Patterns of relative species abundance in rainforests and coral reefs.

A formidable many-body problem in ecology is to understand the complex of factors controlling patterns of relative species abundance (RSA) in communities of interacting species. Unlike many problems in physics, the nature of the interactions in ecological communities is not completely known. Although most contemporary theories in ecology start with the basic premise that species interact, here we show that a theory in which all interspecific interactions are turned off leads to analytical results that are in agreement with RSA data from tropical forests and coral reefs. The assumption of non-interacting species leads to a sampling theory for the RSA that yields a simple approximation at large scales to the exact theory. Our results show that one can make significant theoretical progress in ecology by assuming that the effective interactions among species are weak in the stationary states in species-rich communities such as tropical forests and coral reefs.

Inferring species interactions in tropical forests.

We present 2 distinct and independent approaches to deduce the effective interaction strengths between species and apply it to the 20 most abundant species in the long-term 50-ha plot on Barro Colorado Island, Panama. The first approach employs the principle of maximum entropy, and the second uses a stochastic birth-death model. Both approaches yield very similar answers and show that the collective effects of the pairwise interspecific interaction strengths are weak compared with the intraspecific interactions. Our approaches can be applied to other ecological communities in steady state to evaluate the extent to which interactions need to be incorporated into theoretical explanations for their structure and dynamics.

Seeing the forest for the trees through metabolic scaling.

We demonstrate that when power scaling occurs for an individual tree and in a forest, there is great resulting simplicity notwithstanding the underlying complexity characterizing the system over many size scales. Our scaling framework unifies seemingly distinct trends in a forest and provides a simple yet promising approach to quantitatively understand a bewilderingly complex many-body system with imperfectly known interactions. We show that the effective dimension, D tree , of a tree is close to 3, whereas a mature forest has D forest approaching 1. We discuss the energy equivalence rule and show that the metabolic rate-mass relationship is a power law with an exponent D/(D + 1) in both cases leading to a Kleiber's exponent of 3/4 for a tree and 1/2 for a forest. Our work has implications for understanding carbon sequestration and for climate science.

Density dependence explains tree species abundance and diversity in tropical forests.

The recurrent patterns in the commonness and rarity of species in ecological communities--the relative species abundance--have puzzled ecologists for more than half a century. Here we show that the framework of the current neutral theory in ecology can easily be generalized to incorporate symmetric density dependence. We can calculate precisely the strength of the rare-species advantage that is needed to explain a given RSA distribution. Previously, we demonstrated that a mechanism of dispersal limitation also fits RSA data well. Here we compare fits of the dispersal and density-dependence mechanisms for empirical RSA data on tree species in six New and Old World tropical forests and show that both mechanisms offer sufficient and independent explanations. We suggest that RSA data cannot by themselves be used to discriminate among these explanations of RSA patterns--empirical studies will be required to determine whether RSA patterns are due to one or the other mechanism, or to some combination of both.

South-Siberian mountain mires: Perspectives on a potentially vulnerable remote source of biodiversity.

Changes in climate, land-use and pollution are having disproportionate impacts on ecosystems and biodiversity of arctic and mountain ecosystems. While these impacts are well-documented for many areas of the Arctic and alpine regions, some isolated and inaccessible mountain areas are poorly studied. Furthermore, even in well-studied regions, assessments of biodiversity and species responses to environmental change are biased towards vascular plants and cryptogams, particularly bryophytes are far less represented. This paper aims to document the environments of the remote and inaccessible Altai-Sayan mountain mires and particularly their bryofloras where threatened species exist and species new to the regional flora are still being found. As these mountain mires are relatively inaccessible, changes in drivers of change and their ecosystem and biodiversity impacts have not been monitored. However, the remoteness of the mires has so far protected them and their species. In this study, we describe the mires, their bryophyte species and the expected impacts of environmental stressors to bring attention to the urgency of documenting change and conserving these pristine ecosystems.

The dynamic land-cover of the Altai Mountains: Perspectives based on past and current environmental and biodiversity changes.

We present climate-dependent changes in the high-mountain forest ecotone, old-growth forests, alpine phytocenoses, and deglaciated forelands in the Aktru glacial basin (Altai Republic, Russia). A number of independent sources (variations in upper treeline altitude, dendrochronological data, analysis of lacustrine sediments and botanical and geographical studies linked with the dynamics of glacial-dammed lakes in the Chuya and Kurai intermountain depressions) suggest Holocene temperatures reached about 4 °C higher than today. Unlike the European Alps, glaciers in the continental Altai Mountains disappeared before forming again. Also, the upper altitudinal limit of mountain forests during the Holocene was greater than in the European Alps. The high variability of mountain ecosystems in southern Siberia suggests their potential instability in a currently changing climate. However, periglacial successions associated with the strong continental climate and glacier retreat represent an area of increasing biodiversity and plant cover. The historical and current sensitivity of the continental mountains to climate variations which exceeds that of the European Alps requires greater understanding, environmental protection, and increased social responsibility for the consequences of anthropogenic contributions to climate change: the isolated Altai areas contribute little to climate changes, but are greatly affected by them.

