Phylogenetic topology and timing of New Zealand olive shells are consistent with punctuated equilibrium

The olive shells of the genus Amalda comprises readily recognized species of marine neogastropod mollusks found around the world. The New Zealand Amalda fauna has particular notoriety as providing one of the best demonstrations of evolutionary morphological stasis, a prerequisite for punctuated equilibrium theory. An excellent fossil record includes representation of three extant endemic Amalda species used to explore patterns of form change. However, the phylogenetic relationship of the New Zealand Amalda species and the timing of their lineage splitting have not been studied, even though these would provide valuable evidence to test predictions of punctuated equilibrium. Here, we use entire mitogenome and long nuclear rRNA gene cassette data from 11 Amalda species, selected from New Zealand and around the world in light of high rates of endemicity among extant and fossil Amalda. Our inferred phylogenies do not refute the hypothesis that New Zealand Amalda are a natural monophyletic group and therefore an appropriate example of morphological stasis. Furthermore, estimates of the timing of cladogenesis from the molecular data for the New Zealand group are compatible with the fossil record for extant species and consistent with expectations of punctuated equilibrium.     

Recombination and genetic differentiation among natural populations of the ectomycorrhizal mushroom Tricholoma matsutake from southwestern China

Effective conservation and utilization strategies for natural biological resources require a clear understanding of the natural populations of the target organisms. Tricholoma matsutake is an ectomycorrhizal mushroom that forms symbiotic associations with plants and plays an important ecological role in natural forest ecosystems in many parts of the world. It is also an economically very important gourmet mushroom. Because no artificial cultivation is available, natural populations of this species are under increasing threats, primarily from habitat disturbance and destruction. Despite its economical and ecological importance, little is known about its genetics and population biology. Here, using 14 polymerase chain reaction–restriction fragment length polymorphism markers, we analysed 154 strains from 17 geographical locations in southwestern China, a region where over 25% of the global T. matsutake harvest comes from. Our results revealed abundant genetic variation within individual populations. The analyses of gene and genotype frequencies within populations indicated that most loci did not deviate from Hardy–Weinberg equilibrium in most populations and that alleles among loci were in linkage equilibrium in the majority of the local populations. These results are consistent with the hypothesis that sexual reproduction and recombination play an important role in natural populations of this species. Our analyses indicated low but significant genetic differentiation among the geographical populations, with a significant positive correlation between genetic distance and geographical distance. We discuss the implications of our results to the ecology and resource management of this species.     

Environment and Social Values

This paper suggests three fundamental influences that have led to the development of a socially embedded view of the environment in the United States. While our social relationship to the environment has changed over our history, from one primarily of exploitation to one primarily of stewardship, the natural world continues to be central to the American sense of self. Epistemological evolution also has clearly affected how we understand and relate to the environment, particularly as scientific and other epistemologies have evolved in the context of a country whose people and history are tightly connected to its natural resources. Finally, our society has developed a sense of ethical responsibility to the environment. These three strands have created the intellectual environment within which the scientific tools used to understand the natural world are exercised.     

The Microbial Olympics

Every four years, the Olympic Games plays host to competitors who have built on their natural talent by training for many years to become the best in their chosen discipline. Similar spirit and endeavour can be found throughout the microbial world, in which every day is a competition to survive and thrive. Microorganisms are trained through evolution to become the fittest and the best adapted to a particular environmental niche or lifestyle, and to innovate when the 'rules of the game' are changed by alterations to their natural habitats. In this Essay, we honour the best competitors in the microbial world by inviting them to take part in the inaugural Microbial Olympics.     

Green world maintained by adaptation

An ecological theory (HSS hypothesis) predicts that carnivores maintain the terrestrial ecosystem with abundant plants (green world) by regulating herbivore abundance. However, a weak density dependence of herbivores will make the equilibrium unstable and results in population oscillations with a large amplitude. Here, we study a possibility that the dynamics can be stabilized if defence trait by herbivores and offence trait by carnivores change in an adaptive manner. When the cost constraints on adaptation are strong in both the herbivores and the carnivores, the equilibrium is more likely to be stable if the herbivore adapts more quickly than the carnivore. When the constraints on the adaptation are asymmetric between species, the equilibrium is likely to be unstable. We conclude that the green world may be maintained by fast and costly adaptation by the herbivore through mechanisms such as phenotypic plasticity and behavioural change. Plant defence which is poisonous and prickly has been proposed as one of explanations, however, world can be green through adaptation in higher trophic levels even without plant’s defence.     

