A primer of community ecology using the R language

Community ecology beginners often struggle to understand theories expressed in complex mathematical formulas and to master computer programming. To remedy this situation, this article provides a practical, R-based introduction to community ecology by illustrating core concepts (vital rates, carrying capacity, and density dependence) and models that can be used to explore the patterns of species abundance and diversity. The structure of this article consists of three modeling exercises, each asking a general question that can be answered by a combination of theory and R programming: (1) what determines the abundance of species, and what makes a population persist and go extinct?; (2) what determines the distribution of species and species diversity?; (3) what determines the relative abundance of species and what allows species to coexist? Through the exercises, I discuss the following five concepts and ideas that provide valuable insights into the questions: (i) the tragedy of the commons, (ii) the theory of island biogeography, (iii) competitive exclusion, (iv) the neutral theory of biodiversity, and (v) frequency dependence. These materials are thus designed to guide the reader in developing an intuition for ecological thinking that will help capture the essence of the global environmental and biodiversity crisis. Although this article does not delineate the scope and depth of the vast field of community ecology, I hope that it will motivate the reader to step up to a more formal introduction to community ecology.     

Spatial processes that maintain biodiversity in plant communities

The composition of communities of sessile organisms, and the change in species diversity with time, is a spatially explicit phenomenon. Three spatial factors clearly affect diversity: (1) the structure and heterogeneity of the landscape that limits species immigration and ultimate community size; (2) neighborhood interactions that determine colonization and extinction rates and influence residence times of local populations; and (3) disturbances that open spatially contiguous areas for recolonization by less abundant species. The importance of these three factors was first reviewed and then examined with a spatially explicit, multi-species model of plant dispersal, competition and establishment, with an assumption of neutrality (all species had equivalent life histories) that reduced the initial dimensionality of the problem. The simulations assumed that the probability of immigration was a linear function of mainland abundance and distance to islands, similar to the equilibrium theory of island biogeography and the unified neutral theory of biodiversity. The rate of increase in species richness was not constant across island sizes, declining as island area became very large. This pattern was explained by the spatial dynamics of colonization and establishment, a non-random process that cannot be explained by passive sampling alone. Simulations showed that population establishment depended critically on rare long-distance dispersal events while population persistence was achieved by the formation of aggregated species distributions that developed through restricted dispersal and local competitive interactions. Nevertheless, species richness always declined to a single species in the absence of disturbances, while up to 40 species could persist to 10,000 years when spatially dependent mortality was added. Further explorations with spatially explicit models will be required to fully appreciate the consequence of land use change and altered disturbance regimes on patterns of species distribution and the maintenance of diversity.     

土壤微生物生物地理学研究进展

生物地理学是研究生物（包括种群、群落等不同层次）地理分布格局及成因的一门交叉学科。微生物生物地理学的研究长期滞后于宏生物地理学。鉴于土壤微生物在调控生物地球化学过程和维持生态系统功能方面的重要作用,对其空间分布格局及形成机制的认识具有十分重要的理论和实际意义。随着分子生物学技术的发展,对微生物多样性的认知日益深入。越来越多的证据表明,土壤微生物群落结构和多样性具有一定的时空分布格局,从而对微生物全球性随机分布的传统观点提出了挑战。对当前土壤微生物生物地理学研究中的一些概念性问题,如微生物物种的定义、微生物多样性的定量测度、对微生物全球性随机分布的争论等,进行了系统评述;以微生物种-面积关系和距离-衰减关系为例对当前最新的土壤微生物生物地理学研究成果进行总结,并初步探讨了土壤微生物群落的地带性分布问题;在传统生物地理学理论的指导下,提出了一个可用于验证土壤微生物空间分布格局形成和机制维持的简单研究框架。这些对今后土壤微生物生物地理学的研究有一定借鉴和指导意义。     

Extensions of Island Biogeography Theory predict the scaling of functional trait composition with habitat area and isolation

The Theory of Island Biogeography (TIB) predicts how area and isolation influence species richness equilibrium on insular habitats. However, the TIB remains silent about functional trait composition and provides no information on the scaling of functional diversity with area, an observation that is now documented in many systems. To fill this gap, we develop a probabilistic approach to predict the distribution of a trait as a function of habitat area and isolation, extending the TIB beyond the traditional species–area relationship. We compare model predictions to the body‐size distribution of piscivorous and herbivorous fishes found on tropical reefs worldwide. We find that small and isolated reefs have a higher proportion of large‐sized species than large and connected reefs. We also find that knowledge of species body‐size and trophic position improves the predictions of fish occupancy on tropical reefs, supporting both the allometric and trophic theory of island biogeography. The integration of functional ecology to island biogeography is broadly applicable to any functional traits and provides a general probabilistic approach to study the scaling of trait distribution with habitat area and isolation.     

