All is not loss: plant biodiversity in the anthropocene

Anthropogenic global changes in biodiversity are generally portrayed in terms of massive native species losses or invasions caused by recent human disturbance. Yet these biodiversity changes and others caused directly by human populations and their use of land tend to co-occur as long-term biodiversity change processes in the Anthropocene. Here we explore contemporary anthropogenic global patterns in vascular plant species richness at regional landscape scales by combining spatially explicit models and estimates for native species loss together with gains in exotics caused by species invasions and the introduction of agricultural domesticates and ornamental exotic plants. The patterns thus derived confirm that while native losses are likely significant across at least half of Earth's ice-free land, model predictions indicate that plant species richness has increased overall in most regional landscapes, mostly because species invasions tend to exceed native losses. While global observing systems and models that integrate anthropogenic species loss, introduction and invasion at regional landscape scales remain at an early stage of development, integrating predictions from existing models within a single assessment confirms their vast global extent and significance while revealing novel patterns and their potential drivers. Effective global stewardship of plant biodiversity in the Anthropocene will require integrated frameworks for observing, modeling and forecasting the different forms of anthropogenic biodiversity change processes at regional landscape scales, towards conserving biodiversity within the novel plant communities created and sustained by human systems.     

Biodiversity in tropical agroforests and the ecological role of ants and ant diversity in predatory function

Abstract.  1. Intensive agricultural practices drive biodiversity loss with potentially drastic consequences for ecosystem services. To advance conservation and production goals, agricultural practices should be compatible with biodiversity. Traditional or less intensive systems (i.e. with fewer agrochemicals, less mechanisation, more crop species) such as shaded coffee and cacao agroforests are highlighted for their ability to provide a refuge for biodiversity and may also enhance certain ecosystem functions (i.e. predation).
2. Ants are an important predator group in tropical agroforestry systems. Generally, ant biodiversity declines with coffee and cacao intensification yet the literature lacks a summary of the known mechanisms for ant declines and how this diversity loss may affect the role of ants as predators.
3. Here, how shaded coffee and cacao agroforestry systems protect biodiversity and may preserve related ecosystem functions is discussed in the context of ants as predators. Specifically, the relationships between biodiversity and predation, links between agriculture and conservation, patterns and mechanisms for ant diversity loss with agricultural intensification, importance of ants as control agents of pests and fungal diseases, and whether ant diversity may influence the functional role of ants as predators are addressed. Furthermore, because of the importance of homopteran-tending by ants in the ecological and agricultural literature, as well as to the success of ants as predators, the costs and benefits of promoting ants in agroforests are discussed.
4. Especially where the diversity of ants and other predators is high, as in traditional agroforestry systems, both agroecosystem function and conservation goals will be advanced by biodiversity protection.     

Urbanization promotes the loss of seasonal dynamics in the semi-natural grasslands of an East Asian megacity

The biodiversity of agricultural landscapes has been noticeably affected by rapid urbanization. Although many studies have examined species diversity per unit area (alpha diversity), knowledge about the patterns of species turnover (beta diversity) in urban areas remains limited. Furthermore, most beta diversity studies have focused on spatial heterogeneity; however, losses of temporal heterogeneity resulting from urbanization remain limited. In this study, we examined how urbanization is associated with decreases in the seasonal heterogeneity of species composition, which could be used as an indicator of the loss of seasonality by ecologists and policy makers aiming to conserve biodiversity. We investigated (1) changes in species richness based on seasonal averages (alpha diversity) and (2) the seasonal turnover of species composition (beta diversity) for flowering plants and butterflies along a rural-urban gradient in semi-natural grasslands. The response variables were alpha and beta diversity for flowering plants and butterflies, and the explanatory variables were urban areas within a 1-km radius of the center of each site. Increasing urban area caused both the seasonal alpha and beta diversity of flowering plants and butterflies to decline. These results supported the homogenization hypothesis for the seasonality of plants and butterflies in semi-natural grasslands of dominant urban areas in East Asia. Future studies should focus on investigating how urbanization is causing both declines in seasonality and changes in the spatial heterogeneity of species composition and associated biodiversity loss. Ecologists and policy makers should focus on developing strategies to halt the loss of temporal biological heterogeneity to maintain biodiversity.     

