There's more to macroecology than meets the eye

Macroecology sits at the junction of, and can contribute to, the fields of ecology, biogeography, palaeontology and macroevolution, using a broad range of approaches to tackle a diverse set of questions. Here, we argue that there is more to macroecology than mapping, and that while they are potentially useful, maps are insufficient to assess macroecological pattern and process. The true nature of pattern can only be assessed, and competing hypotheses about process can only be disentangled, by adopting a statistical approach, and it is this that has been key to the development of macroecology as a respected and rigorous scientific discipline.     

Phylogenetic scale in ecology and evolution

Aim

Many important patterns and processes vary across the phylogeny and depend on phylogenetic scale. Nonetheless, phylogenetic scale has never been formally conceptualized, and its potential remains largely unexplored. Here, we formalize the concept of phylogenetic scale, review how phylogenetic scale has been considered across multiple fields and provide practical guidelines for the use of phylogenetic scale to address a range of biological questions.

Innovation

We summarize how phylogenetic scale has been treated in macroevolution, community ecology, biogeography and macroecology, illustrating how it can inform, and possibly resolve, some of the longstanding controversies in these fields. To promote the concept empirically, we define phylogenetic grain and extent, scale dependence, scaling and the domains of phylogenetic scale. We illustrate how existing phylogenetic data and statistical tools can be used to investigate the effects of scale on a variety of well‐known patterns and processes, including diversification rates, community structure, niche conservatism or species‐abundance distributions.

Main conclusions

Explicit consideration of phylogenetic scale can provide new and more complete insight into many longstanding questions across multiple fields (macroevolution, community ecology, biogeography and macroecology). Building on the existing resources and isolated efforts across fields, future research centred on phylogenetic scale might enrich our understanding of the processes that together, but over different scales, shape the diversity of life.     

Unifying ecology and macroevolution with individual‐based theory

A contemporary goal in both ecology and evolutionary biology is to develop theory that transcends the boundary between the two disciplines, to understand phenomena that cannot be explained by either field in isolation. This is challenging because macroevolution typically uses lineage‐based models, whereas ecology often focuses on individual organisms. Here, we develop a new parsimonious individual‐based theory by adding mild selection to the neutral theory of biodiversity. We show that this model generates realistic phylogenies showing a slowdown in diversification and also improves on the ecological predictions of neutral theory by explaining the occurrence of very common species. Moreover, we find the distribution of individual fitness changes over time, with average fitness increasing at a pace that depends positively on community size. Consequently, large communities tend to produce fitter species than smaller communities. These findings have broad implications beyond biodiversity theory, potentially impacting, for example, invasion biology and paleontology.     

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.     

Ecophylogenetics: advances and perspectives

Ecophylogenetics can be viewed as an emerging fusion of ecology, biogeography and macroevolution. This new and fast-growing field is promoting the incorporation of evolution and historical contingencies into the ecological research agenda through the widespread use of phylogenetic data. Including phylogeny into ecological thinking represents an opportunity for biologists from different fields to collaborate and has provided promising avenues of research in both theoretical and empirical ecology, towards a better understanding of the assembly of communities, the functioning of ecosystems and their responses to environmental changes. The time is ripe to assess critically the extent to which the integration of phylogeny into these different fields of ecology has delivered on its promise. Here we review how phylogenetic information has been used to identify better the key components of species interactions with their biotic and abiotic environments, to determine the relationships between diversity and ecosystem functioning and ultimately to establish good management practices to protect overall biodiversity in the face of global change. We evaluate the relevance of information provided by phylogenies to ecologists, highlighting current potential weaknesses and needs for future developments. We suggest that despite the strong progress that has been made, a consistent unified framework is still missing to link local ecological dynamics to macroevolution. This is a necessary step in order to interpret observed phylogenetic patterns in a wider ecological context. Beyond the fundamental question of how evolutionary history contributes to shape communities, ecophylogenetics will help ecology to become a better integrative and predictive science.     

The what,how and why of doing macroecology

Macroecology is a growing and important subdiscipline of ecology, but it is becoming increasingly diffuse, without an organizing principle that is widely agreed upon. I highlight two main current views of macroecology: as the study of large‐scale systems and as the study of emergent systems. I trace the history of both these views through the writings of the founders of macroecology. I also highlight the transmutation principle that identifies serious limitations to the study of large‐scale systems with reductionist approaches. And I suggest that much of the underlying goal of macroecology is the pursuit of general principles and the escape from contingency. I highlight that there are many intertwined aspects of macroecology, with a number of resulting implications. I propose that returning to a focus on studying assemblages of a large number of particles is a helpful view. I propose defining macroecology as “the study at the aggregate level of aggregate ecological entities made up of large numbers of particles for the purposes of pursuing generality”.     