On the semiotic dimension of ecological theory: The case of island biogeography

The Macarthur-Wilson equilibrium theory of island biogeography has had a contradictory role in ecology. As a lasting contribution, the theory has created a new way of viewing insular environments as dynamical systems. On the other hand, many of the applications of the theory have reduced to mere unimaginative curve-fitting. I analyze this paradox in semiotic terms: the theory was mainly equated with the simple species-area relationship which became a signifier of interesting island ecology. The theory is, however, better viewed as a theoretical framework that suggests specific hypotheses on the ecology of colonization of insular environments. This paradox is inherent in the use of simplifying analytic models. Analytic models are necessary and fruitful in the work of ecologists, but they ought to be supplemented with a broader, pluralistic appreciation of the role of theories in general.     

A system dynamics model of island biogeography

The MacArthur-Wilson equilibrium theory of island biogeography has been one of the more influential concepts in modern biogeography and ecology. In this paper, we synthesize the theory and examine effects of different immigration/extinction rate-species diversity curves on original predictions from the theory by using the System Dynamics simulation modeling approach. Moreover, we develop a comprehensive and generic System Dynamics model to incorporate a variety of recent modifications and extensions of the theory, including area effect, distance effect, competition effect, habitat diversity effect, target effect, and rescue effect. Through computer simulation with STELLA, a more profound understanding of the theory of island biogeography can be gained. The System Dynamics modeling approach is especially appropriate for such a study because it maximizes the utilization of the ecological data by incorporating qualitative information so that a complex, imprecisely-defined ecological system can be studied quantitatively, effectively, and comprehensively. Our simulation results show that different monotonic rate-species diversity curves do not affect the essence of the theory of island biogeography, while the magnitude of equilibrium species diversity may be greatly affected. Non-monotonic rate-species diversity curves may result in potential multiple equilibria of species diversity. In addition, our model suggests that a non-monotonic relationship may exist between the equilibrium turnover rate and island area and between the equilibrium turnover rate and distance.     

Predicting community structure in snakes on Eastern Nearctic islands using ecological neutral theory and phylogenetic methods

Predicting species presence and richness on islands is important for understanding the origins of communities and how likely it is that species will disperse and resist extinction. The equilibrium theory of island biogeography (ETIB) and, as a simple model of sampling abundances, the unified neutral theory of biodiversity (UNTB), predict that in situations where mainland to island migration is high, species-abundance relationships explain the presence of taxa on islands. Thus, more abundant mainland species should have a higher probability of occurring on adjacent islands. In contrast to UNTB, if certain groups have traits that permit them to disperse to islands better than other taxa, then phylogeny may be more predictive of which taxa will occur on islands. Taking surveys of 54 island snake communities in the Eastern Nearctic along with mainland communities that have abundance data for each species, we use phylogenetic assembly methods and UNTB estimates to predict island communities. Species richness is predicted by island area, whereas turnover from the mainland to island communities is random with respect to phylogeny. Community structure appears to be ecologically neutral and abundance on the mainland is the best predictor of presence on islands. With regard to young and proximate islands, where allopatric or cladogenetic speciation is not a factor, we find that simple neutral models following UNTB and ETIB predict the structure of island communities.     

A unified model of island biogeography sheds light on the zone of radiation

Islands acquire species through immigration and speciation. Models of island biogeography should capture both processes; however quantitative island biogeography theory has either neglected speciation or treated it unrealistically. We introduce a model where the dominance of immigration on small and near islands gives way to an increasing role for speciation as island area and isolation increase. We examine the contribution of immigration and speciation to the avifauna of 35 archipelagoes and find, consistent with our model, that the zone of radiation comprises two regions: endemic species diverged from mainland sister-species at intermediate isolation and from insular sister-species at higher levels of isolation. Our model also predicts species-area curves in accord with existing research and makes new predictions about species ages and abundances. We argue that a paucity of data and theory on species abundances on isolated islands highlights the need for island biogeography to be reconnected with mainstream ecology.     

