Extracting abundance information from DNA-based data

The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet reconstruction and quantitative food webs, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, capture bias, capture noise, species pipeline biases, and pipeline noise all combine to inject error into DNA-based datasets. We focus on methods for correcting the latter two error sources, as the first two are addressed extensively in the ecological literature. To extract abundance information, it is useful to distinguish two concepts. (1) Across-species quantification describes relative species abundances within one sample. (2) In contrast, within-species quantification describes how the abundance of each individual species varies from sample to sample, as in a time series, an environmental gradient, or different experimental treatments. Firstly, we review methods to remove species pipeline biases and pipeline noise. Secondly, we demonstrate experimentally (with a detailed protocol) how to use a 'DNA spike-in' to remove pipeline noise and recover within-species abundance information. We also introduce a statistical estimator that can partially remove pipeline noise from datasets that lack a physical DNA spike-in.

An updated checklist of marine copepoda from Peninsular Malaysia with notes on their functional traits and distributional records

An up-to-date checklist of marine zooplankton copepods from the water of Peninsular Malaysia is presented, there are 235 species of copepods which consists of 89 genera and 44 families. Extensive list of bibliographical references with synonymy, detailed information on their functional groups, and distributional data are provided for each species. The checklist is based on taxonomic and ecological literature until 28 May 2020. Calanoida recorded the most diverse order with 101 species in total, followed by Harpacticoida with 70 species and 61 species from Cyclopoida. As for Canuelloida, Monstrilloida and Siphonostomatoida all recorded with 1 species respectively. There are 192 species of copepod recorded along the west coast (Malacca Strait) and 123 species on the east coast (South China Sea). Endemicity at species level attains 1% for the whole Peninsular Malaysian coast, with 2 genera restricted to the east coast (Kensakia parva and Brachiella malayensis) and one genus to the west coast (Labidocera jaafari). There are six dominant species that can be found along the coast of Peninsular Malaysia (Acartia erythraea, Acartia pacifica, Bestiolina similis, Euterpina acutifrons, Microsetella norvegica, Paracalanus aculeatus, Oithona nana, Oithona simplex and Temora discaudata).

Linking host plants to damage types in the fossil record of insect herbivory

Studies of insect herbivory on fossilized leaves tend to focus on a few, relatively simple metrics that are agnostic to the distribution of insect damage types among host plants. More complex metrics that link particular damage types to particular host plants have the potential to address additional ecological questions, but such metrics can be biased by sampling incompleteness due to the difficulty of distinguishing the true absence of a particular interaction from the failure to detect it---a challenge that has been raised in the ecological literature. We evaluate a range of methods for characterizing the relationships between damage types and host plants by performing resampling and subsampling exercises on a variety of datasets. We found that the components of beta diversity provide a more valid, reliable, and interpretable method for comparing component communities than do bipartite network metrics. We found the rarefaction of interactions to be a valid, reliable, and interpretable method for comparing compound communities. Both of these methods avoid the potential pitfalls of multiple comparisons. Lastly, we found that the host specificity of individual damage types is challenging to assess. Whereas some previously used methods are sufficiently biased by sampling incompleteness to be inappropriate for fossil herbivory data, alternatives exist that are perfectly suitable for fossil datasets with sufficient sample coverage.

Mythical images in the novel “The Great Wang” by N. A. Baykov

This article analyzes the mythical images in the novel “The Great Wang” by N. A. Baykov. In this work, the writer depicts such mythical images as the tiger – Great Wang, the wise old man – Tong Li, and the lotus flower. The tiger is assigned a significant role in many works by N. A. Baykov – the novels “The Great Wang”, “Tigress”, “The Black Captain”, “On The Hills and Woods of Manchuria”, as well as the scientific articles “The Manchurian Tiger”, “Tigers in The Far East”, "Tiger Hunting" , etc. The unique peculiarity of the novel under review lies in combination of the expressive techniques of Western literature with the exotic themes of Eastern nature, simple natural worldview of inhabitants of the East. The specifics of the novel lies in the fact that the idea “The Great Wang” is based on the Chinese folk myths and legends, which attach a rather mystical and mythical hue. All forest animals anthropomorphized by the writer have their own thoughts and emotions. The conclusion is made that using mythical images, the well versed in the Chinese culture and folklore writer, combined mythical images with his narrative, and expressed his opinion on the man – nature relations. N. A. Baykov was against anthropocentrism, and advocated for the harmonious coexistence of man and nature. In the current context of deterioration of environmental situation, the reflected in “The Great Wang” ecological problems deserve attention of each one of us. The name of N. A. Baykov should be inscribed in the history of the world ecological literature.

