The Neutral—Niche Debate: A Philosophical Perspective

Ecological communities around the world are under threat while a consensus theory of community structure remains elusive. In the last decade ecologists have struggled with two seemingly opposing theories: niche-based theory that explains diversity with species’ differences and the neutral theory of biodiversity that claims that much of the diversity we observe can be explained without explicitly invoking species’ differences. Although ecologists are increasingly attempting to reconcile these two theories, there is still much resistance against the neutral theory of biodiversity. Here we argue that the dispute between the two theories is a classic example of the dichotomy between philosophical perspectives, realism and instrumentalism. Realism is associated with specific, small-scale and detailed explanations, whereas instrumentalism is linked to general, large-scale, but less precise accounts. Recognizing this will help ecologists get both niche-based and neutral theories in perspective as useful tools for understanding biodiversity patterns.     

Trophic separation in planktivorous reef fishes: a new role for mucus?

Oecologia - The feeding apparatus directly influences a species’ trophic ecology. In fishes, our understanding of feeding modes is largely derived from studies of rigid structures (i.e....     

The temporal dimension of marine speciation

Speciation is a process that occurs over time and, as such, can only be fully understood in an explicitly temporal context. Here we discuss three major consequences of speciation’s extended duration. First, the dynamism of environmental change indicates that nascent species may experience repeated changes in population size, genetic diversity, and geographic distribution during their evolution. The present characteristics of species therefore represents a static snapshot of a single time point in a species’ highly dynamic history, and impedes inferences about the strength of selection or the geography of speciation. Second, the process of speciation is open ended—ecological divergence may evolve in the space of a few generations while the fixation of genetic differences and traits that limit outcrossing may require thousands to millions of years to occur. As a result, speciation is only fully recognized long after it occurs, and short-lived species are difficult to discern. Third, the extinction of species or of clades provides a simple, under-appreciated, mechanism for the genetic, biogeographic, and behavioral ‘gaps’ between extant species. Extinction also leads to the systematic underestimation of the frequency of speciation and the overestimation of the duration of species formation. Hence, it is no surprise that a full understanding of speciation has been difficult to achieve. The modern synthesis—which united genetics, development, ecology, biogeography, and paleontology—greatly advanced the study of evolution. Here we argue that a similarly synthetic approach must be taken to further our understanding of the origin of species.     

Emerging zoonotic diseases originating in mammals: a systematic review of effects of anthropogenic land-use change

1. Zoonotic pathogens and parasites that are transmitted from vertebrates to humans are a major public health risk with high associated global economic costs. The spread of these pathogens and risk of transmission accelerate with recent anthropogenic land-use changes (LUC) such as deforestation, urbanisation, and agricultural intensification, factors that are expected to increase in the future due to human population expansion and increasing demand for resources.
2. We systematically review the literature on anthropogenic LUC and zoonotic diseases, highlighting the most prominent mammalian reservoirs and pathogens, and identifying avenues for future research.
3. The majority of studies were global reviews that did not focus on specific taxa. South America and Asia were the most-studied regions, while the most-studied LUC was urbanisation. Livestock were studied more within the context of agricultural intensification, carnivores with urbanisation and helminths, bats with deforestation and viruses, and primates with habitat fragmentation and protozoa.
4. Research into specific animal reservoirs has improved our understanding of how the spread of zoonotic diseases is affected by LUC. The behaviour of hosts can be altered when their habitats are changed, impacting the pathogens they carry and the probability of disease spreading to humans. Understanding this has enabled the identification of factors that alter the risk of emergence (such as virulence, pathogen diversity, and ease of transmission). Yet, many pathogens and impacts of LUC other than urbanisation have been understudied.
5. Predicting how zoonotic diseases emerge and spread in response to anthropogenic LUC requires more empirical and data synthesis studies that link host ecology and responses with pathogen ecology and disease spread. The link between anthropogenic impacts on the natural environment and the recent COVID-19 pandemic highlights the urgent need to understand how anthropogenic LUC affects the risk of spillover to humans and spread of zoonotic diseases originating in mammals.

