An integrative genomic and phenomic analysis to investigate the nature of plant species in Escallonia (Escalloniaceae)

What we mean by species and whether they have any biological reality has been debated since the early days of evolutionary biology. Some biologists even suggest that plant species are created by taxonomists as a subjective, artificial division of nature. However, the nature of plant species has been rarely tested critically with data while ignoring taxonomy. We integrate phenomic and genomic data collected across hundreds of individuals at a continental scale to investigate this question in Escallonia (Escalloniaceae), a group of plants which includes 40 taxonomic species (the species proposed by taxonomists). We first show that taxonomic species may be questionable as they match poorly to patterns of phenotypic and genetic variation displayed by individuals collected in nature. We then use explicit statistical methods for species delimitation designed for phenotypic and genomic data, and show that plant species do exist in Escallonia as an objective, discrete property of nature independent of taxonomy. We show that such species correspond poorly to current taxonomic species ($$< 20\%$$ < 20 % ) and that phenomic and genomic data seldom delimit congruent entities ($$< 20\%$$ < 20 % ). These discrepancies suggest that evolutionary forces additional to gene flow can maintain the cohesion of species. We propose that phenomic and genomic data analyzed on an equal footing build a broader perspective on the nature of plant species by helping delineate different ‘types of species’. Our results caution studies which take the accuracy of taxonomic species for granted and challenge the notion of plant species without empirical evidence. Note: A version of the complete manuscript in Spanish is available in the Supplemental Materials.

Time-free Solution to Independent Set Problem using P Systems with Active Membranes

Membrane computing is a branch of natural computing aiming to abstract computing models from the structure and functioning of living cells. The computation models obtained in the field of membrane computing are usually called P systems. P systems have been used to solve computationally hard problems efficiently on the assumption that the execution of each rule is completed in exactly one time-unit (a global clock is assumed for timing and synchronizing the execution of rules). However, in biological reality, different biological processes take different times to be completed, which can also be influenced by many environmental factors. In this work, with this biological reality, we give a time-free solution to independent set problem using P systems with active membranes, which solve the problem independent of the execution time of the involved rules.

Primary oral mucosa-associated lymphoid tissue (MALT) lymphoma in patient with monoclonale gammopathy: a rare case report

Background Monoclonal gammopathy is a biological reality encountered in approximately 1% of the general population. In the absence of clinical and biological signs, it is considered of undetermined significance; however, it can be a biological signature of a monoclonal lymphocytic or plasma-cell proliferation. Their localisation to the oral mucosa remains rare and difficult to diagnose, particularly in indolent forms that escape imaging techniques. Case presentation Here, we report the case of a 73-year-old woman with a history of IgM kappa gammopathy followed for 13 years. The patient did not have a chronic infection or an autoimmune disease, and all the biological investigations and radiological explorations were unremarkable during this period. The discovery of a submucosal nodule in the cheek led to the diagnosis of MALT lymphoma and regression of half of the IgM kappa level after resection. The review of the literature shows the dominance of clinical signs (i.e., a mass or swelling) in the diagnosis of primary MALT lymphomas of the oral cavity after surgical resection. Conclusions Our case illustrates the role of examination of the oral cavity in the context of a monoclonal gammopathy. The absence of clinical and radiological evidence in favor of lymphoplasmacytic proliferation, does not exclude a primary indolent MALT lymphoma of the oral mucosa.

nQMaker: estimating time non-reversible amino acid substitution models

Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this paper, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation of time non-reversible amino acid substitution models and rooted phylogenetic trees from a set of protein sequence alignments. We show that the non-reversible models estimated with nQMaker are a much better fit to empirical alignments than pre-existing reversible models, across a wide range of datasets including mammals, birds, plants, fungi, and other taxa, and that the improvements in model fit scale with the size of the dataset. Notably, for the recently published plant and bird trees, these non-reversible models correctly recovered the commonly known root placements with very high statistical support without the need to use an outgroup. We provide nQMaker as an easy-to-use feature in the IQ-TREE software (http://www.iqtree.org), allowing users to estimate non-reversible models and rooted phylogenies from their own protein datasets.

