Spatial and temporal variation in the sediment properties of an intertidal mangrove forest: implications for sampling

Studies of the structure or functioning of intertidal soft sediments often involves collection of biogeochemical data over tidal, diel and seasonal time-scales. Little effort has, however, been made to quantify accurately the time-scales at which these properties vary. Many previous studies collected samples from different sites at different times, potentially resulting in the confounding of spatial and temporal variation. This experiment was designed to determine if time of day or time within the exposure period had any significant effect on measurements of 7 different properties of sediments. Samples of sediment were collected using contact cores at the beginning, middle and end of tidal emersion at each of 9 a.m., 12 p.m. and 3 p.m., with two replicate days of each condition, from mangrove forests fringing Glades Bay, Sydney, Australia. These samples were analysed for water-content, pigments, carbohydrates, grain-size and loss on ignition (LOI), to determine the potential effects of time of day and time within the tidal cycle on these properties of the sediments.Whilst both time of day and time within the tidal cycle were found to occasionally have a significant effect upon the measured properties, most of the variation occurred among sites and between replicate days of each set of conditions. The minimal influence of time of day and time within the tidal cycle show that sampling effort should be preferentially placed into replicating days of sampling and sites because these are the scales with the greatest variation. Differences in the patterns found also depended on whether the data were expressed as content or concentration, the consequences of which are briefly described.     

Neighbourhood effects in forests: implications for within-stand patch structure

1 MOSAIC, a spatially referenced Markov model was used to show how interactions among trees in a neighbourhood may influence the patch structure of forests. A series of two-species simulations were conducted with neighbourhood strength ranging from neutral (chances of species replacing each other independent of neighbourhood composition) to strong (chance of replacement for each species proportional to neighbourhood composition), and with neighbourhood sizes including 1–50 neighbours.
2 Neighbourhood strength was positively correlated with the degree of patchiness. Very high neighbourhood strength is necessary to form mono-specific patches composed of hundreds of individual trees. Intermediate neighbourhood sizes (5–12 neighbours) led to the most distinct patches where individuals were arranged so that contact between species was minimized.
3 Neighbourhood effects alone are unlikely to lead to large areas (several ha) dominated by one species. However, simulations showed that neighbourhood effects can augment small differences in the environment, resulting in large mono-specific patches.
4 Simulations with 4 and 5 species indicated that groups of species can interact to form spatially distinct communities, starting from a random mixture on a uniform environment. This implies that neighbourhood effects may be responsible for some unexplained variability in studies that attempt to relate environmental parameters to forest composition.
5 Patch structures that develop due to neighbourhood effects are usually not recognized by current vegetation classification schemes or by forest managers, and this lack of recognition could lead to the loss of certain natural spatial structures on forested landscapes.     

Drivers of phenotypic variation in cartilage: Circadian clock genes

Endogenous homeostasis and peripheral tissue metabolism are disrupted by irregular fluctuations in activation, movement, feeding and temperature, which can accelerate negative biological processes and lead to immune reactions, such as rheumatoid arthritis (RA) and osteoarthritis (OA). This review summarizes abnormal phenotypes in articular joint components such as cartilage, bone and the synovium, attributed to the deletion or overexpression of clock genes in cartilage or chondrocytes. Understanding the functional mechanisms of different genes, the differentiation of mouse phenotypes and the prevention of joint ageing and disease will facilitate future research.     

Drivers of global variation in land ownership

Land ownership shapes natural resource management and social–ecological resilience, but the factors determining ownership norms in human societies remain unclear. Here we conduct a global empirical test of long‐standing theories from ecology, economics and anthropology regarding potential drivers of land ownership and territoriality. Prior theory suggests that resource defensibility, subsistence strategies, population pressure, political complexity and cultural transmission mechanisms may all influence land ownership. We applied multi‐model inference procedures based on logistic regression to cultural and environmental data from 102 societies, 71 with some form of land ownership and 31 with no land ownership. We found an increased probability of land ownership in mountainous environments, where patchy resources may be more cost effective to defend via ownership. We also uncovered support for the role of population pressure, with a greater probability of land ownership in societies living at higher population densities. Our results also show more land ownership when neighboring societies also practiced ownership. We found less support for variables associated with subsistence strategies and political complexity.     