     

Invading with biological weapons: the role of shared disease in ecological invasion

Theory has been developed that examines the role of infectious disease in ecological invasions for particular natural systems. However, a general understanding of the role that shared disease may play in invasions is lacking. Here, we develop a strategic theoretical framework to determine the role of disease, in addition to competition, in ecological invasions and the expansion of species’ spatial range. We investigate the effect of different disease parameters on the replacement time of a native species by an alien invader. The outcome is critically dependent on the relative effects that the disease has on the two species and less dependent on the basic epidemiological characteristics of the interaction. This framework is also used to investigate the effect of disease on the spatial spread of the invader. Our results show an interesting phenomenon where a wave of disease spreads through the landscape ahead of the wave of replacement.     

Macroecological relationships between coral species�� traits and disease potential

Coral disease is a growing problem for reef corals and a primary driver of reef degradation. Incidences of coral disease on the Great Barrier Reef (GBR) are increasing; however, our understanding of differences among species in their potential for contracting disease is poor. In this study, we integrate observations of coral disease on the GBR from the primary literature as well as morphological, ecological and biogeographical traits of coral species that have been hypothesised to influence “disease potential.” Most of the examined traits influence species’ disease potential when considered alone. However, when all traits are analysed together, diversity of predators, geographical range size and characteristic local abundance are the primary predictors of disease potential. Biases associated with species’ local abundance and phylogeny are tested but do not overpower relationships. This large-scale macroecological evaluation of coral disease provides insights into species-level traits that drive disease susceptibility.     

Geographic evaluation of conservation status of African forest squirrels (Sciuridae) considering land use change and climate change: the importance of point data

Known occurrences based on natural history museum voucher specimens for three genera of African forest squirrels were used to develop a detailed, fine-scale distributional under- standing of each species. Considerations of species’ autecology, effects of land use change, and effects of global climate change were all included in our analyses, and negative effects of land use and climate change on species’ distributional areas were roughly equivalent across the species surveyed. We describe geographic patterns of distribution and endemism, and identify areas of potential occurrence of unknown species. Comparing with coarse grid-based approaches currently in vogue in African biodiversity conservation efforts, we suggest that the point-based method offers significant advantages in fine resolution and avoiding loss of information, and yet are feasibly implemented for many vertebrate groups.     

Range shift and loss of genetic diversity under climate change in Caryocar brasiliense, a Neotropical tree species

Many species have suffered reduction in habitable area due to recent climate change, but few studies evaluated how these range collapses will impact genetic diversity. Here, we modeled shifts in the species’ geographical range to evaluate how genetic diversity of Caryocar brasiliense will change as a consequence of predicted climate change in the next 50 years. A total of 135 records of species occurrence were obtained to model species’ distribution based on the current environment using MAXENT and forecasting future distribution using a combination of three coupled atmospheric–oceanic global circulation models. Genetic parameters were estimated based on the polymorphism at ten microsatellite loci for 466 individuals. Our results show that climatic suitable areas for C. brasiliense will be restricted to the southernmost distribution of savanna vegetation. Genetic diversity and the number of alleles may decrease slowly if populations persist in regions up to 0.5 of environmental suitability estimated by MAXENT, but will sharply decrease above this level. Nevertheless, deviation from mutation–drift equilibrium is significant even if a small amount of local populations is lost. More climatic suitable areas in the future will be in the most disturbed regions in Brazil, and populations that will persist there are those with higher levels of inbreeding at present. This may impose several threats to the species, including the limited capacity to cope with ongoing climatic changes by adaptation and constraints to dispersal.     

An evaluation of prior influence on the predictive ability of Bayesian model averaging

Model averaging is gaining popularity among ecologists for making inference and predictions. Methods for combining models include Bayesian model averaging (BMA) and Akaike’s Information Criterion (AIC) model averaging. BMA can be implemented with different prior model weights, including the Kullback–Leibler prior associated with AIC model averaging, but it is unclear how the prior model weight affects model results in a predictive context. Here, we implemented BMA using the Bayesian Information Criterion (BIC) approximation to Bayes factors for building predictive models of bird abundance and occurrence in the Chihuahuan Desert of New Mexico. We examined how model predictive ability differed across four prior model weights, and how averaged coefficient estimates, standard errors and coefficients’ posterior probabilities varied for 16 bird species. We also compared the predictive ability of BMA models to a best single-model approach. Overall, Occam’s prior of parsimony provided the best predictive models. In general, the Kullback–Leibler prior, however, favored complex models of lower predictive ability. BMA performed better than a best single-model approach independently of the prior model weight for 6 out of 16 species. For 6 other species, the choice of the prior model weight affected whether BMA was better than the best single-model approach. Our results demonstrate that parsimonious priors may be favorable over priors that favor complexity for making predictions. The approach we present has direct applications in ecology for better predicting patterns of species’ abundance and occurrence.     