Combining marine macroecology and palaeoecology in understanding biodiversity: microfossils as a model

There is growing interest in the integration of macroecology and palaeoecology towards a better understanding of past, present, and anticipated future biodiversity dynamics. However, the empirical basis for this integration has thus far been limited. Here we review prospects for a macroecology–palaeoecology integration in biodiversity analyses with a focus on marine microfossils [i.e. small (or small parts of) organisms with high fossilization potential, such as foraminifera, ostracodes, diatoms, radiolaria, coccolithophores, dinoflagellates, and ichthyoliths]. Marine microfossils represent a useful model system for such integrative research because of their high abundance, large spatiotemporal coverage, and good taxonomic and temporal resolution. The microfossil record allows for quantitative cross‐scale research designs, which help in answering fundamental questions about marine biodiversity, including the causes behind similarities in patterns of latitudinal and longitudinal variation across taxa, the degree of constancy of observed gradients over time, and the relative importance of hypothesized drivers that may explain past or present biodiversity patterns. The inclusion of a deep‐time perspective based on high‐resolution microfossil records may be an important step for the further maturation of macroecology. An improved integration of macroecology and palaeoecology would aid in our understanding of the balance of ecological and evolutionary mechanisms that have shaped the biosphere we inhabit today and affect how it may change in the future.     

Marine biogeography and ecology: invasions and introductions

Although biogeography and ecology had previously been considered distinct disciplines, this outlook began to change in the early 1990s. Several people expressed interest in creating a link that would help ecologists become more aware of external influences on communities and help biogeographers realize that distribution patterns had their genesis at the community level. They proposed an interdisciplinary approach called macroecology. This concept has been aided by the advent of phylogeography, for a better knowledge of genetic relationships has had great interdisciplinary value. Two areas of research that should obviously benefit from a macroecological approach are: (1) the question of local vs. regional diversity and (2) the question of whether invader species pose a threat to biodiversity. The two questions are related, because both deal with the vulnerability of ecosystems to penetration by invading species. Biogeographers, who have studied the broad oceanic patterns of dispersal and colonization, tend to regard isolated communities as being open to invasion from areas with greater biodiversity. It became evident that many wide‐ranging species were produced in centres of origin, and that the location of communities with respect to such centres had a direct effect on the level of species diversity. Ecologists, in earlier years, thought that a community could become saturated with species and would thereafter be self‐sustaining. But recent research has shown that saturation is probably never achieved and that the assembly of communities and their maintenance is more or less dependent on the invasion of species from elsewhere. The study of invasions that take place in coastal areas, usually the result of ship traffic and/or aquaculture imports, has special importance due to numerous opinions expressed by scientists and policy‐makers that such invasions are a major threat to biodiversity. However, none of the studies so far conducted has identified the extinction of a single, native marine species due to the influence of an exotic invader. Furthermore, fossil evidence of historical invasions does not indicate that invasive species have caused native extinctions or reductions in biodiversity.     

Characterizing common and range expanding species

Climate change and biological invasions have increased the likelihood of the establishment, growth, spread and survival of some species. With the recent and strongly motivated call for balanced consideration of the ecology and conservation of common and rare species, species undergoing range expansion are of particular interest. The notion of essential biodiversity variables has also re‐focussed attention on the value of abundance and occupancy observations for assessing conservation values, threats and targets – species rare or common, contracting or expanding. Changes in the distribution and abundance of common and range expanding species deserve further attention, not only to better understand their dynamics, but also as the basis for monitoring range expansions and their consequences. With the aim of characterizing range expansion, here we combine perspectives from typological approaches to studying species conservation status with perspectives from spread ecology and macroecology. Closer examination of the properties and dynamics of common species is important not only because declines in their conservation status are underappreciated, but also because those species becoming more common have significant implications for biodiversity, ecosystems and society.     

Research frontiers in null model analysis

Null models are pattern‐generating models that deliberately exclude a mechanism of interest, and allow for randomization tests of ecological and biogeographic data. Although they have had a controversial history, null models are widely used as statistical tools by ecologists and biogeographers. Three active research fronts in null model analysis include biodiversity measures, species co‐occurrence patterns, and macroecology. In the analysis of biodiversity, ecologists have used random sampling procedures such as rarefaction to adjust for differences in abundance and sampling effort. In the analysis of species co‐occurrence and assembly rules, null models have been used to detect the signature of species interactions. However, controversy persists over the details of computer algorithms used for randomizing presence–absence matrices. Finally, in the newly emerging discipline of macroecology, null models can be used to identify constraining boundaries in bivariate scatterplots of variables such as body size, range size, and population density. Null models provide specificity and flexibility in data analysis that is often not possible with conventional statistical tests.     