岛屿生物地理学理论：模型与应用

前言岛屿有许多显著特征,如地理隔离,生物类群简单。这些特点为重复性研究和统计学分析奠定了基础,从而有利于许多深入而细致的生物学研究。因此,岛屿为发展和检验自然选择、物种形成及演化,以及生物地理学和生态学诸领域的理论和假设,提供了重要的自然实验室。岛屿生物地理学理论(MacArthurwilson学说)即为岛屿生物学研究中所产生的著名理论之一。该理论发展之     

Towards an integrative understanding of soil biodiversity

Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species–energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale‐dependent nature of soil biodiversity.     

Niche and metabolic principles explain patterns of diversity and distribution: theory and a case study with soil bacterial communities

The causes of biodiversity patterns are controversial and elusive due to complex environmental variation, covarying changes in communities, and lack of baseline and null theories to differentiate straightforward causes from more complex mechanisms. To address these limitations, we developed general diversity theory integrating metabolic principles with niche-based community assembly. We evaluated this theory by investigating patterns in the diversity and distribution of soil bacteria taxa across four orders of magnitude variation in spatial scale on an Antarctic mountainside in low complexity, highly oligotrophic soils. Our theory predicts that lower temperatures should reduce taxon niche widths along environmental gradients due to decreasing growth rates, and the changing niche widths should lead to contrasting α- and β-diversity patterns. In accord with the predictions, α-diversity, niche widths and occupancies decreased while β-diversity increased with increasing elevation and decreasing temperature. The theory also successfully predicts a hump-shaped relationship between α-diversity and pH and a negative relationship between α-diversity and salinity. Thus, a few simple principles explained systematic microbial diversity variation along multiple gradients. Such general theory can be used to disentangle baseline effects from more complex effects of temperature and other variables on biodiversity patterns in a variety of ecosystems and organisms.     

Factors affecting the distribution of vascular plants, springtails, butterflies and birds on small tropical islands

Aim

The primary objective of our study was to examine the factors affecting the distribution of vascular plants, springtails, butterflies and birds on small tropical islands to understand how different groups of organisms with distinct biological traits respond to biogeographical variables, such as island area.

Location

The Republic of Singapore (103°50′E, 1°20′N) located at the southern tip of Peninsular Malaysia.

Methods

Seventeen islands were surveyed for vascular plants, springtails, butterflies and birds. Correlation analysis, simple linear and multiple regression analyses and the nestedness index were used to test the hypotheses that (1) area is the best predictor of species/genus richness at both the community and specific/generic levels; (2) there is no correlation between population density and island area; and (3) species/genera are distributed as nested subsets.

Results

Area was the most significant factor in determining the island distribution of springtails, butterflies and birds at both the community and specific/generic levels, although there were disparate responses to the biogeographical variables between the three taxonomic groups, as well as between common species within each group. Individual species displayed disparate responses to biogeographical variables, suggesting that patterns of distribution at the community level may not be a good indicator of the population dynamics of individual species/genera. Plant species richness did not show any correlation with any of the tested variables. Population densities of springtails, butterflies and birds were positively correlated with area, contradicting the assumption of the equilibrium theory of island biogeography that population density of island species is independent of area. Population densities of plants showed no correlation with any of the tested biogeographical variables. Vascular plant, springtail, butterfly and bird communities on the islands showed significant patterns of nestedness, indicating there may be species/genus‐specific responses to biogeographical variables.

Main conclusions

We conclude that although area was the most important factor affecting the island distribution of springtails, butterflies and birds, conservation planning must take into consideration how target taxonomic groups respond to biogeographical variables, instead of relying on general principles (e.g. those derived from the equilibrium theory). On a local scale, in order to preserve the island biodiversity of Singapore, the highest priority should be given to preserving the larger islands (e.g. Pulau Ubin) which not only have higher numbers of species, but also species that are absent on smaller islands.