Development of polymorphic microsatellite DNA markers from the Korean field mouse, Apodemus peninsulae

We isolated and characterized eight polymorphic microsatellite DNA markers from the Korean field mouse, Apodemus peninsulae. The primers developed in this study yielded an average polymorphic information content of 0.78 (range 0.44–0.90), with an average of 10.9 alleles per locus (range 5–16). Observed and expected heterozygosities ranged from 0.46 to 1.00 and from 0.49 to 0.93, respectively. These polymorphic loci may provide useful tools for understanding the species’ genetic structure and ecology.     

Microbiology and the species problem

This paper examines the species problem in microbiology and its implications for the species problem more generally. Given the different meanings of ‘species’ in microbiology, the use of ‘species’ in biology is more multifarious and problematic than commonly recognized. So much so, that recent work in microbial systematics casts doubt on the existence of a prokaryote species category in nature. It also casts doubt on the existence of a general species category for all of life (one that includes both prokaryotes and eukaryotes). Prokaryote biology also undermines recent attempts to save the species category, such as the suggestion that species are metapopulation lineages and the idea that ‘species’ is a family resemblance concept.     

Tree diseases and landscape processes: the challenge of landscape pathology

Forest pathology inherently involves a landscape perspective, because tree pathogens propagate according to heterogeneous spatial patterns of flow and isolation. Landscape pathology is a field that is now emerging from the transdisciplinary cooperation of forest pathologists with landscape ecologists. Here, we review recent broad-scale assessments of tree disease risk, investigations of site and host preferences for several root rot pathogens, and regional historical analyses of pathogen outbreak in plantations. Crucial topics include fragmentation effects on pathogen spread and geophysical features that predispose forest patches to disease expression. Recent methodological developments facilitate the spatially explicit analysis of reciprocal coarse-scale relationships among hosts and pathogens. Landscape pathology studies fill a significant research gap in the context of our understanding of sustainable forest management, the introduction of exotic organisms and how climate change might affect the spread of disease.     

Using functional morphology to examine the ecology and evolution of specialization

Researchers strive to understand what makes species different,and what allows them to survive in the time and space that theydo. Many models have been advanced which encompass an arrayof ecological, evolutionary, mathematical, and logical principles.The goal has been to develop ecological theories that can, amongother things, make specific and robust predictions about howand where organisms should live and what organisms should utilize.The role of functional morphology is often an under-appreciatedparameter of these models. A more complete understanding ofhow anatomical features work to allow the organism to accomplishcertain tasks has allowed us to revisit some of these ideaswith a new perspective. We illustrate our view of this rolefor functional morphology in ecology by considering the issueof specialization: we attempt to align several definitions ofspecialization based upon shared ecological and evolutionaryprinciples, and we summarize theoretical predictions regardingwhy an organism might specialize. Kinematic studies of preycapture in several types of fishes are explored with regardto the potential ecological and evolutionary consequences ofspecialization, most notably in the area of trade-offs. We suggestthat a functional morphological perspective can increase ourunderstanding of the ecological concepts of specialization andit consequences. The kinds of data that functional morphologistscollect can help us to quantify organismal performance associatedwith specialization and the union of functional morphology withecology can help us to better understand not just how but whyorganisms interact in the manner that they do.     