Modeling extent and distribution of zygotic disequilibrium: implications for a multigenerational canine pedigree

Unlike gametic linkage disequilibrium defined for a random-mating population, zygotic disequilibrium describes the nonrandom association between different loci in a nonequilibrium population that deviates from Hardy-Weinberg equilibrium. Zygotic disequilibrium specifies five different types of disequilibria simultaneously that are (1) Hardy-Weinberg disequilibria at each locus, (2) gametic disequilibrium (including two alleles in the same gamete, each from a different locus), (3) nongametic disequilibrium (including two alleles in different gametes, each from a different locus), (4) trigenic disequilibrium (including a zygote at one locus and an allele at the other), and (5) quadrigenic disequilibrium (including two zygotes each from a different locus). However, because of the uncertainty on the phase of the double heterozygote, gametic and nongametic disequilibria need to be combined into a composite digenic disequilibrium and further define a composite quadrigenic disequilibrium together with the quadrigenic disequilibrium. To investigate the extent and distribution of zygotic disequilibrium across the canine genome, a total of 148 dogs were genotyped at 247 microsatellite markers located on 39 pairs of chromosomes for an outbred multigenerational pedigree, initiated with a limited number of unrelated founders. A major portion of zygotic disequilibrium was contributed by the composite digenic and quadrigenic disequilibrium whose values and numbers of significant marker pairs are both greater than those of trigenic disequilibrium. All types of disequilibrium are extensive in the canine genome, although their values tend to decrease with extended map distances, but with a greater slope for trigenic disequilibrium than for the other types of disequilibrium. Considerable variation in the pattern of disequilibrium reduction was observed among different chromosomes. The results from this study provide scientific guidance about the determination of the number of markers used for whole-genome association studies.     

Drivers of animal migration and implications in changing environments

Migratory species are widespread in terrestrial, aquatic and aerial environments, and are important both ecologically and economically. Since migration is an adaptive response to particular conditions, environmental changes (climate or otherwise) will potentially alter the selective pressures on movement behavior. Such changes may also interfere with, or disrupt, a species’ ability to migrate. In either case, environmental changes could lead to the reduction or total loss of a migration, yet we have little understanding of when to expect these outcomes to occur. Here, I argue that an understanding of both the proximate and ultimate drivers of migration is needed if we are to predict the fate of migrations under changing environmental conditions. I review what is currently known about the drivers of animal migration, but show that we also need a more complete synthesis of migratory patterns across diverse ecosystems and taxonomic groups. The current understanding of migration indicates that (1) drivers of migration vary across species and ecosystems, and (2) a species’ ability to adapt to environmental change successfully depends in part on its migration drivers. Together, these findings suggest a way forward for studying and generating predictions of how changing environmental conditions will differentially impact species by taxonomic group and geographic region of the world.     

Genomics and variation of ionotropic glutamate receptors: implications for neuroplasticity

Summary. We used two approaches to identify sequence variants in ionotropic glutamate receptor (IGR) genes: high-throughput screening and resequencing techniques, and information mining of public (e.g. dbSNP, ENSEMBL) and private (i.e. Celera Discovery System) sequence databases. Each of the 16 known IGRs is represented in these databases, their positions on a canonical physical map are established. Comparisons of mouse, rat, and human sequences revealed substantial conservation among these genes, which are located on different chromosomes but found within syntenic groups of genes. The IGRs are members of a phylogenetically ancient gene family, sharing similarities with glutamate-like receptors in plants. Parsimony analysis of amino acid sequences groups the IGRs into three distinct clades based on ligand-binding specificity and structural features, such as the channel pore and membrane spanning domains. A collection of 38 variants with amino acid changes was obtained by combining screening, resequencing, and informatics approaches for several of the IGR genes. This represents only a fraction of the sequence variation across these genes, but in fact these may constitute a large fraction of the common polymorphisms at these genes and these polymorphisms are a starting point for understanding the role of these variants in function.Genetically influenced human neurobehavioral phenotypes are likely to be linked to IGR genetic variants. Because ionotropic glutamate receptor activation leads to calcium entry, which is fundamental in brain development and in forms of synaptic plasticity essential for learning and memory and is essential for neuronal survival, it is likely that sequence variants in IGR genes may have profound functional roles in neuronal activation and survival mechanisms.     

