in-range extrapolation.
- The document discusses evaluating niche conservatism across different timescales, from short-term invasions to differences between deeply diverged lineages, and how niche modeling approaches need to account for temporal dimensions.
- Issues with detecting niche evolution are discussed, such as distinguishing the fundamental niche from existing niche subsets and overestimating niche evolution due to incomplete characterization of nic
- Spatial autocorrelation measures the correlation of a variable with itself through space and can be positive or negative. It quantifies the degree of spatial clustering or dispersion of values across locations.
- Global measures identify overall patterns of clustering, while local measures identify specific clusters. Spatial weights defining neighbor relationships are required.
- Contiguity-based weights define neighbors based on shared boundaries, while distance-based weights use a threshold distance. Higher order weights incorporate indirect neighbors.
- Spatially lagged variables are weighted averages of neighboring values and are important for spatial autocorrelation tests and regression models.
The document discusses partial least squares structural equation modeling (PLS-SEM). It provides an overview of key concepts in PLS-SEM, including the differences between PLS-SEM and covariance-based SEM, the objectives and assumptions of each method, and guidelines for when each method is most appropriate. The document also outlines the stages of applying PLS-SEM, including specifying measurement and structural models, model estimation, and evaluating results. Examples are provided to illustrate reflective versus formative measurement models.
Metabolomic Data Analysis Workshop and Tutorials (2014)Dmitry Grapov
This document provides an introduction and overview of tutorials for metabolomic data analysis. It discusses downloading required files and software. The goals of the analysis include using statistical and multivariate analyses to identify differences between sample groups and impacted biochemical domains. It also discusses various data analysis techniques including data quality assessment, univariate and multivariate statistical analyses, clustering, principal component analysis, partial least squares modeling, functional enrichment analysis, and network mapping.
Similar to Updating Ecological Niche Modeling Methodologies (20)
An Open Access Solution that is Genuinely and Globally OpenTown Peterson
This document discusses open access to scholarly literature. It defines open access as digital content that is free of charge and most copyright/licensing restrictions. While open access literature is not free to produce, the goal is to make it costless to access. The document outlines various open access models including green (self-archiving), gold (fully open access journals), hybrid (option to pay a fee to make individual articles open), and platinum (no fees for readers or authors, requiring subsidy). It argues that open access is necessary to foster a global scholarly community but that not all solutions are equal, and that platinum open access which removes all barriers ultimately requires sustainable subsidy.
Niche comparisons 201606 para curso LichosTown Peterson
This document discusses different methods for comparing species niches, including comparing niches in geographic space versus environmental space. It outlines the requirements for niche comparisons, such as defining the null hypothesis and measuring observed versus expected similarities. Two main approaches are described: Warren et al.'s method of comparing niches in geographic space using background similarity tests, and Broennimann et al.'s method of comparing niches in environmental space using kernel densities and randomization tests. The document also provides examples of applications of niche comparison methods including studies on squirrels and fire ants.
This document discusses different methods for evaluating species distribution models. It compares threshold-dependent versus threshold-independent approaches. Threshold-dependent approaches like the binomial test assess whether a model's predictions are significantly better than random by using a single threshold. Threshold-independent approaches like ROC curves avoid assumptions around thresholding but have other limitations. The document emphasizes that both significance testing and measures of predictive performance are important for properly evaluating a model.
The document discusses biodiversity informatics training and resources. It notes that biodiversity informatics is a new field without established training programs or textbooks. It proposes the Biodiversity Informatics Training Curriculum (BITC) to address this need. BITC would include in-person training courses along with online videos, subtitles, and translations to make the materials broadly accessible. It outlines the curriculum topics and plans for future expansion, including additional modules, languages, and regions. It also provides suggestions for a Taiwanese biodiversity informatics program, including translating BITC, developing a national biodiversity assessment, capturing older data from overseas collections, and building training opportunities.
This document discusses mapping disease transmission risk from ecological and biogeographic perspectives. It summarizes past work mapping the distributions of diseases like Marburg and Lassa fever in Africa. It outlines a workflow for developing models of disease transmission risk that integrate niche models of relevant host, vector, and pathogen species with human and climate data. Challenges include integrating disease data with environmental data, accounting for species interactions, and evaluating models under future climate scenarios. Addressing these challenges could help create more predictive spatial epidemiology models.