Economic growth and biodiversity

I argue that there is no fundamental conflict between economic growth and biodiversity. Humans can maintain and produce biological diversity just as we can maintain and produce other goods. Efforts to preserve and enhance biodiversity add to the size and growth of the economy. We are losing biodiversity because of human preferences and human inefficiencies, not because of economic growth. Inefficiency occurs when our actions do not reflect our real preferences, and is mainly due to failures of social coordination. To alleviate the problem of biodiversity loss we should address these failures.     

Conservation of endangered species and the patterns and propensities of biodiversity

It is commonly asserted in the ecological and economic literature that habitat loss is the main cause of loss of imperiled species. The evidence clearly shows that habitat loss is a common contributing factor, but there is little evidence that it is the most important factor. Studies that have focused on the mechanisms of species loss have failed to produce models capable of predicting patterns of loss as a function of human activities. I propose that this is because ecologists have employed an unrealistic conceptual model of the functioning of natural systems. Karl Popper's construct of the propensities of natural systems provides a more realistic view, and better potential to yield predictive models. I provide two examples of patterns of biodiversity and species loss in Canada where mechanistic reasoning is inconsistent with the observed propensities of species loss.     

Is population subdivision different from speciation? From phylogeography to species delimitation

Species‐level diversity and the underlying mechanisms that lead to the formation of new species, that is, speciation, have often been confounded with intraspecific diversity and population subdivision. The delineation between intraspecific and interspecific divergence processes has received much less attention than species delimitation. The ramifications of confounding speciation and population subdivision are that the term speciation has been used to describe many different biological divergence processes, rendering the results, or inferences, between studies incomparable. Phylogeographic studies have advanced our understanding of how spatial variation in the pattern of biodiversity can begin, become structured, and persist through time. Studies of species delimitation have further provided statistical and model‐based approaches to determine the phylogeographic entities that merit species status. However, without a proper understanding and delineation between the processes that generate and maintain intraspecific and interspecific diversity in a study system, the delimitation of species may still not be biologically and evolutionarily relevant. I argue that variation in the continuity of the divergence process among biological systems could be a key factor leading to the enduring contention in delineating divergence patterns, or species delimitation, meriting future comparative studies to help us better understand the nature of biological species.     

Relationships between biodiversity and biological control in agroecosystems: Current status and future challenges

Agricultural systems around the world are faced with the challenge of providing for the demands of a growing human population. To meet this demand, agricultural systems have intensified to produce more crops per unit area at the expense of greater inputs. Agricultural intensification, while yielding more crops, generally has detrimental impacts on biodiversity. However, intensified agricultural systems often have fewer pests than more “environmentally-friendly” systems, which is believed to be primarily due to extensive pesticide use on intensive farms. In turn, to be competitive, less-intensive agricultural systems must rely on biological control of pests. Biological pest control is a complex ecosystem service that is generally positively associated with biodiversity of natural enemy guilds. Yet, we still have a limited understanding of the relationships between biodiversity and biological control in agroecosystems, and the mechanisms underlying these relationships. Here, we review the effects of agricultural intensification on the diversity of natural enemy communities attacking arthropod pests and weeds. We next discuss how biodiversity of these communities impacts pest control, and the mechanisms underlying these effects. We focus in particular on novel conceptual issues such as relationships between richness, evenness, abundance, and pest control. Moreover, we discuss novel experimental approaches that can be used to explore the relationships between biodiversity and biological control in agroecosystems. In particular, we highlight new experimental frontiers regarding evenness, realistic manipulations of biodiversity, and functional and genetic diversity. Management shifts that aim to conserve diversity while suppressing both insect and weed pests will help growers to face future challenges. Moreover, a greater understanding of the interactions between diversity components, and the mechanisms underlying biodiversity effects, would improve efforts to strengthen biological control in agroecosystems.     