How big should a mammal be? A macroecological look at mammalian body size over space and time

Macroecology was developed as a big picture statistical approach to the study of ecology and evolution. By focusing on broadly occurring patterns and processes operating at large spatial and temporal scales rather than on localized and/or fine-scaled details, macroecology aims to uncover general mechanisms operating at organism, population, and ecosystem levels of organization. Macroecological studies typically involve the statistical analysis of fundamental species-level traits, such as body size, area of geographical range, and average density and/or abundance. Here, we briefly review the history of macroecology and use the body size of mammals as a case study to highlight current developments in the field, including the increasing linkage with biogeography and other disciplines. Characterizing the factors underlying the spatial and temporal patterns of body size variation in mammals is a daunting task and moreover, one not readily amenable to traditional statistical analyses. Our results clearly illustrate remarkable regularities in the distribution and variation of mammalian body size across both geographical space and evolutionary time that are related to ecology and trophic dynamics and that would not be apparent without a broader perspective.     

Microbiology of the phyllosphere: a playground for testing ecological concepts

Many concepts and theories in ecology are highly debated, because it is often difficult to design decisive tests with sufficient replicates. Examples include biodiversity theories, succession concepts, invasion theories, coexistence theories, and concepts of life history strategies. Microbiological tests of ecological concepts are rapidly accumulating, but have yet to tap into their full potential to complement traditional macroecological theories. Taking the example of microbial communities on leaf surfaces (i.e. the phyllosphere), we show that most explorations of ecological concepts in this field of microbiology focus on autecology and population ecology, while community ecology remains understudied. Notable exceptions are first tests of the island biogeography theory and of biodiversity theories. Here, the phyllosphere provides the unique opportunity to set up replicated experiments, potentially moving fields such as biogeography, macroecology, and landscape ecology beyond theoretical and observational evidence. Future approaches should take advantage of the great range of spatial scales offered by the leaf surface by iteratively linking laboratory experiments with spatial simulation models.     

利用数值模拟重构物种多样性格局的形成过程

生命形成的过程极其漫长, 经历了地球系统复杂的沧海桑田变化。当前人类所观察到的物种分布格局的形成除了由物种本身特征决定外, 还受到环境变化、人类活动以及各种随机事件的影响。受限于实验条件、时间、经费、人力等诸多因素, 我们尚无法完整地观察并记录到物种多样性形成的全过程, 只能通过片段化数据来推测该过程。信息科学中包括数值模拟在内的仿真技术以其高效、可控及全过程记录等优势, 能从某种程度上解决物种多样性格局形成过程中的部分数据黑箱问题。本文介绍了数值模拟的概念和工作原理及在物种多样性研究中应用的特点, 列举了物种生态位、扩散模式、种间互作及物种分布应对气候变化等方面的数值模拟研究, 基于已有研究系统地介绍了如何综合上述数值模拟研究构建虚拟物种、气候和场景来解释物种多样性的形成与维持机制, 并阐述了数值模拟在物种多样性研究中的优缺点及应用前景。     

Movement‐mediated community assembly and coexistence

Organismal movement is ubiquitous and facilitates important ecological mechanisms that drive community and metacommunity composition and hence biodiversity. In most existing ecological theories and models in biodiversity research, movement is represented simplistically, ignoring the behavioural basis of movement and consequently the variation in behaviour at species and individual levels. However, as human endeavours modify climate and land use, the behavioural processes of organisms in response to these changes, including movement, become critical to understanding the resulting biodiversity loss. Here, we draw together research from different subdisciplines in ecology to understand the impact of individual‐level movement processes on community‐level patterns in species composition and coexistence. We join the movement ecology framework with the key concepts from metacommunity theory, community assembly and modern coexistence theory using the idea of micro–macro links, where various aspects of emergent movement behaviour scale up to local and regional patterns in species mobility and mobile‐link‐generated patterns in abiotic and biotic environmental conditions. These in turn influence both individual movement and, at ecological timescales, mechanisms such as dispersal limitation, environmental filtering, and niche partitioning. We conclude by highlighting challenges to and promising future avenues for data generation, data analysis and complementary modelling approaches and provide a brief outlook on how a new behaviour‐based view on movement becomes important in understanding the responses of communities under ongoing environmental change.     