Composite photographic portrait as a tool for visualizing local anthropological variants (using the example of Bashkir men photographic materials)

Based on individual images of Bashkir men from literary sources (early 20th century) and on the basis of our own photographs of the end of the 20th century, composite photographic portraits (full-face, in profile) were compiled using the "FaceOnFace" computer program. Based on the high similarity of composite photographic portraits, two samples (from the beginning and the end of the 20th century) of initial photographs of Bashkir men were combined into a single corpus (N = 85). Individual photographs corresponding to the descriptions of the South Siberian (N = 40) and Ural (N = 20) minor races were selected from the combined sample of photographs of Bashkir men of the 20th century. Results and discussion. Based on these two subsamples, using digital technologies, 2 pairs of high-precision male composite photographic portraits (full-face and in profile) of Bashkir men were created. They represent the two racial variants prevailing in the region. One pair of photo-generalizations characterizes the softened South Siberian (N = 40), and the other, the sub-Ural (N = 20) anthropological variants. All profile composite photographic portraits of the Bashkirs were obtained for the first time. The phantom image obtained by the method is mentally compared with a certain generalized idea of a particular anthropological version of the known racial classifications. Due to the authorial nature of the various racial classifications, the subjective choice of the «typical», «most characteristic» person (or a short series of faces), presented as an illustration, is also inevitable. Conclusion. The resulting photographic portraits are no less recognizable than the illustrations given in anthropology textbooks: two clearly distinguishable anthropologically variants are visualized that occur in Bashkir populations. This result confirms the deeply entrenched opinion of anthropologists about the heterogeneity and population polytypes of the Bashkir ethno-national community. Both population-typological composite photographic portraits of an ethnic group and a typological digital high precision quality composite portrait, which achieves the effect of "personalization" of a phantom image, are cognitive tools that allow one to assess the biological reality of the existence of human populations with biologically meaningful (adequate) visual means. It is necessary to seek visual means that are isomorphic to the nature of a living, lasting composite.

Animatio

The onset of individual human life has fascinated thinkers of all cultures and epochs and the history of their ideas may shed light on an unsettled debate. Aristotle attributed three different souls to subsequent developmental stages. The last, rational soul, was associated with the formed fetus, and entailed fetal movements. With some modifications, the concept of delayed ensoulment—at 30, 42, 60, or 90 days after conception—was adopted by several Christian church fathers and remained valid throughout the Middle Ages. During the Enlightenment, philosophers began to replace the rational soul by the term personhood, basing the latter on self-awareness. Biological reality suggests that personhood accrues slowly, not at a specific date during gestation. Requirements for personhood are present in the embryo, but not in the pre-embryo before implantation: anatomic substrate; no more totipotent cells; and decreased rate of spontaneous loss. But biological facts alone cannot determine the embryo’s moral status. Societies must negotiate and decide on the extent of protection of unborn humans. In the 21st century, fertilization, implantation, extrauterine viability, and birth have become landmarks of change in ontological status.

Animals on display: animal motifs, human-animal relations and social semiotics in the Bronze Age rock carvings from Enköping and Norrköping, Sweden

Animals make up one of the most common motif groups in south Scandinavian Bronze Age rock art, with depictions of pigs and horses, as well as wild animals like red deer and wild boar, occurring in almost all rock art areas. Despite their ubiquity, their treatment in previous research has been inadequate. In this article, the display of animals in the rock art tradition is mapped out and discussed from a perspective based in human-animal relations and social semiotics. The animal figures are analyzed in terms of species, sex, human practice and regional articulations, as well as in relation to the wider archaeological record. The results reveal that animal motifs probably had a dual role during the Bronze Age, showing both the biological reality and the social and symbolic values that were connected to animals. In addition, the animals depicted in rock art also worked as carriers of semiotic resources, which manifested human social and societal ideas and ideals.

Freedom as a concept and as a property of the subject

The other side of the alternative of “objectivism or subjectivism (anti-substantialism”), can appropriately resolve the problem of the essence of freedom. Hegel wrote: “No idea can be said with such full right that it is indefinite, ambiguous, accessible to the greatest misunderstandings and therefore is actually subject to them, as about the idea of freedom, and none of them is usually spoken of with such a small degree of understanding of it. Since the free spirit is a real spirit, to the extent that the misunderstandings associated with it have enormous practical consequences...” (Hegel, 1977: 471) Thus, even the idealist Hegel admits that the problem of freedom has theoretical and particular practical significance. One can agree with I. Kant, G. Hegel, and N. Berdyaev, and many other philosophers that freedom exists only in the world of human reality, that is, in culture and society. In nature, both living and nonliving, it is not freedom that occurs but a necessity dialectically associated with chance and possibility. As Hegel rightly pointed out, “Nature ... manifests in its present being not freedom, but necessity and chance” (Hegel, 1975: 695). This statement certainly needs to be concretized. Freedom cannot coincide with necessity, but it cannot entirely resist it. Freedom that is not based on any form of necessity, as Hegel also showed, is not freedom. It is arbitrariness. Naked arbitrariness, according to him, is will in the form of chance (Hegel, 1974). One should bear in mind that the differences between inanimate (physical and chemical reality) and living (biological reality) nature, and in the latter – between the levels of its organization – are qualitative and even essential.