     

物种保护的理论基础——从岛屿生物地理学理论到集合种群理论

全球面临着生境破碎化的危机,物种保护已成为人类面临的重大课题,并不是所有的人对岛屿生物地理学理论的产生及其关注的海洋岛屿都很熟悉,但是越来越多生物赖以生存的自然栖息地的丧失和破碎化都是有目共睹的,岛屿生物地理学和集合种群理论是目前物种保护的两个基本理论,物种迁入率和绝灭率的动态变化决策岛屿上的物种丰富度是岛屿生物地理学理论的核心内容,而集合种群理论关注的是局部种群之间个体迁移的动态以及物种的续存条件,在概述两个理论形成、发展及其核心内容的基础上,着重比较它们的异同点以及在生态学理论和实践中的应用,并论述物种保护理论范式从岛屿生物地理学向集合种群理论转变的基本背景和原因。     

Concluding remarks: historical perspective and the future of island biogeography theory

MacArthur and Wilson’s equilibrium theory revolutionized the field of island biogeography and, to a large degree, ecology as well. The theory, which quickly became the ruling paradigm of island biogeography, has changed little over the past three decades. It has not kept pace with relevant theory and our growing appreciation for the complexity of nature, especially with empirical findings that species diversity on many islands: 1) is not in equilibrium; 2) is influenced by differences in speciation, colonization, and extinction among taxa; and 3) is influenced by differences among islands in characteristics other than area and isolation. The discipline of biogeography, itself, is in a state of disequilibrium. We may again be about to witness another paradigm shift, which will see the replacement of MacArthur and Wilson’s theory. Wherever this shift may take us, we are confident that the next generation of biogeographers will still look to islands for insights into the forces that shape biological diversity.     

Human biogeography: evidence of our place in nature

Focusing on human biogeography as a research endeavour may make sense to biogeographers, but in the academic world generally this particular scholarly niche has long been filled by other rival disciplines such as sociology, human ecology, geography, anthropology and archaeology. It may be true that having so many ways of looking at ourselves as a species is a good thing, but it can also be argued that this academic fragmentation of effort has often nurtured the commonplace view that we as a species are 'above' or 'not part of' what plain folks call the 'natural world'. Here I review the historical and basic intellectual ingredients of what might be (but often isn't) called human biogeography. I offer a case study drawn from my research work on the Sepik coast of Papua New Guinea. This research illustrates how adopting an explicitly biogeographical approach to human diversity can lead to unexpected insights into the character and history of human settlement in this part of the world. One benefit of having a field with this explicit orientation might be that the conservation of biodiversity would make more sense to more people.     

A general dynamic theory of oceanic island biogeography

Aim MacArthur and Wilson’s dynamic equilibrium model of island biogeography provides a powerful framework for understanding the ecological processes acting on insular populations. However, their model is known to be less successful when applied to systems and processes operating on evolutionary and geological timescales. Here, we present a general dynamic model (GDM) of oceanic island biogeography that aims to provide a general explanation of biodiversity patterns through describing the relationships between fundamental biogeographical processes – speciation, immigration, extinction – through time and in relation to island ontogeny. Location Analyses are presented for the Azores, Canaries, Galápagos, Marquesas and Hawaii. Methods We develop a theoretical argument from first principles using a series of graphical models to convey key properties and mechanisms involved in the GDM. Based on the premises (1) that emergent properties of island biotas are a function of rates of immigration, speciation and extinction, (2) that evolutionary dynamics predominate in large, remote islands, and (3) that oceanic islands are relatively short‐lived landmasses showing a characteristic humped trend in carrying capacity (via island area, topographic variation, etc.) over their life span, we derive a series of predictions concerning biotic properties of oceanic islands. We test a subset of these predictions using regression analyses based largely on data sets for native species and single‐island endemics (SIEs) for particular taxa from each archipelago, and using maximum island age estimates from the literature. The empirical analyses test the power of a simple model of diversity derived from the GDM: the log(Area) + Time + Time² model (ATT²), relative to other simpler time and area models, using several diversity metrics. Results The ATT² model provides a more satisfactory explanation than the alternative models evaluated (for example the standard diversity–area models) in that it fits a higher proportion of the data sets tested, although it is not always the most parsimonious solution. Main conclusions The theoretical model developed herein is based on the key dynamic biological processes (migration, speciation, extinction) combined with a simple but general representation of the life cycle of oceanic islands, providing a framework for explaining patterns of biodiversity, endemism and diversification on a range of oceanic archipelagos. The properties and predictions derived from the model are shown to be broadly supported (1) by the empirical analyses presented, and (2) with reference to previous phylogenetic, ecological and geological studies.     