Empirical and theoretical challenges in aboveground–belowground ecology

A growing body of evidence shows that aboveground and belowground communities and processes are intrinsically linked, and that feedbacks between these subsystems have important implications for community structure and ecosystem functioning. Almost all studies on this topic have been carried out from an empirical perspective and in specific ecological settings or contexts. Belowground interactions operate at different spatial and temporal scales. Due to the relatively low mobility and high survival of organisms in the soil, plants have longer lasting legacy effects belowground than aboveground. Our current challenge is to understand how aboveground–belowground biotic interactions operate across spatial and temporal scales, and how they depend on, as well as influence, the abiotic environment. Because empirical capacities are too limited to explore all possible combinations of interactions and environmental settings, we explore where and how they can be supported by theoretical approaches to develop testable predictions and to generalise empirical results. We review four key areas where a combined aboveground–belowground approach offers perspectives for enhancing ecological understanding, namely succession, agro-ecosystems, biological invasions and global change impacts on ecosystems. In plant succession, differences in scales between aboveground and belowground biota, as well as between species interactions and ecosystem processes, have important implications for the rate and direction of community change. Aboveground as well as belowground interactions either enhance or reduce rates of plant species replacement. Moreover, the outcomes of the interactions depend on abiotic conditions and plant life history characteristics, which may vary with successional position. We exemplify where translation of the current conceptual succession models into more predictive models can help targeting empirical studies and generalising their results. Then, we discuss how understanding succession may help to enhance managing arable crops, grasslands and invasive plants, as well as provide insights into the effects of global change on community re-organisation and ecosystem processes.     

Propagule Pressure: A Null Model for Biological Invasions

Invasion ecology has been criticised for its lack of general principles. To explore this criticism, we conducted a meta-analysis that examined characteristics of invasiveness (i.e. the ability of species to establish in, spread to, or become abundant in novel communities) and invasibility (i.e. the susceptibility of habitats to the establishment or proliferation of invaders). There were few consistencies among invasiveness characteristics (3 of 13): established and abundant invaders generally occupy similar habitats as native species, while abundant species tend to be less affected by enemies; germination success and reproductive output were significantly positively associated with invasiveness when results from both stages (establishment/spread and abundance/impact) were combined. Two of six invasibility characteristics were also significant: communities experiencing more disturbance and with higher resource availability sustained greater establishment and proliferation of invaders. We also found that even though ‘propagule pressure’ was considered in only ~29% of studies, it was a significant predictor of both invasiveness and invasibility (55 of 64 total cases). Given that nonindigenous species are likely introduced non-randomly, we contend that ‘propagule biases’ may confound current paradigms in invasion ecology. Examples of patterns that could be confounded by propagule biases include characteristics of good invaders and susceptible habitats, release from enemies, evolution of ‘invasiveness’, and invasional meltdown. We conclude that propagule pressure should serve as the basis of a null model for studies of biological invasions when inferring process from patterns of invasion. An erratum to this article can be found at     

A theoretical model linking interspecific variation in density dependence to species abundances

Understanding the factors that govern the commonness and rarity of individual species is a central challenge in community ecology. Empirical studies have often found that abundance is related to traits associated with competitive ability and suitability to the local environment and, more recently, also to negative conspecific density dependence. Here, we construct a theoretical framework to show how a species’ abundance is, in general, expected to be dependent on its per-capita growth rate when rare and the rate at which its growth rate declines with increasing abundance (strength of stabilization). We argue that per-capita growth rate when rare can be interpreted as competitive ability and that strength of stabilization largely reflects negative conspecific inhibition. We then analyze a simple spatially implicit model in which each species is defined by three parameters that affect its juvenile survival: its generalized competitive effect on others, its generalized response to competition, and an additional negative effect on conspecifics. This model facilitates the stable coexistence of an arbitrarily large number of species and qualitatively reproduces empirical relationships between abundance, competitive ability, and negative conspecific density dependence. Our results provide theoretical support for the combined roles of competitive ability and negative density dependence in the determination of species abundances in real ecosystems, and suggest new avenues of research for understanding abundance in models and in real communities.     

Biogeography and conservation in Southeast Asia: how 2.7 million years of repeated environmental fluctuations affect today’s patterns and the future of the remaining refugial-phase biodiversity