The effect of evolution on host-parasitoid systems

It is well known that a simple first-order difference equation can exhibit complex population dynamics, such as sustained oscillations and chaos. An interesting problem is whether such oscillatory dynamics are expected to occur in real populations. This paper assumes that the resident system is composed of 1-host and 1-parasitoid and that only the host is allowed to evolve, but not the parasitoid. Based on the invasibility of a host to host-parasitoid systems, we investigate the dynamics of the host-parasitoid system favored by natural selection. We consider two cases. In the first case, the host's evolution involving both the intrinsic growth rate and the sensitivity to density is considered. In the second case, the host's evolution involving both the intrinsic growth rate and the vulnerability to the parasitoid is considered. In both cases, we see that the dynamics with a stable equilibrium will not be favored by natural selection without the trade-off between the host's traits which are allowed to evolve. The host-parasitoid system with a stable equilibrium will be eventually invaded by a host type that develops an unstable equilibrium with the parasitoid. If there is a trade-off between the host's traits which are allowed to evolve, a host-parasitoid system with a stable equilibrium can be favored by natural selection.     

Ethnobiology and the evolution of the human mind

An evolutionary perspective on human thought and behaviour indicates that we should expect to find universal systems of perception, classification, and decision-making regarding the natural world. It is the interaction between these evolved aspects of the human mind, the biodiversity of the natural world, and unique historical, social, and economic contexts within which individuals develop and act that gives rise to cultural diversity. The palaeoanthropological record also indicates that language is a recently evolved phenomenon. This suggests that linguistic approaches in ethnobiology are likely to provide only a partial understanding of how humans perceive, classify, and engage with the natural world.     

The range of time delay and the global stability of the equilibrium for an IVGTT model

Diabetes mellitus has become a prevalent disease in the world. Diagnostic protocol for the onset of diabetes mellitus is the initial step in the treatments. The intravenous glucose tolerance test (IVGTT) has been considered as the most accurate method to determine the insulin sensitivity and glucose effectiveness. It is well known that there exists a time delay in insulin secretion stimulated by the elevated glucose concentration level. However, the range of the length of the delay in the existing IVGTT models are not fully discussed and thus in many cases the time delay may be assigned to a value out of its reasonable range. In addition, several attempts had been made to determine when the unique equilibrium point is globally asymptotically stable. However, all these conditions are delay-independent. In this paper, we discuss the range of the time delay and provide easy-to-check delay-dependent conditions for the global asymptotic stability of the equilibrium point for a recent IVGTT model through Liapunov function approach. Estimates of the upper bound of the delay for global stability are given in corollaries. In addition, the numerical simulation in this paper is fully incorporated with functional initial conditions, which is natural and more appropriate in delay differential equation systems.     

The priority of prediction in ecological understanding

The objective of science is to understand the natural world; we argue that prediction is the only way to demonstrate scientific understanding, implying that prediction should be a fundamental aspect of all scientific disciplines. Reproducibility is an essential requirement of good science and arises from the ability to develop models that make accurate predictions on new data. Ecology, however, with a few exceptions, has abandoned prediction as a central focus and faces its own crisis of reproducibility. Models are where ecological understanding is stored and they are the source of all predictions – no prediction is possible without a model of the world. Models can be improved in three ways: model variables, functional relationships among dependent and independent variables, and in parameter estimates. Ecologists rarely test to assess whether new models have made advances by identifying new and important variables, elucidating functional relationships, or improving parameter estimates. Without these tests it is difficult to know if we understand more today than we did yesterday. A new commitment to prediction in ecology would lead to, among other things, more mature (i.e. quantitative) hypotheses, prioritization of modeling techniques that are more appropriate for prediction (e.g. using continuous independent variables rather than categorical) and, ultimately, advancement towards a more general understanding of the natural world. Synthesis Ecology, with a few exceptions, has abandoned prediction and therefore the ability to demonstrate understanding. Here we address how this has inhibited progress in ecology and explore how a renewed focus on prediction would benefit ecologists. The lack of emphasis on prediction has resulted in a discipline that tests qualitative, imprecise hypotheses with little concern for whether the results are generalizable beyond where and when the data were collected. A renewed commitment to prediction would allow ecologists to address critical questions about the generalizability of our results and the progress we are making towards understanding the natural world.     

Trophic interactions and range limits: the diverse roles of predation

Interactions between natural enemies and their victims are a pervasive feature of the natural world. In this paper, we discuss trophic interactions as determinants of geographic range limits. Predators can directly limit ranges, or do so in conjunction with competition. Dispersal can at times permit a specialist predator to constrain the distribution of its prey—and thus itself—along a gradient. Conversely, we suggest that predators can also at times permit prey to have larger ranges than would be seen without predation. We discuss several ecological and evolutionary mechanisms that can lead to this counter-intuitive outcome.     