Great Vasyugan Mire: How the world's largest peatland helps addressing the world's largest problems.

Peatlands cover 3% of the land, occur in 169 countries, and have-by sequestering 600 Gt of carbon-cooled the global climate by 0.6 °C. After a general review about peatlands worldwide, this paper describes the importance of the Great Vasyugan Mire and presents suggestions about its protection and future research. The World's largest peatland, the Great Vasyugan Mire in West-Siberia, forms the border between the Taiga and the Forest-Steppe biomes and harbours rare species and mire types and globally unique self-organizing patterns. Current oil and gas exploitation may arguably be largely phased out by 2050, which will pave the way for a stronger focus on the mire's role in buffering climate change, maintaining ecosystem diversity, and providing other ecosystem services. Relevant new research lines will benefit from the extensive data sets that earlier studies have gathered for other purposes. Its globally unique character as the 'largest life form on land' qualifies the Great Vasyugan Mire in its entirety to be designated as a UNESCO World Heritage Site and a Ramsar Wetland of International Importance.

Impacts of environmental change on biodiversity and vegetation dynamics in Siberia.

Biological diversity is the basis for, and an indicator of biosphere integrity. Together with climate change, its loss is one of the two most important planetary boundaries. A halt in biodiversity loss is one of the UN Sustainable Development Goals. Current changes in biodiversity in the vast landmass of Siberia are at an initial stage of inventory, even though the Siberian environment is experiencing rapid climate change, weather extremes and transformation of land use and management. Biodiversity changes affect traditional land use by Indigenous People and multiple ecosystem services with implications for local and national economies. Here we review and analyse a large number of scientific publications, which are little known outside Russia, and we provide insights into Siberian biodiversity issues for the wider international research community. Case studies are presented on biodiversity changes for insect pests, fish, amphibians and reptiles, birds, mammals and steppe vegetation, and we discuss their causes and consequences.

Neutral theory: the stability of forest biodiversity.

The unified neutral theory of biodiversity and biogeography provides a dynamic null hypothesis for the assembly of natural communities. It is also useful for understanding the influence of speciation, extinction, dispersal and ecological drift on patterns of relative species abundance, species-area relationships and phylogeny. Clark and McLachlan argue that neutral drift is inconsistent with the palaeorecord of stability in fossil pollen assemblages of the Holocene forests of southern Canada. We show here that their analysis is based on a partial misunderstanding of neutral theory and that their data alone cannot unambiguously test its validity.

Neutral theory and relative species abundance in ecology.

The theory of island biogeography asserts that an island or a local community approaches an equilibrium species richness as a result of the interplay between the immigration of species from the much larger metacommunity source area and local extinction of species on the island (local community). Hubbell generalized this neutral theory to explore the expected steady-state distribution of relative species abundance (RSA) in the local community under restricted immigration. Here we present a theoretical framework for the unified neutral theory of biodiversity and an analytical solution for the distribution of the RSA both in the metacommunity (Fisher's log series) and in the local community, where there are fewer rare species. Rare species are more extinction-prone, and once they go locally extinct, they take longer to re-immigrate than do common species. Contrary to recent assertions, we show that the analytical solution provides a better fit, with fewer free parameters, to the RSA distribution of tree species on Barro Colorado Island, Panama, than the lognormal distribution.

Stochastic processes are key determinants of short-term evolution in influenza a virus.

Understanding the evolutionary dynamics of influenza A virus is central to its surveillance and control. While immune-driven antigenic drift is a key determinant of viral evolution across epidemic seasons, the evolutionary processes shaping influenza virus diversity within seasons are less clear. Here we show with a phylogenetic analysis of 413 complete genomes of human H3N2 influenza A viruses collected between 1997 and 2005 from New York State, United States, that genetic diversity is both abundant and largely generated through the seasonal importation of multiple divergent clades of the same subtype. These clades cocirculated within New York State, allowing frequent reassortment and generating genome-wide diversity. However, relatively low levels of positive selection and genetic diversity were observed at amino acid sites considered important in antigenic drift. These results indicate that adaptive evolution occurs only sporadically in influenza A virus; rather, the stochastic processes of viral migration and clade reassortment play a vital role in shaping short-term evolutionary dynamics. Thus, predicting future patterns of influenza virus evolution for vaccine strain selection is inherently complex and requires intensive surveillance, whole-genome sequencing, and phenotypic analysis.

Functional localization of auditory cortical fields of human: click-train stimulation.