Understanding the historical biogeography of this global biodiversity hotspot is as important to long-term conservation goals as ecology and evolution are to understanding current patterns and processes. Today’s geography is, however, misleading and typical of only ~2% of the last million years; >90% of that time the region’s land area was 1.5–2.0 times larger as mean sea levels were 62 m below today’s, climates were cooler, and extensive forests and savanna covered the emerged Sunda plains. The region’s land area varied two-fold as sea levels fluctuated up to ±50 m with each of ~50 Pleistocene glacial cycles, and forests expanded and contracted with oscillations in land area and seasonality. This dynamic geographic history is relevant to the development of biogeographic regionalism and shows that it is today’s forests that are refugial, not those of the Last Glacial Maximum. This history affects how species will adapt or shift their ranges in response to global warming and further decreases in land area (submergence of low-lying coastal areas) during the 21st century. The alternative is mass species extinction. The biota is also threatened by the continued destruction of forest, destruction of Mekong River flood-pulse based ecosystems, and continued human population growth. Human biogeography will become more important in conservation planning as tens of millions of people who depend on protected area forests, riverine ecosystems, and coastal habitats become environmental refugees. Conservation scientists need to become more involved in regional ecological education, environmental stewardship, and ecosystem-based adaptation to sustain as much as possible of this rich biota and the ecological services it provides.     

Dietary isotopic discrimination in gentoo penguin (Pygoscelis papua) feathers

Feathers are used commonly for stable isotope analysis to assess the foraging ecology and migration patterns of birds. However, these studies often require knowledge of species-specific feather isotopic discrimination factors (the differences in isotopic ratios between a species’ diet and feathers), which can be influenced by a species’ physiological state during molt. In this study, we determined the isotopic discrimination factors (Δ¹³C_{diet−feather} and Δ¹⁵N_{diet−feather}) between adult gentoo penguin (Pygoscelis papua) diet and feathers in a controlled study. In addition, we tested whether molt duration or the magnitude of voluntary dietary reduction during molt influenced isotopic discrimination, as previous studies have found that nutritional stress can exaggerate ¹⁵N enrichment and in some cases lead to ¹³C depletion in feathers. Contrary to this hypothesis, we found no effect of molt duration or dietary reduction on discrimination factors, suggesting that isotopic discrimination is not linearly related to these measures of fasting intensity in penguins. Furthermore, we found that the range of Δ¹⁵N_{diet−feather} found in several species of penguins, which fast while they molt, was similar to discrimination factors in fish-eating birds, which do not fast during molt. It is likely that species-specific metabolic adaptations that limit nutritional stress while fasting and variation in their relative reliance on endogenous vs. dietary pools during feather growth may confound the use of Δ¹⁵N_{diet−feather} as a general measure of nutritional stress when comparing among species.     

Going through the motions: incorporating movement analyses into disease research

Though epidemiology dates back to the 1700s, most mathematical representations of epidemics still use transmission rates averaged at the population scale, especially for wildlife diseases. In simplifying the contact process, we ignore the heterogeneities in host movements that complicate the real world, and overlook their impact on spatiotemporal patterns of disease burden. Movement ecology offers a set of tools that help unpack the transmission process, letting researchers more accurately model how animals within a population interact and spread pathogens. Analytical techniques from this growing field can also help expose the reverse process: how infection impacts movement behaviours, and therefore other ecological processes like feeding, reproduction, and dispersal. Here, we synthesise the contributions of movement ecology in disease research, with a particular focus on studies that have successfully used movement‐based methods to quantify individual heterogeneity in exposure and transmission risk. Throughout, we highlight the rapid growth of both disease and movement ecology and comment on promising but unexplored avenues for research at their overlap. Ultimately, we suggest, including movement empowers ecologists to pose new questions, expanding our understanding of host–pathogen dynamics and improving our predictive capacity for wildlife and even human diseases.     

Challenges in modelling complexity of fungal entomopathogens in semi-natural populations of insects

The use of fungal entomopathogens as microbial control agents has driven studies into their ecology in crop ecosystems. Yet, there is still a lack of understanding of the ecology of these insect pathogens in semi-natural habitats and communities. We review the literature on prevalence of fungal entomopathogens in insect populations and highlight the difficulties in making such measurements. We then describe the theoretical host-pathogen models available to examine the role that fungal entomopathogens could play in regulating insect populations in semi-natural habitats, much of the inspiration for which has been drawn from managed systems, particularly forests. We further emphasise the need to consider the complexity, and particularly the heterogeneity, of semi-natural habitats within the context of theoretical models and as a framework for empirical studies. We acknowledge that fundamental gaps in understanding fungal entomopathogens from an ecological perspective coupled with a lack of empirical data to test theoretical predictions is impeding progress. There is an increasing need, especially under current rapid environmental change, to improve our understanding of the role of fungi in insect population dynamics beyond the context of forestry and agriculture.