On the relationships between rarity, uniqueness, distinctiveness, originality and functional/phylogenetic diversity

Rarity reflects the low abundance of a species while distinctiveness reflects its quality of being easy to recognize because it has unique functional characteristics and/or an isolated phylogenetic position. As such, the assemblage-level rarity of a species' functional and phylogenetic characteristics (that we name 'effective originality') results from both the rarity and the distinctiveness of this species. The functional and phylogenetic diversity of an assemblage then results from a compromise between the abundances and the effective originalities of the species it contains. Although the distinctiveness of a species itself depends on the abundance of the other species in the assemblage, distinctiveness indices that are available in the ecological literature scarcely consider abundance data. We develop a unifying framework that demonstrates the direct connections between measures of diversity, rarity, distinctiveness and effective originality. While developing our framework, we discovered a family of distinctiveness indices that permit a full control of the influence one wants to give to the strict uniqueness of a species (=its smallest functional or phylogenetic distance to another species in the assemblage). Illustrating our framework with bat phylogenetic diversity along a disturbance gradient in Mexico, we show how each component of rarity, distinctiveness and originality can be controlled to obtain efficient indicators for conservation. Overall our framework is aimed to improve conservation actions directed towards highly diverse areas and/or towards species whose loss would considerably decrease biodiversity by offering flexible quantitative tools where the influence of abundant versus rare, and ordinary versus original, species is understood and controlled.

Checklist of Staphylinidae (Coleoptera) of El Salvador

This paper is primarily a compilation of published data on the staphylinid beetle species reported for El Salvador. It is based on taxonomic and ecological literature, with inclusion of some new records from different entomological collections. Thirty eight genera and 96 species are reported in the list, including a first country record: Eulissus chalybaeus. Country-level distribution outside of El Salvador, locality references and topographic zones are included for each species. In the list, three endemic species are recorded: Seeversiella badia, S. minima and Stenus salvadorensis. It is remarkable that 14 genera (37%) and 52 species (54%) have only been reported at a country level in the literature, without a specific locality of collection, indicating the need for local inventories of this coleopteran family in the salvadoran territory.

Using ecological evidence to refine approaches to deploying offshore artificial reefs for recreational fisheries

Artificial reefs have many applications but are best known for their deployments to enhance recreational fisheries by creating new habitat in areas where natural reef is otherwise limited. The expectation is that fish assemblages will take up residence on artificial reefs and that these assemblages will become at least similar, if not more diverse and abundant, to those on natural reefs. Although designed, purpose-built artificial reefs are becoming more widely used in support of recreational fisheries and many of the historic issues have been resolved, conservation practitioners and managers still face challenges as to the type, number, and arrangement of structures and where to deploy them to maximize benefits and minimize risks. The ecological literature was reviewed to develop and enhance contemporary principles of artificial reef best practices for utilization. Our review identified optimal shapes, vertical relief, void spaces, and unit arrangements for increasing volumes and diversity of catch to recreational fishers and we provide a tool for identifying the least constrained areas for artificial reef deployment. We suggest; (a) monitoring of noncatch motivators in combination with quantitative indicators of the fishing activity (e.g., catch rate and effort) will provide the best understanding of success or failure of an artificial reef deployment; (b) choosing target species for informing purpose-built artificial reef designs to be reef-associated, demersal, philopatric, territorial, and obligatory reef species that are desired by local recreational fishers; and (c) considering the ecosystem services provided by artificial reefs beyond those associated with recreational fishing.

Philosophy of ecology of Justus von Liebig: different Liebig

German chemist Justus von Liebig is known in the ecological literature as the author of Liebigs law of the minimum. But the law of the minimum is absent in his publications, which ecologists cite. The law is nothing more than an interpretation of some of Liebigs statements. However, irrespective of the law of the minimum, Liebigs outstanding contribution to the theory of ecology is obvious: Liebig was one of the first who drew attention to the sustainability of the phenomenon of life organized into supraorganismal systems. Liebig showed that as a result of the interaction of plants and animals and as a result of their life processes, such as nutrition and respiration, there is a continuous transformation of a substance consisting of the same elements. On the example of the constancy of the gas composition of the atmosphere, Liebig comes to a generalization that is crucial for ecology: the interaction of plants and animals is a factor of sustainability of their own environment, which they create themselves and support for an unlimited time in a stable state.

Our Current Understanding of Commensalism

Commensalisms, interactions between two species in which one species benefits and the other experiences no net effect, are frequently mentioned in the ecological literature but are surprisingly little studied. Here we review and synthesize our limited understanding of commensalism. We then argue that commensalism is not a single type of interaction; rather, it is a suite of phenomena associated with distinct ecological processes and evolutionary consequences. For each form of commensalism we define, we present evidence for how, where, and why it occurs, including when it is evolutionarily persistent and when it is an occasional outcome of interactions that are usually mutualistic or antagonistic. We argue that commensalism should be of great interest in the study of species interactions due to its location at the center of the continuum between positive and negative outcomes. Finally, we offer a roadmap for future research.