MaxEnt is a program for modelling species distributions from presence-only species records. This paper is written for ecologists and describes the MaxEnt model from a statistical perspective, making ...explicit links between the structure of the model, decisions required in producing a modelled distribution, and knowledge about the species and the data that might affect those decisions. To begin we discuss the characteristics of presence-only data, highlighting implications for modelling distributions. We particularly focus on the problems of sample bias and lack of information on species prevalence. The keystone of the paper is a new statistical explanation of MaxEnt which shows that the model minimizes the relative entropy between two probability densities (one estimated from the presence data and one, from the landscape) defined in covariate space. For many users, this viewpoint is likely to be a more accessible way to understand the model than previous ones that rely on machine learning concepts. We then step through a detailed explanation of MaxEnt describing key components (e.g. covariates and features, and definition of the landscape extent), the mechanics of model fitting (e.g. feature selection, constraints and regularization) and outputs. Using case studies for a Banksia species native to south-west Australia and a riverine fish, we fit models and interpret them, exploring why certain choices affect the result and what this means. The fish example illustrates use of the model with vector data for linear river segments rather than raster (gridded) data. Appropriate treatments for survey bias, unprojected data, locally restricted species, and predicting to environments outside the range of the training data are demonstrated, and new capabilities discussed. Online appendices include additional details of the model and the mathematical links between previous explanations and this one, example code and data, and further information on the case studies.
Despite repeated calls to action, proposals for urban conservation are often met with surprise or scepticism. There remains a pervasive narrative in policy, practice, and the public psyche that urban ...environments, although useful for engaging people with nature or providing ecosystem services, are of little conservation value. We argue that the tendency to overlook the conservation value of urban environments stems from misconceptions about the ability of native species to persist within cities and towns and that this, in turn, hinders effective conservation action. However, recent scientific evidence shows that these assumptions do not always hold. Although it is generally true that increasing the size, quality, and connectivity of habitat patches will improve the probability that a species can persist, the inverse is not that small, degraded, or fragmented habitats found in urban environments are worthless. In light of these findings we propose updated messages that guide and inspire researchers, practitioners, and decision makers to undertake conservation action in urban environments: consider small spaces, recognize unconventional habitats, test creative solutions, and use science to minimize the impacts of future urban development.
Corrección de Ideas Erróneas para Inspirar Acciones de Conservación en Ambientes Urbanos
Resumen
A pesar de las repetidas llamadas a actuar, las propuestas para la conservación urbana con frecuencia se enfrentan a reacciones de sorpresa o escepticismo. Todavía existe una narrativa penetrante en la política, la práctica y el psique del público que dicta que los ambientes urbanos, aunque sean útiles para comprometer a las personas con la naturaleza o para proporcionar servicios ambientales, tienen poco valor para la conservación. Argumentamos que la tendencia de pasar por alto el valor para la conservación de los ambientes urbanos surge de las ideas erróneas sobre la habilidad que tienen las especies nativas para persistir dentro de ciudades y pueblos y que esto, en cambio, impide la acción efectiva de la conservación. A pesar de esto, la evidencia científica reciente muestra que estas suposiciones no siempre se sostienen. Aunque casi siempre es verdad que incrementar el tamaño, la calidad y la conectividad de los fragmentos de hábitat mejorará la probabilidad de que una especie pueda persistir, lo contrario, que los hábitats fragmentados, degradados y pequeños que se encuentran en los ambientes urbanos son inútiles, no lo es. A la luz de estos hallazgos proponemos mensajes actualizados que guíen e inspiren a los investigadores, practicantes y a los tomadores de decisiones a emprender acciones de conservación en ambientes urbanos: considerar espacios pequeños, reconocer hábitats poco convencionales, probar con soluciones creativas, y utilizar la ciencia para minimizar los impactos de desarrollos urbanos futuros.
摘要
尽管人们一再呼吁要采取城市保护行动, 然而却常常对相关提案表示诧异或怀疑。在政策制定、实践行动和公众心理中仍存在一种普遍的认识, 即城市环境虽然有助于人们亲近自然并提供生态系统服务, 但其保护价值微乎其微。我们认为, 这种忽视城市环境保护价值的倾向来源于对本地物种在城市和乡镇间续存能力的误解, 而这反过来又阻碍了有效的保护行动。然而, 最近的科学证据表明这些种种假设并不总是成立。虽然通常情况下增加生境斑块的大小、提高其质量和连接度可以提高物种续存的可能性, 但反过来看, 并不是说退化或碎片化的小面积生境在城市环境中就毫无价值。鉴于以上发现, 我们建议更新这些指导和激励研究者、实践者和决策者采取城市环境保护行动的信息, 应考虑小尺度空间的保护、认识非传统生境、尝试创新性解决方案, 并利用科学知识来减少未来城市发展带来的影响。 【翻译: 胡怡思; 审校: 聂永刚】
Article impact statement: Conserving native biodiversity is both important and achievable in urban environments.