Averaged auditory evoked potentials (AEPs) to bilaterally presented 100 Hz click trains were recorded from multiple sites simultaneously within Heschl's gyrus (HG) and on the posterolateral surface of the superior temporal gyrus (STG) in epilepsy-surgery patients. Three auditory fields were identified based on AEP waveforms and their distribution. Primary (core) auditory cortex was localized to posteromedial HG. Here the AEP was characterized by a robust polyphasic low-frequency field potential having a short onset latency and on which was superimposed a smaller frequency-following response to the click train. Core AEPs exhibited the lowest response threshold and highest response amplitude at one HG site with threshold rising and amplitude declining systematically on either side of it. The AEPs recorded anterolateral to the core, if present, were typically of low amplitude, with little or no evidence of short-latency waves or the frequency-following response that characterized core AEPs. We suggest that this area is part of a lateral auditory belt system. Robust AEPs, with waveforms demonstrably different from those of the core or lateral belt, were localized to the posterolateral surface of the STG and conform to previously described field PLST.

The last 50 years of climate-induced melting of the Maliy Aktru glacier (Altai Mountains, Russia) revealed in a primary ecological succession.

In this article, we report and discuss the results obtained from a survey of plants, microorganisms (bacteria and fungi), and soil elements along a chronosequence in the first 600 m of the Maliy Aktru glacier's forefront (Altai Mountains, Russia). Many glaciers of the world show effects of climate change. Nonetheless, except for some local reports, the ecological effects of deglaciation have been poorly studied and have not been quantitatively assessed in the Altai Mountains. Here, we studied the ecological changes of plants, fungi, bacteria, and soil elements that take the form of a primary ecological succession and that took place over the deglaciated soil of the Maliy Aktru glacier during the last 50 year. According to our measurements, the glacier lost about 12 m per year during the last 50 years. Plant succession shows clear signs of changes along the incremental distance from the glacier forefront. The analysis of the plant α- and ß-diversity confirmed an expected increase of them with increasing distance from the glacier forefront. Moreover, the analysis of ß-diversity confirmed the hypothesis of the presence of three main stages of the plant succession: (a) initial (pioneer species) from 30 to 100 m; (b) intermediate (r-selected species) from 110 to 120-150 m; and (c) final (K-selected species) from 150 to 550. Our study also shows that saprotrophic communities of fungi are widely distributed in the glacier retreating area with higher relative abundances of saprotroph ascomycetes at early successional stages. The evolution of a primary succession is also evident for bacteria, soil elements, and CO 2 emission and respiration. The development of biological communities and the variation in geochemical parameters represent an irrefutable proof that climate change is altering soils that have been long covered by ice.

Functional connections within the human inferior frontal gyrus.

The highly convoluted and cytoarchitectonically diverse inferior frontal gyrus (IFG) of humans is known to be critically involved in a wide range of complex operations including speech and language processing. The neural circuitry that underlies these operations is not fully understood. We hypothesized that this neural circuitry includes functional connections within and between the three major IFG subgyri: the pars orbitalis, pars triangularis, and pars opercularis. To test this hypothesis we employed electrical stimulation tract-tracing techniques in 10 human patients undergoing surgical treatment for intractable epilepsy. The approach involved delivering repeated bipolar electrical stimuli to one site on the IFG while recording the electrical response evoked by that stimulus from a 64-contact grid overlying more distant IFG sites. In all subjects, stimulation of a site on one subgyrus evoked polyphasic potentials at distant sites, either on the same subgyrus or on an adjacent subgyrus. This provided prima facie evidence for a functional connection between the site of stimulation and the sites of the evoked response. The averaged evoked potentials tended to aggregate as response fields. The spatial spread of a response field indicated a divergent projection from the site of stimulation. When two or more sites were stimulated, the resulting evoked potentials exhibited different waveforms while the respective response fields could overlap substantially, suggesting that input from multiple sites converged but by engaging different neural circuits. The earliest deflection in the evoked potential ranged from 2 to 10 msec. No differences were noted between language-dominant and language-nondominant hemispheres.

Functional connections between auditory cortical fields in humans revealed by Granger causality analysis of intra-cranial evoked potentials to sounds: comparison of two methods.

Knowledge of neural interactions amongst cortical sites is important for understanding higher brain function. We studied such interactions using Granger causality (GC) to analyze auditory event-related potentials (ERPs) recorded directly and simultaneously from two physiologically identified and functionally interconnected auditory areas of cerebral cortex in human neurosurgical patients. Two methods of GC analysis were used and the results compared. Both approaches involved adaptive autoregressive modeling but differed from each other in other ways. Results obtained by using the two methods also differed. Fewer false-positive results were obtained using the method that suppressed the ERP non-stationarity and that expressed the GC as the sum of model coefficients, which suggests that this is the more appropriate approach for analyzing ERPs recorded directly from the human cortex.