This document discusses using niche modeling techniques to project the potential distributions of invasive species. It notes that such projections require comprehensive data from the species' native range and any other invaded areas to characterize the environmental conditions where the species is known to occur. Where possible, data from the target invaded range should also be used to test the model projections. The document recommends exploring different algorithms, environmental data sets, and extrapolation techniques to develop robust projections of areas at risk of invasion.
D2T3 exploring past distributions of speciesTown Peterson
This document discusses how Pleistocene climate changes may have impacted forest bird speciation patterns globally. It presents evidence that:
1) Forest bird distributions were fragmented into refugia during glacial periods, driving speciation as suggested by Haffer. Molecular and distribution data from Amazonian birds support this.
2) Different regions experienced warming or cooling phases that isolated populations, with adjacent areas sometimes experiencing opposite phases.
3) Speciation timing may have been out of phase between regions. Molecular clocks estimating pre-Pleistocene speciation may be inaccurate. Understanding species' ecological requirements and range shifts over time provides new insights.
D2T2 predicting species range under climate changeTown Peterson
The document discusses several potential drivers of biodiversity change including climate change, land use change, sea level rise, and direct exploitation. It explores approaches to studying both present-day models and future projections of driver impacts, as well as documenting changes that have already occurred. Specific methods examined include projecting future climate conditions, adding effects of land use and sea level rise changes, and measuring avifaunal turnover in recent historical times. The results indicate that observed temperature changes have had a significant effect on species turnover while human landscape impacts and precipitation changes have not. Land use change, climate change, and sea level rise are highlighted as diverse drivers of biodiversity change, with their impacts being complex to study and dependent on available before-and-after
A study examined the distribution of Spanish moss, an epiphytic bromeliad, across its range and related its distribution to climate data to test if its distribution could be anticipated based on optimal physiological conditions. Detailed physiological studies of Spanish moss from the 1970s-1980s were used alongside a climate data set providing global climate information every 6 hours for decades. The study aimed to scale from the micro level of Spanish moss physiology to the macro level of climate and geography to model its potential distribution using climate variables alone and with dispersal factors added.
This document discusses methods for ecological niche modeling (ENM). It covers the major steps in the ENM process:
1) Accumulating occurrence and environmental data
2) Integrating the data and assessing scenarios of how available habitat relates to a species' distribution
3) Calibrating models using various algorithms and evaluating model performance
The document emphasizes best practices such as considering biases in occurrence data, reducing dimensionality, assessing spatial autocorrelation, and using multiple model algorithms and evaluation metrics to identify the best model for a given situation. Thresholding is discussed as a key step to convert model outputs to predicted distributions.
D1T1 overview of the theoretical foundations for ecological niche modelsTown Peterson
The document discusses the BAM (Biotic, Abiotic, Movement) diagram, which is a heuristic for conceptualizing species' ecological niches and geographic distributions. It describes the three components of the BAM diagram - the abiotic niche defined by physiological requirements, the biotic niche defined by biotic interactions, and accessibility defined by a species' ability to disperse. The document also discusses Hutchinson's distinction between scenopoetic and bionomic variables and provides examples demonstrating the importance of dispersal limitations on species' distributions.
Early History of Ecological Niche Modeling and Species Distribution ModelingTown Peterson
Ecological niche modeling (ENM) and species distribution modeling (SDM) emerged in the early 1900s from Grinnell's concept of the ecological niche and has grown tremendously, with key early developments including models from Australia, Mexico, CLIMEX, and GAP analyses. Major algorithms improved upon BIOCLIM and included GARP and statistical approaches, and the field solidified with broad model testing by Elith et al. in 2006 and Phillips et al.'s influential 2006 paper launching maximum entropy modeling.
José Mariano Mociño: A First Light in Mexican OrnithologyTown Peterson
A talk presented to the Facultad de Ciencias, UNAM, in Mexico City. Accompanied the presentation of a new book publication on the ornithological results of the Sessé-Mociño expeditions in the late 1700s.
José Mariano Mociño: A First Light in Mexican OrnithologyTown Peterson
Talk presented (in Spanish) to the Facultad de Ciencias, UNAM, in celebration of the publication of a book presenting the 'ornithology' of the Sessé-Mociño Expedition in the late 1700s.
This document discusses the importance and benefits of global academic collaboration. It provides examples of the author's international field expeditions and collaborative research projects studying biodiversity in China and Peru. It also highlights a long-term research project analyzing changes in bird populations and species turnover in Mexico over time, finding temperature changes to be a significant driver of turnover. The document stresses that to best collaborate globally, researchers should learn the local language and culture, understand the history, make genuine local friends, and collaborate openly and respectfully while accounting for cultural differences.