Altered climate leads to positive density‐dependent feedbacks in a tropical wet forest

Climate change is predicted to result in warmer and drier Neotropical forests relative to current conditions. Negative density‐dependent feedbacks, mediated by natural enemies, are key to maintaining the high diversity of tree species found in the tropics, yet we have little understanding of how projected changes in climate are likely to affect these critical controls. Over 3 years, we evaluated the effects of a natural drought and in situ experimental warming on density‐dependent feedbacks on seedling demography in a wet tropical forest in Puerto Rico. In the +4°C warming treatment, we found that seedling survival increased with increasing density of the same species (conspecific). These positive density‐dependent feedbacks were not associated with a decrease in aboveground natural enemy pressure. If positive density‐dependent feedbacks are not transient, the diversity of tropical wet forests, which may rely on negative density dependence to drive diversity, could decline in a future warmer, drier world.     

From traditional Chinese medicine to rational cancer therapy

Many natural products and derivatives thereof belong to the standard repertoire of cancer chemotherapy. Examples are Vinca alkaloids, taxanes and camptothecins. In recent years, the potential of natural products from plants, notably from medicinal plants used in traditional Chinese medicine (TCM), has been recognized by the scientific community in the Western world. To provide an example of the most recent developments in this field, we have selected several compounds, namely artesunate, homoharringtonine, arsenic trioxide and cantharidin, that are found in natural TCM products and that have the potential for use in cancer therapy. Controlled clinical studies have shown that homoharringtonine and arsenic trioxide can exert profound activity against leukaemia. Increased knowledge of the molecular mechanisms of TCM-derived drugs and recent developments in their applications demonstrate that the combination of TCM with modern cutting-edge technologies provides an attractive strategy for the development of novel and improved cancer therapeutics.     

Phylogenetic approaches for studying diversification

Estimating rates of speciation and extinction, and understanding how and why they vary over evolutionary time, geographical space and species groups, is a key to understanding how ecological and evolutionary processes generate biological diversity. Such inferences will increasingly benefit from phylogenetic approaches given the ever‐accelerating rates of genetic sequencing. In the last few years, models designed to understand diversification from phylogenetic data have advanced significantly. Here, I review these approaches and what they have revealed about diversification in the natural world. I focus on key distinctions between different models, and I clarify the conclusions that can be drawn from each model. I identify promising areas for future research. A major challenge ahead is to develop models that more explicitly take into account ecology, in particular the interaction of species with each other and with their environment. This will not only improve our understanding of diversification; it will also present a new perspective to the use of phylogenies in community ecology, the science of interaction networks and conservation biology, and might shift the current focus in ecology on equilibrium biodiversity theories to non‐equilibrium theories recognising the crucial role of history.     

How do we make indoor environments and healthcare settings healthier?

It is now well accepted that our modern lifestyle has certain implications for our health (Schaub et al., 2006 ), mainly as a result of our willingness to remove ourselves from the biological diversity of our natural environments (Roduit et al., 2016 ), while still being drawn inextricably to interact with it (Kellert and Wilson, 1995 ). Much of our interaction with the biological world is shaped by our interaction with the microbiological world. The bacteria, fungi, viruses, archaea and protists that comprise the microbiome of this planet, are also key to the development and normal functioning of our bodies. Our immune system is built to shepherd our microbial exposure, ensuring that microbial organisms that we need are kept close (but not too close), and that less‐desirable organisms are expelled or killed before they can do too much damage. By moving from a life interacting with nature on a regular basis, to a life in which we isolate ourselves physically from natural microbial exposure, we may have instigated one of the great plagues of the 21st century; chronic immune disorders.     

A snapshot of the population structure of Branchiostoma lanceolatum in the Racou beach, France, during its spawning season

A methodology for inducing spawning in captivity of the lancelet Branchiostoma lanceolatum has been developed recently with animals collected at the Racou beach, in the southern coast of France. An increasing amount of laboratories around the world are now working on the evolution of developmental mechanisms (Evo-Devo) using amphioxus collected in this site. Thus, today, the development of new aquaculture techniques for keeping amphioxus in captivity is needed and the study of the natural conditions at which amphioxus is exposed in the Racou beach during their spawning season becomes necessary. We have investigated the amphioxus distribution, size frequency, and population structure in the Racou beach during its natural spawning season using multivariate methods (redundancy analysis and multiple regression). We found a clear preference of amphioxus for sandy sites, something that seems to be a general behaviour of different amphioxus species around the world. We have also estimated the amphioxus growth rate and we show how the animals are preferentially localized in shallow waters during April and June.     