Upscaling species richness and abundances in tropical forests.

The quantification of tropical tree biodiversity worldwide remains an open and challenging problem. More than two-fifths of the number of worldwide trees can be found either in tropical or in subtropical forests, but only ≈0.000067% of species identities are known. We introduce an analytical framework that provides robust and accurate estimates of species richness and abundances in biodiversity-rich ecosystems, as confirmed by tests performed on both in silico-generated and real forests. Our analysis shows that the approach outperforms other methods. In particular, we find that upscaling methods based on the log-series species distribution systematically overestimate the number of species and abundances of the rare species. We finally apply our new framework on 15 empirical tropical forest plots and quantify the minimum percentage cover that should be sampled to achieve a given average confidence interval in the upscaled estimate of biodiversity. Our theoretical framework confirms that the forests studied are comprised of a large number of rare or hyper-rare species. This is a signature of critical-like behavior of species-rich ecosystems and can provide a buffer against extinction.

Hearing suppression induced by electrical stimulation of human auditory cortex.

In the course of performing electrical stimulation functional mapping (ESFM) in neurosurgery patients, we identified three subjects who experienced hearing suppression during stimulation of sites within the superior temporal gyrus (STG). One of these patients had long standing tinnitus that affected both ears. In all subjects, auditory event related potentials (ERPs) were recorded from chronically implanted intracranial electrodes and the results were used to localize auditory cortical fields within the STG. Hearing suppression sites were identified within anterior lateral Heschl's gyrus (HG) and posterior lateral STG, in what may be auditory belt and parabelt fields. Cortical stimulation suppressed hearing in both ears, which persisted beyond the period of electrical stimulation. Subjects experienced other stimulation-evoked perceptions at some of these same sites, including symptoms of vestibular activation and alteration of audio-visual speech processing. In contrast, stimulation of presumed core auditory cortex within posterior medial HG evoked sound perceptions, or in one case an increase in tinnitus intensity, that affected the contralateral ear and did not persist beyond the period of stimulation. The current results confirm a rarely reported experimental observation, and correlate the cortical sites associated with hearing suppression with physiologically identified auditory cortical fields.

Molecular dynamics simulations of crystallization of hard spheres.

We have carried out molecular dynamics simulations of the crystallization of hard spheres modeling colloidal systems that are studied in conventional and space-based experiments. We use microscopic probes to investigate the effects of gravitational forces, polydispersity, and of bounding walls on the phase structure. The simulations employed an extensive exclusive particle grid method and the type and degree of crystalline order was studied in two independent ways: by the structure factor, as in experiments, and through local rotational invariants. We present quantitative comparisons of the nucleation rates of monodisperse and polydisperse hard-sphere systems and benchmark them against experimental results. We show how the presence of bounding walls leads to wall-induced nucleation and rapid crystallization, and discuss the role of gravity on the dynamics of crystallization.

Applications of the principle of maximum entropy: from physics to ecology.

There are numerous situations in physics and other disciplines which can be described at different levels of detail in terms of probability distributions. Such descriptions arise either intrinsically as in quantum mechanics, or because of the vast amount of details necessary for a complete description as, for example, in Brownian motion and in many-body systems. We show that an application of the principle of maximum entropy for estimating the underlying probability distribution can depend on the variables used for describing the system. The choice of characterization of the system carries with it implicit assumptions about fundamental attributes such as whether the system is classical or quantum mechanical or equivalently whether the individuals are distinguishable or indistinguishable. We show that the correct procedure entails the maximization of the relative entropy subject to known constraints and, additionally, requires knowledge of the behavior of the system in the absence of these constraints. We present an application of the principle of maximum entropy to understanding species diversity in ecology and introduce a new statistical ensemble corresponding to the distribution of a variable population of individuals into a set of species not defined a priori.

Synthesizing within-host and population-level selective pressures on viral populations: the impact of adaptive immunity on viral immune escape.

The evolution of viruses to escape prevailing host immunity involves selection at multiple integrative scales, from within-host viral and immune kinetics to the host population level. In order to understand how viral immune escape occurs, we develop an analytical framework that links the dynamical nature of immunity and viral variation across these scales. Our epidemiological model incorporates within-host viral evolutionary dynamics for a virus that causes acute infections (e.g. influenza and norovirus) with changes in host immunity in response to genetic changes in the virus population. We use a deterministic description of the within-host replication dynamics of the virus, the pool of susceptible host cells and the host adaptive immune response. We find that viral immune escape is most effective at intermediate values of immune strength. At very low levels of immunity, selection is too weak to drive immune escape in recovered hosts, while very high levels of immunity impose such strong selection that viral subpopulations go extinct before acquiring enough genetic diversity to escape host immunity. This result echoes the predictions of simpler models, but our formulation allows us to dissect the combination of within-host and transmission-level processes that drive immune escape.