A systemic view of biodiversity and its conservation: processes, interrelationships, and human culture: presentation of a systemic view of biodiversity and its conservation that emphasizes complex interrelationships among subsystems and includes human culture

Historically, views and measurements of biodiversity have had a narrow focus, for instance, characterizing the attributes of observable patterns but affording less attention to processes. Here, we explore the question: how does a systems thinking view – one where the world is seen as elements and processes that connect and interact in dynamic ways to form a whole – affect the way we understand biodiversity and practice conservation? We answer this question by illustrating the systemic properties of biodiversity at multiple levels, and show that biodiversity is a collection of dynamic systems linking seemingly disparate biological and cultural components and requiring an understanding of the system as a whole. We conclude that systems thinking calls traditional views of species, ecosystem function, and human relationships with the rest of biodiversity into question. Finally, we suggest some of the ways in which this view can impact the science and practice of conservation, particularly through affecting our conservation targets and strategies.     

Biodiversity conservation in cocoa production landscapes: an overview

Cocoa agroforests that retain a floristically diverse and structurally complex shade canopy have the potential to harbour significant levels of biodiversity, yet few studies have documented the plant and animal species occurring within these systems or within landscapes dominated by cocoa production. In this special issue, we bring together nine studies from Latin America, Africa and Asia that document the contribution of cocoa agroforestry systems to biodiversity conservation, and explore how the design, management and location of these systems within the broader landscape influence their value as habitats, resources and biological corridors. Tree diversity within the cocoa production systems is variable, depending on management, cultural differences, location and farm history, among other factors. Animal diversity is typically highest in those cocoa agroforests that have high plant diversity, structurally complex canopies, and abundant surrounding forest cover. In general, both plant and animal diversity within cocoa agroforests is greater than those of other agricultural land uses, but lower than in the original forest habitat. There are several emerging threats to biodiversity conservation within cocoa production landscapes, including the loss of remaining forest cover, the simplification of cocoa shade canopies and the conversion of cocoa agroforestry systems to other agricultural land uses with lower biodiversity value. To counter these threats and conserve biodiversity over the long-term, land management should focus on conserving native forest habitat within cocoa production landscapes, maintaining or restoring floristically diverse and structurally complex shade canopies within cocoa agroforests, and retaining other types of on-farm tree cover to enhance landscape connectivity and habitat availability.     

Biodiversity of soil microbial communities in agricultural systems

The productivity and health of agricultural systems depend greatly upon the functional processes carried out by soil microorganisms and soil microbial communities. The biodiversity of the soil microbial communities and the effect of diversity on the stability of the agricultural system, is unknown. Taxonomic approaches to estimating biodiversity of soil microbial communities are limited by difficulties in defining suitable taxonomic units and the apparent non-culturability of the majority of the microbial species present in the soil. Analysis of functional diversity may be a more meaningful approach but is also limited by the need to culture organisms. Approaches which do not rely on culturing organisms such as fatty acid analysis and 16S/18S rRNA analysis have provided an insight into the extent of genetic diversity within communities and may be useful in the analysis of community structure. Scale effects, including successional processes associated with organic matter decomposition, local effects associated with abiotic soil factors, and regional effects including the effect of agricultural management practices, on the diversity of microbial communities are considered. Their impact is important in relation to the minimum biodiversity required to maintain system function.     