The taxonomic history of bats of the tribe Lasiurini (Chiroptera: Vespertilionidae) has undergone significant changes over time. Authors at different times have recognized various numbers of genera and subgenera within the tribe. The most recent proposed change to generic level taxonomy (that there should be three genera recognized instead of a single genus) has been debated in the literature. We reviewed papers that commented on the recent changes to lasiurine generic taxonomy, as well as those that have adopted the new taxonomy and the ones that have not. We also reviewed the relevant taxonomic literature from 1942 to the present that shows the fluid taxonomic history of these bats. The literature review shows that the recently proposed taxonomic change recognizing the three groups of lasiurine bats as distinct genera is the only taxonomy that differentiates the tribe from the genera. Examination of times to most recent common ancestor (TMRCA) of 24 vespertilionid genera shows Lasiurus, if it comprises all Lasiurini, to be an outlier. Here, we support the recognition of three genera and explain how this arrangement best reflects the evolutionary history and biodiversity of the tribe by bringing the three distinct lineages in line with other vespertilionid genera with respect to divergence times and genetic distances. Considering the Lasiurini to comprise a single genus, Lasiurus, that genus has the greatest TMRCA of all vespertilionid genera analyzed, comparable only to the genus Kerivoula of the monotypic subfamily Kerivoulinae. However, recognizing the three deeply diverged lasiurine lineages (red bats, yellow bats, and hoary bats) as genera brings their TMRCAs in line with other genera and approximates the mean TMRCA of the 24 genera analyzed. Opponents of Baird et al.’s taxonomy argued that these three lineages should be considered as subgenera to avoid changing scientific names for purpose of nomenclatural stability and ease of conducting a literature search and because the three deep lineages are all monophyletic. That argument ignores the biological reality that these lineages are morphologically distinct, and that they are genetically as distinct from one another as other genera of vespertilionid bats; there is ample precedent in the mammalian literature to use values of TMRCA as a metric to maintain consistency of higher taxonomic categories such as genus. We encourage other mammalogists to utilize taxonomy to its maximum descriptive potential, while taking into account phylogenetic relationships of the taxa of interest.

The taxonomic history of bats of the tribe Lasiurini (Chiroptera: Vespertilionidae) has undergone significant changes over time. Authors at different times have recognized various numbers of genera and subgenera within the tribe. The most recent proposed change to generic level taxonomy (that there should be three genera recognized instead of a single genus) has been debated in the literature. We reviewed papers that commented on the recent changes to lasiurine generic taxonomy, as well as those that have adopted the new taxonomy and the ones that have not. We also reviewed the relevant taxonomic literature from 1942 to the present that shows the fluid taxonomic history of these bats. The literature review shows that the recently proposed taxonomic change recognizing the three groups of lasiurine bats as distinct genera is the only taxonomy that differentiates the tribe from the genera. Examination of times to most recent common ancestor (TMRCA) of 24 vespertilionid genera shows Lasiurus, if it comprises all Lasiurini, to be an outlier. Here, we support the recognition of three genera and explain how this arrangement best reflects the evolutionary history and biodiversity of the tribe by bringing the three distinct lineages in line with other vespertilionid genera with respect to divergence times and genetic distances. Considering the Lasiurini to comprise a single genus, Lasiurus, that genus has the greatest TMRCA of all vespertilionid genera analyzed, comparable only to the genus Kerivoula of the monotypic subfamily Kerivoulinae. However, recognizing the three deeply diverged lasiurine lineages (red bats, yellow bats, and hoary bats) as genera brings their TMRCAs in line with other genera and approximates the mean TMRCA of the 24 genera analyzed. Opponents of Baird et al.’s taxonomy argued that these three lineages should be considered as subgenera to avoid changing scientific names for purpose of nomenclatural stability and ease of conducting a literature search and because the three deep lineages are all monophyletic. That argument ignores the biological reality that these lineages are morphologically distinct, and that they are genetically as distinct from one another as other genera of vespertilionid bats; there is ample precedent in the mammalian literature to use values of TMRCA as a metric to maintain consistency of higher taxonomic categories such as genus. We encourage other mammalogists to utilize taxonomy to its maximum descriptive potential, while taking into account phylogenetic relationships of the taxa of interest.