Nonbiological factors affecting track censuses: implications for sampling design and reliability

Track census is a widely used method for rapid faunal assessments, which assumes that differences in track count numbers mainly reflect differences in species abundance due to some biological factors. However, some methodological and climatic variables might affect results of track censuses. Here, we tested the effect of climatic variables, such as maximum temperature, humidity, wind speed or days since last rain, and methodological factors such as censusing day period, distance from transect to vegetation edge, substrate condition or observer, on the number of tracks of mammal carnivores and some of their potential prey detected in sandy substrates. We sampled 2?×?2 km² located within the scrubland area of Doñana National Park (southwestern Spain) for carnivore and several potential prey tracks. Our results showed differences in the number of tracks detected between observers and a significant interaction between observers and the day period when censuses were carried out. Moreover, the variables increasing the quality of the substrate (higher environmental humidity, lower wind speed and days since last rain) not only led to a greater detection of carnivore tracks but, depending on the size of the species sampled other variables such as distance from transects to the vegetation border, also affected results. We recommend restricting sampling to certain fixed weather conditions when planning to monitor relative animal abundance from track censuses. When not possible, climatic or methodological variables should be included as covariates in analyses that try to test for the biological factors affecting wildlife abundance, taking into account that these variables, which affect the number of tracks detected could vary between years.     

Biological invasions in the Antarctic: extent, impacts and implications

Alien microbes, fungi, plants and animals occur on most of the sub-Antarctic islands and some parts of the Antarctic continent. These have arrived over approximately the last two centuries, coincident with human activity in the region. Introduction routes have varied, but are largely associated with movement of people and cargo in connection with industrial, national scientific program and tourist operations. The large majority of aliens are European in origin. They have both direct and indirect impacts on the functioning of species-poor Antarctic ecosystems, in particular including substantial loss of local biodiversity and changes to ecosystem processes. With rapid climate change occurring in some parts of Antarctica, elevated numbers of introductions and enhanced success of colonization by aliens are likely, with consequent increases in impacts on ecosystems. Mitigation measures that will substantially reduce the risk of introductions to Antarctica and the sub-Antarctic must focus on reducing propagule loads on humans, and their food, cargo, and transport vessels.     

新型冠状病毒序列变异时空分析系统的设计与实现

新型冠状病毒肺炎目前已进入全球大流行状态,多个国家出现疫情爆发。美国疾病管制局期刊《新兴传染病》发表的关于新型冠状病毒的最新研究结论显示,新型冠状病毒基本传染数R0的中位数高达5.7,这意味着在未来较长时间内新型冠状病毒可能会在人群中持续传播并发生变异。在这一背景下,如何监视病毒的变异,对于冠状病毒的研究和药物研发具有重要意义。本文基于来自GISAID的病毒基因组序列数据,设计和实现了新型冠状病毒变异时空分析系统。该系统可对来自不同国家和地区的新型冠状病毒序列数进行统计,对病毒序列在不同时间、不同空间内的变异情况进行分析和可视化,同时还支持不同序列之间的差异比对。该系统可为新型冠状病毒肺炎的研究和政府的疾病控制机构的决策提供支持。     

Small-scale temporal variability in assemblages of larval fishes: implications for sampling