Equilibrium of global amphibian species distributions with climate

A common assumption in bioclimatic envelope modeling is that species distributions are in equilibrium with contemporary climate. A number of studies have measured departures from equilibrium in species distributions in particular regions, but such investigations were never carried out for a complete lineage across its entire distribution. We measure departures of equilibrium with contemporary climate for the distributions of the world amphibian species. Specifically, we fitted bioclimatic envelopes for 5544 species using three presence-only models. We then measured the proportion of the modeled envelope that is currently occupied by the species, as a metric of equilibrium of species distributions with climate. The assumption was that the greater the difference between modeled bioclimatic envelope and the occupied distribution, the greater the likelihood that species distribution would not be at equilibrium with contemporary climate. On average, amphibians occupied 30% to 57% of their potential distributions. Although patterns differed across regions, there were no significant differences among lineages. Species in the Neotropic, Afrotropics, Indo-Malay, and Palaearctic occupied a smaller proportion of their potential distributions than species in the Nearctic, Madagascar, and Australasia. We acknowledge that our models underestimate non equilibrium, and discuss potential reasons for the observed patterns. From a modeling perspective our results support the view that at global scale bioclimatic envelope models might perform similarly across lineages but differently across regions.     

Genetic variation of Ardisia crenata in south China revealed by nuclear microsatellite

Ardisia crenata Sims,one of the most widely distributed Ardisia in the world,is an important ornamental and medicinal plant species.Using seven polymorphic nuclear microsatellite loci,we studied the genetic variation of 20 natural populations of A.crenata across its distribution center in south China.Significant deviation from the Hardy-Weinberg equilibrium in all populations and at all loci were detected,and the fixation index was high(FIS = 0.725),indicating that inbreeding may be dominant in the mixed mating system of this self-compatible species.The average genetic diversity within populations was relatively low(HS = 0.321).There was significant genetic differentiation among populations(FST = 0.583),which may have resulted from a high level of inbreeding and a low level of gene flow.Ardisia crenata in south China can be roughly divided into an eastern group and a western group,consistent with the floristic division of the Sino-Himalayan forest subkingdom and the Sino-Japanese forest subkingdom.There may be separated glacial refugia in each region.     

海南潜在世界自然遗产地的突出普遍价值初探

世界自然遗产地是全球最具有保护价值的自然保护地,强调全球突出普遍价值的完整性和在全球的唯一性。世界自然遗产有助于更好地保护生态系统的完整性和原真性,促进人类与自然的可持续发展。该研究在大量文献资料的基础上,以海南潜在世界自然遗产地(海南热带雨林国家公园)原生动植物及植被群落(亚洲北缘热带雨林)为研究对象,从植被类型、物种多样性、区系组成、特有种等生物生态过程方面,评估海南潜在世界自然遗产地的全球突出普遍价值。结果表明:(1)海南潜在世界自然遗产地分布有3 653种野生维管植物,资源植物种类丰富。陆栖脊椎动物有540种,各类野生动物占全国的比例高达10%～30%,生物多样性极高。(2)植物区系独特,海南岛的热带雨林植被区划属于印度-马来雨林群系,属马来区的部分呈现出热带性和与中国华南大陆的共源性显示出明显的热带边缘性质,为中国华南植物区系与亚洲热带雨林的过渡类型。(3)植物区系中的植物物种特有性较低,特有属仅有7个,特有种仅约占岛内植物的1/10,较低的特有性表明了其大陆起源特征,是生物多样性不可替代的元素,具有鲜明的环境指示特色。该研究明确了海南潜在世界自然遗产地在全球背景下的突出普遍价值,为海南未来申遗提供科学依据和技术支撑。     

Unnatural history: is a paradigm shift of natural history in 21st century ornithology needed?

Natural history, across disciplines, is essential for the continuation of science, especially as we attempt to identify the myriad of threats that biodiversity faces in this rapidly changing world. Recording the natural history of birds is perhaps the most prominent, widespread and long‐standing pursuit of this activity. Yet, there is a distinct decrease in publishing of natural history in the ornithological sciences. Concomitantly, the natural history information being published is often in small and regional journals, less accessible by the global ornithological community. We argue that historical natural history needs a modern reinvigoration, and should focus on placing natural history observations in the context of an anthropogenically altered world – ‘unnatural history’. This includes, but is not limited to, behavioural adaptations, novel diet choices, hybridization and novel adaptations to urbanization. Here, we elaborate on natural history's place in modern ornithology, how this relates to citizen science and the potential cost of ignoring it. Ultimately, increased accessibility of natural history observations, encouragement of amateur ornithologists' participation in professional societies (and vice versa) and targeted citizen science projects are potential mechanisms by which to reinvigorate natural history in 21st century ornithology.