Biological images of geological history: through a glass darkly or brightly face to face?

Abstract Aim To explore the implications for historical biogeography of a recent review of island biogeographical theory in three main thematic areas and to suggest ways in which a synthesis between the two approaches might be achieved to the benefit of both. Location The Indo‐Australian tropics. Theme 1 discusses the relationship of species number to area, and how the nestedness of faunas may influence the methodology used for some types of analysis and also the quality of data expected from an archipelago embracing an extreme range of island sizes. Theme 2 examines the way in which the processes of speciation may lead to development of biogeographical patterns through a complex archipelago, illustrated in particular with reference to Sulawesi where biotic enrichment from different lepidopteran groups follows predictions from island biogeographical theory. This also has implications for patterns of endemism in the archipelago, another constraint on the quality of data available for historical biogeography. Theme 3 addresses ecological determinism as an influence in development of biogeographical pattern, focusing on the theme of specificity in insect–plant relationships and the potential for parallel development of pattern in an insect group and its particular plant host group. This theme is developed with particular reference to moth and plant groups that may represent Gondwanan elements in the Oriental fauna, with an analysis of Sarcinodes, a geometrid moth genus associated with Proteaceae. Main conclusions Prospects are assessed for the synthesis of the two approaches of island biogeography and historical biogeography. Modelling pattern development with the former may complement the methods of analysis of the latter, particularly if some satisfactory method for dating events of pattern development can also be incorporated.     

历史生物地理学进展

生物地理学研究动植物的地理分布。历史生物地理学重建生物区系历史。分替理论的复兴动摇了散布理论的上百年统治。最近10年主要是分替理论推动了历史生物地理学,出现了多个途径——种系发生物地理学、分支分替生物地理学、特有性的俭吝分析和泛生物地理学。岛屿生物地理学理论有了改进和严格的实验检验;庇所学说产生了新的模型。最后就我国如何发展生物地理学提出了对策措施。     

Island biogeography and the reproductive ecology of great tits Parus major

Island biogeography theory has contributed greatly to both theoretical and applied studies of conservation biology (e.g., design of nature reserves, minimum viable population sizes, extinction risk) and community composition. However, little theoretical and empirical work has addressed how island isolation and size affect reproductive ecology. We investigated the reproductive ecology of great tits (Parus major) on one offshore and one nearshore island, as well as on the Danish mainland. Tits breeding on the offshore island bred later, laid smaller clutches, and laid larger eggs than those on the nearshore island and mainland. In addition, the level of ectoparasite infestation in nests was highest on the offshore island, intermediate on the nearshore island, and lowest on the mainland. These insular effects may occur due to lower food abundance on islands, to density-dependent effects, or to effects related to low genetic diversity within island populations. Whatever the cause, the results emphasize that future studies of forest fragmentation/population isolation should consider not only gross measures of reproductive success, but also fine-scale measures such as clutch size, timing of breeding, and parasite prevalence. Received: 10 November 1997 / Accepted: 9 March 1998     

On the definition of element,chorotype and component in biogeography

Terms such as element, chorotype and component are widely used to indicate biogeographical units. As a result of variation in approaches and methodologies, these terms do not have a single definitive meaning, and similar concepts have been defined under different labels. As originally defined, element denotes a group of species that occur in previously defined biogeographical areas, while chorotype denotes a group of species with a similar distribution. The term component is widely used in ecology to denote the biotic or abiotic constituent of an ecosystem; within biogeography it has typically been used as a synonym for element. Applying the original meanings, current usage within the tradition of systematic biogeography should regard element as referring to groups of taxa defined according to the biogeographical areas they occupy. Within quantitative and evolutionary biogeography, chorotype should be used to define patterns of distribution that can be used to generate hypotheses about their causes and origins. In this paper I argue that component expresses a generic concept rather than a chorological category and should be avoided in biogeography.