This document discusses experiments to determine phenotypic traits that indicate genetic purity in Red Junglefowl (RJF). Crosses were performed between pure RJF and feral Carolina Bantam chickens. Results showed that some traits like leg color were expressed in hybrids, making them unreliable indicators of purity. The absence of hens' combs was lost in first generation hybrids but returned in backcrosses, indicating it only shows extreme contamination. Molecular studies reveal RJF genomes are contaminated by chickens, even in historical specimens. This raises questions about RJF conservation status and purity of remaining wild and captive populations.
Presented to Wildlife Institute of India, treating each step in the process of publishing scientific results, from the basic writing skills to considerations of open access to scientific results.
This document discusses using ecological niche modeling to map disease transmission risk. It describes how spatial models can help identify areas to focus disease prevention and treatment resources. The document presents examples of past models mapping the distributions of Marburg virus in Africa and the sand fly Lutzomyia longipalpis. It advocates developing models that consider interactions between relevant species like pathogens, vectors and hosts to better anticipate transmission risk. The document outlines a proposed workflow for building such integrated models and applying them under future climate change scenarios. It acknowledges gaps in data and approaches that need more development to create truly predictive spatial epidemiology models.
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...Scintica Instrumentation
Targeting Hsp90 and its pathogen Orthologs with Tethered Inhibitors as a Diagnostic and Therapeutic Strategy for cancer and infectious diseases with Dr. Timothy Haystead.
Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDSSérgio Sacani
The pathway(s) to seeding the massive black holes (MBHs) that exist at the heart of galaxies in the present and distant Universe remains an unsolved problem. Here we categorise, describe and quantitatively discuss the formation pathways of both light and heavy seeds. We emphasise that the most recent computational models suggest that rather than a bimodal-like mass spectrum between light and heavy seeds with light at one end and heavy at the other that instead a continuum exists. Light seeds being more ubiquitous and the heavier seeds becoming less and less abundant due the rarer environmental conditions required for their formation. We therefore examine the different mechanisms that give rise to different seed mass spectrums. We show how and why the mechanisms that produce the heaviest seeds are also among the rarest events in the Universe and are hence extremely unlikely to be the seeds for the vast majority of the MBH population. We quantify, within the limits of the current large uncertainties in the seeding processes, the expected number densities of the seed mass spectrum. We argue that light seeds must be at least 103 to 105 times more numerous than heavy seeds to explain the MBH population as a whole. Based on our current understanding of the seed population this makes heavy seeds (Mseed > 103 M⊙) a significantly more likely pathway given that heavy seeds have an abundance pattern than is close to and likely in excess of 10−4 compared to light seeds. Finally, we examine the current state-of-the-art in numerical calculations and recent observations and plot a path forward for near-future advances in both domains.
Candidate young stellar objects in the S-cluster: Kinematic analysis of a sub...Sérgio Sacani
Context. The observation of several L-band emission sources in the S cluster has led to a rich discussion of their nature. However, a definitive answer to the classification of the dusty objects requires an explanation for the detection of compact Doppler-shifted Brγ emission. The ionized hydrogen in combination with the observation of mid-infrared L-band continuum emission suggests that most of these sources are embedded in a dusty envelope. These embedded sources are part of the S-cluster, and their relationship to the S-stars is still under debate. To date, the question of the origin of these two populations has been vague, although all explanations favor migration processes for the individual cluster members. Aims. This work revisits the S-cluster and its dusty members orbiting the supermassive black hole SgrA* on bound Keplerian orbits from a kinematic perspective. The aim is to explore the Keplerian parameters for patterns that might imply a nonrandom distribution of the sample. Additionally, various analytical aspects are considered to address the nature of the dusty sources. Methods. Based on the photometric analysis, we estimated the individual H−K and K−L colors for the source sample and compared the results to known cluster members. The classification revealed a noticeable contrast between the S-stars and the dusty sources. To fit the flux-density distribution, we utilized the radiative transfer code HYPERION and implemented a young stellar object Class I model. We obtained