Short-term changes in the assemblages of larval fishes in watersover the inner continental shelf off Sydney (Australia) wereexamined.This was done to highlight the potential sampling problemof confounding short-term variability with longer-term and spatialvariability in plankton communities. Assemblages at the surfaceand at 30 m depth were sampled twice a day over consecutivedays at two locations 5 km apart. The assemblages and the densitiesof individual taxa varied greatly between sampling times anddays. The small-scale temporal changes in densities of larvaewere not the same at both locations or between depths. Largeand consistent depth-related differences in assemblages andabundances of most taxa were evident. The consequences of small-scaletemporal variations are discussed relative to the design ofsampling programs for ecological and environmental purposes.Studies that include the double sampling of some stations arerecommended. Greater emphasis needs to be placed on fine-scaleoceanography and larval behaviour to determine causative mechanismsof short-term changes in assemblages of larval fishes.     

Modelling the spatio-temporal dynamics of multi-species host-parasitoid interactions: heterogeneous patterns and ecological implications

A mathematical model of the spatio-temporal dynamics of a two host, two parasitoid system is presented. There is a coupling of the four species through parasitism of both hosts by one of the parasitoids. The model comprises a system of four reaction-diffusion equations. The underlying system of ordinary differential equations, modelling the host-parasitoid population dynamics, has a unique positive steady state and is shown to be capable of undergoing Hopf bifurcations, leading to limit cycle kinetics which give rise to oscillatory temporal dynamics. The stability of the positive steady state has a fundamental impact on the spatio-temporal dynamics: stable travelling waves of parasitoid invasion exhibit increasingly irregular periodic travelling wave behaviour when key parameter values are increased beyond their Hopf bifurcation point. These irregular periodic travelling waves give rise to heterogeneous spatio-temporal patterns of host and parasitoid abundance. The generation of heterogeneous patterns has ecological implications and the concepts of temporary host refuge and niche formation are considered.     

Adult sex ratio variation: implications for breeding system evolution

Adult sex ratio (ASR) exhibits immense variation in nature, although neither the causes nor the implications of this variation are fully understood. According to theory, the ASR is expected to influence sex roles and breeding systems, as the rarer sex in the population has more potential partners to mate with than the more common sex. Changes in mate choice, mating systems and parental care suggest that the ASR does influence breeding behaviour, although there is a need for more tests, especially experimental ones. In the context of breeding system evolution, the focus is currently on operational sex ratios (OSRs). We argue that the ASR plays a role of similar importance and urge researchers to study the ASR and the OSR side by side. Finally, we plead for a dynamic view of breeding system evolution with feedbacks between mating, parenting, OSR and ASR on both ecological and evolutionary time scales.     

The circular definition of populations and its implications for biological sampling

Application of population-based theoretical models to the study of real world populations requires the relationship between the real and theoretical populations to be defined. Otherwise, it is not possible to take a representative field sample or census of a population. I demonstrate that the concept of a biological population is based on a circular definition and is logically untenable. A population is composed of a number of individuals whose membership of the population is determined by their relationship to the rest of the population. This has serious implications for common practice in a range of ecological and evolutionary disciplines.     

Resource exploitation and relatedness: implications for offspring size variation within broods

Much of the theory on offspring size variation within a brood relies on unequal maternal allocation of resources to each embryo. However, maternal allocation strategies are subject to an inherent conflict between mothers and offspring: individual offspring, being more closely related to themselves than to their siblings, should always prefer a larger share of the available resources than that which is optimal from their mother's perspective. Thus, in species where mothers cannot unilaterally impose a resource allocation strategy, offspring can respond to this conflict by competing for more resources than is maternally optimal. Here we show that variation in offspring size within a brood can arise as a by‐product of competition between siblings over a common resource, even when 1) there are no competitive inequalities within families, and 2) maternal investment per brood is fixed. Moreover, we show that size variance among offspring increases with increasing levels of competition, brought about by decreasing relatedness among siblings. Conflict thus offers a simple, testable and, potentially general, explanation for the wide variability in offspring size seen in nature. This extends explanatory hypotheses for offspring size variation beyond those of maternal effects, under which most explanations have been subsumed to date.     