Temperature‐dependent oxygen limitation and the rise of Bergmann's rule in species with aquatic respiration

Bergmann's rule is the propensity for species‐mean body size to decrease with increasing temperature. Temperature‐dependent oxygen limitation has been hypothesized to help drive temperature–size relationships among ectotherms, including Bergmann's rule, where organisms reduce body size under warm oxygen‐limited conditions, thereby maintaining aerobic scope. Temperature‐dependent oxygen limitation should be most pronounced among aquatic ectotherms that cannot breathe aerially, as oxygen solubility in water decreases with increasing temperature. We use phylogenetically explicit analyses to show that species‐mean adult size of aquatic salamanders with branchial or cutaneous oxygen uptake becomes small in warm environments and large in cool environments, whereas body size of aquatic species with lungs (i.e., that respire aerially), as well as size of semiaquatic and terrestrial species do not decrease with temperature. We argue that oxygen limitation drives the evolution of small size in warm aquatic environments for species with aquatic respiration. More broadly, the stronger decline in size with temperature observed in aquatic versus terrestrial salamander species mirrors the relatively strong plastic declines in size observed previously among aquatic versus terrestrial invertebrates, suggesting that temperature‐dependent oxygen availability can help drive patterns of plasticity, micro‐ and macroevolution.     

Metabolic partitioning across individuals in ecological communities

The mechanistic origin and shape of body‐size distributions within communities are of considerable interest in ecology. A recently proposed light‐limitation model provides a good fit to the distribution of tree sizes in a tropical forest plot. The maximum entropy theory of ecology (METE) also predicts size distributions, but without explicit mechanistic assumptions, and thus its predictions should hold in ecosystems generally, regardless of whether they are light limited. A comparison of the form and success of the predictions of the model and the theory can provide insight into the role that mechanisms play in shaping patterns in macroecology. The prediction by the METE of the size distribution of organisms is remarkably similar in form to that of the model: power‐law behaviour in the size range where the light‐limitation model predicts a power law, and exponential behaviour in the size range where the model predicts an exponential tail. The METE prediction matches data widely, including data in ecosystems where light is not limiting. We show examples for three disparate communities: trees in a tropical forest plot; herbaceous plants in a treeless subalpine meadow; and island arthropods. We conclude that the success of METE's predicted form across systems, including those that are clearly not light limited, enriches our capacity to predict patterns in macroecology without making explicit mechanistic assumptions and provides a unified framework that can capture ubiquitous features of those patterns across diverse ecosystems governed by a variety of mechanisms.     

Effects of allometry,productivity and lifestyle on rates and limits of body size evolution

Body size affects nearly all aspects of organismal biology, so it is important to understand the constraints and dynamics of body size evolution. Despite empirical work on the macroevolution and macroecology of minimum and maximum size, there is little general quantitative theory on rates and limits of body size evolution. We present a general theory that integrates individual productivity, the lifestyle component of the slow–fast life-history continuum, and the allometric scaling of generation time to predict a clade''s evolutionary rate and asymptotic maximum body size, and the shape of macroevolutionary trajectories during diversifying phases of size evolution. We evaluate this theory using data on the evolution of clade maximum body sizes in mammals during the Cenozoic. As predicted, clade evolutionary rates and asymptotic maximum sizes are larger in more productive clades (e.g. baleen whales), which represent the fast end of the slow–fast lifestyle continuum, and smaller in less productive clades (e.g. primates). The allometric scaling exponent for generation time fundamentally alters the shape of evolutionary trajectories, so allometric effects should be accounted for in models of phenotypic evolution and interpretations of macroevolutionary body size patterns. This work highlights the intimate interplay between the macroecological and macroevolutionary dynamics underlying the generation and maintenance of morphological diversity.     

区域生态学研究热点及进展

区域生态学是近年才发展起来的一门新兴学科,综述了区域生态学的学科特点、近期研究进展,以及区域生态学发展中存在的主要问题及其主要的研究热点。其研究热点主要集中在物种分布-多度模型、体型与分布范围、物种多样性纬度梯度格局、区域生态学与生物保护及区域生态学的新陈代谢理论等几个方面。尽管目前区域生态学研究中还存在研究方法、数据质量限制、数据统计、研究尺度不确定等一系列问题,它对于解决目前紧迫的区域环境问题及生物保护仍然具有重要意义,而且随着其研究方法和手段的进步,将发挥越来越重要的作用。