the position angle from the Keplerian fit results; additionally, we analyzed the distribution of the inclinations and the longitudes of the ascending node. Results. The colors of the dusty sources suggest a stellar nature consistent with the spectral energy distribution in the near and midinfrared domains. Furthermore, the evaporation timescales of dusty and gaseous clumps in the vicinity of SgrA* are much shorter ( 2yr) than the epochs covered by the observations (≈15yr). In addition to the strong evidence for the stellar classification of the D-sources, we also find a clear disk-like pattern following the arrangements of S-stars proposed in the literature. Furthermore, we find a global intrinsic inclination for all dusty sources of 60 ± 20◦, implying a common formation process. Conclusions. The pattern of the dusty sources manifested in the distribution of the position angles, inclinations, and longitudes of the ascending node strongly suggests two different scenarios: the main-sequence stars and the dusty stellar S-cluster sources share a common formation history or migrated with a similar formation channel in the vicinity of SgrA*. Alternatively, the gravitational influence of SgrA* in combination with a massive perturber, such as a putative intermediate mass black hole in the IRS 13 cluster, forces the dusty objects and S-stars to follow a particular orbital arrangement. Key words. stars: black holes– stars: formation– Galaxy: center– galaxies: star formation
TOPIC OF DISCUSSION: CENTRIFUGATION SLIDESHARE.pptxshubhijain836
Centrifugation is a powerful technique used in laboratories to separate components of a heterogeneous mixture based on their density. This process utilizes centrifugal force to rapidly spin samples, causing denser particles to migrate outward more quickly than lighter ones. As a result, distinct layers form within the sample tube, allowing for easy isolation and purification of target substances.
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...Advanced-Concepts-Team
Presentation in the Science Coffee of the Advanced Concepts Team of the European Space Agency on the 07.06.2024.
Speaker: Diego Blas (IFAE/ICREA)
Title: Gravitational wave detection with orbital motion of Moon and artificial
Abstract:
In this talk I will describe some recent ideas to find gravitational waves from supermassive black holes or of primordial origin by studying their secular effect on the orbital motion of the Moon or satellites that are laser ranged.
PPT on Direct Seeded Rice presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 2024.
BIRDS DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptxgoluk9330
Ahota Beel, nestled in Sootea Biswanath Assam , is celebrated for its extraordinary diversity of bird species. This wetland sanctuary supports a myriad of avian residents and migrants alike. Visitors can admire the elegant flights of migratory species such as the Northern Pintail and Eurasian Wigeon, alongside resident birds including the Asian Openbill and Pheasant-tailed Jacana. With its tranquil scenery and varied habitats, Ahota Beel offers a perfect haven for birdwatchers to appreciate and study the vibrant birdlife that thrives in this natural refuge.
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...Creative-Biolabs
Neutralizing antibodies, pivotal in immune defense, specifically bind and inhibit viral pathogens, thereby playing a crucial role in protecting against and mitigating infectious diseases. In this slide, we will introduce what antibodies and neutralizing antibodies are, the production and regulation of neutralizing antibodies, their mechanisms of action, classification and applications, as well as the challenges they face.
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆Sérgio Sacani
Context. The early-type galaxy SDSS J133519.91+072807.4 (hereafter SDSS1335+0728), which had exhibited no prior optical variations during the preceding two decades, began showing significant nuclear variability in the Zwicky Transient Facility (ZTF) alert stream from December 2019 (as ZTF19acnskyy). This variability behaviour, coupled with the host-galaxy properties, suggests that SDSS1335+0728 hosts a ∼ 106M⊙ black hole (BH) that is currently in the process of ‘turning on’. Aims. We present a multi-wavelength photometric analysis and spectroscopic follow-up performed with the aim of better understanding the origin of the nuclear variations detected in SDSS1335+0728. Methods. We used archival photometry (from WISE, 2MASS, SDSS, GALEX, eROSITA) and spectroscopic data (from SDSS and LAMOST) to study the state of SDSS1335+0728 prior to December 2019, and new observations from Swift, SOAR/Goodman, VLT/X-shooter, and Keck/LRIS taken after its turn-on to characterise its current state. We analysed the variability of SDSS1335+0728 in the X-ray/UV/optical/mid-infrared range, modelled its spectral energy distribution prior to and after December 2019, and studied the evolution of its UV/optical spectra. Results. From our multi-wavelength photometric analysis, we find that: (a) since 2021, the UV flux (from Swift/UVOT observations) is four times brighter than the flux reported by