To make progress scientists need to know what other researchers have found and how they found it. However, transparency is often insufficient across much of ecology and evolution. Researchers often ...fail to report results and methods in detail sufficient to permit interpretation and meta-analysis, and many results go entirely unreported. Further, these unreported results are often a biased subset. Thus the conclusions we can draw from the published literature are themselves often biased and sometimes might be entirely incorrect. Fortunately there is a movement across empirical disciplines, and now within ecology and evolution, to shape editorial policies to better promote transparency. This can be done by either requiring more disclosure by scientists or by developing incentives to encourage disclosure.
Evidence suggests that insufficient transparency is a problem across much of ecology and evolution. Results and methods are often reported in insufficient detail or go entirely unreported. Further, these unreported results are often a biased subset, thus substantially hampering interpretation and meta-analysis.
Journals and other institutions, such as funding agencies, influence researchers’ decisions about disseminating results. There is a movement across empirical disciplines, including ecology and evolution, to shape institutional policies to better promote transparency.
Institutions can promote transparency by requiring or encouraging more disclosure, as with the now-familiar data archiving, or by developing an incentive structure promoting disclosure, such as preregistration of studies and analysis plans.
Ecosystem services are the conditions and processes through which natural ecosystems and the species that make them up, sustain and fulfil human life. Ecosystem service valuation is being developed ...as a vehicle to integrate ecological understanding and economic considerations to redress the traditional neglect of ecosystem services in policy decisions. This paper presents a critical review on the neoclassical economic framework, tools used for economic valuation of ecosystem services and the economic welfare approach to collective decision-making, from an ecological perspective. The applicability of the framework and techniques for valuing ecosystem services are evaluated in light of the challenges posed by the complex, non-linear nature of many ecosystem services. Decisions concerning ecosystem management are often complex, socially contentious and fraught with uncertainty. Although judicious application of economic valuation techniques to ecosystem services can provide valuable information for conceptualizing decision choices and evaluating management options, there are serious limitations in the economic welfare approach to decision-making. These shortcomings and their implications for ecosystem management are elucidated and alternative approaches that emphasize participation, explicit treatment of uncertainty and transparent decision-making processes are discussed.
Iran is one of the world's fish biodiversity hotspots. Most riverine fish species in this country are currently under threat by human activities. In addition to those threats, climate change is ...expected to alter rainfall and temperature regimes, imposing further limitations, particularly to endemic fishes. Therefore, understanding how these species respond to climate change is an important issue in the conservation of Iranian freshwater biodiversity.
This study aimed to predict the potential distribution of 16 endemic fish species under two climate change scenarios (i.e., RCP 4.5 and RCP 8.5) in river habitats of Iran in the 2050s and the 2080s. The analysis is conducted using the MaxEnt model. Seven environmental variables were used for modelling: maximum width, elevation, river slope, the basins occupied by the target species, average annual precipitation, annual mean temperature, and the temperature difference between the coldest and hottest months of the year .
The validation of the model for each species showed that AUC (area under the ROC curve) scores range from 0.87 to 0.99. Under optimistic (RCP 4.5) and pessimistic (RCP 8.5) scenarios in the 2050s and the 2080s, species will face four different outcomes to their habitat range: reduction (three species), expansion (five species), reduction and expansion (seven species) and no change (one species).
It is concluded that most species that are unique in their geographical area will face serious challenges from climate change. Delineating species range changes under climate change scenarios can help prioritise conservation measures for these valuable species. Considering our results, the translocation of species to new locations also should be investigated.
