The multilevel organismal diversity approach deciphers difficult to distinguish nudibranch species complex

Species identification is a key procedure for broad-scoped ecological, phylogeographic and evolutionary studies. However, to perform a taxonomic study in the molecular era is a complicated task that has many pitfalls. In the present study we use particular examples of common but difficult to distinguish European species within the genus of Polycera (Nudibranchia, Mollusca) to discuss the general issues of the “cryptic species” problem that has broad biological and interdisciplinary importance and can significantly impede ecological, evolutionary, and other biodiversity-related research. The largest dataset of molecular and morphological information for European nudibranchs ever applied encompasses a wide geographical area and shapes a robust framework in this study. Four species are recognized in the species complex, including a new one. It is shown that a lack of appropriate taxonomic analysis led recently to considerable errors in species identity assessment of this complex. Chromatic polymorphism for each species is mapped in a periodic-like framework and combined with statistical analysis of the diagnostic features that considerably facilitates identification of particular species in the complex for biologists and practitioners. The present study evidently shows that “cryptic” and “non-cryptic” components are present within the same species. Therefore, this species complex is well suited for the exploring and testing of general biological problems. One of the main conclusions of this study is that division of biological diversity into “cryptic” and “non-cryptic” components is counterproductive. We propose that the central biological phenomenon of a species can instead be universally designated as multilevel organismal diversity thereby provide a practical set of methods for its investigation.

Conceptualization of the species problem

The species problem is understood as a result of the contradiction between aspiration and inability to reduce diversity of species conceptions (SCs) to a single one. Any SC represents the natural spe-cies phenomenon in a certain cognitive situation and serves as a heuristic model of this phenomenon in the latter. SCs of various levels of generality emerge as a result of sequential multiple reduction cascade; the more reduction steps lead to a particular SC, the less it is adequate to the natural species phenomenon. The entire array of SCs can be represented by a conceptual pyramid, within which various SCs occur as particular interpretations of more general (inclusive) concepts and have no sense without contexts imposed by them. It is suggested that, in order to define natural “species in general,” a certain concept of biota should be fixed at the top of conceptual pyramid allowing to dis-tinguish between species and non-species (such as life form, syntaxa, guilds) phenomena. The on-tology of the natural species phenomenon is presumably determined by its essence, viz. species-hood. The latter is a part of the entire natural history of organisms, so its manifestations are group-specific and evolve with the evolutionary development of the structure of biota.

Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision

Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).

Problem-solving performance in wild Steller’s jays using a string-pulling task

Animals that exploit resources from human-modified environments may encounter unique problems when searching for food. Pulling a string tied to a food reward (string-pulling task) is one of the most widespread methods of testing a species’ problem-solving performance in non-human animals. Performance in problem-solving tasks may be influenced by an individual’s characteristics and social interactions, especially in its natural habitat. We examined problem solving by free-ranging Steller’s jays (Cyanocitta stelleri) when extracting food from a string-pulling task presented in their natural habitat. During the study, seven of 50 jays successfully solved the task on their first to eighteenth experimental opportunity; solvers differed from nonsolvers by showing higher levels of persistence by pulling the string in more trials. Of the successful jays, five birds solved without observing others, while two birds were present during successful trials and subsequently completed the task. All seven jays demonstrated improvement in the task by using less string pulls over additional successful trials. Nineteen other jays in the population interacted with the apparatus and pulled the string, but not enough to acquire the food. These 19 jays were significantly bolder (shorter latencies to approach), more explorative (contacted more parts of the apparatus), and had observed solvers more than the 24 individuals that did not pull the string. These results indicate a broad spectrum of individual differences in propensity for solving novel tasks in our population of Steller’s jays.

Aesthetics at the Intersection of the Species Problem and De-Extinction Technology

De-extinction technology aims to bring extinct species back into existence, often with the goal of releasing created organisms into natural environments. In this paper, I argue that there are aesthetic reasons to avoid engaging in de-extinction and release projects, even if they pass moral permissibility criteria. The strength of these reasons depends on conclusions regarding species authenticity - a problem that arises at the intersection of de-extinction technology and the 'species problem' in the philosophy of biology. Since species authenticity affects the perceived naturalness of 'natural' environments, and thus the aesthetic judgments thereof, I contend that there will be negative aesthetic consequences of de-extinction efforts that ought to be further explored before such projects move forward.

The Origin of Specious: misunderstandings about Patrick Matthew’s evolutionary thinking

Many ambiguities in Patrick Matthew’s evolutionary ideas can be resolved upon rejecting the presumption that his mechanism was identical to Darwin’s. This presumption has led to two ingrained interpretations which we show are false. First, competitive natural selection plays no role in Matthew’s lineage splitting. On the contrary, it is absent during his comparably short phases of adaptive radiation occurring after catastrophes. Catastrophes eliminate competition, and the competitive vacuum pulls the surviving species apart and unleashes their indwelling variational force. Separate populations adapt to new circumstances through variation and non-competitive survival. Second, competitive natural selection does not drive Matthew’s lineage adaptation either. When it is active, during the comparably long phases of conformity that follow adaptive radiation, the environment directly leads the system towards adaptation. Lineages adapt to changing circumstances but do not split. Interpreting Matthew’s statements accordingly makes sense of his evolutionary thinking that seemed obscure for over a century, especially his statements about the fixity of species and the species problem.

The Clostridioides difficile species problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies

Clostridioides difficile infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across C. difficile underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 C. difficile genomes spanning the eight currently defined phylogenetic clades. Through whole-genome average nucleotide identity, pangenomic and Bayesian analyses, we identified major taxonomic incoherence with clear species boundaries for each of the recently described cryptic clades CI-III. The emergence of these three novel genomospecies predates clades C1-5 by millions of years, rewriting the global population structure of C. difficile specifically and taxonomy of the Peptostreptococcaceae in general. These genomospecies all show unique and highly divergent toxin gene architecture, advancing our understanding of the evolution of C. difficile and close relatives. Beyond the taxonomic ramifications, this work impacts the diagnosis of CDI worldwide.

On the Plakobranchidae (Gastropoda, Sacoglossa) from soft sediment habitats of Koh Tao, Gulf of Thailand, with descriptions of two new species

Research in recent years have provided rapid advances in biogeographic and taxonomic documentation of sea slugs around the world. However, efforts are lacking in surveying most coastlines and habitats in South-East Asia. Recent studies from the Gulf of Thailand have indicated that a wealth of unexplored sea slug diversity and ecology may be gained from an investigation of soft sediment habitats beyond the reef slopes. Additionally, the waters of Koh Tao have been found to host regionally high levels of sea slug diversity with several species awaiting taxonomic clarification. In this work the initial findings of an expanded survey effort from the waters around Koh Tao are provided, with the identity of two soft sediment-associated sacoglossan species in the family Plakobranchidae being investigated. By integrating morphological and molecular analyses, the species Plakobranchus noctisstellatussp. nov. and Elysia aowthaisp. nov. are described and species complexes surrounding Plakobranchus ocellatus van Hasselt, 1824 and Elysia japonica Eliot, 1913 are discussed. The topics of morphological variability and the cryptic species problem are also discussed.