GALEX in 2004; (b) since June 2022, the mid-infrared flux has risen more than two times, and the W1−W2 WISE colour has become redder; and (c) since February 2024, the source has begun showing X-ray emission. From our spectroscopic follow-up, we see that (i) the narrow emission line ratios are now consistent with a more energetic ionising continuum; (ii) broad emission lines are not detected; and (iii) the [OIII] line increased its flux ∼ 3.6 years after the first ZTF alert, which implies a relatively compact narrow-line-emitting region. Conclusions. We conclude that the variations observed in SDSS1335+0728 could be either explained by a ∼ 106M⊙ AGN that is just turning on or by an exotic tidal disruption event (TDE). If the former is true, SDSS1335+0728 is one of the strongest cases of an AGNobserved in the process of activating. If the latter were found to be the case, it would correspond to the longest and faintest TDE ever observed (or another class of still unknown nuclear transient). Future observations of SDSS1335+0728 are crucial to further understand its behaviour. Key words. galaxies: active– accretion, accretion discs– galaxies: individual: SDSS J133519.91+072807.4
2. It Is A Bit Too Easy …
• Very easy access to lots of
occurrence data
• Very easy access to rich
geospatial data
• Easy-to-use modeling tools
• Lots of literature setting out
the examples
3. Ecological Niche Modeling
1. Accumulate Input Data
2. Integrate Occurrence and Environmental Data
3. Model Calibration
4. Model Evaluation
5. Summary and Interpretation
4. Accumulate Input Data
Collate primary
biodiversity data
documenting
occurrences
Process environmental
layers to be maximally
relevant to distributional
ecology of species in
question
Collate GIS database
of relevant data
layers
Assess spatial precision
of occurrence data;
adjust inclusion of data
accordingly
Data subsetting for
model evaluation
Occurrence and
environmental data
Assess spatial
autocorrelation
5. Occurrence Data in Niche Modeling
• Goal is to represent the full diversity of
situations under which a particular species
maintains populations
• Spatial biases (i.e., non-random or non-
uniform distribution within G) is not damning
• Biases within E are catastrophic, and will
translate directly into biases in any niche
estimate
• More is usually better, but not always…
8. Georeferencing should …
• Represent the place at which the species was
found
• Represent the certainty and uncertainty with
which that place is characterized
• Summarize the methods used to establish that
place
• Preserve all of the original information for
possible reinterpretation
12. Data Cleaning
• Attempt to detect meaningfully erroneous records,
so that they can be treated with caution in analysis
• Use internal consistency to detect initial problems
– Species names consistent?
– Terrestrial species on land, marine species in the ocean?
– Latlong matches country, state, district, etc.
• Use external consistency to go deeper
– Occurrence data match known distribution spatially?
– Occurrence data match known distribution
environmentally?
• If precision data are available, filter to retain only
records that are precise enough for the study
• Iterative process with important consequences
13.
14. Data Subsetting
• Must respond to the question at hand … why
are you doing the study?
• Ideally completely independent data streams
• Failing that, can be
– Macrospatial
– Microspatial (but see spatial autocorrelation)
– Random
• Will return to this point later…
15. Generalities: Environmental Data
• Raster format: i.e., information exists across
entire region of interest
• Relevant information as regards the
distributional potential of the species of
interest
• More dimensions = better (generally), BUT
– collinearity is bad
– too many dimensions is bad
16. Major Sources
• Climate data – long time span, but low
temporal resolution
• Remote-sensing data – high temporal
resolution, diverse products, short time span
• Topographic data – high temporal resolution,
uncertain connection to species’ distributional
ecology
• Soils data – uneven global coverage,
categorical data
• Others
18. Two Major Implications
• Non-independence in model evaluation
– Available data are often split into data sets for
calibration and evaluation
– Data points that are not independent of one another
may end up in different data sets, thereby
compromising the robustness of the test
• Inflation of sample sizes
– Because individual data points may be non-
independent of one another, sample sizes may appear
larger than they actually are
– This inflation may create opportunity for Type 1 errors
in model evaluation and model comparisons
21. Integrate Occurrence and Environmental Data
Assess BAM scenario for
species in question; avoid
M-limited situations
Saupe et al. 2012. Variation in niche and distribution model performance: The need
for a priori assessment of key causal factors. Ecological Modelling, 237–238, 11-22.
Estimate M and S
as area of analysis
in study
Barve et al. 2011. The crucial role of the
accessible area in ecological niche modeling
and species distribution modeling. Ecological
Modelling, 222, 1810-1819.