Globally, urban expansion and climate change interact to threaten stream ecosystems and are accelerating the loss of aquatic biodiversity. Waterway managers urgently need tools to understand the ...potential combined impacts of urbanization and climate change and to identify effective mitigating management interventions for protecting freshwater biota. We address this challenge using the semi‐aquatic mammal the platypus (Ornithorhynchus anatinus) as a focal species. We developed high‐resolution environmental spatial data for stream networks and spatially explicit habitat suitability models (HSMs) to explore the impact of threats and to identify the combination of management actions most likely to maintain or improve habitat suitability over the next 50 years in greater Melbourne, Australia. We developed and evaluated platypus HSMs (males‐and‐females and females‐only) including validation using an independent environmental DNA data set. Platypus occurred more commonly in larger, cooler streams with greater catchment‐weighted discharge, following periods of greater stream flow. They were positively associated with near‐stream forest cover and negatively associated with annual air temperature and urban stormwater runoff. Extensive reductions in suitable platypus habitat are predicted to occur under urbanization and climate change scenarios, with the greatest threat expected from reduced streamflows. This emphasizes the importance of maintaining flow regimes as part of conserving platypus in the region; however, substantial additional benefit is predicted by concurrent riparian revegetation and urban stormwater management efforts (that also have the potential to contribute to the streamflow objectives). Provision of adequate streamflows in a future with increasing water demands and water security requirements will likely require creative integrated water management solutions. Our high‐resolution stream network and HSMs have allowed predictions of potential range‐shifts due to urban expansion and climate change impacts at management‐relevant scales and at the whole‐of‐landscape scale. This has enabled systematic strategic planning, priority action planning and target setting in strategic policy development.
Using habitat suitability models, we explored the potential impact of urban growth and climate change on the distribution of threatened platypus (Ornithorhynchus anatinus) in Greater Melbourne, Victoria, Australia. We then identified the combination of management actions most likely to maintain or improve habitat suitability. Compared with the current distribution (1), we predict extensive reductions in suitable platypus habitat from our business‐as‐usual future scenario (2). The protection of natural flow regimes was identified as the most important action to protect platypus habitat, although, substantial additional benefit is predicted by concurrent riparian revegetation and urban stormwater management.
Unreliable research programmes waste funds, time, and even the lives of the organisms we seek to help and understand. Reducing this waste and increasing the value of scientific evidence require ...changing the actions of both individual researchers and the institutions they depend on for employment and promotion. While ecologists and evolutionary biologists have somewhat improved research transparency over the past decade (e.g. more data sharing), major obstacles remain. In this commentary, we lift our gaze to the horizon to imagine how researchers and institutions can clear the path towards more credible and effective research programmes.
Globally, offset schemes have emerged in many statutory frameworks relating to development activities with the aim of balancing biodiversity conservation and development. Although the theory and use ...of biodiversity offsets in terrestrial environments is broadly documented, little attention has been paid to offsets in stream ecosystems. Here we examine the application of offset schemes to stream ecosystems and explore whether they suffer similar shortcomings to those of offset schemes focused on terrestrial biodiversity. To challenge the applicability of offsets further, we discuss typical trajectories of urban expansion and their cascading physical, chemical and biological impacts on stream ecosystems. We argue that the highly connected nature of stream ecosystems and urban drainage networks can transfer impacts of urbanization across wide areas, complicating the notion of like-for-like exchange and the prospect of effectively mitigating biodiversity loss. Instead, we identify in-catchment options for stormwater control, which can avoid or minimize the impacts of development on downstream ecosystems, while presenting additional public and private benefits. We describe the underlying principles of these alternatives, some of the challenges associated with their uptake, and policy initiatives being trialed to facilitate adoption. In conclusion, we argue that strongerpolicies to avoid and minimize the impacts of urbanization provide better prospects for protecting downstream ecosystems, and can additionally, stimulate economic opportunities and improve urban liveability. A nivel m undial han surgido estrategias de compensaciones en muchos marcos de trabajo reglamentarios con miras a balancear la conservación de la biodiversidad con el desarrollo. Aunque la teoría y el uso de las compensaciones por biodiversidad en los ecosistemas terrestres están ampliamente documentados, se le ha prestado muy poca atención a las compensaciones en los ecosistemas fluviales. Examinamos la aplicación de las estrategias de compensación a los ecosistemas fluviales y exploramos si sus limitaciones son similares a aquellas de las estrategias de compensación enfocadas en la biodiversidad terrestre. Consideramos las trayectorias