整合空间信息在生物多样性丧失等研究中的重要性

无数证据表明,地球可能正经历着有史以来的第六次物种大灭绝。在这一背景下,研究生物多样性丧失机制及其对生态系统功能的影响具有重要意义。从先前的相关研究中,已逐渐清晰地认识到造成多样性丧失的几大机制,并对这些机制发生的空间尺度有了一定了解。然而,空间本身对多样性丧失研究的影响仍被该领域的很多研究所忽视。因为生物多样性丧失过程发生在不同空间尺度中,所造成的多样性丧失格局也具有不同的空间尺度特征。忽略空间信息很可能会对多样性丧失等相关研究造成很大干扰,甚至得出错误的结论,其结果也很难正确地运用于不同空间尺度的多样性保护当中。整合空间信息已成为当前生物多样性丧失研究,乃至整个生态学研究的前沿和热点之一。为促进这一趋势在国内的发展,将结合多样性丧失的估计与监测、几大多样性丧失机制(全球环境变化与生境片段化、生物入侵等)来阐述空间信息对当前及今后多样性丧失机制研究的重要性,并用实例展示未充分考虑空间信息而可能造成的后果。最后探讨我国当前科技条件下进行整合空间信息的生物多样性丧失等研究的可行性。     

土壤动物群落空间格局和构建机制研究进展

群落空间格局和构建机制一直是生态学研究的核心内容。在生物多样性严重丧失的背景下, 揭示群落空间格局及其构建机制, 有助于深刻理解生物多样性丧失的原因, 更有助于应对生物多样性保护等重大生态环境问题。然而, 陆地生态系统的研究多集中于地上生物群落, 对地下生态系统, 尤其是土壤动物空间格局和构建机制的研究尚不充分。事实上, 土壤动物多样性是全球生物多样性的关键组成之一, 是地下生态系统结构和功能维持的重要部分。对土壤动物空间格局和构建机制的研究, 能明确不同空间尺度条件下土壤动物多样性的维持机制。土壤动物群落常在多种空间尺度形成复杂的空间分布格局, 因此, 本文首先介绍了不同空间尺度主要土壤动物群落的空间自相关性特征, 阐述了土壤动物群落斑块和孔隙镶嵌分布的复杂空间格局。继而阐明这种空间格局主要受生物间作用、环境过滤和随机扩散的调控, 并说明这三个过程对土壤动物群落的调控能力和作用方式。作者提出, 这三个过程仍是今后土壤动物群落空间格局和构建机制研究的重点内容, 需要进一步加强以土壤动物为研究对象的群落构建理论的验证和发展。我国土壤动物群落空间格局和构建机制起步较晚, 希望本文能够促进我国土壤动物生态学相关领域的研究。     

农业活动对生物多样性的影响

农业生产活动如土地的农业利用、耕作、作物间套种植方式、放牧、农药化肥的使用以及农业动植物遗传改良（包括外来种引入）等是农业生产力提高的重要途径,同时也是影响生物多样性的重要因素之一。土地的不合理开发利用易导致生境破碎、生物多样性下降;大规模的机械耕作导致土壤动植物区系的变化,甚至某些物种的消失;农药（除草剂、杀虫剂等）的高度使用使非靶标动植物受到伤害;品种改良、外来种的引入以及远缘外源遗传物质的利用（如远缘杂交和ＤＮＡ导入分子育种）在丰富了遗传多样性的同时导致农作物类型和品种的简单化、一些古老的地方种和农家种等传统资源丢失等;而一些合理的农业措施（间套作、实行有机农场等）将有利于生物多样性的保持。农业活动注重的是农业生产力的提高而往往忽视其对农业系统中野生动植物（包括有害和无害）的影响以及野生动植物在维持系统稳定和平衡的作用。本文论述农业活动对生物多样性的影响以及生物多样性保护对提高农业生产力的作用,启示人们采取合理的农业活动方式,合理管理有害生物,减少农业活动对生物多样性的负面影响。     

gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity

Understanding the origins of biodiversity has been an aspiration since the days of early naturalists. The immense complexity of ecological, evolutionary, and spatial processes, however, has made this goal elusive to this day. Computer models serve progress in many scientific fields, but in the fields of macroecology and macroevolution, eco-evolutionary models are comparatively less developed. We present a general, spatially explicit, eco-evolutionary engine with a modular implementation that enables the modeling of multiple macroecological and macroevolutionary processes and feedbacks across representative spatiotemporally dynamic landscapes. Modeled processes can include species’ abiotic tolerances, biotic interactions, dispersal, speciation, and evolution of ecological traits. Commonly observed biodiversity patterns, such as α, β, and γ diversity, species ranges, ecological traits, and phylogenies, emerge as simulations proceed. As an illustration, we examine alternative hypotheses expected to have shaped the latitudinal diversity gradient (LDG) during the Earth’s Cenozoic era. Our exploratory simulations simultaneously produce multiple realistic biodiversity patterns, such as the LDG, current species richness, and range size frequencies, as well as phylogenetic metrics. The model engine is open source and available as an R package, enabling future exploration of various landscapes and biological processes, while outputs can be linked with a variety of empirical biodiversity patterns. This work represents a key toward a numeric, interdisciplinary, and mechanistic understanding of the physical and biological processes that shape Earth’s biodiversity.

This study describes a novel mechanistic engine that predicts a realistic global latitudinal diversity gradient, species richness distribution and phylogenies. This approach is a step towards the interdisciplinary numeric understanding of the physical and biological processes that have shaped Earth’s biodiversity.     

Ecology and evolution of mammalian biodiversity

Mammals have incredible biological diversity, showing extreme flexibility in eco-morphology, physiology, life history and behaviour across their evolutionary history. Undoubtedly, mammals play an important role in ecosystems by providing essential services such as regulating insect populations, seed dispersal and pollination and act as indicators of general ecosystem health. However, the macroecological and macroevolutionary processes underpinning past and present biodiversity patterns are only beginning to be explored on a global scale. It is also particularly important, in the face of the global extinction crisis, to understand these processes in order to be able to use this knowledge to prevent future biodiversity loss and loss of ecosystem services. Unfortunately, efforts to understand mammalian biodiversity have been hampered by a lack of data. New data compilations on current species' distributions, ecologies and evolutionary histories now allow an integrated approach to understand this biodiversity. We review and synthesize these new studies, exploring the past and present ecology and evolution of mammalian biodiversity, and use these findings to speculate about the mammals of our future.     

Monitoring global rates of biodiversity change: challenges that arise in meeting the Convention on Biological Diversity (CBD) 2010 goals

By agreeing to strive for 'a significant reduction in the current rate of loss of biological diversity' by the year 2010, political leaders at the 2002 World Summit on Sustainable Development (held in Johannesburg, South Africa) presented conservation scientists with a great opportunity, but also one of their most significant challenges. This is an extremely exciting and laudable development, but this reporting process could be made yet more powerful if it incorporates, from the outset, independent scientific assessment of the measures, how they are analysed, and practical ways of plugging key gaps. This input is crucial if the measures are to be widely owned, credible and robust to the vigorous external scrutiny to which they will doubtless be exposed. Assessing how rates of biodiversity loss have changed from current levels by 2010 will require that a given attribute has been measured at least three times; however, most habitats, species, populations and ecosystem services have not been assessed even once. Furthermore, the best data on which to base estimates of biodiversity loss are biased towards the charismatic vertebrate species; unfortunately, these supply minimal services to the human economy. We have to find ways to redress this taxonomic imbalance and expand our analyses to consider the vast diversity of invertebrate, fungal and microbial species that play a role in determining human health and economic welfare. In the first part of this paper I will use examples from local and regional monitoring of biological diversity to examine the desired properties of 'ideal indicators'. I will then change focus and examine an initial framework that asks how we might monitor changes in the economic goods and services provided by natural ecosystems. I will use this exercise to examine how the set of possible indicators given by the Convention on Biological Diversity might be modified in ways that provide a more critical assay of the economic value of biological diversity. Here I will emphasize that we need not only to monitor these benefits, but also to significantly increase public awareness of human dependence upon the role that non-voting species play in driving the world's financial economy.     