Reduce dimensionality (PCA
or correlation analysis)
Occurrence and
environmental data
Occurrence and
environmental data
ready for analysis
27. BAM Conclusions
• Some situations are not amenable to fitting
ecological niche models that will have
predictive power
• Models tend much more to good fitting of the
potential distribution, rather than the actual
distribution
• Must ponder carefully the BAM configuration
in a particular study situation to avoid
configurations that will not yield usable
models
34. M
• When the species has no history in an area:
– Use a radius related to dispersal distances
• When history is short (i.e., environment
constant):
– Use a radius representing compounding of
dispersal distances
• When history is long (i.e., environmental
change is a factor)
– Seek ways of assessing areas that the species’
distribution through time has covered…
37. Model Calibration
Estimate ecological niche
(various algorithms)
Model calibration,
adjusting parameters to
maximize quality
Model
thresholding
Peterson et al. 2007. Transferability and model
evaluation in ecological niche modeling: A
comparison of GARP and Maxent. Ecography,
30, 550-560.
Occurrence and
environmental data
ready for analysis
“No Silver Bullet” paper to appear
Warren, D. L. and S. N. Seifert. 2011. Ecological niche
modeling in Maxent: The importance of model complexity
and the performance of model selection criteria. Ecological
Applications 21:335-342.
Preliminary
models
47. No Silver Bullets in ENM
• Single algorithms may perform ‘best’ on average
• The best algorithm in any given situation,
however, may be other than the ‘best’
• NSB thinking suggests that we should not use a
single approach
• Use a suite of approaches (e.g., as implemented
in OM, BIOMOD, BIOENSEMBLES, etc.), challenge
to predict, choose best for that situation
• Maxent is good, but it is not the only algorithm …
50. Thresholding
• Use an approach that prioritizes omission
error over commission error, in view of the
greater reliability of presence data
• Minimum training presence thresholding
seeks the highest suitability value that
includes 100% of the calibration data
• Suggest (strongly) using a parallel approach
that seeks that highest suitability value that
includes (100-E)% of the calibration data
52. Model Evaluation
Project niche model
to geographic space
Model
evaluation
Peterson et al. 2008. Rethinking receiver operating characteristic
analysis applications in ecological niche modelling. Ecological
Modelling, 213, 63-72.
Preliminary
models
Reset data subsets based
on evaluation results
Corroborated models
ready for projection to
geographic
times/regions of
interest
53.
54. If predicted suitable area covers
15% of the testing area, then
15% of evaluation points are
expected to fall in the predicted
suitable area by chance.
• p = proportion of area
predicted suitable
• s = number of successes
• n = number of evaluation
points
Cumulative binomial distribution calculates the probability of
obtaining s successes out of n trials in a situation in which p
proportion of the testing area is predicted present. If this probability
is below 0.05, we interpret the situation as indicating that the
model’s predictions are significantly better than random.
Threshold-
dependent
Approach
59. Significance vs Performance
• Predictions that are significantly better than
random is important, and is a sine qua non for
model interpretation
• BUT, it is also important to assure that the
model performs sufficiently well for the
intended uses of the output
• Performance measures include omission rate,
correct classification rate, etc.
60. Summary and Interpretation
Evaluation of model
transfer results
Transfer to other
situations (time
and space)
Assess extrapolation
(MESS and MOP)
Owens, H. L., L. P. Campbell, L. Dornak, E. E. Saupe, N.
Barve, J. Soberón, K. Ingenloff, A. Lira-Noriega, C. M.
Hensz, C. E. Myers, and A. T. Peterson. 2013.
Constraints on interpretation of ecological niche
models by limited environmental ranges on calibration
areas. Ecological Modelling 263:10-18.
Refine estimate of
current distribution
via land use, etc.
Compare present and
“other” to assess
effects of change
Models calibrated and
evaluated, and transferred
to present and “other”
situations
61.
62.
63.
64.
65.
66. MESS and MOP
• Both have the intention of detecting extrapolative
situations
• MESS is implemented within Maxent
• MESS compares the area in question to the
centroid of the calibration cloud
• MOP compares the area in question to the
nearest part of the calibration cloud
• Agree on ‘out of range’ conditions
• MOP better characterizes similarities between
calibration and transfer regions, and thus is more
optimistic as regards in-range extrapolation
67.
68. Ecological Niche Modeling
1. Accumulate Input Data
2. Integrate Occurrence and Environmental Data
3. Model Calibration
4. Model Evaluation
5. Summary and Interpretation