Interpopulation variation in Chrysoperla carnea reproduction: implications for mass-rearing and storage

To determine whether diverse populations and biotypes of Chrysoperla carnea (Stephens) (Neuroptera: Chrysopidae) can be mass-produced and stored under uniform conditions, we assessed reproduction in five North American populations, four from the carnea biotype and one from the mohave biotype. Non-diapause adults from the carnea biotype varied significantly in only one aspect of reproduction, viz., the preoviposition period, whereas the duration and rate of oviposition, as well as fecundity, did not vary significantly. Relative to the carnea populations, the mohave population typically had delayed oviposition and a lower rate of oviposition; however, its oviposition period was long, and thus its fecundity differed only from that of the most productive carnea populations.The shelf-life (= survival during storage, and subsequent survival and reproduction after storage) was evaluated for four populations of the carnea biotype. Survival of diapausing adults during the first 18 weeks of storage was high among all four populations; adults from three populations also showed high survival after 35 weeks of storage. A high incidence of females from all four populations laid some fertile eggs after being stored for up to 31 weeks or longer. After six or more weeks of storage, average fecundity was high and ranged from 400–900 eggs/female. Duration of storage (up to 39 weeks) was a significant determinant of fecundity in two of the four populations.In practice, diverse populations of C. carnea can be efficiently mass-produced (with or without storage) under uniform conditions in the insectary. Thus, the choice of which populations to mass-produce and use in augmentation can be based primarily on the characteristics (e.g., climate, habitat, crop) of the intended area of release, rather than on considerations concerning mass-rearing.     

Discovery of a large clonal patch of a social amoeba: implications for social evolution

Studies of genetic population structures of clonally reproducing macro-organisms have revealed large areas where only one clone is found. These areas, referred to as clonal patches, have not been shown to occur in free-living microbes until now. In free-living microbes, high genetic diversity at local scales is usually maintained by high rates of dispersal. We report, however, a highly dense, 12-m clonal patch of the social amoeba Dictyostelium discoideum in a cattle pasture located in a Texas Gulf Coast prairie. We confirm the presence of only one clone by the analysis of 65 samples and amplification of 10 polymorphic microsatellite loci. Samplings of additional cattle pastures nearby showed higher clonal diversity, but with a density of D. discoideum isolates lower than in the clonal patch. These findings show that high rates of microbial dispersal do not always produce genetic diversity at local scales, contrary to the findings of previous studies. The existence of clonal patches may be particularly important for microbial social evolution.     

Analysis and implications of mutational variation

Variation from new mutations is important for several questions in quantitative genetics. Key parameters are the genomic mutation rate and the distribution of effects of mutations (DEM), which determine the amount of new quantitative variation that arises per generation from mutation (V _M ). Here, we review methods and empirical results concerning mutation accumulation (MA) experiments that have shed light on properties of mutations affecting quantitative traits. Surprisingly, most data on fitness traits from laboratory assays of MA lines indicate that the DEM is platykurtic in form (i.e., substantially less leptokurtic than an exponential distribution), and imply that most variation is produced by mutations of moderate to large effect. This finding contrasts with results from MA or mutagenesis experiments in which mutational changes to the DNA can be assayed directly, which imply that the vast majority of mutations have very small phenotypic effects, and that the distribution has a leptokurtic form. We compare these findings with recent approaches that attempt to infer the DEM for fitness based on comparing the frequency spectra of segregating nucleotide polymorphisms at putatively neutral and selected sites in population samples. When applied to data for humans and Drosophila, these analyses also indicate that the DEM is strongly leptokurtic. However, by combining the resultant estimates of parameters of the DEM with estimates of the mutation rate per nucleotide, the predicted V _M for fitness is only a tiny fraction of V _M observed in MA experiments. This discrepancy can be explained if we postulate that a few deleterious mutations of large effect contribute most of the mutational variation observed in MA experiments and that such mutations segregate at very low frequencies in natural populations, and effectively are never seen in population samples.