Weed invasions in wetlands of Australia's Top End: reasons and solutions

Weed invasions are an increasing threat to the extensive wetlands of the Northern Territory's wet-dry tropics. Although the conservation value of these wetlands is in some ways undisputed, it is evident from the Government's multiple land use policy that it is also misunderstood. This policy aims to maximise economic returns from wetlands while protecting their ecological integrity at a time when ecological and economic costs associated with weeds are, at least in the short term, set to worsen. The underlying reasons behind wetland loss and degradation in Australia parallel those identified in Mediterranean Europe where there was antipathy from bureaucracies toward science and ecology. Several case studies from the Northern Territory explore how ecological, anthropogenic, political and economic factors contribute to weed problems. Caution is necessary when translating experience from agricultural weeds to environmental weeds. Managers have not always heeded the advice of specialists and practitioners, whose understanding of the ecological basis to weed invasions is not in as parlous a state as sometimes thought. Even when faced with sound information from which to manage, it was non-ecological reasons that slowed down or prevented effective weed control. If the floristic identity and diversity of Australia's natural wetlands is to be retained, then weeds need serious and immediate attention. Weed impacts progress beyond loss of wetland habitat and biodiversity to regional changes in landscape processes. We advocate that governments and industry recognise and address the underlying non-ecological reasons that exacerbate weed problems and set priorities to fund relevant practical studies and control programs that enable inventive weed management. Cooperation between land users, custodians and the wider community can help to overcome bureaucratic obstacles and enable judicious weed control that contributes effectively to wetland protection.     

Biodiversity conservation in metacommunity networks: linking pattern and persistence

A central goal of conservation science is to identify the most important habitat patches for maintaining biodiversity on a landscape. Spatial biodiversity patterns are often used for such assessments, and patches that harbor unique diversity are generally prioritized over those with high community similarity to other areas. This places an emphasis on biodiversity representation, but removing a patch can have cascading effects on biodiversity persistence in the remaining ecological communities. Metacommunity theory provides a mechanistic route to the linking of biodiversity patterns on a landscape with the subsequent dynamics of diversity loss after habitat is degraded. Using spatially explicit neutral theory, I focus on the situation where spatial patterns of diversity and similarity are generated by the structure of dispersal networks and not environmental gradients. I find that gains in biodiversity representation are nullified by losses in persistence, and as a result the effects of removing a patch on metacommunity diversity are essentially independent of complementarity or other biodiversity patterns. In this scenario, maximizing protected area and not biodiversity representation is the key to maintaining diversity in the long term. These results highlight the need for a broader understanding of how conservation paradigms perform under different models of metacommunity dynamics.     

Studying and modelling dynamic biological processes using time-series gene expression data

Biological processes are often dynamic, thus researchers must monitor their activity at multiple time points. The most abundant source of information regarding such dynamic activity is time-series gene expression data. These data are used to identify the complete set of activated genes in a biological process, to infer their rates of change, their order and their causal effects and to model dynamic systems in the cell. In this Review we discuss the basic patterns that have been observed in time-series experiments, how these patterns are combined to form expression programs, and the computational analysis, visualization and integration of these data to infer models of dynamic biological systems.     

Separating Macroecological Pattern and Process: Comparing Ecological,Economic, and Geological Systems

Theories of biodiversity rest on several macroecological patterns describing the relationship between species abundance and diversity. A central problem is that all theories make similar predictions for these patterns despite disparate assumptions. A troubling implication is that these patterns may not reflect anything unique about organizational principles of biology or the functioning of ecological systems. To test this, we analyze five datasets from ecological, economic, and geological systems that describe the distribution of objects across categories in the United States. At the level of functional form (‘first-order effects’), these patterns are not unique to ecological systems, indicating they may reveal little about biological process. However, we show that mechanism can be better revealed in the scale-dependency of first-order patterns (‘second-order effects’). These results provide a roadmap for biodiversity theory to move beyond traditional patterns, and also suggest ways in which macroecological theory can constrain the dynamics of economic systems.