típicas de la expansión urbana y sus impactos secundarios físicos, químicos y biológicos sobre los ecosistemas fluviales para presentar un mayor reto para la utilidad de las compensaciones. Argumentamos que la conectividad natural de los ecosistemasfluvialesy las redes de drenaje urbano pueden transferir los impactos de la urbanización a lo largo de áreas extensas que complica la lo noción de la compensación de igual-por-igual y la mitigación efectiva de la pérdida de la biodiversidad. Como alternativas a las compensaciones identificamos opciones en las cuencas de entrada para el control de aguas pluviales como tanques de lluvia, sistemas de biofiltración, y humedales construidos que pueden evitar o minimizar los impactos de las aguas pluviales sobre los ecosistemas fluviales mientras proporcionan beneficios públicos y privados como áreas verdes enfriamiento local, y amenidades mejoradas en paisajes urbanos. El principio subyacente del manejo efectivo requiere que los vertidos de aguas pluviales desde los desarrollos urbanos sean capturados tratados, y utilizados de tal manera que el régimen de vertidos resultantes imite detenidamente al régimen previo al desarrollo urbano. Los obstáculos a enfrentar incluyen la implementación de un manejo afectivo a escala. Se requieren cambios operativos y sociales para superar dichos obstáculos, y se están intentando algunas iniciativas políticas para facilitar la adopción de las opciones en las cuencas de entrada. Creemos que políticas más severas para evitar y minimizar los impactos de la urbanización protegerán de mejor manera a los ecosistemas fluviales y pueden estimular las oportunidades económicas y mejorar la habitabilidad urbana. 为了平衡生物多祥性保护与发展，全球范围内许多法规框架中都納入了生物多祥性补偿计划。尽管陆生 环境生物多祥性补偿的理论和实践巳被广泛报道，但是河流生态系统的补偿却少受到关注。我们检验了生物多 样性补偿计划在河流生态系统中的应用，并探讨了它们是否与陆生环境的生物多祥性补偿计划面临相似的问 题。为了进一歩探究补偿计划的适用性，我们还考虑了城市扩张的典型轨迹及其在河流生态系统的物理、化学 和生物方面的级联效应。我们认为，河流生态系统和城市排水网络本身紧密相连，这导致城市化的影响范围大大 増加，使实现同等补偿和有效减缓生物多样性丧失变得更加复杂。作为生物多样性补偿的替代方案，我们确定了 雨水控制中既能避免或減少雨水对下游生态系统的影响，又能带来附加的公共及私人收益（如绿地、局部降温 及更舒适的城市景观) 的集水措施，包括雨水储水池、生物过滤系统和人工湿地等。有效管理的基本原则要求 开发区的雨水径流经过拦截、处理和利用后，最终与流经未开发区的径流高度相似。这ー实践的ー个挑战在于 如何在大尺度上实施有效管理。要克服这个挑战需要运作上和社会上的变革，目前已有政策在尝试推进采用这 些集水措施。我们相信致力于避免和减少城市化影响的更有力的政策将保护好下游生态系统、带来经济机会，并提高城市的宜居性。
Recent replication projects in other disciplines have uncovered disturbingly low levels of reproducibility, suggesting that those research literatures may contain unverifiable claims. The conditions ...contributing to irreproducibility in other disciplines are also present in ecology. These include a large discrepancy between the proportion of “positive” or “significant” results and the average statistical power of empirical research, incomplete reporting of sampling stopping rules and results, journal policies that discourage replication studies, and a prevailing publish-or-perish research culture that encourages questionable research practices. We argue that these conditions constitute sufficient reason to systematically evaluate the reproducibility of the evidence base in ecology and evolution. In some cases, the direct replication of ecological research is difficult because of strong temporal and spatial dependencies, so here, we propose metaresearch projects that will provide proxy measures of reproducibility.
1. Overabundant wildlife can cause economic and ecological damage. Therefore population control typically seeks to maintain species' abundance within desired control limits. Efficient control ...requires targets, methods for estimating population size before and after control, and reliable means of forecasting population size. Demographic stochasticity, environmental variability and model uncertainty complicate these tasks. Monitoring provides critical feedback in the control process, yet examples of integrated monitoring and management are scarce. 2. We developed an integrated Bayesian population modelling and monitoring algorithm to assist with dynamic cull control of an overabundant population. We describe components of the control algorithm and their combination to produce a structured, sequential prescription for implementing control of a kangaroo population. We demonstrate its application within a single management year and evaluate its performance over a multi‐year horizon under a range of scenarios reflecting uncertainties about population dynamics. 3. Simulation testing of the algorithm demonstrates that it provides a coherent, flexible, efficient and robust basis for managing population control. It is coherent in that connections between management objectives, models and operating rules are explicit and logically integrated. It is flexible in that the management objectives can be freely varied. It is both cost and operationally efficient because: (i) it avoids the need for an expensive, dedicated sampling process to estimate population size prior to culling; (ii) a relatively small number of culls produces reasonable population size estimates and (iii) the estimation by removal process enables direct assessment of whether control has been achieved. Lastly, it is robust because even when there is substantial uncertainty about system state and dynamics, the algorithm performs well at keeping the population under control over the duration of the management horizon. 4. Synthesis and applications. We provide a general and flexible framework for integrated monitoring and culling when the objective is to keep a species' abundance within control limits. Our framework explicitly deals with uncertainty arising from demographic stochasticity, ecological complexity and lack of knowledge, and provides the foundation for maximizing efficiency and cost‐effectiveness of control operations. Our approach could be applied in any instances where control is effected via culling.
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